Add workflow: genome annotation with Maker #631

rlibouba · 2024-12-11T09:33:21Z

Hello,
I would like to propose this workflow for annotating a genome from the GTN "Genome annotation with Maker (short)".

Thank you! Have a nice day!

wm75 · 2024-12-12T10:19:06Z

This looks really cool already, thanks!

When I'm importing the WF on Galaxy Europe, it complains about

So I guess that needs to be fixed.

In the README I would not discuss inputs/outputs per tool but at the WF level to avoid redundancy.
You can just list the inputs, their expected format and what the WF will use them for.
Likewise, you can have one list of all outputs, what they are for and (if that's relevant/helpful) which tool produced them.

Without knowing too much about the details of the WF, would a MultiQC combined report of some of the results make sense?

workflows/genome_annotation/annotation_maker/Genome_annotation_with_maker_short_tests.yml

github-actions · 2024-12-17T17:43:00Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

github-actions · 2024-12-18T10:13:48Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

github-actions · 2024-12-18T11:01:53Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

github-actions · 2024-12-18T14:46:54Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

Problems:

Output with path /tmp/tmptsq1_ptk/Busco on data 15 GFF__7e7e240c-881c-416b-a5ba-93611220de80 different than expected
Expected text 'snap-NC_003421.2-processed-gene-12.94-mRNA-1' in output ('##gff-version 3
snap-NC_003421.2-processed-gene-12.33-mRNA-1	MetaEuk	gene	6745	8037	61	+	.	Target_ID=118701at4751_402676_1:00055d;TCS_ID=118701at4751_402676_1:00055d|snap-NC_003421.2-processed-gene-12.33-mRNA-1|+|6744
snap-NC_003421.2-processed-gene-12.33-mRNA-1	MetaEuk	gene	6745	8037	61	+	.	Target_ID=118701at4751_402676_1:00055d;TCS_ID=118701at4751_402676_1:00055d|snap-NC_003421.2-processed-gene-12.33-mRNA-1|+|6744
snap-NC_003421.2-processed-gene-4.105-mRNA-1	MetaEuk	gene	2380	2757	123	+	.	Target_ID=119833at4751_61395_1:00030d;TCS_ID=119833at4751_61395_1:00030d|snap-NC_003421.2-processed-gene-4.105-mRNA-1|+|2379
snap-NC_003421.2-processed-gene-4.105-mRNA-1	MetaEuk	gene	2380	2757	123	+	.	Target_ID=119833at4751_61395_1:00030d;TCS_ID=119833at4751_61395_1:00030d|snap-NC_003421.2-processed-gene-4.105-mRNA-1|+|2379
maker-NC_003421.2-augustus-gene-18.1-mRNA-1	MetaEuk	gene	95	802	349	+	.	Target_ID=189573at4751_483514_1:00063e;TCS_ID=189573at4751_483514_1:00063e|maker-NC_003421.2-augustus-gene-18.1-mRNA-1|+|94
maker-NC_003421.2-augustus-gene-18.1-mRNA-1	MetaEuk	gene	95	802	349	+	.	Target_ID=189573at4751_483514_1:00063e;TCS_ID=189573at4751_483514_1:00063e|maker-NC_003421.2-augustus-gene-18.1-mRNA-1|+|94
snap-NC_003421.2-processed-gene-1.33-mRNA-1	MetaEuk	gene	55	969	203	+	.	Target_ID=198196at4751_13706_1:00058d;TCS_ID=198196at4751_13706_1:00058d|snap-NC_003421.2-processed-gene-1.33-mRNA-1|+|54
snap-NC_003421.2-processed-gene-1.33-mRNA-1	MetaEuk	gene	55	969	203	+	.	Target_ID=198196at4751_13706_1:00058d;TCS_ID=198196at4751_13706_1:00058d|snap-NC_003421.2-processed-gene-1.33-mRNA-1|+|54
snap-NC_003421.2-processed-gene-13.65-mRNA-1	MetaEuk	gene	292	1110	76	+	.	Target_ID=320638at4751_684364_1:000687;TCS_ID=320638at4751_684364_1:000687|snap-NC_003421.2-processed-gene-13.65-mRNA-1|+|291
maker-NC_003421.2-augustus-gene-23.147-mRNA-1	MetaEuk	gene	151	564	53	+	.	Target_ID=396842at4751_881290_1:0007d0;TCS_ID=396842at4751_881290_1:0007d0|maker-NC_003421.2-augustus-gene-23.147-mRNA-1|+|150
snap-NC_003421.2-processed-gene-16.18-mRNA-1	MetaEuk	gene	490	1224	88	+	.	Target_ID=4466at4751_200324_1:000152;TCS_ID=4466at4751_200324_1:000152|snap-NC_003421.2-processed-gene-16.18-mRNA-1|+|489
maker-NC_003421.2-augustus-gene-5.100-mRNA-1	MetaEuk	gene	210	3200	224	+	.	Target_ID=56432at4751_1408658_1:000b00;TCS_ID=56432at4751_1408658_1:000b00|maker-NC_003421.2-augustus-gene-5.100-mRNA-1|+|209
maker-NC_003421.2-augustus-gene-5.100-mRNA-1	MetaEuk	gene	210	3200	224	+	.	Target_ID=56432at4751_1408658_1:000b00;TCS_ID=56432at4751_1408658_1:000b00|maker-NC_003421.2-augustus-gene-5.100-mRNA-1|+|209
augustus-NC_003421.2-processed-gene-15.71-mRNA-1	MetaEuk	gene	79	2817	143	+	.	Target_ID=6377at4751_1128425_1:0022e4;TCS_ID=6377at4751_1128425_1:0022e4|augustus-NC_003421.2-processed-gene-15.71-mRNA-1|+|78
augustus-NC_003421.2-processed-gene-15.71-mRNA-1	MetaEuk	gene	79	2817	143	+	.	Target_ID=6377at4751_1128425_1:0022e4;TCS_ID=6377at4751_1128425_1:0022e4|augustus-NC_003421.2-processed-gene-15.71-mRNA-1|+|78
maker-NC_003421.2-snap-gene-14.45-mRNA-1	MetaEuk	gene	56	2500	709	+	.	Target_ID=76975at4751_483514_1:00079d;TCS_ID=76975at4751_483514_1:00079d|maker-NC_003421.2-snap-gene-14.45-mRNA-1|+|55
maker-NC_003421.2-snap-gene-14.45-mRNA-1	MetaEuk	gene	56	2500	709	+	.	Target_ID=76975at4751_483514_1:00079d;TCS_ID=76975at4751_483514_1:00079d|maker-NC_003421.2-snap-gene-14.45-mRNA-1|+|55
maker-NC_003421.2-augustus-gene-12.92-mRNA-1	MetaEuk	gene	1	2754	442	+	.	Target_ID=85793at4751_653667_1:000c86;TCS_ID=85793at4751_653667_1:000c86|maker-NC_003421.2-augustus-gene-12.92-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-12.92-mRNA-1	MetaEuk	gene	1	2754	442	+	.	Target_ID=85793at4751_653667_1:000c86;TCS_ID=85793at4751_653667_1:000c86|maker-NC_003421.2-augustus-gene-12.92-mRNA-1|+|0
maker-NC_003421.2-snap-gene-15.45-mRNA-1	MetaEuk	gene	1134	1880	337	-	.	Target_ID=298379at4751_653667_1:000bde;TCS_ID=298379at4751_653667_1:000bde|maker-NC_003421.2-snap-gene-15.45-mRNA-1|-|1133
snap-NC_003421.2-processed-gene-15.30-mRNA-1	MetaEuk	gene	58	804	337	+	.	Target_ID=298379at4751_653667_1:000bde;TCS_ID=298379at4751_653667_1:000bde|snap-NC_003421.2-processed-gene-15.30-mRNA-1|+|57
snap-NC_003421.2-processed-gene-13.73-mRNA-1	MetaEuk	gene	1	1653	933	+	.	Target_ID=101133at4751_483514_1:001111;TCS_ID=101133at4751_483514_1:001111|snap-NC_003421.2-processed-gene-13.73-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-5.79-mRNA-1	MetaEuk	gene	395	3025	1345	+	.	Target_ID=103183at4751_653667_1:00105f;TCS_ID=103183at4751_653667_1:00105f|augustus-NC_003421.2-processed-gene-5.79-mRNA-1|+|394
snap-NC_003421.2-processed-gene-5.5-mRNA-1	MetaEuk	gene	1	3042	1347	+	.	Target_ID=103461at4751_483514_1:00091c;TCS_ID=103461at4751_483514_1:00091c|snap-NC_003421.2-processed-gene-5.5-mRNA-1|+|0
snap-NC_003421.2-processed-gene-22.10-mRNA-1	MetaEuk	gene	1	4125	1542	+	.	Target_ID=11636at4751_653667_1:000a79;TCS_ID=11636at4751_653667_1:000a79|snap-NC_003421.2-processed-gene-22.10-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-10.35-mRNA-1	MetaEuk	gene	22	2298	1103	+	.	Target_ID=122507at4751_483514_1:000f4c;TCS_ID=122507at4751_483514_1:000f4c|augustus-NC_003421.2-processed-gene-10.35-mRNA-1|+|21
snap-NC_003421.2-processed-gene-1.41-mRNA-1	MetaEuk	gene	1	3282	1315	+	.	Target_ID=126037at4751_653667_1:001091;TCS_ID=126037at4751_653667_1:001091|snap-NC_003421.2-processed-gene-1.41-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-19.53-mRNA-1	MetaEuk	gene	146	1849	978	+	.	Target_ID=126256at4751_653667_1:000aef;TCS_ID=126256at4751_653667_1:000aef|maker-NC_003421.2-augustus-gene-19.53-mRNA-1|+|145
snap-NC_003421.2-processed-gene-20.57-mRNA-1	MetaEuk	gene	1	4896	2105	+	.	Target_ID=130930at4751_653667_1:000b5f;TCS_ID=130930at4751_653667_1:000b5f|snap-NC_003421.2-processed-gene-20.57-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-3.0-mRNA-1	MetaEuk	gene	405	2126	777	+	.	Target_ID=130976at4751_483514_1:0007e4;TCS_ID=130976at4751_483514_1:0007e4|maker-NC_003421.2-augustus-gene-3.0-mRNA-1|+|404
maker-NC_003421.2-augustus-gene-3.11-mRNA-1	MetaEuk	gene	305	1552	745	+	.	Target_ID=165243at4751_653667_1:00104c;TCS_ID=165243at4751_653667_1:00104c|maker-NC_003421.2-augustus-gene-3.11-mRNA-1|+|304
maker-NC_003421.2-snap-gene-14.51-mRNA-1	MetaEuk	gene	124	1689	921	+	.	Target_ID=167498at4751_653667_1:000a63;TCS_ID=167498at4751_653667_1:000a63|maker-NC_003421.2-snap-gene-14.51-mRNA-1|+|123
snap-NC_003421.2-processed-gene-23.35-mRNA-1	MetaEuk	gene	46	1779	844	+	.	Target_ID=168092at4751_653667_1:001122;TCS_ID=168092at4751_653667_1:001122|snap-NC_003421.2-processed-gene-23.35-mRNA-1|+|45
snap-NC_003421.2-processed-gene-21.19-mRNA-1	MetaEuk	gene	1	1299	747	+	.	Target_ID=171238at4751_653667_1:000c64;TCS_ID=171238at4751_653667_1:000c64|snap-NC_003421.2-processed-gene-21.19-mRNA-1|+|0
snap-NC_003421.2-processed-gene-9.98-mRNA-1	MetaEuk	gene	85	3054	1363	+	.	Target_ID=17174at4751_483514_1:000959;TCS_ID=17174at4751_483514_1:000959|snap-NC_003421.2-processed-gene-9.98-mRNA-1|+|84
snap-NC_003421.2-processed-gene-3.83-mRNA-1	MetaEuk	gene	13	1818	724	+	.	Target_ID=173428at4751_483514_1:000b3b;TCS_ID=173428at4751_483514_1:000b3b|snap-NC_003421.2-processed-gene-3.83-mRNA-1|+|12
snap-NC_003421.2-processed-gene-4.115-mRNA-1	MetaEuk	gene	16	1542	629	+	.	Target_ID=176648at4751_483514_1:000b29;TCS_ID=176648at4751_483514_1:000b29|snap-NC_003421.2-processed-gene-4.115-mRNA-1|+|15
maker-NC_003421.2-snap-gene-17.42-mRNA-1	MetaEuk	gene	176	1633	846	+	.	Target_ID=179437at4751_653667_1:0009e6;TCS_ID=179437at4751_653667_1:0009e6|maker-NC_003421.2-snap-gene-17.42-mRNA-1|+|175
maker-NC_003421.2-augustus-gene-20.44-mRNA-1	MetaEuk	gene	258	1160	505	+	.	Target_ID=183801at4751_653667_1:000bc2;TCS_ID=183801at4751_653667_1:000bc2|maker-NC_003421.2-augustus-gene-20.44-mRNA-1|+|257
maker-NC_003421.2-augustus-gene-6.35-mRNA-1	MetaEuk	gene	78	2381	1122	+	.	Target_ID=185196at4751_653667_1:00101f;TCS_ID=185196at4751_653667_1:00101f|maker-NC_003421.2-augustus-gene-6.35-mRNA-1|+|77
augustus-NC_003421.2-processed-gene-13.36-mRNA-1	MetaEuk	gene	1	3126	879	+	.	Target_ID=186701at4751_653667_1:000c7d;TCS_ID=186701at4751_653667_1:000c7d|augustus-NC_003421.2-processed-gene-13.36-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-4.63-mRNA-1	MetaEuk	gene	37	1200	739	+	.	Target_ID=188070at4751_653667_1:0010e8;TCS_ID=188070at4751_653667_1:0010e8|maker-NC_003421.2-augustus-gene-4.63-mRNA-1|+|36
maker-NC_003421.2-augustus-gene-21.55-mRNA-1	MetaEuk	gene	219	2036	880	+	.	Target_ID=189234at4751_653667_1:000c0f;TCS_ID=189234at4751_653667_1:000c0f|maker-NC_003421.2-augustus-gene-21.55-mRNA-1|+|218
maker-NC_003421.2-augustus-gene-23.143-mRNA-1	MetaEuk	gene	141	1439	712	+	.	Target_ID=190183at4751_653667_1:0010d8;TCS_ID=190183at4751_653667_1:0010d8|maker-NC_003421.2-augustus-gene-23.143-mRNA-1|+|140
snap-NC_003421.2-processed-gene-23.46-mRNA-1	MetaEuk	gene	1	1956	936	+	.	Target_ID=190475at4751_653667_1:00113c;TCS_ID=190475at4751_653667_1:00113c|snap-NC_003421.2-processed-gene-23.46-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-8.68-mRNA-1	MetaEuk	gene	1	969	381	+	.	Target_ID=200331at4751_653667_1:0010d1;TCS_ID=200331at4751_653667_1:0010d1|augustus-NC_003421.2-processed-gene-8.68-mRNA-1|+|0
maker-NC_003421.2-snap-gene-7.36-mRNA-1	MetaEuk	gene	63	1217	657	+	.	Target_ID=203109at4751_483514_1:0008b9;TCS_ID=203109at4751_483514_1:0008b9|maker-NC_003421.2-snap-gene-7.36-mRNA-1|+|62
snap-NC_003421.2-processed-gene-18.93-mRNA-1	MetaEuk	gene	1	1182	707	+	.	Target_ID=204087at4751_483514_1:0009f3;TCS_ID=204087at4751_483514_1:0009f3|snap-NC_003421.2-processed-gene-18.93-mRNA-1|+|0
snap-NC_003421.2-processed-gene-4.104-mRNA-1	MetaEuk	gene	1	2226	874	+	.	Target_ID=204341at4751_483514_1:0008f8;TCS_ID=204341at4751_483514_1:0008f8|snap-NC_003421.2-processed-gene-4.104-mRNA-1|+|0
snap-NC_003421.2-processed-gene-10.5-mRNA-1	MetaEuk	gene	4	1209	555	+	.	Target_ID=209619at4751_653667_1:00112e;TCS_ID=209619at4751_653667_1:00112e|snap-NC_003421.2-processed-gene-10.5-mRNA-1|+|3
snap-NC_003421.2-processed-gene-17.97-mRNA-1	MetaEuk	gene	7	1686	771	+	.	Target_ID=211442at4751_483514_1:001292;TCS_ID=211442at4751_483514_1:001292|snap-NC_003421.2-processed-gene-17.97-mRNA-1|+|6
snap-NC_003421.2-processed-gene-3.97-mRNA-1	MetaEuk	gene	79	1287	574	+	.	Target_ID=216683at4751_483514_1:000954;TCS_ID=216683at4751_483514_1:000954|snap-NC_003421.2-processed-gene-3.97-mRNA-1|+|78
maker-NC_003421.2-augustus-gene-7.63-mRNA-1	MetaEuk	gene	133	1488	791	+	.	Target_ID=216747at4751_653667_1:0010ff;TCS_ID=216747at4751_653667_1:0010ff|maker-NC_003421.2-augustus-gene-7.63-mRNA-1|+|132
augustus-NC_003421.2-processed-gene-5.71-mRNA-1	MetaEuk	gene	95	2800	1405	+	.	Target_ID=21689at4751_653667_1:0010d2;TCS_ID=21689at4751_653667_1:0010d2|augustus-NC_003421.2-processed-gene-5.71-mRNA-1|+|94
snap-NC_003421.2-processed-gene-9.105-mRNA-1	MetaEuk	gene	1	1308	638	+	.	Target_ID=225535at4751_483514_1:0008ee;TCS_ID=225535at4751_483514_1:0008ee|snap-NC_003421.2-processed-gene-9.105-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-7.56-mRNA-1	MetaEuk	gene	53	4708	1367	+	.	Target_ID=234548at4751_483514_1:000c48;TCS_ID=234548at4751_483514_1:000c48|maker-NC_003421.2-augustus-gene-7.56-mRNA-1|+|52
maker-NC_003421.2-snap-gene-2.18-mRNA-1	MetaEuk	gene	492	1916	400	+	.	Target_ID=237276at4751_402676_1:0003b9;TCS_ID=237276at4751_402676_1:0003b9|maker-NC_003421.2-snap-gene-2.18-mRNA-1|+|491
snap-NC_003421.2-processed-gene-9.106-mRNA-1	MetaEuk	gene	1	1065	594	+	.	Target_ID=237533at4751_653667_1:0010be;TCS_ID=237533at4751_653667_1:0010be|snap-NC_003421.2-processed-gene-9.106-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-4.76-mRNA-1	MetaEuk	gene	673	2325	767	+	.	Target_ID=241079at4751_483514_1:000ccb;TCS_ID=241079at4751_483514_1:000ccb|maker-NC_003421.2-augustus-gene-4.76-mRNA-1|+|672
maker-NC_003421.2-augustus-gene-16.113-mRNA-1	MetaEuk	gene	16	1869	711	+	.	Target_ID=247129at4751_483514_1:000ff4;TCS_ID=247129at4751_483514_1:000ff4|maker-NC_003421.2-augustus-gene-16.113-mRNA-1|+|15
snap-NC_003421.2-processed-gene-14.99-mRNA-1	MetaEuk	gene	1	1083	551	+	.	Target_ID=247383at4751_483514_1:000531;TCS_ID=247383at4751_483514_1:000531|snap-NC_003421.2-processed-gene-14.99-mRNA-1|+|0
maker-NC_003421.2-snap-gene-6.71-mRNA-1	MetaEuk	gene	97	972	200	+	.	Target_ID=252314at4751_1507870_1:001c80;TCS_ID=252314at4751_1507870_1:001c80|maker-NC_003421.2-snap-gene-6.71-mRNA-1|+|96
snap-NC_003421.2-processed-gene-23.17-mRNA-1	MetaEuk	gene	1	1794	674	+	.	Target_ID=264164at4751_653667_1:001020;TCS_ID=264164at4751_653667_1:001020|snap-NC_003421.2-processed-gene-23.17-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-1.46-mRNA-1	MetaEuk	gene	1	1278	563	+	.	Target_ID=265325at4751_653667_1:000877;TCS_ID=265325at4751_653667_1:000877|augustus-NC_003421.2-processed-gene-1.46-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-21.46-mRNA-1	MetaEuk	gene	46	1647	802	+	.	Target_ID=281920at4751_483514_1:000457;TCS_ID=281920at4751_483514_1:000457|maker-NC_003421.2-augustus-gene-21.46-mRNA-1|+|45
maker-NC_003421.2-augustus-gene-8.50-mRNA-1	MetaEuk	gene	64	2553	1089	+	.	Target_ID=284377at4751_653667_1:001120;TCS_ID=284377at4751_653667_1:001120|maker-NC_003421.2-augustus-gene-8.50-mRNA-1|+|63
snap-NC_003421.2-processed-gene-21.9-mRNA-1	MetaEuk	gene	1545	2417	484	+	.	Target_ID=289666at4751_653667_1:000b78;TCS_ID=289666at4751_653667_1:000b78|snap-NC_003421.2-processed-gene-21.9-mRNA-1|+|1544
augustus-NC_003421.2-processed-gene-5.90-mRNA-1	MetaEuk	gene	1	852	474	+	.	Target_ID=295692at4751_653667_1:0010dd;TCS_ID=295692at4751_653667_1:0010dd|augustus-NC_003421.2-processed-gene-5.90-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-21.52-mRNA-1	MetaEuk	gene	127	1455	514	+	.	Target_ID=297671at4751_483514_1:0000ad;TCS_ID=297671at4751_483514_1:0000ad|maker-NC_003421.2-augustus-gene-21.52-mRNA-1|+|126
maker-NC_003421.2-snap-gene-0.26-mRNA-1	MetaEuk	gene	260	1132	460	+	.	Target_ID=299330at4751_483514_1:000f99;TCS_ID=299330at4751_483514_1:000f99|maker-NC_003421.2-snap-gene-0.26-mRNA-1|+|259
maker-NC_003421.2-snap-gene-11.39-mRNA-1	MetaEuk	gene	73	1146	654	+	.	Target_ID=299509at4751_653667_1:000d1c;TCS_ID=299509at4751_653667_1:000d1c|maker-NC_003421.2-snap-gene-11.39-mRNA-1|+|72
maker-NC_003421.2-augustus-gene-16.99-mRNA-1	MetaEuk	gene	1	918	555	+	.	Target_ID=299583at4751_483514_1:00051f;TCS_ID=299583at4751_483514_1:00051f|maker-NC_003421.2-augustus-gene-16.99-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-4.66-mRNA-1	MetaEuk	gene	2915	3778	461	+	.	Target_ID=304341at4751_653667_1:00104e;TCS_ID=304341at4751_653667_1:00104e|maker-NC_003421.2-augustus-gene-4.66-mRNA-1|+|2914
maker-NC_003421.2-augustus-gene-19.45-mRNA-1	MetaEuk	gene	47	2662	1201	+	.	Target_ID=305061at4751_653667_1:000ab2;TCS_ID=305061at4751_653667_1:000ab2|maker-NC_003421.2-augustus-gene-19.45-mRNA-1|+|46
maker-NC_003421.2-augustus-gene-13.61-mRNA-1	MetaEuk	gene	57	1367	632	+	.	Target_ID=306594at4751_653667_1:000986;TCS_ID=306594at4751_653667_1:000986|maker-NC_003421.2-augustus-gene-13.61-mRNA-1|+|56
maker-NC_003421.2-snap-gene-2.14-mRNA-1	MetaEuk	gene	7	2199	1034	+	.	Target_ID=310718at4751_653667_1:000ffc;TCS_ID=310718at4751_653667_1:000ffc|maker-NC_003421.2-snap-gene-2.14-mRNA-1|+|6
maker-NC_003421.2-augustus-gene-1.104-mRNA-1	MetaEuk	gene	336	1130	400	+	.	Target_ID=312209at4751_653667_1:00105d;TCS_ID=312209at4751_653667_1:00105d|maker-NC_003421.2-augustus-gene-1.104-mRNA-1|+|335
snap-NC_003421.2-processed-gene-14.91-mRNA-1	MetaEuk	gene	1	3294	1030	+	.	Target_ID=31256at4751_653667_1:000a33;TCS_ID=31256at4751_653667_1:000a33|snap-NC_003421.2-processed-gene-14.91-mRNA-1|+|0
snap-NC_003421.2-processed-gene-14.97-mRNA-1	MetaEuk	gene	55	957	529	+	.	Target_ID=321728at4751_653667_1:000c26;TCS_ID=321728at4751_653667_1:000c26|snap-NC_003421.2-processed-gene-14.97-mRNA-1|+|54
maker-NC_003421.2-augustus-gene-14.61-mRNA-1	MetaEuk	gene	118	1137	631	+	.	Target_ID=323327at4751_653667_1:000c51;TCS_ID=323327at4751_653667_1:000c51|maker-NC_003421.2-augustus-gene-14.61-mRNA-1|+|117
maker-NC_003421.2-augustus-gene-1.93-mRNA-1	MetaEuk	gene	1539	2384	450	+	.	Target_ID=325992at4751_653667_1:00083f;TCS_ID=325992at4751_653667_1:00083f|maker-NC_003421.2-augustus-gene-1.93-mRNA-1|+|1538
maker-NC_003421.2-augustus-gene-19.56-mRNA-1	MetaEuk	gene	1	936	492	+	.	Target_ID=327884at4751_483514_1:00063c;TCS_ID=327884at4751_483514_1:00063c|maker-NC_003421.2-augustus-gene-19.56-mRNA-1|+|0
snap-NC_003421.2-processed-gene-21.6-mRNA-1	MetaEuk	gene	1	759	487	+	.	Target_ID=331763at4751_483514_1:000028;TCS_ID=331763at4751_483514_1:000028|snap-NC_003421.2-processed-gene-21.6-mRNA-1|+|0
snap-NC_003421.2-processed-gene-1.10-mRNA-1	MetaEuk	gene	1	1902	1054	+	.	Target_ID=332876at4751_653667_1:0010fc;TCS_ID=332876at4751_653667_1:0010fc|snap-NC_003421.2-processed-gene-1.10-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-4.70-mRNA-1	MetaEuk	gene	117	1016	547	+	.	Target_ID=335719at4751_653667_1:0010bc;TCS_ID=335719at4751_653667_1:0010bc|maker-NC_003421.2-augustus-gene-4.70-mRNA-1|+|116
snap-NC_003421.2-processed-gene-13.94-mRNA-1	MetaEuk	gene	1	1020	594	+	.	Target_ID=336181at4751_653667_1:0008f0;TCS_ID=336181at4751_653667_1:0008f0|snap-NC_003421.2-processed-gene-13.94-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-8.49-mRNA-1	MetaEuk	gene	245	880	274	+	.	Target_ID=336187at4751_653667_1:001126;TCS_ID=336187at4751_653667_1:001126|maker-NC_003421.2-augustus-gene-8.49-mRNA-1|+|244
snap-NC_003421.2-processed-gene-5.33-mRNA-1	MetaEuk	gene	7	2760	1653	+	.	Target_ID=33984at4751_653667_1:001087;TCS_ID=33984at4751_653667_1:001087|snap-NC_003421.2-processed-gene-5.33-mRNA-1|+|6
augustus-NC_003421.2-processed-gene-7.2-mRNA-1	MetaEuk	gene	1	1086	551	+	.	Target_ID=348111at4751_653667_1:001029;TCS_ID=348111at4751_653667_1:001029|augustus-NC_003421.2-processed-gene-7.2-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-13.54-mRNA-1	MetaEuk	gene	38	895	541	+	.	Target_ID=351482at4751_653667_1:000cd2;TCS_ID=351482at4751_653667_1:000cd2|maker-NC_003421.2-augustus-gene-13.54-mRNA-1|+|37
maker-NC_003421.2-snap-gene-22.56-mRNA-1	MetaEuk	gene	10	738	343	+	.	Target_ID=351646at4751_653667_1:000ab5;TCS_ID=351646at4751_653667_1:000ab5|maker-NC_003421.2-snap-gene-22.56-mRNA-1|+|9
maker-NC_003421.2-augustus-gene-22.98-mRNA-1	MetaEuk	gene	28	759	477	+	.	Target_ID=351858at4751_483514_1:0005da;TCS_ID=351858at4751_483514_1:0005da|maker-NC_003421.2-augustus-gene-22.98-mRNA-1|+|27
maker-NC_003421.2-augustus-gene-17.61-mRNA-1	MetaEuk	gene	42	1655	739	+	.	Target_ID=355454at4751_653667_1:000a48;TCS_ID=355454at4751_653667_1:000a48|maker-NC_003421.2-augustus-gene-17.61-mRNA-1|+|41
maker-NC_003421.2-augustus-gene-21.48-mRNA-1	MetaEuk	gene	177	1010	430	+	.	Target_ID=355781at4751_483514_1:00043e;TCS_ID=355781at4751_483514_1:00043e|maker-NC_003421.2-augustus-gene-21.48-mRNA-1|+|176
snap-NC_003421.2-processed-gene-6.22-mRNA-1	MetaEuk	gene	1	648	404	+	.	Target_ID=356743at4751_653667_1:0010d9;TCS_ID=356743at4751_653667_1:0010d9|snap-NC_003421.2-processed-gene-6.22-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-21.83-mRNA-1	MetaEuk	gene	1	792	411	+	.	Target_ID=362250at4751_653667_1:000af6;TCS_ID=362250at4751_653667_1:000af6|augustus-NC_003421.2-processed-gene-21.83-mRNA-1|+|0
snap-NC_003421.2-processed-gene-9.97-mRNA-1	MetaEuk	gene	7	735	434	+	.	Target_ID=369435at4751_653667_1:0010fd;TCS_ID=369435at4751_653667_1:0010fd|snap-NC_003421.2-processed-gene-9.97-mRNA-1|+|6
maker-NC_003421.2-augustus-gene-9.74-mRNA-1	MetaEuk	gene	304	1119	504	+	.	Target_ID=372972at4751_402676_1:000dbb;TCS_ID=372972at4751_402676_1:000dbb|maker-NC_003421.2-augustus-gene-9.74-mRNA-1|+|303
snap-NC_003421.2-processed-gene-12.21-mRNA-1	MetaEuk	gene	346	2865	551	+	.	Target_ID=37642at4751_483514_1:001272;TCS_ID=37642at4751_483514_1:001272|snap-NC_003421.2-processed-gene-12.21-mRNA-1|+|345
augustus-NC_003421.2-processed-gene-3.53-mRNA-1	MetaEuk	gene	4	1626	628	+	.	Target_ID=378436at4751_653667_1:000ff9;TCS_ID=378436at4751_653667_1:000ff9|augustus-NC_003421.2-processed-gene-3.53-mRNA-1|+|3
snap-NC_003421.2-processed-gene-21.2-mRNA-1	MetaEuk	gene	1	570	340	+	.	Target_ID=379525at4751_483514_1:00015b;TCS_ID=379525at4751_483514_1:00015b|snap-NC_003421.2-processed-gene-21.2-mRNA-1|+|0
snap-NC_003421.2-processed-gene-8.36-mRNA-1	MetaEuk	gene	1	612	391	+	.	Target_ID=385139at4751_653667_1:001005;TCS_ID=385139at4751_653667_1:001005|snap-NC_003421.2-processed-gene-8.36-mRNA-1|+|0
snap-NC_003421.2-processed-gene-22.20-mRNA-1	MetaEuk	gene	1	543	314	+	.	Target_ID=387347at4751_653667_1:000a8c;TCS_ID=387347at4751_653667_1:000a8c|snap-NC_003421.2-processed-gene-22.20-mRNA-1|+|0
maker-NC_003421.2-snap-gene-1.88-mRNA-1	MetaEuk	gene	178	708	295	+	.	Target_ID=387759at4751_653667_1:001031;TCS_ID=387759at4751_653667_1:001031|maker-NC_003421.2-snap-gene-1.88-mRNA-1|+|177
augustus-NC_003421.2-processed-gene-12.39-mRNA-1	MetaEuk	gene	4589	5641	531	+	.	Target_ID=389547at4751_483514_1:0012bb;TCS_ID=389547at4751_483514_1:0012bb|augustus-NC_003421.2-processed-gene-12.39-mRNA-1|+|4588
maker-NC_003421.2-augustus-gene-4.62-mRNA-1	MetaEuk	gene	92	1057	567	+	.	Target_ID=390518at4751_653667_1:0010c6;TCS_ID=390518at4751_653667_1:0010c6|maker-NC_003421.2-augustus-gene-4.62-mRNA-1|+|91
snap-NC_003421.2-processed-gene-17.96-mRNA-1	MetaEuk	gene	1	621	314	+	.	Target_ID=399413at4751_653667_1:0008a0;TCS_ID=399413at4751_653667_1:0008a0|snap-NC_003421.2-processed-gene-17.96-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-9.65-mRNA-1	MetaEuk	gene	26	652	337	+	.	Target_ID=399810at4751_483514_1:000dc5;TCS_ID=399810at4751_483514_1:000dc5|maker-NC_003421.2-augustus-gene-9.65-mRNA-1|+|25
snap-NC_003421.2-processed-gene-11.7-mRNA-1	MetaEuk	gene	28	924	409	+	.	Target_ID=401387at4751_483514_1:0010b5;TCS_ID=401387at4751_483514_1:0010b5|snap-NC_003421.2-processed-gene-11.7-mRNA-1|+|27
maker-NC_003421.2-augustus-gene-22.102-mRNA-1	MetaEuk	gene	159	1013	414	+	.	Target_ID=403079at4751_483514_1:000201;TCS_ID=403079at4751_483514_1:000201|maker-NC_003421.2-augustus-gene-22.102-mRNA-1|+|158
maker-NC_003421.2-augustus-gene-19.47-mRNA-1	MetaEuk	gene	383	1582	520	+	.	Target_ID=407348at4751_653667_1:000c1f;TCS_ID=407348at4751_653667_1:000c1f|maker-NC_003421.2-augustus-gene-19.47-mRNA-1|+|382
snap-NC_003421.2-processed-gene-14.77-mRNA-1	MetaEuk	gene	10	981	557	+	.	Target_ID=410782at4751_653667_1:0009f5;TCS_ID=410782at4751_653667_1:0009f5|snap-NC_003421.2-processed-gene-14.77-mRNA-1|+|9
maker-NC_003421.2-snap-gene-15.45-mRNA-1	MetaEuk	gene	156	758	178	+	.	Target_ID=411130at4751_237631_1:0017a8;TCS_ID=411130at4751_237631_1:0017a8|maker-NC_003421.2-snap-gene-15.45-mRNA-1|+|155
maker-NC_003421.2-augustus-gene-1.96-mRNA-1	MetaEuk	gene	65	604	366	+	.	Target_ID=412006at4751_653667_1:00105b;TCS_ID=412006at4751_653667_1:00105b|maker-NC_003421.2-augustus-gene-1.96-mRNA-1|+|64
snap-NC_003421.2-processed-gene-9.76-mRNA-1	MetaEuk	gene	1	699	418	+	.	Target_ID=419200at4751_653667_1:00115a;TCS_ID=419200at4751_653667_1:00115a|snap-NC_003421.2-processed-gene-9.76-mRNA-1|+|0
maker-NC_003421.2-snap-gene-6.66-mRNA-1	MetaEuk	gene	205	729	255	+	.	Target_ID=419667at4751_653667_1:00111e;TCS_ID=419667at4751_653667_1:00111e|maker-NC_003421.2-snap-gene-6.66-mRNA-1|+|204
maker-NC_003421.2-snap-gene-7.34-mRNA-1	MetaEuk	gene	1836	2375	319	+	.	Target_ID=421097at4751_483514_1:0007c7;TCS_ID=421097at4751_483514_1:0007c7|maker-NC_003421.2-snap-gene-7.34-mRNA-1|+|1835
maker-NC_003421.2-augustus-gene-1.94-mRNA-1	MetaEuk	gene	84	1199	433	+	.	Target_ID=422764at4751_653667_1:0009be;TCS_ID=422764at4751_653667_1:0009be|maker-NC_003421.2-augustus-gene-1.94-mRNA-1|+|83
maker-NC_003421.2-augustus-gene-13.53-mRNA-1	MetaEuk	gene	505	921	280	+	.	Target_ID=423166at4751_483514_1:000e4a;TCS_ID=423166at4751_483514_1:000e4a|maker-NC_003421.2-augustus-gene-13.53-mRNA-1|+|504
snap-NC_003421.2-processed-gene-8.1-mRNA-1	MetaEuk	gene	1	459	273	+	.	Target_ID=428342at4751_653667_1:0010cf;TCS_ID=428342at4751_653667_1:0010cf|snap-NC_003421.2-processed-gene-8.1-mRNA-1|+|0
snap-NC_003421.2-processed-gene-22.32-mRNA-1	MetaEuk	gene	22	582	213	+	.	Target_ID=433384at4751_483514_1:000619;TCS_ID=433384at4751_483514_1:000619|snap-NC_003421.2-processed-gene-22.32-mRNA-1|+|21
snap-NC_003421.2-processed-gene-13.100-mRNA-1	MetaEuk	gene	1	570	224	+	.	Target_ID=444602at4751_653667_1:0008e0;TCS_ID=444602at4751_653667_1:0008e0|snap-NC_003421.2-processed-gene-13.100-mRNA-1|+|0
maker-NC_003421.2-snap-gene-7.44-mRNA-1	MetaEuk	gene	96	521	222	+	.	Target_ID=445954at4751_483514_1:000b1c;TCS_ID=445954at4751_483514_1:000b1c|maker-NC_003421.2-snap-gene-7.44-mRNA-1|+|95
maker-NC_003421.2-augustus-gene-14.60-mRNA-1	MetaEuk	gene	200	880	396	+	.	Target_ID=449717at4751_653667_1:0009c2;TCS_ID=449717at4751_653667_1:0009c2|maker-NC_003421.2-augustus-gene-14.60-mRNA-1|+|199
augustus-NC_003421.2-processed-gene-7.11-mRNA-1	MetaEuk	gene	245	946	274	+	.	Target_ID=449803at4751_653667_1:001145;TCS_ID=449803at4751_653667_1:001145|augustus-NC_003421.2-processed-gene-7.11-mRNA-1|+|244
snap-NC_003421.2-processed-gene-11.9-mRNA-1	MetaEuk	gene	55	792	334	+	.	Target_ID=454840at4751_653667_1:000c80;TCS_ID=454840at4751_653667_1:000c80|snap-NC_003421.2-processed-gene-11.9-mRNA-1|+|54
augustus-NC_003421.2-processed-gene-21.98-mRNA-1	MetaEuk	gene	1	1002	368	+	.	Target_ID=458980at4751_653667_1:000bec;TCS_ID=458980at4751_653667_1:000bec|augustus-NC_003421.2-processed-gene-21.98-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-22.105-mRNA-1	MetaEuk	gene	160	684	307	+	.	Target_ID=459844at4751_653667_1:000a84;TCS_ID=459844at4751_653667_1:000a84|maker-NC_003421.2-augustus-gene-22.105-mRNA-1|+|159
maker-NC_003421.2-augustus-gene-3.1-mRNA-1	MetaEuk	gene	79	3078	1535	+	.	Target_ID=46098at4751_653667_1:000fef;TCS_ID=46098at4751_653667_1:000fef|maker-NC_003421.2-augustus-gene-3.1-mRNA-1|+|78
snap-NC_003421.2-processed-gene-9.78-mRNA-1	MetaEuk	gene	1	624	341	+	.	Target_ID=464711at4751_653667_1:0010d7;TCS_ID=464711at4751_653667_1:0010d7|snap-NC_003421.2-processed-gene-9.78-mRNA-1|+|0
snap-NC_003421.2-processed-gene-21.39-mRNA-1	MetaEuk	gene	1	1005	261	+	.	Target_ID=474125at4751_653667_1:000b29;TCS_ID=474125at4751_653667_1:000b29|snap-NC_003421.2-processed-gene-21.39-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-21.86-mRNA-1	MetaEuk	gene	70	453	244	+	.	Target_ID=474374at4751_653667_1:000c1d;TCS_ID=474374at4751_653667_1:000c1d|augustus-NC_003421.2-processed-gene-21.86-mRNA-1|+|69
maker-NC_003421.2-snap-gene-21.69-mRNA-1	MetaEuk	gene	121	1023	345	+	.	Target_ID=482337at4751_653667_1:000c60;TCS_ID=482337at4751_653667_1:000c60|maker-NC_003421.2-snap-gene-21.69-mRNA-1|+|120
maker-NC_003421.2-augustus-gene-11.45-mRNA-1	MetaEuk	gene	62	580	186	+	.	Target_ID=485650at4751_483514_1:000dfb;TCS_ID=485650at4751_483514_1:000dfb|maker-NC_003421.2-augustus-gene-11.45-mRNA-1|+|61
maker-NC_003421.2-snap-gene-6.72-mRNA-1	MetaEuk	gene	1	387	182	+	.	Target_ID=490662at4751_653667_1:001012;TCS_ID=490662at4751_653667_1:001012|maker-NC_003421.2-snap-gene-6.72-mRNA-1|+|0
snap-NC_003421.2-processed-gene-19.64-mRNA-1	MetaEuk	gene	1	14151	5082	+	.	Target_ID=494at4751_653667_1:000b57;TCS_ID=494at4751_653667_1:000b57|snap-NC_003421.2-processed-gene-19.64-mRNA-1|+|0
snap-NC_003421.2-processed-gene-12.13-mRNA-1	MetaEuk	gene	178	3867	1647	+	.	Target_ID=58127at4751_653667_1:000d01;TCS_ID=58127at4751_653667_1:000d01|snap-NC_003421.2-processed-gene-12.13-mRNA-1|+|177
maker-NC_003421.2-augustus-gene-22.99-mRNA-1	MetaEuk	gene	211	2910	1286	+	.	Target_ID=61438at4751_483514_1:0001db;TCS_ID=61438at4751_483514_1:0001db|maker-NC_003421.2-augustus-gene-22.99-mRNA-1|+|210
maker-NC_003421.2-augustus-gene-6.53-mRNA-1	MetaEuk	gene	117	2045	1059	+	.	Target_ID=65334at4751_483514_1:000920;TCS_ID=65334at4751_483514_1:000920|maker-NC_003421.2-augustus-gene-6.53-mRNA-1|+|116
snap-NC_003421.2-processed-gene-23.20-mRNA-1	MetaEuk	gene	1	2505	1125	+	.	Target_ID=65499at4751_653667_1:000b7a;TCS_ID=65499at4751_653667_1:000b7a|snap-NC_003421.2-processed-gene-23.20-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-13.58-mRNA-1	MetaEuk	gene	522	2678	1025	+	.	Target_ID=66151at4751_653667_1:00087c;TCS_ID=66151at4751_653667_1:00087c|maker-NC_003421.2-augustus-gene-13.58-mRNA-1|+|521
maker-NC_003421.2-augustus-gene-3.16-mRNA-1	MetaEuk	gene	226	2325	1214	+	.	Target_ID=67399at4751_653667_1:001114;TCS_ID=67399at4751_653667_1:001114|maker-NC_003421.2-augustus-gene-3.16-mRNA-1|+|225
maker-NC_003421.2-augustus-gene-16.101-mRNA-1	MetaEuk	gene	222	2606	1189	+	.	Target_ID=71046at4751_653667_1:000af4;TCS_ID=71046at4751_653667_1:000af4|maker-NC_003421.2-augustus-gene-16.101-mRNA-1|+|221
maker-NC_003421.2-augustus-gene-11.47-mRNA-1	MetaEuk	gene	1	3948	1940	+	.	Target_ID=75709at4751_653667_1:000d74;TCS_ID=75709at4751_653667_1:000d74|maker-NC_003421.2-augustus-gene-11.47-mRNA-1|+|0
snap-NC_003421.2-processed-gene-9.112-mRNA-1	MetaEuk	gene	1	1755	1067	+	.	Target_ID=79294at4751_483514_1:001102;TCS_ID=79294at4751_483514_1:001102|snap-NC_003421.2-processed-gene-9.112-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-8.75-mRNA-1	MetaEuk	gene	1	2331	1223	+	.	Target_ID=79797at4751_483514_1:000aaa;TCS_ID=79797at4751_483514_1:000aaa|augustus-NC_003421.2-processed-gene-8.75-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-21.51-mRNA-1	MetaEuk	gene	204	2411	676	+	.	Target_ID=79988at4751_653667_1:000bf1;TCS_ID=79988at4751_653667_1:000bf1|maker-NC_003421.2-augustus-gene-21.51-mRNA-1|+|203
snap-NC_003421.2-processed-gene-6.6-mRNA-1	MetaEuk	gene	1	5052	2277	+	.	Target_ID=81614at4751_653667_1:00109f;TCS_ID=81614at4751_653667_1:00109f|snap-NC_003421.2-processed-gene-6.6-mRNA-1|+|0
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Genome sequence:
- step_state: scheduled
Step 2: Genome assembly:
- step_state: scheduled

Step 11: Map annotation ids:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat' '/tmp/tmp9cvtqig0/job_working_directory/000/11/outputs/dataset_97ca84e4-a0f2-4f87-9407-2d9484e00683.dat' && maker_map_ids --prefix 'TEST_' --justify 6 '/tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat' > '/tmp/tmp9cvtqig0/job_working_directory/000/11/outputs/dataset_3c0f8748-863d-446f-ac8c-aafcddc2c395.dat' && map_gff_ids '/tmp/tmp9cvtqig0/job_working_directory/000/11/outputs/dataset_3c0f8748-863d-446f-ac8c-aafcddc2c395.dat' '/tmp/tmp9cvtqig0/job_working_directory/000/11/outputs/dataset_97ca84e4-a0f2-4f87-9407-2d9484e00683.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
justify	`"6"`
prefix	`"TEST_"`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp9cvtqig0/files/9/3/2/dataset_93278d3b-41ee-48e7-908b-e13196d0f653.dat' --mode 'tran' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-12-18 14:45:08 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-12-18 14:37:45 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 12/18/2024 14:37:45 *****
2024-12-18 14:37:45 INFO:	Configuring BUSCO with local environment
2024-12-18 14:37:45 INFO:	Running transcriptome mode
2024-12-18 14:37:45 INFO:	Input file is /tmp/tmp9cvtqig0/files/9/3/2/dataset_93278d3b-41ee-48e7-908b-e13196d0f653.dat
2024-12-18 14:37:45 WARNING:	Option contig_break was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:37:45 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:37:45 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:37:45 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2024-12-18 14:37:45 INFO:	Running 1 job(s) on metaeuk, starting at 12/18/2024 14:37:45
2024-12-18 14:40:26 INFO:	[metaeuk]	1 of 1 task(s) completed
2024-12-18 14:40:26 INFO:	***** Run HMMER on gene sequences *****
2024-12-18 14:40:26 INFO:	Running 758 job(s) on hmmsearch, starting at 12/18/2024 14:40:26
2024-12-18 14:40:29 INFO:	[hmmsearch]	76 of 758 task(s) completed
2024-12-18 14:40:30 INFO:	[hmmsearch]	152 of 758 task(s) completed
2024-12-18 14:40:32 INFO:	[hmmsearch]	228 of 758 task(s) completed
2024-12-18 14:40:34 INFO:	[hmmsearch]	304 of 758 task(s) completed
2024-12-18 14:40:35 INFO:	[hmmsearch]	379 of 758 task(s) completed
2024-12-18 14:40:36 INFO:	[hmmsearch]	455 of 758 task(s) completed
2024-12-18 14:40:37 INFO:	[hmmsearch]	531 of 758 task(s) completed
2024-12-18 14:40:38 INFO:	[hmmsearch]	607 of 758 task(s) completed
2024-12-18 14:40:39 INFO:	[hmmsearch]	683 of 758 task(s) completed
2024-12-18 14:40:41 INFO:	[hmmsearch]	758 of 758 task(s) completed
2024-12-18 14:40:41 INFO:	140 exons in total
2024-12-18 14:40:41 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-12-18 14:41:02 INFO:	Running 1 job(s) on metaeuk, starting at 12/18/2024 14:41:02
2024-12-18 14:44:53 INFO:	[metaeuk]	1 of 1 task(s) completed
2024-12-18 14:44:53 INFO:	***** Run HMMER on gene sequences *****
2024-12-18 14:44:53 INFO:	Running 630 job(s) on hmmsearch, starting at 12/18/2024 14:44:53
2024-12-18 14:44:55 INFO:	[hmmsearch]	63 of 630 task(s) completed
2024-12-18 14:44:56 INFO:	[hmmsearch]	126 of 630 task(s) completed
2024-12-18 14:44:57 INFO:	[hmmsearch]	189 of 630 task(s) completed
2024-12-18 14:44:58 INFO:	[hmmsearch]	252 of 630 task(s) completed
2024-12-18 14:44:59 INFO:	[hmmsearch]	315 of 630 task(s) completed
2024-12-18 14:45:00 INFO:	[hmmsearch]	378 of 630 task(s) completed
2024-12-18 14:45:01 INFO:	[hmmsearch]	441 of 630 task(s) completed
2024-12-18 14:45:02 INFO:	[hmmsearch]	504 of 630 task(s) completed
2024-12-18 14:45:03 INFO:	[hmmsearch]	567 of 630 task(s) completed
2024-12-18 14:45:04 INFO:	[hmmsearch]	630 of 630 task(s) completed
2024-12-18 14:45:05 INFO:	1 candidate overlapping regions found
2024-12-18 14:45:05 INFO:	143 exons in total
2024-12-18 14:45:05 INFO:	Results:	C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758	   

2024-12-18 14:45:05 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758      |
    |128    Complete BUSCOs (C)                        |
    |127    Complete and single-copy BUSCOs (S)        |
    |1    Complete and duplicated BUSCOs (D)           |
    |11    Fragmented BUSCOs (F)                       |
    |619    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-12-18 14:45:05 INFO:	BUSCO analysis done with WARNING(s). Total running time: 440 seconds

***** Summary of warnings: *****
2024-12-18 14:37:45 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:37:45 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:37:45 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2024-12-18 14:45:05 INFO:	Results written in /tmp/tmp9cvtqig0/job_working_directory/000/12/working/busco_galaxy
2024-12-18 14:45:05 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-12-18 14:45:05 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 64
drwxr-xr-x 5 1001 118  4096 Dec 18 14:37 busco_sequences
-rw-r--r-- 1 1001 118 36033 Dec 18 14:45 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Dec 18 14:40 hmmer_output
drwxr-xr-x 4 1001 118  4096 Dec 18 14:45 metaeuk_output
-rw-r--r-- 1 1001 118  8066 Dec 18 14:45 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2395 Dec 18 14:45 short_summary.json
-rw-r--r-- 1 1001 118   761 Dec 18 14:45 short_summary.txt
2024-12-18 14:45:06 INFO:	****************** Start plot generation at 12/18/2024 14:45:06 ******************
2024-12-18 14:45:06 INFO:	Load data ...
2024-12-18 14:45:06 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2024-12-18 14:45:06 INFO:	Generate the R code ...
2024-12-18 14:45:06 INFO:	Run the R code ...
2024-12-18 14:45:08 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-12-18 14:45:08 INFO:	Plot generation done. Total running time: 2.167381525039673 seconds
2024-12-18 14:45:08 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image", "gff"]`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmp9cvtqig0/job_working_directory/000/13/outputs/dataset_fd23a98e-ab40-4e23-ae8d-f9fc83c80cb7_files &&  cp /tmp/tmp9cvtqig0/job_working_directory/000/13/configs/tmpzlqn969i /tmp/tmp9cvtqig0/job_working_directory/000/13/outputs/dataset_fd23a98e-ab40-4e23-ae8d-f9fc83c80cb7_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp9cvtqig0/job_working_directory/000/13/outputs/dataset_fd23a98e-ab40-4e23-ae8d-f9fc83c80cb7_files /tmp/tmp9cvtqig0/job_working_directory/000/13/configs/tmpzlqn969i &&  cp /tmp/tmp9cvtqig0/job_working_directory/000/13/outputs/dataset_fd23a98e-ab40-4e23-ae8d-f9fc83c80cb7_files/index.html /tmp/tmp9cvtqig0/job_working_directory/000/13/outputs/dataset_fd23a98e-ab40-4e23-ae8d-f9fc83c80cb7.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Maker annotation / Map annotation ids on data 12: renamed GFF
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Maker annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 18, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 3: Protein sequences:
- step_state: scheduled
Step 4: Augustus training:
- step_state: scheduled
Step 5: SNAP training:
- step_state: scheduled

**Step 6: Fasta Statistics **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmp9cvtqig0/files/d/6/1/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.dat' --stats_output '/tmp/tmp9cvtqig0/job_working_directory/000/6/outputs/dataset_e8e5918e-83c5-4043-b6e9-a0061e7cbbbe.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp9cvtqig0/files/d/6/1/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.dat' --mode 'tran' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-12-18 14:24:55 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-12-18 14:14:03 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 12/18/2024 14:14:03 *****
2024-12-18 14:14:03 INFO:	Configuring BUSCO with local environment
2024-12-18 14:14:03 INFO:	Running transcriptome mode
2024-12-18 14:14:05 INFO:	Input file is /tmp/tmp9cvtqig0/files/d/6/1/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.dat
2024-12-18 14:14:05 WARNING:	Option contig_break was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:14:05 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:14:05 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:14:05 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2024-12-18 14:14:05 INFO:	Running 1 job(s) on metaeuk, starting at 12/18/2024 14:14:05
2024-12-18 14:17:18 INFO:	[metaeuk]	1 of 1 task(s) completed
2024-12-18 14:17:18 INFO:	***** Run HMMER on gene sequences *****
2024-12-18 14:17:18 INFO:	Running 758 job(s) on hmmsearch, starting at 12/18/2024 14:17:18
2024-12-18 14:17:26 INFO:	[hmmsearch]	76 of 758 task(s) completed
2024-12-18 14:17:33 INFO:	[hmmsearch]	152 of 758 task(s) completed
2024-12-18 14:17:40 INFO:	[hmmsearch]	228 of 758 task(s) completed
2024-12-18 14:17:47 INFO:	[hmmsearch]	304 of 758 task(s) completed
2024-12-18 14:17:53 INFO:	[hmmsearch]	379 of 758 task(s) completed
2024-12-18 14:17:59 INFO:	[hmmsearch]	455 of 758 task(s) completed
2024-12-18 14:18:05 INFO:	[hmmsearch]	531 of 758 task(s) completed
2024-12-18 14:18:11 INFO:	[hmmsearch]	607 of 758 task(s) completed
2024-12-18 14:18:17 INFO:	[hmmsearch]	683 of 758 task(s) completed
2024-12-18 14:18:24 INFO:	[hmmsearch]	758 of 758 task(s) completed
2024-12-18 14:18:24 INFO:	1 candidate overlapping regions found
2024-12-18 14:18:24 INFO:	265 exons in total
2024-12-18 14:18:25 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-12-18 14:18:46 INFO:	Running 1 job(s) on metaeuk, starting at 12/18/2024 14:18:46
2024-12-18 14:24:40 INFO:	[metaeuk]	1 of 1 task(s) completed
2024-12-18 14:24:40 INFO:	***** Run HMMER on gene sequences *****
2024-12-18 14:24:40 INFO:	Running 630 job(s) on hmmsearch, starting at 12/18/2024 14:24:40
2024-12-18 14:24:42 INFO:	[hmmsearch]	63 of 630 task(s) completed
2024-12-18 14:24:43 INFO:	[hmmsearch]	126 of 630 task(s) completed
2024-12-18 14:24:44 INFO:	[hmmsearch]	189 of 630 task(s) completed
2024-12-18 14:24:45 INFO:	[hmmsearch]	252 of 630 task(s) completed
2024-12-18 14:24:46 INFO:	[hmmsearch]	315 of 630 task(s) completed
2024-12-18 14:24:47 INFO:	[hmmsearch]	378 of 630 task(s) completed
2024-12-18 14:24:48 INFO:	[hmmsearch]	441 of 630 task(s) completed
2024-12-18 14:24:49 INFO:	[hmmsearch]	504 of 630 task(s) completed
2024-12-18 14:24:50 INFO:	[hmmsearch]	567 of 630 task(s) completed
2024-12-18 14:24:51 INFO:	[hmmsearch]	630 of 630 task(s) completed
2024-12-18 14:24:52 INFO:	5 candidate overlapping regions found
2024-12-18 14:24:52 INFO:	273 exons in total
2024-12-18 14:24:52 INFO:	Results:	C:16.9%[S:16.9%,D:0.0%],F:1.3%,M:81.8%,n:758	   

2024-12-18 14:24:52 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:16.9%[S:16.9%,D:0.0%],F:1.3%,M:81.8%,n:758      |
    |128    Complete BUSCOs (C)                        |
    |128    Complete and single-copy BUSCOs (S)        |
    |0    Complete and duplicated BUSCOs (D)           |
    |10    Fragmented BUSCOs (F)                       |
    |620    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-12-18 14:24:52 INFO:	BUSCO analysis done with WARNING(s). Total running time: 647 seconds

***** Summary of warnings: *****
2024-12-18 14:14:05 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:14:05 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:14:05 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2024-12-18 14:24:52 INFO:	Results written in /tmp/tmp9cvtqig0/job_working_directory/000/7/working/busco_galaxy
2024-12-18 14:24:52 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-12-18 14:24:52 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 60
drwxr-xr-x 5 1001 118  4096 Dec 18 14:14 busco_sequences
-rw-r--r-- 1 1001 118 32181 Dec 18 14:24 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Dec 18 14:18 hmmer_output
drwxr-xr-x 4 1001 118  4096 Dec 18 14:24 metaeuk_output
-rw-r--r-- 1 1001 118  8079 Dec 18 14:24 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2393 Dec 18 14:24 short_summary.json
-rw-r--r-- 1 1001 118   761 Dec 18 14:24 short_summary.txt
2024-12-18 14:24:53 INFO:	****************** Start plot generation at 12/18/2024 14:24:53 ******************
2024-12-18 14:24:53 INFO:	Load data ...
2024-12-18 14:24:53 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2024-12-18 14:24:53 INFO:	Generate the R code ...
2024-12-18 14:24:53 INFO:	Run the R code ...
2024-12-18 14:24:55 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-12-18 14:24:55 INFO:	Plot generation done. Total running time: 2.2214157581329346 seconds
2024-12-18 14:24:55 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: Maker:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

RM_PATH=$(which RepeatMasker) && if [ -z "$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH ($PATH)" >&2 ; exit 1 ; fi &&  LIBDIR=$(dirname "$RM_PATH")/../share/RepeatMasker/Libraries &&  export LIBDIR &&  maker -CTL  &&  cp '/tmp/tmp9cvtqig0/job_working_directory/000/8/configs/tmp0heb0krf' maker_opts.ctl  &&    cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&  mkdir -p 'augustus_dir/species/' &&  tar -C 'augustus_dir/species/' -xzvf '/tmp/tmp9cvtqig0/files/9/8/2/dataset_982d13e6-6f2c-4fb1-9ee6-7f668291f94e.dat' > /dev/null &&  export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&  MPI_CMD="" && if [ "$MAKER_MPI" == "1" ]; then MPI_CMD="mpiexec -n ${GALAXY_SLOTS:-4}"; fi &&  ${MPI_CMD} maker --ignore_nfs_tmp  maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null  &&  gff3_merge -d *.maker.output/*_master_datastore_index.log -o '/tmp/tmp9cvtqig0/job_working_directory/000/8/outputs/dataset_8a2dba4b-91ab-451a-8041-524f850cb4c8.dat'  &&  awk '{if ($2 == "maker" || $1 ~ /^#/) {print}}' '/tmp/tmp9cvtqig0/job_working_directory/000/8/outputs/dataset_8a2dba4b-91ab-451a-8041-524f850cb4c8.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmp9cvtqig0/job_working_directory/000/8/outputs/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat'  &&  awk '{if ($2 != "maker") {print}}' '/tmp/tmp9cvtqig0/job_working_directory/000/8/outputs/dataset_8a2dba4b-91ab-451a-8041-524f850cb4c8.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmp9cvtqig0/job_working_directory/000/8/outputs/dataset_20ce8a00-e1f3-449d-a8c1-cb8d901133b1.dat'

Exit Code:

```
0
```

Standard Error:

Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore

To access files for individual sequences use the datastore index:
/tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: NC_003421.2
Length: 2452883
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat /tmp/tmp9cvtqig0/tmp/maker_cn677n/NC_003421%2E2.abinit_nomask.0 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/NC_003421%2E2.abinit_nomask.0.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e%2Edat.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --UTR=off /tmp/tmp9cvtqig0/tmp/maker_cn677n/NC_003421%2E2.abinit_nomask.0 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/NC_003421%2E2.abinit_nomask.0.local.augustus
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.0
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.0 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.0.blastn
#-------------------------------#
deleted:2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.1 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.1.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.2
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.2 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.2.blastn
#-------------------------------#
deleted:1 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.3
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.3 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.3.blastn
#-------------------------------#
deleted:0 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.4
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.4 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.4.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.5
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.5 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.5.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.6
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.6 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.6.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.7
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.7 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.7.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.8
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.8 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.8.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.9
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.9 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.9.blastn
#-------------------------------#
deleted:-1 hits
collecting blastn reports
in cluster::shadow_cluster...
...finished clustering.
polishig ESTs
running  est2genome search.
#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/bin/exonerate  -q /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/TRINITY_DN2776_c0_g1_i1.for.1209-2601.0.fasta -t /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1209-2601.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1209-2601.TRINITY_DN2776_c0_g1_i1.e.exonerate
#-------------------------------#
running  est2genome search.
#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/bin/exonerate  -q /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/TRINITY_DN2776_c0_g1_i2.for.1417-2601.0.fasta -t /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1417-2601.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1417-2601.TRINITY_DN2776_c0_g1_i2.e.exonerate
#-------------------------------#
running  est2genome search.
#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/bin/exonerate  -q /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/TRINITY_DN2776_c0_g3_i1.for.1209-2201.0.fasta -t /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1209-2201.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1209-2201.TRINITY_DN2776_c0_g3_i1.e.exonerate
#-------------------------------#
running  est2genome search.
#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/bin/exonerate  -q /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/TRINITY_DN2776_c0_g1_i3.for.1451-2601.0.fasta -t /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1451-2601.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1451-2601.TRINITY_DN2776_c0_g1_i3.e.exonerate
#-------------------------------#
running  est2genome search.
#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/bin/exonerate  -q /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/TRINITY_DN2776_c0_g2_i1.for.1962-3582.0.fasta -t /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1962-3582.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1962-3582.TRINITY_DN2776_c0_g2_i1.e.exonerate
#-------------------------------#
running  est2genome search.
#--------- command -------------#
Widget::exonerate:
..
2-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/132_0.2303936-2305950.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/132_0.2303936-2305950.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/132_0.2303936-2305950.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/132_0.2303936-2305950.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output


Maker is now finished!!!

Standard Output:

Start_time: 1734531234
End_time:   1734532644
Elapsed:    1410

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
abinitio_gene_prediction	`{"aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 4, "src": "hda"}]}}, "snaphmm": {"values": [{"id": 5, "src": "hda"}]}, "unmask": false}`
advanced	`{"AED_threshold": "1.0", "alt_peptide": "C", "alt_splice": false, "always_complete": false, "correct_est_fusion": false, "fix_nucleotides": false, "keep_preds": "0.0", "map_forward": false, "max_dna_len": "100000", "min_contig": "1", "min_protein": "0", "other_gff": null, "pred_flank": "200", "pred_stats": false, "single_exon": {"__current_case__": 0, "single_exon": "0"}, "split_hit": "10000"}`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
est_evidences	`{"altest": null, "altest_gff": null, "est": {"values": [{"id": 2, "src": "hda"}]}, "est2genome": false, "est_gff": null}`
gene_prediction	`{"model_gff": null, "pred_gff": null, "snoscan_rrna": null, "trna": false}`
license_agreement	`true`
organism_type	`"eukaryotic"`
protein_evidences	`{"protein": {"values": [{"id": 3, "src": "hda"}]}, "protein2genome": false, "protein_gff": null}`
reannotation	`{"__current_case__": 0, "reannotate": "no"}`
repeat_masking	`{"repeat_source": {"__current_case__": 3, "source_type": "no"}}`

Step 9: GFFRead:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9cvtqig0/files/d/6/1/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.dat' genomeref.fa &&  gffread '/tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat' -g genomeref.fa  -F -D -E  -w exons.fa

Exit Code:

```
0
```

Standard Error:

Command line was:
gffread /tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat -g genomeref.fa -F -D -E -w exons.fa
FASTA index file genomeref.fa.fai created.
   .. loaded 864 genomic features from /tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
chr_replace	`None`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`true`
expose	`true`
filtering	`None`
full_gff_attribute_preservation	`true`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-w exons.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 10: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp9cvtqig0/job_working_directory/000/10/outputs/dataset_753f9010-5b18-4355-955e-39c082dc5a54.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp9cvtqig0/files/d/6/1/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.dat' 2>&1 | tail -n +3 >> '/tmp/tmp9cvtqig0/job_working_directory/000/10/outputs/dataset_753f9010-5b18-4355-955e-39c082dc5a54.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp9cvtqig0/job_working_directory/000/10/outputs/dataset_753f9010-5b18-4355-955e-39c082dc5a54.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp9cvtqig0/job_working_directory/000/10/outputs/dataset_1894acd3-9681-47ef-a814-19f0303449f3.dat'

Exit Code:

```
0
```

Standard Error:

�[0;33m14:38:07 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m14:38:09 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m14:38:09 [base]�[0m�[0;35m Imported 864 records from `transcript.sizes`.�[0m
�[0;33m14:38:09 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m14:38:09 [base]�[0m�[0;35m Imported 864 records from `transcript.sizes`.�[0m
�[0;33m14:38:09 [stats]�[0m�[0;35m A total of 864 transcripts populated.�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m platform is linux2�[0m
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'unittest.suite', '_ctypes', 'xml.etree', 'json.scanner', 'codecs', 'Bio.collections', 'numpy.os', 'jcvi.annotation.jcvi', 'mkl_fft._numpy_fft', 'StringIO', 'Bio.Alphabet.IUPAC', 'weakref', 'numpy.core._internal', 'distutils.sys', 'numpy.lib.arraypad', 'pprint', 'Bio.SeqIO.math', 'Bio.warnings', 'jcvi.apps.httplib', 'sqlite3.dbapi2', 'select', 'ctypes._ctypes', '_heapq', 'six.moves.urllib', 'numpy.lib.financial', 'Bio.Align.Generic', 'binascii', 'jcvi.formats.sizes', 'unittest.loader', 'unittest.fnmatch', 'numpy.polynomial.chebyshev', '_functools', 'cPickle', 'numpy.polynomial.hermite_e', 'jcvi.apps.urllib', 'jcvi', 'numpy.testing.utils', 'jcvi.graphics.histogram', 'jcvi.utils.UserDict', 'numpy.core.fromnumeric', 'unicodedata', 'numpy.ctypeslib', 'matplotlib._version', '_ast', 'jcvi.utils.range', 'encodings.aliases', 'Bio.SeqIO.SeqXmlIO', 'fnmatch', 'sre_parse', 'pickle', 'Bio.SeqIO.AceIO', 'numpy.random.warnings', 'xml.sax.types', 'jcvi.utils.itertools', 'logging.cStringIO', 'Bio.SeqIO.os', 'numpy.lib.polynomial', 'numpy.compat', 'numbers', 'numpy.core.records', 'strop', 'xml.etree.ElementPath', 'numpy.core.numeric', 'six', 'Bio.array', 'jcvi.apps', 'matplotlib.testing', 'Bio.Alphabet.Bio', 'numpy.lib.utils', 'numpy.lib.arrayterator', 'os.path', 'Bio.GenBank.__future__', '_weakrefset', 'Bio.SeqIO.warnings', 'unittest.traceback', 'unittest.os', 'jcvi.utils.table', 'functools', 'sysconfig', 'sqlite3.collections', 'numpy.polynomial.legendre', 'numpy.matrixlib.defmatrix', 'tempfile', 'imp', 'jcvi.apps.subprocess', 'jcvi.formats.urllib', 'Bio._py3k.commands', 'Bio.SeqIO.Interfaces', 'numpy.linalg.info', 'jcvi.utils.re', 'jcvi.formats.Bio', 'xml.etree._elementtree', 'unittest.util', 'Bio.SeqIO.struct', 'jcvi.apps.time', 'httplib', 'decimal', 'numpy.lib._datasource', 'Bio._py3k.__builtin__', 'jcvi.formats.os', 'jcvi.apps.unicodedata', 'numpy.linalg._umath_linalg', 'cStringIO', 'numpy.polynomial', 'jcvi.annotation.reformat', 'jcvi.graphics.sys', 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'logging.traceback', 'numpy.matrixlib', 'Bio.SeqIO.xml', 'numpy.testing.nose_tools.decorators', 'token', 'backports', 'numpy.lib.mixins', '_posixsubprocess32', 'Bio.SeqIO', 'glob', 'Bio.GenBank.Scanner', 'mpl_toolkits', 'jcvi.utils.sys', 'UserDict', 'inspect', 'jcvi.utils.bisect', 'logging.sys', 'Bio.SeqIO.collections', 'Bio.itertools', 'Bio.Sequencing.__future__', 'Bio.SeqUtils.CheckSum', 'socket', 'numpy.core.memmap', 'cython_runtime', 'Bio.Align.__future__', 'numpy.linalg.lapack_lite', 'Bio.Seq', 'os', 'marshal', '__future__', 'Bio.Alphabet', 'numpy.core.shape_base', 'jcvi.apps.errno', 'matplotlib.compat', '__builtin__', 'xml.sax.xmlreader', 'operator', 'xml.dom.pulldom', 'distutils.string', 'Bio.GenBank.re', 'jcvi.apps.optparse', 'errno', '_socket', 'json', 'jcvi.apps.shutil', 'Bio.SeqIO.PdbIO', 'xml.sax.handler', 'numpy.testing.nose_tools.utils', 'jcvi.formats.hashlib', 'jcvi.utils.urlparse', '_warnings', 'encodings.__builtin__', 'tokenize', 'numpy._distributor_init', 'pwd', 'numpy.core.getlimits', '_sysconfigdata', 'Bio.SeqIO.SffIO', 'numpy.fft', 'numpy.random.numpy', 'logging.time', 'Bio.GenBank.collections', 'jcvi.formats.gff', 'numpy.lib.function_base', 'logging.warnings', 'mimetools', 'xml.sax', 'Bio._py3k.cStringIO', 'logging.codecs', 'numpy.compat.py3k', 'Bio.Data.CodonTable', 'numpy.polynomial._polybase', 'numpy.polynomial.hermite', 'contextlib', 'numpy.polynomial.polynomial', 'grp', 'numpy.core.defchararray', 'gettext', '_abcoll', 'Bio.SeqFeature', 'xml.sax._exceptions', 'genericpath', 'stat', 'urllib2', 'unittest.signals', 'backports.functools_lru_cache', 'ctypes.ctypes', 'numpy.lib.format', 'numpy.testing.nosetester', 'xml.dom', 'time', 'jcvi.apps.socket', 'jcvi.annotation.os', 'Bio.Sequencing.Ace']�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m CACHEDIR=/tmp/tmp9cvtqig0/tmp/matplotlib-KOboYv�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m font search path ['/usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf', '/usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm', '/usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts']�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono-Oblique.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSans-Oblique.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansDisplay.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmr10.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizFourSymReg.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizTwoSymReg.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizThreeSymBol.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralBolIta.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmtt10.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizTwoSymBol.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneral.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmmi10.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizOneSymBol.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmb10.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizThreeSymReg.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniIta.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralItalic.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmss10.ttf�[0m
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Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Other invocation details
- history_id
  - 5319e1fa34219f11
- history_state
  - ok
- invocation_id
  - 5319e1fa34219f11
- invocation_state
  - scheduled
- workflow_id
  - 5319e1fa34219f11

rlibouba · 2025-03-10T14:17:26Z

Hello,
I have made some changes, in particular to the selection of the lineage for BUSCO. In this workflow, you run BUSCO twice using the same lineage. I'd like to do this so that the user can select the line only once :

But I have a problem with the execution of BUSCO. For the lineage_dataset parameter instead of having "--lineage_dataset fungi__odb10", I have this "--lineage_dataset '__lt__galaxy.tools.parameters.workflow_utils.ConnectedValue object at 0x7fc7ac5a78d0__gt__'".

I can't figure out what to put for this parameter. Does anyone have any ideas?

github-actions · 2025-03-10T15:10:14Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

github-actions · 2025-03-10T15:42:06Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

github-actions · 2025-03-10T17:24:40Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

github-actions · 2025-03-11T13:18:27Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

Problems:

Output with path /tmp/tmp_av0iymc/Busco on data 1 short summary__dc403069-a649-4b4a-a746-bafe9c0fe4bb different than expected
Expected 32+-0 lines in the output found 0

Output with path /tmp/tmpbdbsh3i5/Busco on data 1 full table__0a4a75ed-eb61-4594-8aed-9a2af2438cc8 different than expected
Expected text 'BUSCO version is: 5.7.1' in output ('')

Output with path /tmp/tmp4kw0tkmi/Busco on data 1 missing buscos__490e73bf-9fa4-4cc8-9557-60974f77e13c different than expected
Expected text 'BUSCO version is: 5.7.1' in output ('')

Output with path /tmp/tmplzgqc8b_/Map annotation ids on data 12 ID map__df3372cf-5237-4983-a6ec-4c85ff321631 different than expected
Expected text 'snap-NC_003421.2-processed-gene-0.0' in output ('snap_masked-NC_003421.2-processed-gene-0.27	000001
snap_masked-NC_003421.2-processed-gene-0.27-mRNA-1	000001-RA
augustus_masked-NC_003421.2-processed-gene-0.12	000002
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snap_masked-NC_003421.2-processed-gene-0.28	000003
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augustus_masked-NC_003421.2-processed-gene-0.1	000004
augustus_masked-NC_003421.2-processed-gene-0.1-mRNA-1	000004-RA
snap_masked-NC_003421.2-processed-gene-0.31	000005
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snap_masked-NC_003421.2-processed-gene-0.32	000006
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augustus_masked-NC_003421.2-processed-gene-0.3	000007
augustus_masked-NC_003421.2-processed-gene-0.3-mRNA-1	000007-RA
snap_masked-NC_003421.2-processed-gene-0.43	000008
snap_masked-NC_003421.2-processed-gene-0.43-mRNA-1	000008-RA
snap_masked-NC_003421.2-processed-gene-0.44	000009
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maker-NC_003421.2-augustus-gene-0.22	000010
maker-NC_003421.2-augustus-gene-0.22-mRNA-1	000010-RA
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maker-NC_003421.2-augustus-gene-1.38	000027
maker-NC_003421.2-augustus-gene-1.38-mRNA-1	000027-RA
augustus_masked-NC_003421.2-processed-gene-1.4	000028
augustus_masked-NC_003421.2-processed-gene-1.4-mRNA-1	000028-RA
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augustus_masked-NC_003421.2-processed-gene-1.5-mRNA-1	000029-RA
augustus_masked-NC_003421.2-processed-gene-1.19	000030
augustus_masked-NC_003421.2-processed-gene-1.19-mRNA-1	000030-RA
maker-NC_003421.2-augustus-gene-1.39	000031
maker-NC_003421.2-augustus-gene-1.39-mRNA-1	000031-RA
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maker-NC_003421.2-snap-gene-1.57-mRNA-1	000033-RA
augustus_masked-NC_003421.2-processed-gene-1.22	000034
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augustus_masked-NC_003421.2-processed-gene-1.25	000039
augustus_masked-NC_003421.2-processed-gene-1.25-mRNA-1	000039-RA
snap_masked-NC_003421.2-processed-gene-1.71	000040
snap_masked-NC_003421.2-processed-gene-1.71-mRNA-1	000040-RA
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snap_masked-NC_003421.2-processed-gene-1.93	000044
snap_masked-NC_003421.2-processed-gene-1.93-mRNA-1	000044-RA
augustus_masked-NC_003421.2-processed-gene-1.11	000045
augustus_masked-NC_003421.2-processed-gene-1.11-mRNA-1	000045-RA
snap_masked-NC_003421.2-processed-gene-1.94	000046
snap_masked-NC_003421.2-processed-gene-1.94-mRNA-1	000046-RA
snap_masked-NC_003421.2-processed-gene-1.95	000047
snap_masked-NC_003421.2-processed-gene-1.95-mRNA-1	000047-RA
snap_masked-NC_003421.2-processed-gene-1.76	000048
snap_masked-NC_003421.2-processed-gene-1.76-mRNA-1	000048-RA
maker-NC_003421.2-snap-gene-1.58	000049
maker-NC_003421.2-snap-gene-1.58-mRNA-1	000049-RA
maker-NC_003421.2-augustus-gene-1.40	000050
maker-NC_003421.2-augustus-gene-1.40-mRNA-1	000050-RA
maker-NC_003421.2-augustus-gene-1.45	000051
maker-NC_003421.2-augustus-gene-1.45-mRNA-1	000051-RA
maker-NC_003421.2-snap-gene-1.59	000052
maker-NC_003421.2-snap-gene-1.59-mRNA-1	000052-RA
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snap_masked-NC_003421.2-processed-gene-23.39-mRNA-1	000846-RA
augustus_masked-NC_003421.2-processed-gene-23.146	000847
augustus_masked-NC_003421.2-processed-gene-23.146-mRNA-1	000847-RA
maker-NC_003421.2-snap-gene-23.3	000848
maker-NC_003421.2-snap-gene-23.3-mRNA-1	000848-RA
maker-NC_003421.2-augustus-gene-23.93	000849
maker-NC_003421.2-augustus-gene-23.93-mRNA-1	000849-RA
maker-NC_003421.2-augustus-gene-23.81	000850
maker-NC_003421.2-augustus-gene-23.81-mRNA-1	000850-RA
snap_masked-NC_003421.2-processed-gene-23.43	000851
snap_masked-NC_003421.2-processed-gene-23.43-mRNA-1	000851-RA
augustus_masked-NC_003421.2-processed-gene-23.118	000852
augustus_masked-NC_003421.2-processed-gene-23.118-mRNA-1	000852-RA
augustus_masked-NC_003421.2-processed-gene-23.148	000853
augustus_masked-NC_003421.2-processed-gene-23.148-mRNA-1	000853-RA
snap_masked-NC_003421.2-processed-gene-23.74	000854
snap_masked-NC_003421.2-processed-gene-23.74-mRNA-1	000854-RA
augustus_masked-NC_003421.2-processed-gene-23.149	000855
augustus_masked-NC_003421.2-processed-gene-23.149-mRNA-1	000855-RA
snap_masked-NC_003421.2-processed-gene-23.45	000856
snap_masked-NC_003421.2-processed-gene-23.45-mRNA-1	000856-RA
maker-NC_003421.2-snap-gene-23.18	000857
maker-NC_003421.2-snap-gene-23.18-mRNA-1	000857-RA
augustus_masked-NC_003421.2-processed-gene-23.120	000858
augustus_masked-NC_003421.2-processed-gene-23.120-mRNA-1	000858-RA
augustus_masked-NC_003421.2-processed-gene-23.121	000859
augustus_masked-NC_003421.2-processed-gene-23.121-mRNA-1	000859-RA
snap_masked-NC_003421.2-processed-gene-23.77	000860
snap_masked-NC_003421.2-processed-gene-23.77-mRNA-1	000860-RA
')

Workflow invocation details

Invocation Messages

Steps

Step 1: BUSCO lineage:
- step_state: scheduled
Step 2: Genome sequence:
- step_state: scheduled

Step 11: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp59rld10r/files/4/5/8/dataset_458fc7db-bcdc-4002-ac1d-8e611cab431c.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp59rld10r/job_working_directory/000/10/outputs/dataset_816c433a-ead8-4b3f-bbc1-f6104abd3798.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp59rld10r/files/2/6/c/dataset_26c632f3-2942-4af4-832d-28af90393a17.dat' 2>&1 | tail -n +3 >> '/tmp/tmp59rld10r/job_working_directory/000/10/outputs/dataset_816c433a-ead8-4b3f-bbc1-f6104abd3798.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp59rld10r/job_working_directory/000/10/outputs/dataset_816c433a-ead8-4b3f-bbc1-f6104abd3798.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp59rld10r/job_working_directory/000/10/outputs/dataset_61ee4c42-bb64-4984-934f-837b45a70b1d.dat'

Exit Code:

```
0
```

Standard Error:

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�[0;33m13:09:30 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m13:09:30 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m13:09:30 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m13:09:30 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m13:09:30 [stats]�[0m�[0;35m A total of 860 transcripts populated.�[0m
�[0;33m13:09:32 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m13:09:32 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m13:09:32 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m13:09:32 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m13:09:32 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m13:09:32 [__init__]�[0m�[0;35m platform is linux2�[0m
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�[0;33m13:09:32 [__init__]�[0m�[0;35m CACHEDIR=/tmp/tmp59rld10r/tmp/matplotlib-YtnIWC�[0m
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�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono-Oblique.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSans-Oblique.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansDisplay.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmr10.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizFourSymReg.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizTwoSymReg.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizThreeSymBol.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralBolIta.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmtt10.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizTwoSymBol.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneral.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmmi10.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizOneSymBol.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmb10.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizThreeSymReg.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizFiveSymReg.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralItalic.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmss10.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSerif-BoldItalic.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniBolIta.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniBol.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono-Bold.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSerif-Bold.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizOneSymReg.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralBol.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUni.ttf�[0m
�[0;33m13:09:32 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmex10.ttf�[0m
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Saving 7 x 7 in image
Warning message:
Removed 428 rows containing non-finite values (stat_bin). 
�[0;33m13:09:35 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
Intron_Length/input.txt: Min=4 Max=6176 N=1041 Mean=113.748318924 SD=293.903841208 Median=60.0 Sum=118412
�[0;33m13:09:35 [base]�[0m�[0;35m Rscript /tmp/tmp59rld10r/tmp/tmpXvZDWz�[0m
Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
�[0;33m13:09:38 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=42 Max=14154 N=860 Mean=1426.46511628 SD=1122.12972862 Median=1123.5 Sum=1226760
�[0;33m13:09:38 [base]�[0m�[0;35m Rscript /tmp/tmp59rld10r/tmp/tmpYhWyWs�[0m
Warning message:
Removed 29 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 29 rows containing non-finite values (stat_bin). 
�[0;33m13:09:41 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=860 Mean=2.21046511628 SD=1.74039083219 Median=2.0 Sum=1901
�[0;33m13:09:41 [base]�[0m�[0;35m Rscript /tmp/tmp59rld10r/tmp/tmpnBPjW9�[0m
Saving 7 x 7 in image

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6a4816afe7411ef8d457c1e5222e1a9"`
chromInfo	`"/tmp/tmp59rld10r/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 12: Map annotation ids:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmp59rld10r/files/4/5/8/dataset_458fc7db-bcdc-4002-ac1d-8e611cab431c.dat' '/tmp/tmp59rld10r/job_working_directory/000/11/outputs/dataset_0e95cfc1-56cf-429a-afa6-a871f7f234df.dat' && maker_map_ids --prefix '' --justify 6 '/tmp/tmp59rld10r/files/4/5/8/dataset_458fc7db-bcdc-4002-ac1d-8e611cab431c.dat' > '/tmp/tmp59rld10r/job_working_directory/000/11/outputs/dataset_df3372cf-5237-4983-a6ec-4c85ff321631.dat' && map_gff_ids '/tmp/tmp59rld10r/job_working_directory/000/11/outputs/dataset_df3372cf-5237-4983-a6ec-4c85ff321631.dat' '/tmp/tmp59rld10r/job_working_directory/000/11/outputs/dataset_0e95cfc1-56cf-429a-afa6-a871f7f234df.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6a4816afe7411ef8d457c1e5222e1a9"`
chromInfo	`"/tmp/tmp59rld10r/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
justify	`"6"`
prefix	`None`

Step 13: BUSCO on the predicted protein sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp59rld10r/files/2/0/3/dataset_2037c1e2-c284-4078-b7c8-cfb0b06a375b.dat' --mode 'tran' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2025-03-11 13:17:00 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-03-11 13:08:50 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/11/2025 13:08:50 *****
2025-03-11 13:08:50 INFO:	Configuring BUSCO with local environment
2025-03-11 13:08:50 INFO:	Running transcriptome mode
2025-03-11 13:08:50 INFO:	Input file is /tmp/tmp59rld10r/files/2/0/3/dataset_2037c1e2-c284-4078-b7c8-cfb0b06a375b.dat
2025-03-11 13:08:50 WARNING:	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-11 13:08:50 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-11 13:08:50 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2025-03-11 13:08:50 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-11 13:08:50 INFO:	Running 1 job(s) on metaeuk, starting at 03/11/2025 13:08:50
2025-03-11 13:11:28 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-11 13:11:28 INFO:	***** Run HMMER on gene sequences *****
2025-03-11 13:11:28 INFO:	Running 758 job(s) on hmmsearch, starting at 03/11/2025 13:11:28
2025-03-11 13:11:37 INFO:	[hmmsearch]	76 of 758 task(s) completed
2025-03-11 13:11:44 INFO:	[hmmsearch]	152 of 758 task(s) completed
2025-03-11 13:11:51 INFO:	[hmmsearch]	228 of 758 task(s) completed
2025-03-11 13:11:58 INFO:	[hmmsearch]	304 of 758 task(s) completed
2025-03-11 13:12:05 INFO:	[hmmsearch]	379 of 758 task(s) completed
2025-03-11 13:12:11 INFO:	[hmmsearch]	455 of 758 task(s) completed
2025-03-11 13:12:17 INFO:	[hmmsearch]	531 of 758 task(s) completed
2025-03-11 13:12:23 INFO:	[hmmsearch]	607 of 758 task(s) completed
2025-03-11 13:12:30 INFO:	[hmmsearch]	683 of 758 task(s) completed
2025-03-11 13:12:37 INFO:	[hmmsearch]	758 of 758 task(s) completed
2025-03-11 13:12:38 INFO:	142 exons in total
2025-03-11 13:12:38 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2025-03-11 13:12:58 INFO:	Running 1 job(s) on metaeuk, starting at 03/11/2025 13:12:58
2025-03-11 13:16:45 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-11 13:16:45 INFO:	***** Run HMMER on gene sequences *****
2025-03-11 13:16:45 INFO:	Running 630 job(s) on hmmsearch, starting at 03/11/2025 13:16:45
2025-03-11 13:16:47 INFO:	[hmmsearch]	63 of 630 task(s) completed
2025-03-11 13:16:48 INFO:	[hmmsearch]	126 of 630 task(s) completed
2025-03-11 13:16:49 INFO:	[hmmsearch]	189 of 630 task(s) completed
2025-03-11 13:16:50 INFO:	[hmmsearch]	252 of 630 task(s) completed
2025-03-11 13:16:51 INFO:	[hmmsearch]	315 of 630 task(s) completed
2025-03-11 13:16:52 INFO:	[hmmsearch]	378 of 630 task(s) completed
2025-03-11 13:16:53 INFO:	[hmmsearch]	441 of 630 task(s) completed
2025-03-11 13:16:54 INFO:	[hmmsearch]	504 of 630 task(s) completed
2025-03-11 13:16:55 INFO:	[hmmsearch]	567 of 630 task(s) completed
2025-03-11 13:16:56 INFO:	[hmmsearch]	630 of 630 task(s) completed
2025-03-11 13:16:56 INFO:	1 candidate overlapping regions found
2025-03-11 13:16:56 INFO:	145 exons in total
2025-03-11 13:16:56 INFO:	Results:	C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758	   

2025-03-11 13:16:56 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758      |
    |128    Complete BUSCOs (C)                        |
    |127    Complete and single-copy BUSCOs (S)        |
    |1    Complete and duplicated BUSCOs (D)           |
    |11    Fragmented BUSCOs (F)                       |
    |619    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2025-03-11 13:16:56 INFO:	BUSCO analysis done with WARNING(s). Total running time: 487 seconds

***** Summary of warnings: *****
2025-03-11 13:08:50 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-11 13:08:50 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-11 13:08:50 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2025-03-11 13:16:56 INFO:	Results written in /tmp/tmp59rld10r/job_working_directory/000/12/working/busco_galaxy
2025-03-11 13:16:56 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-03-11 13:16:56 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 64
drwxr-xr-x 5 1001 118  4096 Mar 11 13:08 busco_sequences
-rw-r--r-- 1 1001 118 36531 Mar 11 13:16 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Mar 11 13:12 hmmer_output
drwxr-xr-x 4 1001 118  4096 Mar 11 13:16 metaeuk_output
-rw-r--r-- 1 1001 118  8066 Mar 11 13:16 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2395 Mar 11 13:16 short_summary.json
-rw-r--r-- 1 1001 118   761 Mar 11 13:16 short_summary.txt
2025-03-11 13:16:58 INFO:	****************** Start plot generation at 03/11/2025 13:16:58 ******************
2025-03-11 13:16:58 INFO:	Load data ...
2025-03-11 13:16:58 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2025-03-11 13:16:58 INFO:	Generate the R code ...
2025-03-11 13:16:58 INFO:	Run the R code ...
2025-03-11 13:17:00 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-03-11 13:17:00 INFO:	Plot generation done. Total running time: 2.3292088508605957 seconds
2025-03-11 13:17:00 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6a4816afe7411ef8d457c1e5222e1a9"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
chromInfo	`"/tmp/tmp59rld10r/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 14: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmp59rld10r/job_working_directory/000/13/outputs/dataset_fc3d4977-1a33-4d64-94dd-26fa8b0fdd4f_files &&  cp /tmp/tmp59rld10r/job_working_directory/000/13/configs/tmpgu2kehf6 /tmp/tmp59rld10r/job_working_directory/000/13/outputs/dataset_fc3d4977-1a33-4d64-94dd-26fa8b0fdd4f_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp59rld10r/job_working_directory/000/13/outputs/dataset_fc3d4977-1a33-4d64-94dd-26fa8b0fdd4f_files /tmp/tmp59rld10r/job_working_directory/000/13/configs/tmpgu2kehf6 &&  cp /tmp/tmp59rld10r/job_working_directory/000/13/outputs/dataset_fc3d4977-1a33-4d64-94dd-26fa8b0fdd4f_files/index.html /tmp/tmp59rld10r/job_working_directory/000/13/outputs/dataset_fc3d4977-1a33-4d64-94dd-26fa8b0fdd4f.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Maker annotation / Map annotation ids on data 12: renamed GFF
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"f6a4816afe7411ef8d457c1e5222e1a9"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp59rld10r/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Maker annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 18, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 3: Genome assembly:
- step_state: scheduled
Step 4: Protein sequences:
- step_state: scheduled
Step 5: Augustus training:
- step_state: scheduled
Step 6: SNAP training:
- step_state: scheduled

**Step 7: Fasta Statistics **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmp59rld10r/files/2/6/c/dataset_26c632f3-2942-4af4-832d-28af90393a17.dat' --stats_output '/tmp/tmp59rld10r/job_working_directory/000/6/outputs/dataset_2238127b-f10f-4b8a-a076-ae18801bb4d6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6a4816afe7411ef8d457c1e5222e1a9"`
chromInfo	`"/tmp/tmp59rld10r/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 8: BUSCO on the genome sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp59rld10r/files/2/6/c/dataset_26c632f3-2942-4af4-832d-28af90393a17.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

/tmp/tmp59rld10r/job_working_directory/000/7/tool_script.sh: line 23:    11 Killed                  busco --in '/tmp/tmp59rld10r/files/2/6/c/dataset_26c632f3-2942-4af4-832d-28af90393a17.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5 --lineage_dataset 'fungi_odb10' --miniprot

Standard Output:

2025-03-11 12:35:11 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/11/2025 12:35:11 *****
2025-03-11 12:35:11 INFO:	Configuring BUSCO with local environment
2025-03-11 12:35:11 INFO:	Running genome mode
2025-03-11 12:35:13 INFO:	Input file is /tmp/tmp59rld10r/files/2/6/c/dataset_26c632f3-2942-4af4-832d-28af90393a17.dat
2025-03-11 12:35:13 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2025-03-11 12:35:13 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2025-03-11 12:35:13 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-11 12:35:13 INFO:	Running 1 job(s) on bbtools, starting at 03/11/2025 12:35:13
2025-03-11 12:35:14 INFO:	[bbtools]	1 of 1 task(s) completed
2025-03-11 12:35:14 INFO:	Running 1 job(s) on miniprot_index, starting at 03/11/2025 12:35:14
2025-03-11 12:35:15 INFO:	[miniprot_index]	1 of 1 task(s) completed
2025-03-11 12:35:15 INFO:	Running 1 job(s) on miniprot_align, starting at 03/11/2025 12:35:15
2025-03-11 12:52:51 INFO:	[miniprot_align]	1 of 1 task(s) completed

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6a4816afe7411ef8d457c1e5222e1a9"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmp59rld10r/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 9: Maker:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

RM_PATH=$(which RepeatMasker) && if [ -z "$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH ($PATH)" >&2 ; exit 1 ; fi &&  LIBDIR=$(dirname "$RM_PATH")/../share/RepeatMasker/Libraries &&  export LIBDIR &&  maker -CTL  &&  cp '/tmp/tmp59rld10r/job_working_directory/000/8/configs/tmph4ze02lj' maker_opts.ctl  &&    cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&  mkdir -p 'augustus_dir/species/' &&  tar -C 'augustus_dir/species/' -xzvf '/tmp/tmp59rld10r/files/b/f/4/dataset_bf481956-663b-4097-9e50-35423d75e25a.dat' > /dev/null &&  export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&  MPI_CMD="" && if [ "$MAKER_MPI" == "1" ]; then MPI_CMD="mpiexec -n ${GALAXY_SLOTS:-4}"; fi &&  ${MPI_CMD} maker --ignore_nfs_tmp  maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null  &&  gff3_merge -d *.maker.output/*_master_datastore_index.log -o '/tmp/tmp59rld10r/job_working_directory/000/8/outputs/dataset_72d2aba8-e3fd-4ca9-a0fa-e2e0f934099c.dat'  &&  awk '{if ($2 == "maker" || $1 ~ /^#/) {print}}' '/tmp/tmp59rld10r/job_working_directory/000/8/outputs/dataset_72d2aba8-e3fd-4ca9-a0fa-e2e0f934099c.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmp59rld10r/job_working_directory/000/8/outputs/dataset_458fc7db-bcdc-4002-ac1d-8e611cab431c.dat'  &&  awk '{if ($2 != "maker") {print}}' '/tmp/tmp59rld10r/job_working_directory/000/8/outputs/dataset_72d2aba8-e3fd-4ca9-a0fa-e2e0f934099c.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmp59rld10r/job_working_directory/000/8/outputs/dataset_79499f1d-e374-45e5-8baf-d5d74c0e2abf.dat'

Exit Code:

```
0
```

Standard Error:

Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore

To access files for individual sequences use the datastore index:
/tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: NC_003421.2
Length: 2452883
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.1.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.2.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.3.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.4.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.5.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.6.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.7.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.8.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.9.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.10.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.11.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.12.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.13.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.14.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.15.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.16.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.17.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.18.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp59rld10r/tmp/maker_TOuc2o; /usr/local/bin/RepeatMasker /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.19.human.rb -species human -dir /tmp/tmp59rld10r/job_working_directory/000/8/working/dataset_26c632f3-2942-4af4-832d-28af90393a17.maker.output/dataset_26c632f3-2942-4af4-832d-28af90393a17_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -----
..
b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/130_0.2303936-2305953.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/130_0.2303936-2305953.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/130_0.2303936-2305953.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/130_0.2303936-2305953.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/131_0.2317785-2319394.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/131_0.2317785-2319394.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/131_0.2317785-2319394.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/131_0.2317785-2319394.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/131_0.2317785-2319394.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/131_0.2317785-2319394.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/132_0.2326855-2328897.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/132_0.2326855-2328897.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/132_0.2326855-2328897.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/132_0.2326855-2328897.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/132_0.2326855-2328897.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/132_0.2326855-2328897.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/133_0.2329261-2334928.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/133_0.2329261-2334928.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/133_0.2329261-2334928.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/133_0.2329261-2334928.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/133_0.2329261-2334928.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/133_0.2329261-2334928.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/134_0.2341240-2344143.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/134_0.2341240-2344143.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/134_0.2341240-2344143.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/134_0.2341240-2344143.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/134_0.2341240-2344143.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/134_0.2341240-2344143.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/135_0.2349164-2354609.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/135_0.2349164-2354609.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/135_0.2349164-2354609.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/135_0.2349164-2354609.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/135_0.2349164-2354609.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/135_0.2349164-2354609.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/136_0.2366363-2370156.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/136_0.2366363-2370156.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/136_0.2366363-2370156.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/136_0.2366363-2370156.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/136_0.2366363-2370156.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/136_0.2366363-2370156.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/137_0.2373919-2380223.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/137_0.2373919-2380223.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/137_0.2373919-2380223.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/137_0.2373919-2380223.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/137_0.2373919-2380223.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/137_0.2373919-2380223.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/138_0.2381056-2382231.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/138_0.2381056-2382231.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/138_0.2381056-2382231.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/138_0.2381056-2382231.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/138_0.2381056-2382231.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/138_0.2381056-2382231.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/139_0.2384415-2388063.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/139_0.2384415-2388063.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/139_0.2384415-2388063.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/139_0.2384415-2388063.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/139_0.2384415-2388063.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/139_0.2384415-2388063.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/140_0.2388096-2391775.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/140_0.2388096-2391775.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/140_0.2388096-2391775.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/140_0.2388096-2391775.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/140_0.2388096-2391775.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/140_0.2388096-2391775.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/141_0.2407535-2408933.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/141_0.2407535-2408933.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/141_0.2407535-2408933.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/141_0.2407535-2408933.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/141_0.2407535-2408933.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/141_0.2407535-2408933.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp59rld10r/files/1/a/3/dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat -xdef /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/142_0.2428734-2431724.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.xdef.snap  /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/142_0.2428734-2431724.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/142_0.2428734-2431724.dataset_1a33b36b-8bb8-4d56-badc-b9d4187866de.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp59rld10r/tmp/maker_TOuc2o/0/142_0.2428734-2431724.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp59rld10r/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/142_0.2428734-2431724.local.auto_annotator.augustus.fasta > /tmp/tmp59rld10r/tmp/maker_TOuc2o/0/142_0.2428734-2431724.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output


Maker is now finished!!!

Standard Output:

Start_time: 1741696511
End_time:   1741698507
Elapsed:    1996

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6a4816afe7411ef8d457c1e5222e1a9"`
abinitio_gene_prediction	`{"aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 4, "src": "hda"}]}}, "snaphmm": {"values": [{"id": 5, "src": "hda"}]}, "unmask": false}`
advanced	`{"AED_threshold": "1.0", "alt_peptide": "C", "alt_splice": false, "always_complete": false, "correct_est_fusion": false, "fix_nucleotides": false, "keep_preds": "0.0", "map_forward": false, "max_dna_len": "100000", "min_contig": "1", "min_protein": "0", "other_gff": null, "pred_flank": "200", "pred_stats": false, "single_exon": {"__current_case__": 0, "single_exon": "0"}, "split_hit": "10000"}`
chromInfo	`"/tmp/tmp59rld10r/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
est_evidences	`{"altest": null, "altest_gff": null, "est": {"values": [{"id": 2, "src": "hda"}]}, "est2genome": false, "est_gff": null}`
gene_prediction	`{"model_gff": null, "pred_gff": null, "snoscan_rrna": null, "trna": false}`
license_agreement	`true`
organism_type	`"eukaryotic"`
protein_evidences	`{"protein": {"values": [{"id": 3, "src": "hda"}]}, "protein2genome": false, "protein_gff": null}`
reannotation	`{"__current_case__": 0, "reannotate": "no"}`
repeat_masking	`{"repeat_source": {"__current_case__": 0, "softmask": true, "source_type": "dfam", "species_source": {"__current_case__": 0, "species_from_list": "yes", "species_list": "human"}}}`

Step 10: GFFRead:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp59rld10r/files/2/6/c/dataset_26c632f3-2942-4af4-832d-28af90393a17.dat' genomeref.fa &&  gffread '/tmp/tmp59rld10r/files/4/5/8/dataset_458fc7db-bcdc-4002-ac1d-8e611cab431c.dat' -g genomeref.fa      -w exons.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6a4816afe7411ef8d457c1e5222e1a9"`
chr_replace	`None`
chromInfo	`"/tmp/tmp59rld10r/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-w exons.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Other invocation details
- history_id
  - 08b364631a0b5164
- history_state
  - ok
- invocation_id
  - 08b364631a0b5164
- invocation_state
  - scheduled
- workflow_id
  - 08b364631a0b5164

github-actions · 2025-03-11T15:10:59Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

Problems:

Output with path /tmp/tmpbr1ront1/Busco on data 1 short summary__a1a5c905-b03a-4961-a1d3-633b74d21fd7 different than expected
Expected 32+-0 lines in the output found 0

Output with path /tmp/tmp1t2hnipp/Busco on data 1 full table__9abcd496-3c2d-45d1-9095-4b3ddb465184 different than expected
Expected text 'BUSCO version is: 5.7.1' in output ('')

Output with path /tmp/tmphfgxf6ky/Busco on data 1 missing buscos__c99275e4-a869-4682-938c-c69ce06ba784 different than expected
Expected text 'BUSCO version is: 5.7.1' in output ('')

Output with path /tmp/tmp8rtn18p1/Map annotation ids on data 12 ID map__4fd36ea6-4849-4ec9-b741-ac59116f00d7 different than expected
Expected text 'snap-NC_003421.2-processed-gene-0.0' in output ('snap_masked-NC_003421.2-processed-gene-0.27	000001
snap_masked-NC_003421.2-processed-gene-0.27-mRNA-1	000001-RA
augustus_masked-NC_003421.2-processed-gene-0.17	000002
augustus_masked-NC_003421.2-processed-gene-0.17-mRNA-1	000002-RA
snap_masked-NC_003421.2-processed-gene-0.28	000003
snap_masked-NC_003421.2-processed-gene-0.28-mRNA-1	000003-RA
augustus_masked-NC_003421.2-processed-gene-0.6	000004
augustus_masked-NC_003421.2-processed-gene-0.6-mRNA-1	000004-RA
snap_masked-NC_003421.2-processed-gene-0.31	000005
snap_masked-NC_003421.2-processed-gene-0.31-mRNA-1	000005-RA
snap_masked-NC_003421.2-processed-gene-0.32	000006
snap_masked-NC_003421.2-processed-gene-0.32-mRNA-1	000006-RA
augustus_masked-NC_003421.2-processed-gene-0.8	000007
augustus_masked-NC_003421.2-processed-gene-0.8-mRNA-1	000007-RA
snap_masked-NC_003421.2-processed-gene-0.43	000008
snap_masked-NC_003421.2-processed-gene-0.43-mRNA-1	000008-RA
snap_masked-NC_003421.2-processed-gene-0.44	000009
snap_masked-NC_003421.2-processed-gene-0.44-mRNA-1	000009-RA
maker-NC_003421.2-augustus-gene-0.50	000010
maker-NC_003421.2-augustus-gene-0.50-mRNA-1	000010-RA
snap_masked-NC_003421.2-processed-gene-0.45	000011
snap_masked-NC_003421.2-processed-gene-0.45-mRNA-1	000011-RA
snap_masked-NC_003421.2-processed-gene-0.46	000012
snap_masked-NC_003421.2-processed-gene-0.46-mRNA-1	000012-RA
maker-NC_003421.2-augustus-gene-0.53	000013
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snap_masked-NC_003421.2-processed-gene-21.101	000757
snap_masked-NC_003421.2-processed-gene-21.101-mRNA-1	000757-RA
snap_masked-NC_003421.2-processed-gene-21.81	000758
snap_masked-NC_003421.2-processed-gene-21.81-mRNA-1	000758-RA
maker-NC_003421.2-snap-gene-21.18	000759
maker-NC_003421.2-snap-gene-21.18-mRNA-1	000759-RA
maker-NC_003421.2-snap-gene-21.6	000760
maker-NC_003421.2-snap-gene-21.6-mRNA-1	000760-RA
snap_masked-NC_003421.2-processed-gene-21.83	000761
snap_masked-NC_003421.2-processed-gene-21.83-mRNA-1	000761-RA
maker-NC_003421.2-snap-gene-21.19	000762
maker-NC_003421.2-snap-gene-21.19-mRNA-1	000762-RA
snap_masked-NC_003421.2-processed-gene-21.84	000763
snap_masked-NC_003421.2-processed-gene-21.84-mRNA-1	000763-RA
snap_masked-NC_003421.2-processed-gene-21.105	000764
snap_masked-NC_003421.2-processed-gene-21.105-mRNA-1	000764-RA
maker-NC_003421.2-snap-gene-21.7	000765
maker-NC_003421.2-snap-gene-21.7-mRNA-1	000765-RA
maker-NC_003421.2-augustus-gene-21.113	000766
maker-NC_003421.2-augustus-gene-21.113-mRNA-1	000766-RA
maker-NC_003421.2-augustus-gene-22.63	000767
maker-NC_003421.2-augustus-gene-22.63-mRNA-1	000767-RA
maker-NC_003421.2-augustus-gene-22.55	000768
maker-NC_003421.2-augustus-gene-22.55-mRNA-1	000768-RA
snap_masked-NC_003421.2-processed-gene-22.76	000769
snap_masked-NC_003421.2-processed-gene-22.76-mRNA-1	000769-RA
maker-NC_003421.2-augustus-gene-22.64	000770
maker-NC_003421.2-augustus-gene-22.64-mRNA-1	000770-RA
snap_masked-NC_003421.2-processed-gene-22.78	000771
snap_masked-NC_003421.2-processed-gene-22.78-mRNA-1	000771-RA
maker-NC_003421.2-augustus-gene-22.56	000772
maker-NC_003421.2-augustus-gene-22.56-mRNA-1	000772-RA
maker-NC_003421.2-augustus-gene-22.65	000773
maker-NC_003421.2-augustus-gene-22.65-mRNA-1	000773-RA
maker-NC_003421.2-augustus-gene-22.57	000774
maker-NC_003421.2-augustus-gene-22.57-mRNA-1	000774-RA
maker-NC_003421.2-snap-gene-22.12	000775
maker-NC_003421.2-snap-gene-22.12-mRNA-1	000775-RA
augustus_masked-NC_003421.2-processed-gene-22.27	000776
augustus_masked-NC_003421.2-processed-gene-22.27-mRNA-1	000776-RA
snap_masked-NC_003421.2-processed-gene-22.82	000777
snap_masked-NC_003421.2-processed-gene-22.82-mRNA-1	000777-RA
snap_masked-NC_003421.2-processed-gene-22.98	000778
snap_masked-NC_003421.2-processed-gene-22.98-mRNA-1	000778-RA
snap_masked-NC_003421.2-processed-gene-22.83	000779
snap_masked-NC_003421.2-processed-gene-22.83-mRNA-1	000779-RA
maker-NC_003421.2-augustus-gene-22.67	000780
maker-NC_003421.2-augustus-gene-22.67-mRNA-1	000780-RA
maker-NC_003421.2-augustus-gene-22.68	000781
maker-NC_003421.2-augustus-gene-22.68-mRNA-1	000781-RA
snap_masked-NC_003421.2-processed-gene-22.84	000782
snap_masked-NC_003421.2-processed-gene-22.84-mRNA-1	000782-RA
maker-NC_003421.2-augustus-gene-22.58	000783
maker-NC_003421.2-augustus-gene-22.58-mRNA-1	000783-RA
maker-NC_003421.2-augustus-gene-22.69	000784
maker-NC_003421.2-augustus-gene-22.69-mRNA-1	000784-RA
augustus_masked-NC_003421.2-processed-gene-22.32	000785
augustus_masked-NC_003421.2-processed-gene-22.32-mRNA-1	000785-RA
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snap_masked-NC_003421.2-processed-gene-22.102-mRNA-1	000786-RA
maker-NC_003421.2-snap-gene-22.16	000787
maker-NC_003421.2-snap-gene-22.16-mRNA-1	000787-RA
maker-NC_003421.2-augustus-gene-22.70	000788
maker-NC_003421.2-augustus-gene-22.70-mRNA-1	000788-RA
snap_masked-NC_003421.2-processed-gene-22.87	000789
snap_masked-NC_003421.2-processed-gene-22.87-mRNA-1	000789-RA
maker-NC_003421.2-augustus-gene-22.59	000790
maker-NC_003421.2-augustus-gene-22.59-mRNA-1	000790-RA
maker-NC_003421.2-snap-gene-22.4	000791
maker-NC_003421.2-snap-gene-22.4-mRNA-1	000791-RA
snap_masked-NC_003421.2-processed-gene-22.105	000792
snap_masked-NC_003421.2-processed-gene-22.105-mRNA-1	000792-RA
snap_masked-NC_003421.2-processed-gene-22.106	000793
snap_masked-NC_003421.2-processed-gene-22.106-mRNA-1	000793-RA
snap_masked-NC_003421.2-processed-gene-22.90	000794
snap_masked-NC_003421.2-processed-gene-22.90-mRNA-1	000794-RA
maker-NC_003421.2-augustus-gene-22.60	000795
maker-NC_003421.2-augustus-gene-22.60-mRNA-1	000795-RA
maker-NC_003421.2-augustus-gene-22.71	000796
maker-NC_003421.2-augustus-gene-22.71-mRNA-1	000796-RA
maker-NC_003421.2-snap-gene-22.18	000797
maker-NC_003421.2-snap-gene-22.18-mRNA-1	000797-RA
snap_masked-NC_003421.2-processed-gene-22.109	000798
snap_masked-NC_003421.2-processed-gene-22.109-mRNA-1	000798-RA
snap_masked-NC_003421.2-processed-gene-22.110	000799
snap_masked-NC_003421.2-processed-gene-22.110-mRNA-1	000799-RA
snap_masked-NC_003421.2-processed-gene-22.111	000800
snap_masked-NC_003421.2-processed-gene-22.111-mRNA-1	000800-RA
maker-NC_003421.2-snap-gene-22.7	000801
maker-NC_003421.2-snap-gene-22.7-mRNA-1	000801-RA
snap_masked-NC_003421.2-processed-gene-22.93	000802
snap_masked-NC_003421.2-processed-gene-22.93-mRNA-1	000802-RA
snap_masked-NC_003421.2-processed-gene-22.94	000803
snap_masked-NC_003421.2-processed-gene-22.94-mRNA-1	000803-RA
maker-NC_003421.2-augustus-gene-22.62	000804
maker-NC_003421.2-augustus-gene-22.62-mRNA-1	000804-RA
snap_masked-NC_003421.2-processed-gene-23.77	000805
snap_masked-NC_003421.2-processed-gene-23.77-mRNA-1	000805-RA
snap_masked-NC_003421.2-processed-gene-23.78	000806
snap_masked-NC_003421.2-processed-gene-23.78-mRNA-1	000806-RA
snap_masked-NC_003421.2-processed-gene-23.76	000807
snap_masked-NC_003421.2-processed-gene-23.76-mRNA-1	000807-RA
snap_masked-NC_003421.2-processed-gene-23.79	000808
snap_masked-NC_003421.2-processed-gene-23.79-mRNA-1	000808-RA
snap_masked-NC_003421.2-processed-gene-23.80	000809
snap_masked-NC_003421.2-processed-gene-23.80-mRNA-1	000809-RA
snap_masked-NC_003421.2-processed-gene-23.81	000810
snap_masked-NC_003421.2-processed-gene-23.81-mRNA-1	000810-RA
snap_masked-NC_003421.2-processed-gene-23.82	000811
snap_masked-NC_003421.2-processed-gene-23.82-mRNA-1	000811-RA
snap_masked-NC_003421.2-processed-gene-23.104	000812
snap_masked-NC_003421.2-processed-gene-23.104-mRNA-1	000812-RA
snap_masked-NC_003421.2-processed-gene-23.83	000813
snap_masked-NC_003421.2-processed-gene-23.83-mRNA-1	000813-RA
snap_masked-NC_003421.2-processed-gene-23.84	000814
snap_masked-NC_003421.2-processed-gene-23.84-mRNA-1	000814-RA
snap_masked-NC_003421.2-processed-gene-23.85	000815
snap_masked-NC_003421.2-processed-gene-23.85-mRNA-1	000815-RA
snap_masked-NC_003421.2-processed-gene-23.86	000816
snap_masked-NC_003421.2-processed-gene-23.86-mRNA-1	000816-RA
maker-NC_003421.2-augustus-gene-23.135	000817
maker-NC_003421.2-augustus-gene-23.135-mRNA-1	000817-RA
maker-NC_003421.2-augustus-gene-23.140	000818
maker-NC_003421.2-augustus-gene-23.140-mRNA-1	000818-RA
augustus_masked-NC_003421.2-processed-gene-23.49	000819
augustus_masked-NC_003421.2-processed-gene-23.49-mRNA-1	000819-RA
snap_masked-NC_003421.2-processed-gene-23.88	000820
snap_masked-NC_003421.2-processed-gene-23.88-mRNA-1	000820-RA
maker-NC_003421.2-augustus-gene-23.141	000821
maker-NC_003421.2-augustus-gene-23.141-mRNA-1	000821-RA
maker-NC_003421.2-snap-gene-23.9	000822
maker-NC_003421.2-snap-gene-23.9-mRNA-1	000822-RA
snap_masked-NC_003421.2-processed-gene-23.110	000823
snap_masked-NC_003421.2-processed-gene-23.110-mRNA-1	000823-RA
snap_masked-NC_003421.2-processed-gene-23.89	000824
snap_masked-NC_003421.2-processed-gene-23.89-mRNA-1	000824-RA
maker-NC_003421.2-augustus-gene-23.142	000825
maker-NC_003421.2-augustus-gene-23.142-mRNA-1	000825-RA
snap_masked-NC_003421.2-processed-gene-23.90	000826
snap_masked-NC_003421.2-processed-gene-23.90-mRNA-1	000826-RA
snap_masked-NC_003421.2-processed-gene-23.113	000827
snap_masked-NC_003421.2-processed-gene-23.113-mRNA-1	000827-RA
snap_masked-NC_003421.2-processed-gene-23.114	000828
snap_masked-NC_003421.2-processed-gene-23.114-mRNA-1	000828-RA
maker-NC_003421.2-snap-gene-23.11	000829
maker-NC_003421.2-snap-gene-23.11-mRNA-1	000829-RA
snap_masked-NC_003421.2-processed-gene-23.116	000830
snap_masked-NC_003421.2-processed-gene-23.116-mRNA-1	000830-RA
snap_masked-NC_003421.2-processed-gene-23.91	000831
snap_masked-NC_003421.2-processed-gene-23.91-mRNA-1	000831-RA
maker-NC_003421.2-augustus-gene-23.144	000832
maker-NC_003421.2-augustus-gene-23.144-mRNA-1	000832-RA
maker-NC_003421.2-augustus-gene-23.145	000833
maker-NC_003421.2-augustus-gene-23.145-mRNA-1	000833-RA
maker-NC_003421.2-augustus-gene-23.146	000834
maker-NC_003421.2-augustus-gene-23.146-mRNA-1	000834-RA
snap_masked-NC_003421.2-processed-gene-23.92	000835
snap_masked-NC_003421.2-processed-gene-23.92-mRNA-1	000835-RA
augustus_masked-NC_003421.2-processed-gene-23.62	000836
augustus_masked-NC_003421.2-processed-gene-23.62-mRNA-1	000836-RA
snap_masked-NC_003421.2-processed-gene-23.121	000837
snap_masked-NC_003421.2-processed-gene-23.121-mRNA-1	000837-RA
snap_masked-NC_003421.2-processed-gene-23.122	000838
snap_masked-NC_003421.2-processed-gene-23.122-mRNA-1	000838-RA
snap_masked-NC_003421.2-processed-gene-23.123	000839
snap_masked-NC_003421.2-processed-gene-23.123-mRNA-1	000839-RA
snap_masked-NC_003421.2-processed-gene-23.93	000840
snap_masked-NC_003421.2-processed-gene-23.93-mRNA-1	000840-RA
maker-NC_003421.2-snap-gene-23.15	000841
maker-NC_003421.2-snap-gene-23.15-mRNA-1	000841-RA
maker-NC_003421.2-augustus-gene-23.149	000842
maker-NC_003421.2-augustus-gene-23.149-mRNA-1	000842-RA
maker-NC_003421.2-augustus-gene-23.136	000843
maker-NC_003421.2-augustus-gene-23.136-mRNA-1	000843-RA
augustus_masked-NC_003421.2-processed-gene-23.69	000844
augustus_masked-NC_003421.2-processed-gene-23.69-mRNA-1	000844-RA
snap_masked-NC_003421.2-processed-gene-23.127	000845
snap_masked-NC_003421.2-processed-gene-23.127-mRNA-1	000845-RA
snap_masked-NC_003421.2-processed-gene-23.96	000846
snap_masked-NC_003421.2-processed-gene-23.96-mRNA-1	000846-RA
snap_masked-NC_003421.2-processed-gene-23.128	000847
snap_masked-NC_003421.2-processed-gene-23.128-mRNA-1	000847-RA
maker-NC_003421.2-snap-gene-23.3	000848
maker-NC_003421.2-snap-gene-23.3-mRNA-1	000848-RA
maker-NC_003421.2-augustus-gene-23.150	000849
maker-NC_003421.2-augustus-gene-23.150-mRNA-1	000849-RA
maker-NC_003421.2-augustus-gene-23.138	000850
maker-NC_003421.2-augustus-gene-23.138-mRNA-1	000850-RA
snap_masked-NC_003421.2-processed-gene-23.100	000851
snap_masked-NC_003421.2-processed-gene-23.100-mRNA-1	000851-RA
snap_masked-NC_003421.2-processed-gene-23.101	000852
snap_masked-NC_003421.2-processed-gene-23.101-mRNA-1	000852-RA
snap_masked-NC_003421.2-processed-gene-23.130	000853
snap_masked-NC_003421.2-processed-gene-23.130-mRNA-1	000853-RA
snap_masked-NC_003421.2-processed-gene-23.131	000854
snap_masked-NC_003421.2-processed-gene-23.131-mRNA-1	000854-RA
snap_masked-NC_003421.2-processed-gene-23.132	000855
snap_masked-NC_003421.2-processed-gene-23.132-mRNA-1	000855-RA
snap_masked-NC_003421.2-processed-gene-23.102	000856
snap_masked-NC_003421.2-processed-gene-23.102-mRNA-1	000856-RA
maker-NC_003421.2-snap-gene-23.18	000857
maker-NC_003421.2-snap-gene-23.18-mRNA-1	000857-RA
augustus_masked-NC_003421.2-processed-gene-23.45	000858
augustus_masked-NC_003421.2-processed-gene-23.45-mRNA-1	000858-RA
snap_masked-NC_003421.2-processed-gene-23.103	000859
snap_masked-NC_003421.2-processed-gene-23.103-mRNA-1	000859-RA
snap_masked-NC_003421.2-processed-gene-23.134	000860
snap_masked-NC_003421.2-processed-gene-23.134-mRNA-1	000860-RA
')

Workflow invocation details

Invocation Messages

Steps

Step 1: BUSCO lineage:
- step_state: scheduled
Step 2: Genome sequence:
- step_state: scheduled

Step 11: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp4n70qbf_/files/b/8/0/dataset_b80d9e43-9e9f-4bba-82d8-0f5ee143f453.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp4n70qbf_/job_working_directory/000/10/outputs/dataset_1b08a7be-f5aa-42ea-9c5d-a9cca20afdf8.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp4n70qbf_/files/6/c/4/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.dat' 2>&1 | tail -n +3 >> '/tmp/tmp4n70qbf_/job_working_directory/000/10/outputs/dataset_1b08a7be-f5aa-42ea-9c5d-a9cca20afdf8.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp4n70qbf_/job_working_directory/000/10/outputs/dataset_1b08a7be-f5aa-42ea-9c5d-a9cca20afdf8.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp4n70qbf_/job_working_directory/000/10/outputs/dataset_3b13f007-8efa-49bb-9a56-b30ce3b5cb04.dat'

Exit Code:

```
0
```

Standard Error:

�[0;33m15:01:41 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m15:01:42 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m15:01:42 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m15:01:42 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m15:01:42 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m15:01:42 [stats]�[0m�[0;35m A total of 860 transcripts populated.�[0m
�[0;33m15:01:44 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m15:01:44 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m15:01:44 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m15:01:44 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m15:01:44 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m15:01:44 [__init__]�[0m�[0;35m platform is linux2�[0m
�[0;33m15:01:44 [__init__]�[0m�[0;35m loaded modules: ['numpy.core.info', 'Bio.SeqIO.UniprotIO', 'jcvi.apps.base', 'ctypes.os', 'Bio.os', 'runpy', 'gc', 'distutils.sysconfig', 'matplotlib.cbook._backports', 'Bio._py3k.urllib2', 'logging.weakref', 'base64', 'jcvi.utils', 'jcvi.apps.signal', 'unittest.sys', 'numpy.core.umath', 'string', 'Bio.SeqIO.InsdcIO', 'numpy.lib.arraysetops', '_elementtree', 'xml.etree.warnings', 'xml.etree.sys', 'Bio.SeqUtils.binascii', 'json.encoder', 'Bio.SeqIO.QualityIO', 'numpy.core.machar', 'jcvi.formats.collections', 'unittest.StringIO', 'unittest.types', 'jcvi.apps.threading', 'numpy.ma.extras', 'numpy.fft.fftpack_lite', 'matplotlib.cbook', 'dis', 'zlib', 'logging.threading', 'jcvi.annotation', 'Bio.SeqIO.Bio', '_json', 'Bio.GenBank.warnings', 'matplotlib.cbook.warnings', 'pyparsing', 'matplotlib.cbook.textwrap', 'abc', 'numpy._globals', 'numpy.lib.npyio', 'xml.sax.io', 'Bio._py3k.sys', 'Bio.SeqIO.sys', 'numpy.fft.helper', 'matplotlib.rcsetup', 'optparse', 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�[0;33m15:01:44 [font_manager]�[0m�[0;35m generated new fontManager�[0m
�[0;33m15:01:44 [__init__]�[0m�[0;35m backend agg version v2.2�[0m
�[0;33m15:01:44 [stats]�[0m�[0;35m Parsing files in `Exon_Length`..�[0m
Exon_Length/input.txt: Min=2 Max=14154 N=1898 Mean=646.258166491 SD=928.852859224 Median=267.0 Sum=1226598
�[0;33m15:01:44 [base]�[0m�[0;35m Rscript /tmp/tmp4n70qbf_/tmp/tmp0TbHaB�[0m
Warning message:
Removed 428 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 428 rows containing non-finite values (stat_bin). 
�[0;33m15:01:47 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
Intron_Length/input.txt: Min=4 Max=6176 N=1038 Mean=114.487475915 SD=294.619481795 Median=60.0 Sum=118838
�[0;33m15:01:47 [base]�[0m�[0;35m Rscript /tmp/tmp4n70qbf_/tmp/tmpMIrKFF�[0m
Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
�[0;33m15:01:51 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=42 Max=14154 N=860 Mean=1426.27674419 SD=1121.61646646 Median=1123.5 Sum=1226598
�[0;33m15:01:51 [base]�[0m�[0;35m Rscript /tmp/tmp4n70qbf_/tmp/tmpmX56ME�[0m
Warning message:
Removed 28 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 28 rows containing non-finite values (stat_bin). 
�[0;33m15:01:54 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=860 Mean=2.20697674419 SD=1.71896336377 Median=2.0 Sum=1898
�[0;33m15:01:54 [base]�[0m�[0;35m Rscript /tmp/tmp4n70qbf_/tmp/tmp2MBpTU�[0m
Saving 7 x 7 in image

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a77d3b30fe8411efbdfa7c1e5242529a"`
chromInfo	`"/tmp/tmp4n70qbf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 12: Map annotation ids:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmp4n70qbf_/files/b/8/0/dataset_b80d9e43-9e9f-4bba-82d8-0f5ee143f453.dat' '/tmp/tmp4n70qbf_/job_working_directory/000/11/outputs/dataset_0aceec12-273a-43bb-b0bd-a7e9cb48398d.dat' && maker_map_ids --prefix '' --justify 6 '/tmp/tmp4n70qbf_/files/b/8/0/dataset_b80d9e43-9e9f-4bba-82d8-0f5ee143f453.dat' > '/tmp/tmp4n70qbf_/job_working_directory/000/11/outputs/dataset_4fd36ea6-4849-4ec9-b741-ac59116f00d7.dat' && map_gff_ids '/tmp/tmp4n70qbf_/job_working_directory/000/11/outputs/dataset_4fd36ea6-4849-4ec9-b741-ac59116f00d7.dat' '/tmp/tmp4n70qbf_/job_working_directory/000/11/outputs/dataset_0aceec12-273a-43bb-b0bd-a7e9cb48398d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a77d3b30fe8411efbdfa7c1e5242529a"`
chromInfo	`"/tmp/tmp4n70qbf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
justify	`"6"`
prefix	`None`

Step 13: BUSCO on the predicted protein sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp4n70qbf_/files/9/7/8/dataset_9784fa55-4b89-4761-b73a-d056a4d70699.dat' --mode 'tran' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2025-03-11 15:09:24 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-03-11 15:01:21 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/11/2025 15:01:21 *****
2025-03-11 15:01:21 INFO:	Configuring BUSCO with local environment
2025-03-11 15:01:21 INFO:	Running transcriptome mode
2025-03-11 15:01:21 INFO:	Input file is /tmp/tmp4n70qbf_/files/9/7/8/dataset_9784fa55-4b89-4761-b73a-d056a4d70699.dat
2025-03-11 15:01:21 WARNING:	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-11 15:01:21 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-11 15:01:21 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2025-03-11 15:01:21 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-11 15:01:21 INFO:	Running 1 job(s) on metaeuk, starting at 03/11/2025 15:01:21
2025-03-11 15:03:59 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-11 15:03:59 INFO:	***** Run HMMER on gene sequences *****
2025-03-11 15:03:59 INFO:	Running 758 job(s) on hmmsearch, starting at 03/11/2025 15:03:59
2025-03-11 15:04:05 INFO:	[hmmsearch]	76 of 758 task(s) completed
2025-03-11 15:04:09 INFO:	[hmmsearch]	152 of 758 task(s) completed
2025-03-11 15:04:16 INFO:	[hmmsearch]	228 of 758 task(s) completed
2025-03-11 15:04:22 INFO:	[hmmsearch]	304 of 758 task(s) completed
2025-03-11 15:04:28 INFO:	[hmmsearch]	379 of 758 task(s) completed
2025-03-11 15:04:33 INFO:	[hmmsearch]	455 of 758 task(s) completed
2025-03-11 15:04:39 INFO:	[hmmsearch]	531 of 758 task(s) completed
2025-03-11 15:04:44 INFO:	[hmmsearch]	607 of 758 task(s) completed
2025-03-11 15:04:50 INFO:	[hmmsearch]	683 of 758 task(s) completed
2025-03-11 15:04:59 INFO:	[hmmsearch]	758 of 758 task(s) completed
2025-03-11 15:04:59 INFO:	140 exons in total
2025-03-11 15:04:59 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2025-03-11 15:05:20 INFO:	Running 1 job(s) on metaeuk, starting at 03/11/2025 15:05:20
2025-03-11 15:09:09 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-11 15:09:09 INFO:	***** Run HMMER on gene sequences *****
2025-03-11 15:09:09 INFO:	Running 630 job(s) on hmmsearch, starting at 03/11/2025 15:09:09
2025-03-11 15:09:10 INFO:	[hmmsearch]	63 of 630 task(s) completed
2025-03-11 15:09:12 INFO:	[hmmsearch]	126 of 630 task(s) completed
2025-03-11 15:09:13 INFO:	[hmmsearch]	189 of 630 task(s) completed
2025-03-11 15:09:14 INFO:	[hmmsearch]	252 of 630 task(s) completed
2025-03-11 15:09:15 INFO:	[hmmsearch]	315 of 630 task(s) completed
2025-03-11 15:09:16 INFO:	[hmmsearch]	378 of 630 task(s) completed
2025-03-11 15:09:17 INFO:	[hmmsearch]	441 of 630 task(s) completed
2025-03-11 15:09:18 INFO:	[hmmsearch]	504 of 630 task(s) completed
2025-03-11 15:09:19 INFO:	[hmmsearch]	567 of 630 task(s) completed
2025-03-11 15:09:20 INFO:	[hmmsearch]	630 of 630 task(s) completed
2025-03-11 15:09:20 INFO:	1 candidate overlapping regions found
2025-03-11 15:09:20 INFO:	143 exons in total
2025-03-11 15:09:20 INFO:	Results:	C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758	   

2025-03-11 15:09:21 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758      |
    |128    Complete BUSCOs (C)                        |
    |127    Complete and single-copy BUSCOs (S)        |
    |1    Complete and duplicated BUSCOs (D)           |
    |11    Fragmented BUSCOs (F)                       |
    |619    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2025-03-11 15:09:21 INFO:	BUSCO analysis done with WARNING(s). Total running time: 480 seconds

***** Summary of warnings: *****
2025-03-11 15:01:21 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-11 15:01:21 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-11 15:01:21 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2025-03-11 15:09:21 INFO:	Results written in /tmp/tmp4n70qbf_/job_working_directory/000/12/working/busco_galaxy
2025-03-11 15:09:21 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-03-11 15:09:21 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 64
drwxr-xr-x 5 1001 118  4096 Mar 11 15:01 busco_sequences
-rw-r--r-- 1 1001 118 36536 Mar 11 15:09 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Mar 11 15:04 hmmer_output
drwxr-xr-x 4 1001 118  4096 Mar 11 15:09 metaeuk_output
-rw-r--r-- 1 1001 118  8066 Mar 11 15:09 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2395 Mar 11 15:09 short_summary.json
-rw-r--r-- 1 1001 118   761 Mar 11 15:09 short_summary.txt
2025-03-11 15:09:22 INFO:	****************** Start plot generation at 03/11/2025 15:09:22 ******************
2025-03-11 15:09:22 INFO:	Load data ...
2025-03-11 15:09:22 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2025-03-11 15:09:22 INFO:	Generate the R code ...
2025-03-11 15:09:22 INFO:	Run the R code ...
2025-03-11 15:09:24 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-03-11 15:09:24 INFO:	Plot generation done. Total running time: 2.3384671211242676 seconds
2025-03-11 15:09:24 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a77d3b30fe8411efbdfa7c1e5242529a"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
chromInfo	`"/tmp/tmp4n70qbf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 14: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmp4n70qbf_/job_working_directory/000/13/outputs/dataset_356ddee9-6df1-431e-b71c-20f4135d2714_files &&  cp /tmp/tmp4n70qbf_/job_working_directory/000/13/configs/tmp3x021cfe /tmp/tmp4n70qbf_/job_working_directory/000/13/outputs/dataset_356ddee9-6df1-431e-b71c-20f4135d2714_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp4n70qbf_/job_working_directory/000/13/outputs/dataset_356ddee9-6df1-431e-b71c-20f4135d2714_files /tmp/tmp4n70qbf_/job_working_directory/000/13/configs/tmp3x021cfe &&  cp /tmp/tmp4n70qbf_/job_working_directory/000/13/outputs/dataset_356ddee9-6df1-431e-b71c-20f4135d2714_files/index.html /tmp/tmp4n70qbf_/job_working_directory/000/13/outputs/dataset_356ddee9-6df1-431e-b71c-20f4135d2714.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Maker annotation / Map annotation ids on data 12: renamed GFF
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"a77d3b30fe8411efbdfa7c1e5242529a"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp4n70qbf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Maker annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 18, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 3: Genome assembly:
- step_state: scheduled
Step 4: Protein sequences:
- step_state: scheduled
Step 5: Augustus training:
- step_state: scheduled
Step 6: SNAP training:
- step_state: scheduled

**Step 7: Fasta Statistics **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmp4n70qbf_/files/6/c/4/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.dat' --stats_output '/tmp/tmp4n70qbf_/job_working_directory/000/6/outputs/dataset_c2059f84-d9d5-4039-be53-e9e6fb791426.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a77d3b30fe8411efbdfa7c1e5242529a"`
chromInfo	`"/tmp/tmp4n70qbf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 8: BUSCO on the genome sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp4n70qbf_/files/6/c/4/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

/tmp/tmp4n70qbf_/job_working_directory/000/7/tool_script.sh: line 23:    11 Killed                  busco --in '/tmp/tmp4n70qbf_/files/6/c/4/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5 --lineage_dataset 'fungi_odb10' --miniprot

Standard Output:

2025-03-11 14:26:49 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/11/2025 14:26:49 *****
2025-03-11 14:26:49 INFO:	Configuring BUSCO with local environment
2025-03-11 14:26:49 INFO:	Running genome mode
2025-03-11 14:27:06 INFO:	Input file is /tmp/tmp4n70qbf_/files/6/c/4/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.dat
2025-03-11 14:27:06 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2025-03-11 14:27:06 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2025-03-11 14:27:07 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-11 14:27:07 INFO:	Running 1 job(s) on bbtools, starting at 03/11/2025 14:27:07
2025-03-11 14:27:07 INFO:	[bbtools]	1 of 1 task(s) completed
2025-03-11 14:27:07 INFO:	Running 1 job(s) on miniprot_index, starting at 03/11/2025 14:27:07
2025-03-11 14:27:08 INFO:	[miniprot_index]	1 of 1 task(s) completed
2025-03-11 14:27:08 INFO:	Running 1 job(s) on miniprot_align, starting at 03/11/2025 14:27:08
2025-03-11 14:44:50 INFO:	[miniprot_align]	1 of 1 task(s) completed

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a77d3b30fe8411efbdfa7c1e5242529a"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmp4n70qbf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 9: Maker:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

RM_PATH=$(which RepeatMasker) && if [ -z "$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH ($PATH)" >&2 ; exit 1 ; fi &&  LIBDIR=$(dirname "$RM_PATH")/../share/RepeatMasker/Libraries &&  export LIBDIR &&  maker -CTL  &&  cp '/tmp/tmp4n70qbf_/job_working_directory/000/8/configs/tmpx6892ipw' maker_opts.ctl  &&    cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&  mkdir -p 'augustus_dir/species/' &&  tar -C 'augustus_dir/species/' -xzvf '/tmp/tmp4n70qbf_/files/d/c/3/dataset_dc30591f-7b12-4b4c-8825-bf82fb5e3234.dat' > /dev/null &&  export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&  MPI_CMD="" && if [ "$MAKER_MPI" == "1" ]; then MPI_CMD="mpiexec -n ${GALAXY_SLOTS:-4}"; fi &&  ${MPI_CMD} maker --ignore_nfs_tmp  maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null  &&  gff3_merge -d *.maker.output/*_master_datastore_index.log -o '/tmp/tmp4n70qbf_/job_working_directory/000/8/outputs/dataset_01c15257-67fd-4bc5-b78d-1cc1e1388b85.dat'  &&  awk '{if ($2 == "maker" || $1 ~ /^#/) {print}}' '/tmp/tmp4n70qbf_/job_working_directory/000/8/outputs/dataset_01c15257-67fd-4bc5-b78d-1cc1e1388b85.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmp4n70qbf_/job_working_directory/000/8/outputs/dataset_b80d9e43-9e9f-4bba-82d8-0f5ee143f453.dat'  &&  awk '{if ($2 != "maker") {print}}' '/tmp/tmp4n70qbf_/job_working_directory/000/8/outputs/dataset_01c15257-67fd-4bc5-b78d-1cc1e1388b85.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmp4n70qbf_/job_working_directory/000/8/outputs/dataset_1890f0c9-f625-4182-8cb3-957106a63e18.dat'

Exit Code:

```
0
```

Standard Error:

Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore

To access files for individual sequences use the datastore index:
/tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: NC_003421.2
Length: 2452883
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.1.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.2.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.3.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.4.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.5.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.6.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.7.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.8.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.9.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.10.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.11.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.12.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.13.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.14.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.15.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.16.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.17.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.18.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp4n70qbf_/tmp/maker_oWDGec; /usr/local/bin/RepeatMasker /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.19.human.rb -species human -dir /tmp/tmp4n70qbf_/job_working_directory/000/8/working/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.maker.output/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -----
..
1-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/130_0.2303936-2305953.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/130_0.2303936-2305953.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/130_0.2303936-2305953.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/130_0.2303936-2305953.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/131_0.2317785-2319394.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/131_0.2317785-2319394.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/131_0.2317785-2319394.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/131_0.2317785-2319394.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/131_0.2317785-2319394.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/131_0.2317785-2319394.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/132_0.2326855-2328897.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/132_0.2326855-2328897.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/132_0.2326855-2328897.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/132_0.2326855-2328897.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/132_0.2326855-2328897.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/132_0.2326855-2328897.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/133_0.2329261-2334928.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/133_0.2329261-2334928.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/133_0.2329261-2334928.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/133_0.2329261-2334928.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/133_0.2329261-2334928.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/133_0.2329261-2334928.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/134_0.2341240-2344143.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/134_0.2341240-2344143.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/134_0.2341240-2344143.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/134_0.2341240-2344143.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/134_0.2341240-2344143.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/134_0.2341240-2344143.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/135_0.2349164-2354609.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/135_0.2349164-2354609.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/135_0.2349164-2354609.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/135_0.2349164-2354609.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/135_0.2349164-2354609.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/135_0.2349164-2354609.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/136_0.2366363-2370156.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/136_0.2366363-2370156.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/136_0.2366363-2370156.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/136_0.2366363-2370156.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/136_0.2366363-2370156.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/136_0.2366363-2370156.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/137_0.2373919-2380223.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/137_0.2373919-2380223.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/137_0.2373919-2380223.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/137_0.2373919-2380223.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/137_0.2373919-2380223.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/137_0.2373919-2380223.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/138_0.2381056-2382231.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/138_0.2381056-2382231.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/138_0.2381056-2382231.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/138_0.2381056-2382231.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/138_0.2381056-2382231.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/138_0.2381056-2382231.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/139_0.2384415-2388063.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/139_0.2384415-2388063.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/139_0.2384415-2388063.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/139_0.2384415-2388063.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/139_0.2384415-2388063.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/139_0.2384415-2388063.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/140_0.2388096-2391775.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/140_0.2388096-2391775.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/140_0.2388096-2391775.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/140_0.2388096-2391775.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/140_0.2388096-2391775.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/140_0.2388096-2391775.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/141_0.2407535-2408933.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/141_0.2407535-2408933.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/141_0.2407535-2408933.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/141_0.2407535-2408933.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/141_0.2407535-2408933.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/141_0.2407535-2408933.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp4n70qbf_/files/8/9/c/dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat -xdef /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/142_0.2428734-2431724.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.xdef.snap  /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/142_0.2428734-2431724.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/142_0.2428734-2431724.dataset_89c0cc01-1949-4ca7-8b0c-fae3072fd44c.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/142_0.2428734-2431724.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp4n70qbf_/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/142_0.2428734-2431724.local.auto_annotator.augustus.fasta > /tmp/tmp4n70qbf_/tmp/maker_oWDGec/0/142_0.2428734-2431724.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output


Maker is now finished!!!

Standard Output:

Start_time: 1741703217
End_time:   1741705260
Elapsed:    2043

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a77d3b30fe8411efbdfa7c1e5242529a"`
abinitio_gene_prediction	`{"aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 4, "src": "hda"}]}}, "snaphmm": {"values": [{"id": 5, "src": "hda"}]}, "unmask": false}`
advanced	`{"AED_threshold": "1.0", "alt_peptide": "C", "alt_splice": false, "always_complete": false, "correct_est_fusion": false, "fix_nucleotides": false, "keep_preds": "0.0", "map_forward": false, "max_dna_len": "100000", "min_contig": "1", "min_protein": "0", "other_gff": null, "pred_flank": "200", "pred_stats": false, "single_exon": {"__current_case__": 0, "single_exon": "0"}, "split_hit": "10000"}`
chromInfo	`"/tmp/tmp4n70qbf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
est_evidences	`{"altest": null, "altest_gff": null, "est": {"values": [{"id": 2, "src": "hda"}]}, "est2genome": false, "est_gff": null}`
gene_prediction	`{"model_gff": null, "pred_gff": null, "snoscan_rrna": null, "trna": false}`
license_agreement	`true`
organism_type	`"eukaryotic"`
protein_evidences	`{"protein": {"values": [{"id": 3, "src": "hda"}]}, "protein2genome": false, "protein_gff": null}`
reannotation	`{"__current_case__": 0, "reannotate": "no"}`
repeat_masking	`{"repeat_source": {"__current_case__": 0, "softmask": true, "source_type": "dfam", "species_source": {"__current_case__": 0, "species_from_list": "yes", "species_list": "human"}}}`

Step 10: GFFRead:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp4n70qbf_/files/6/c/4/dataset_6c4b7e2f-41da-4d32-aee6-e0be9f74b436.dat' genomeref.fa &&  gffread '/tmp/tmp4n70qbf_/files/b/8/0/dataset_b80d9e43-9e9f-4bba-82d8-0f5ee143f453.dat' -g genomeref.fa      -w exons.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a77d3b30fe8411efbdfa7c1e5242529a"`
chr_replace	`None`
chromInfo	`"/tmp/tmp4n70qbf_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-w exons.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Other invocation details
- history_id
  - 07a32aa5caa9cc00
- history_state
  - ok
- invocation_id
  - 07a32aa5caa9cc00
- invocation_state
  - scheduled
- workflow_id
  - 07a32aa5caa9cc00

github-actions · 2025-03-12T13:17:13Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

Problems:

Output with path /tmp/tmpl_6087jh/Busco on data 1 short summary__3e6d29b2-f58e-4fc9-9976-96651e26b2da different than expected
Expected 32+-0 lines in the output found 0

Output with path /tmp/tmpc8w7cb2c/Busco on data 1 full table__f4c8887e-bc5c-4c0f-af7d-453126cbfeed different than expected
Expected text 'BUSCO version is: 5.7.1' in output ('')

Output with path /tmp/tmpfnl4zl19/Busco on data 1 missing buscos__a089e192-a5f8-45f3-8cad-aee9efe1c33f different than expected
Expected text 'BUSCO version is: 5.7.1' in output ('')

Workflow invocation details

Invocation Messages

Steps

Step 1: BUSCO lineage:
- step_state: scheduled
Step 2: Genome sequence:
- step_state: scheduled

Step 11: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpkb4nkc5a/files/1/4/b/dataset_14b3110f-11f0-424d-93d7-6cf23f9b9898.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpkb4nkc5a/job_working_directory/000/10/outputs/dataset_03e78245-4a27-4875-8e3f-937b8f5e8d4c.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpkb4nkc5a/files/a/b/b/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.dat' 2>&1 | tail -n +3 >> '/tmp/tmpkb4nkc5a/job_working_directory/000/10/outputs/dataset_03e78245-4a27-4875-8e3f-937b8f5e8d4c.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpkb4nkc5a/job_working_directory/000/10/outputs/dataset_03e78245-4a27-4875-8e3f-937b8f5e8d4c.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpkb4nkc5a/job_working_directory/000/10/outputs/dataset_5a159bb5-49c9-4c48-bb48-6c917f88cc23.dat'

Exit Code:

```
0
```

Standard Error:

�[0;33m13:08:49 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m13:08:50 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m13:08:50 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m13:08:50 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m13:08:50 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m13:08:50 [stats]�[0m�[0;35m A total of 860 transcripts populated.�[0m
�[0;33m13:08:52 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m13:08:52 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m13:08:52 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m13:08:52 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m13:08:52 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m13:08:52 [__init__]�[0m�[0;35m platform is linux2�[0m
�[0;33m13:08:52 [__init__]�[0m�[0;35m loaded modules: ['numpy.core.info', 'Bio.SeqIO.UniprotIO', 'jcvi.apps.base', 'ctypes.os', 'Bio.os', 'runpy', 'gc', 'distutils.sysconfig', 'matplotlib.cbook._backports', 'Bio._py3k.urllib2', 'logging.weakref', 'base64', 'jcvi.utils', 'jcvi.apps.signal', 'unittest.sys', 'numpy.core.umath', 'string', 'Bio.SeqIO.InsdcIO', 'numpy.lib.arraysetops', '_elementtree', 'xml.etree.warnings', 'xml.etree.sys', 'Bio.SeqUtils.binascii', 'json.encoder', 'Bio.SeqIO.QualityIO', 'numpy.core.machar', 'jcvi.formats.collections', 'unittest.StringIO', 'unittest.types', 'jcvi.apps.threading', 'numpy.ma.extras', 'numpy.fft.fftpack_lite', 'matplotlib.cbook', 'dis', 'zlib', 'logging.threading', 'jcvi.annotation', 'Bio.SeqIO.Bio', '_json', 'Bio.GenBank.warnings', 'matplotlib.cbook.warnings', 'pyparsing', 'matplotlib.cbook.textwrap', 'abc', 'numpy._globals', 'numpy.lib.npyio', 'xml.sax.io', 'Bio._py3k.sys', 'Bio.SeqIO.sys', 'numpy.fft.helper', 'matplotlib.rcsetup', 'optparse', 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�[0;33m13:08:52 [base]�[0m�[0;35m Rscript /tmp/tmpkb4nkc5a/tmp/tmpqgbQyj�[0m
Warning message:
Removed 428 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 428 rows containing non-finite values (stat_bin). 
�[0;33m13:08:56 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
Intron_Length/input.txt: Min=4 Max=6176 N=1043 Mean=114.04506232 SD=293.834008623 Median=60.0 Sum=118949
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Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
�[0;33m13:08:59 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=42 Max=14154 N=860 Mean=1426.9255814 SD=1121.71613602 Median=1123.5 Sum=1227156
�[0;33m13:08:59 [base]�[0m�[0;35m Rscript /tmp/tmpkb4nkc5a/tmp/tmp4fx2MP�[0m
Warning message:
Removed 28 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 28 rows containing non-finite values (stat_bin). 
�[0;33m13:09:01 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=860 Mean=2.21279069767 SD=1.72669172264 Median=2.0 Sum=1903
�[0;33m13:09:01 [base]�[0m�[0;35m Rscript /tmp/tmpkb4nkc5a/tmp/tmpplNOYI�[0m
Saving 7 x 7 in image

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"347aa644ff3e11ef8d456045bd7d2ea5"`
chromInfo	`"/tmp/tmpkb4nkc5a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 12: Map annotation ids:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpkb4nkc5a/files/1/4/b/dataset_14b3110f-11f0-424d-93d7-6cf23f9b9898.dat' '/tmp/tmpkb4nkc5a/job_working_directory/000/11/outputs/dataset_b77e9a0d-2dd0-47e1-b7e5-3fe6b0a886de.dat' && maker_map_ids --prefix '' --justify 6 '/tmp/tmpkb4nkc5a/files/1/4/b/dataset_14b3110f-11f0-424d-93d7-6cf23f9b9898.dat' > '/tmp/tmpkb4nkc5a/job_working_directory/000/11/outputs/dataset_35d80700-6e0f-4148-a681-e98be9f8d71e.dat' && map_gff_ids '/tmp/tmpkb4nkc5a/job_working_directory/000/11/outputs/dataset_35d80700-6e0f-4148-a681-e98be9f8d71e.dat' '/tmp/tmpkb4nkc5a/job_working_directory/000/11/outputs/dataset_b77e9a0d-2dd0-47e1-b7e5-3fe6b0a886de.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"347aa644ff3e11ef8d456045bd7d2ea5"`
chromInfo	`"/tmp/tmpkb4nkc5a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
justify	`"6"`
prefix	`None`

Step 13: BUSCO on the predicted protein sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpkb4nkc5a/files/6/e/b/dataset_6ebc9c09-270c-4bd4-88be-7d1d155a4d92.dat' --mode 'tran' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2025-03-12 13:15:51 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-03-12 13:08:21 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/12/2025 13:08:21 *****
2025-03-12 13:08:21 INFO:	Configuring BUSCO with local environment
2025-03-12 13:08:21 INFO:	Running transcriptome mode
2025-03-12 13:08:21 INFO:	Input file is /tmp/tmpkb4nkc5a/files/6/e/b/dataset_6ebc9c09-270c-4bd4-88be-7d1d155a4d92.dat
2025-03-12 13:08:21 WARNING:	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-12 13:08:21 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-12 13:08:21 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2025-03-12 13:08:21 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-12 13:08:21 INFO:	Running 1 job(s) on metaeuk, starting at 03/12/2025 13:08:21
2025-03-12 13:10:57 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-12 13:10:57 INFO:	***** Run HMMER on gene sequences *****
2025-03-12 13:10:58 INFO:	Running 758 job(s) on hmmsearch, starting at 03/12/2025 13:10:58
2025-03-12 13:11:03 INFO:	[hmmsearch]	76 of 758 task(s) completed
2025-03-12 13:11:07 INFO:	[hmmsearch]	152 of 758 task(s) completed
2025-03-12 13:11:10 INFO:	[hmmsearch]	228 of 758 task(s) completed
2025-03-12 13:11:13 INFO:	[hmmsearch]	304 of 758 task(s) completed
2025-03-12 13:11:16 INFO:	[hmmsearch]	379 of 758 task(s) completed
2025-03-12 13:11:19 INFO:	[hmmsearch]	455 of 758 task(s) completed
2025-03-12 13:11:22 INFO:	[hmmsearch]	531 of 758 task(s) completed
2025-03-12 13:11:24 INFO:	[hmmsearch]	607 of 758 task(s) completed
2025-03-12 13:11:27 INFO:	[hmmsearch]	683 of 758 task(s) completed
2025-03-12 13:11:32 INFO:	[hmmsearch]	758 of 758 task(s) completed
2025-03-12 13:11:32 INFO:	141 exons in total
2025-03-12 13:11:33 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2025-03-12 13:11:52 INFO:	Running 1 job(s) on metaeuk, starting at 03/12/2025 13:11:52
2025-03-12 13:15:36 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-12 13:15:36 INFO:	***** Run HMMER on gene sequences *****
2025-03-12 13:15:36 INFO:	Running 630 job(s) on hmmsearch, starting at 03/12/2025 13:15:36
2025-03-12 13:15:37 INFO:	[hmmsearch]	63 of 630 task(s) completed
2025-03-12 13:15:38 INFO:	[hmmsearch]	126 of 630 task(s) completed
2025-03-12 13:15:40 INFO:	[hmmsearch]	189 of 630 task(s) completed
2025-03-12 13:15:41 INFO:	[hmmsearch]	252 of 630 task(s) completed
2025-03-12 13:15:42 INFO:	[hmmsearch]	315 of 630 task(s) completed
2025-03-12 13:15:43 INFO:	[hmmsearch]	378 of 630 task(s) completed
2025-03-12 13:15:44 INFO:	[hmmsearch]	441 of 630 task(s) completed
2025-03-12 13:15:44 INFO:	[hmmsearch]	504 of 630 task(s) completed
2025-03-12 13:15:45 INFO:	[hmmsearch]	567 of 630 task(s) completed
2025-03-12 13:15:47 INFO:	[hmmsearch]	630 of 630 task(s) completed
2025-03-12 13:15:47 INFO:	1 candidate overlapping regions found
2025-03-12 13:15:47 INFO:	144 exons in total
2025-03-12 13:15:47 INFO:	Results:	C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758	   

2025-03-12 13:15:48 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758      |
    |128    Complete BUSCOs (C)                        |
    |127    Complete and single-copy BUSCOs (S)        |
    |1    Complete and duplicated BUSCOs (D)           |
    |11    Fragmented BUSCOs (F)                       |
    |619    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2025-03-12 13:15:48 INFO:	BUSCO analysis done with WARNING(s). Total running time: 446 seconds

***** Summary of warnings: *****
2025-03-12 13:08:21 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-12 13:08:21 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-12 13:08:21 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2025-03-12 13:15:48 INFO:	Results written in /tmp/tmpkb4nkc5a/job_working_directory/000/12/working/busco_galaxy
2025-03-12 13:15:48 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-03-12 13:15:48 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 64
drwxr-xr-x 5 1001 118  4096 Mar 12 13:08 busco_sequences
-rw-r--r-- 1 1001 118 36733 Mar 12 13:15 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Mar 12 13:11 hmmer_output
drwxr-xr-x 4 1001 118  4096 Mar 12 13:15 metaeuk_output
-rw-r--r-- 1 1001 118  8066 Mar 12 13:15 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2395 Mar 12 13:15 short_summary.json
-rw-r--r-- 1 1001 118   761 Mar 12 13:15 short_summary.txt
2025-03-12 13:15:49 INFO:	****************** Start plot generation at 03/12/2025 13:15:49 ******************
2025-03-12 13:15:49 INFO:	Load data ...
2025-03-12 13:15:49 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2025-03-12 13:15:49 INFO:	Generate the R code ...
2025-03-12 13:15:49 INFO:	Run the R code ...
2025-03-12 13:15:51 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-03-12 13:15:51 INFO:	Plot generation done. Total running time: 2.2918801307678223 seconds
2025-03-12 13:15:51 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"347aa644ff3e11ef8d456045bd7d2ea5"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
chromInfo	`"/tmp/tmpkb4nkc5a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 14: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmpkb4nkc5a/job_working_directory/000/13/outputs/dataset_44be092b-3e3b-4247-bb68-e9becf0a1531_files &&  cp /tmp/tmpkb4nkc5a/job_working_directory/000/13/configs/tmpeqktk8tr /tmp/tmpkb4nkc5a/job_working_directory/000/13/outputs/dataset_44be092b-3e3b-4247-bb68-e9becf0a1531_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpkb4nkc5a/job_working_directory/000/13/outputs/dataset_44be092b-3e3b-4247-bb68-e9becf0a1531_files /tmp/tmpkb4nkc5a/job_working_directory/000/13/configs/tmpeqktk8tr &&  cp /tmp/tmpkb4nkc5a/job_working_directory/000/13/outputs/dataset_44be092b-3e3b-4247-bb68-e9becf0a1531_files/index.html /tmp/tmpkb4nkc5a/job_working_directory/000/13/outputs/dataset_44be092b-3e3b-4247-bb68-e9becf0a1531.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Maker annotation / Map annotation ids on data 12: renamed GFF
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"347aa644ff3e11ef8d456045bd7d2ea5"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpkb4nkc5a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Maker annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 18, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 3: Genome assembly:
- step_state: scheduled
Step 4: Protein sequences:
- step_state: scheduled
Step 5: Augustus training:
- step_state: scheduled
Step 6: SNAP training:
- step_state: scheduled

**Step 7: Fasta Statistics **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmpkb4nkc5a/files/a/b/b/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.dat' --stats_output '/tmp/tmpkb4nkc5a/job_working_directory/000/6/outputs/dataset_a24aa367-2a3c-43d9-8e5e-5f62a9333496.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"347aa644ff3e11ef8d456045bd7d2ea5"`
chromInfo	`"/tmp/tmpkb4nkc5a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 8: BUSCO on the genome sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpkb4nkc5a/files/a/b/b/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

/tmp/tmpkb4nkc5a/job_working_directory/000/7/tool_script.sh: line 23:    11 Killed                  busco --in '/tmp/tmpkb4nkc5a/files/a/b/b/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5 --lineage_dataset 'fungi_odb10' --miniprot

Standard Output:

2025-03-12 12:35:04 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/12/2025 12:35:04 *****
2025-03-12 12:35:04 INFO:	Configuring BUSCO with local environment
2025-03-12 12:35:04 INFO:	Running genome mode
2025-03-12 12:35:13 INFO:	Input file is /tmp/tmpkb4nkc5a/files/a/b/b/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.dat
2025-03-12 12:35:13 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2025-03-12 12:35:13 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2025-03-12 12:35:13 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-12 12:35:13 INFO:	Running 1 job(s) on bbtools, starting at 03/12/2025 12:35:13
2025-03-12 12:35:14 INFO:	[bbtools]	1 of 1 task(s) completed
2025-03-12 12:35:14 INFO:	Running 1 job(s) on miniprot_index, starting at 03/12/2025 12:35:14
2025-03-12 12:35:15 INFO:	[miniprot_index]	1 of 1 task(s) completed
2025-03-12 12:35:15 INFO:	Running 1 job(s) on miniprot_align, starting at 03/12/2025 12:35:15
2025-03-12 12:52:52 INFO:	[miniprot_align]	1 of 1 task(s) completed

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"347aa644ff3e11ef8d456045bd7d2ea5"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmpkb4nkc5a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 9: Maker:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

RM_PATH=$(which RepeatMasker) && if [ -z "$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH ($PATH)" >&2 ; exit 1 ; fi &&  LIBDIR=$(dirname "$RM_PATH")/../share/RepeatMasker/Libraries &&  export LIBDIR &&  maker -CTL  &&  cp '/tmp/tmpkb4nkc5a/job_working_directory/000/8/configs/tmp7yrwu5v3' maker_opts.ctl  &&    cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&  mkdir -p 'augustus_dir/species/' &&  tar -C 'augustus_dir/species/' -xzvf '/tmp/tmpkb4nkc5a/files/8/4/1/dataset_841edf9e-b391-4dfd-abc8-a97d9b80d4bd.dat' > /dev/null &&  export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&  MPI_CMD="" && if [ "$MAKER_MPI" == "1" ]; then MPI_CMD="mpiexec -n ${GALAXY_SLOTS:-4}"; fi &&  ${MPI_CMD} maker --ignore_nfs_tmp  maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null  &&  gff3_merge -d *.maker.output/*_master_datastore_index.log -o '/tmp/tmpkb4nkc5a/job_working_directory/000/8/outputs/dataset_a9888a00-31c9-4987-8fd1-7e090a23cac4.dat'  &&  awk '{if ($2 == "maker" || $1 ~ /^#/) {print}}' '/tmp/tmpkb4nkc5a/job_working_directory/000/8/outputs/dataset_a9888a00-31c9-4987-8fd1-7e090a23cac4.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmpkb4nkc5a/job_working_directory/000/8/outputs/dataset_14b3110f-11f0-424d-93d7-6cf23f9b9898.dat'  &&  awk '{if ($2 != "maker") {print}}' '/tmp/tmpkb4nkc5a/job_working_directory/000/8/outputs/dataset_a9888a00-31c9-4987-8fd1-7e090a23cac4.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmpkb4nkc5a/job_working_directory/000/8/outputs/dataset_dd9dd7b3-7a11-401d-b13f-964d152dc679.dat'

Exit Code:

```
0
```

Standard Error:

Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore

To access files for individual sequences use the datastore index:
/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: NC_003421.2
Length: 2452883
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.1.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.2.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.3.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.4.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.5.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.6.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.7.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.8.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.9.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.10.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.11.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.12.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.13.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.14.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.15.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.16.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.17.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.18.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpkb4nkc5a/tmp/maker_zyokUx; /usr/local/bin/RepeatMasker /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.19.human.rb -species human -dir /tmp/tmpkb4nkc5a/job_working_directory/000/8/working/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.maker.output/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -----
..
aker_zyokUx/0/130_0.2303936-2305953.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/130_0.2303936-2305953.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/130_0.2303936-2305953.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/130_0.2303936-2305953.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/130_0.2303936-2305953.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/131_0.2317785-2319394.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/131_0.2317785-2319394.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/131_0.2317785-2319394.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/131_0.2317785-2319394.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/131_0.2317785-2319394.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/131_0.2317785-2319394.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/132_0.2326855-2328897.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/132_0.2326855-2328897.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/132_0.2326855-2328897.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/132_0.2326855-2328897.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/132_0.2326855-2328897.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/132_0.2326855-2328897.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/133_0.2329261-2334928.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/133_0.2329261-2334928.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/133_0.2329261-2334928.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/133_0.2329261-2334928.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/133_0.2329261-2334928.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/133_0.2329261-2334928.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/134_0.2341240-2344143.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/134_0.2341240-2344143.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/134_0.2341240-2344143.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/134_0.2341240-2344143.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/134_0.2341240-2344143.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/134_0.2341240-2344143.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/135_0.2349164-2354609.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/135_0.2349164-2354609.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/135_0.2349164-2354609.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/135_0.2349164-2354609.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/135_0.2349164-2354609.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/135_0.2349164-2354609.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/136_0.2366363-2370156.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/136_0.2366363-2370156.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/136_0.2366363-2370156.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/136_0.2366363-2370156.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/136_0.2366363-2370156.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/136_0.2366363-2370156.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/137_0.2373919-2380223.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/137_0.2373919-2380223.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/137_0.2373919-2380223.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/137_0.2373919-2380223.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/137_0.2373919-2380223.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/137_0.2373919-2380223.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/138_0.2381056-2382231.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/138_0.2381056-2382231.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/138_0.2381056-2382231.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/138_0.2381056-2382231.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/138_0.2381056-2382231.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/138_0.2381056-2382231.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/139_0.2384415-2388063.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/139_0.2384415-2388063.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/139_0.2384415-2388063.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/139_0.2384415-2388063.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/139_0.2384415-2388063.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/139_0.2384415-2388063.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/140_0.2388096-2391775.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/140_0.2388096-2391775.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/140_0.2388096-2391775.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/140_0.2388096-2391775.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/140_0.2388096-2391775.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/140_0.2388096-2391775.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/141_0.2407535-2408933.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/141_0.2407535-2408933.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/141_0.2407535-2408933.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/141_0.2407535-2408933.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/141_0.2407535-2408933.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/141_0.2407535-2408933.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/142_0.2428734-2431724.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpkb4nkc5a/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/142_0.2428734-2431724.local.auto_annotator.augustus.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/142_0.2428734-2431724.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpkb4nkc5a/files/4/4/b/dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat -xdef /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/142_0.2428734-2431724.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.xdef.snap  /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/142_0.2428734-2431724.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap.fasta > /tmp/tmpkb4nkc5a/tmp/maker_zyokUx/0/142_0.2428734-2431724.dataset_44b7ed86-f610-4f8a-a3d7-a142bb6672b5.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output


Maker is now finished!!!

Standard Output:

Start_time: 1741782902
End_time:   1741784880
Elapsed:    1978

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"347aa644ff3e11ef8d456045bd7d2ea5"`
abinitio_gene_prediction	`{"aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 4, "src": "hda"}]}}, "snaphmm": {"values": [{"id": 5, "src": "hda"}]}, "unmask": false}`
advanced	`{"AED_threshold": "1.0", "alt_peptide": "C", "alt_splice": false, "always_complete": false, "correct_est_fusion": false, "fix_nucleotides": false, "keep_preds": "0.0", "map_forward": false, "max_dna_len": "100000", "min_contig": "1", "min_protein": "0", "other_gff": null, "pred_flank": "200", "pred_stats": false, "single_exon": {"__current_case__": 0, "single_exon": "0"}, "split_hit": "10000"}`
chromInfo	`"/tmp/tmpkb4nkc5a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
est_evidences	`{"altest": null, "altest_gff": null, "est": {"values": [{"id": 2, "src": "hda"}]}, "est2genome": false, "est_gff": null}`
gene_prediction	`{"model_gff": null, "pred_gff": null, "snoscan_rrna": null, "trna": false}`
license_agreement	`true`
organism_type	`"eukaryotic"`
protein_evidences	`{"protein": {"values": [{"id": 3, "src": "hda"}]}, "protein2genome": false, "protein_gff": null}`
reannotation	`{"__current_case__": 0, "reannotate": "no"}`
repeat_masking	`{"repeat_source": {"__current_case__": 0, "softmask": true, "source_type": "dfam", "species_source": {"__current_case__": 0, "species_from_list": "yes", "species_list": "human"}}}`

Step 10: GFFRead:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpkb4nkc5a/files/a/b/b/dataset_abb17ae0-b974-4363-8573-eb8b63c9db53.dat' genomeref.fa &&  gffread '/tmp/tmpkb4nkc5a/files/1/4/b/dataset_14b3110f-11f0-424d-93d7-6cf23f9b9898.dat' -g genomeref.fa      -w exons.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"347aa644ff3e11ef8d456045bd7d2ea5"`
chr_replace	`None`
chromInfo	`"/tmp/tmpkb4nkc5a/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-w exons.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Other invocation details
- history_id
  - b867ef2de3b2f07f
- history_state
  - ok
- invocation_id
  - b867ef2de3b2f07f
- invocation_state
  - scheduled
- workflow_id
  - b867ef2de3b2f07f

github-actions · 2025-03-12T15:51:35Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

Problems:

Output with path /tmp/tmpylbrb80q/Busco on data 1 short summary__4148418c-21e9-4853-a672-edb557a850c3 different than expected
Expected 32+-0 lines in the output found 0

Output with path /tmp/tmpbf6yu2k9/Busco on data 1 full table__103a4d74-37ca-4717-8d42-4d2429662bd1 different than expected
Expected text '# BUSCO version is: 5.7.1' in output ('')

Output with path /tmp/tmpdxzhu095/Busco on data 1 missing buscos__d7e0c1f5-467f-4dba-b645-d2df7af24ac5 different than expected
Expected text '# BUSCO version is: 5.7.1' in output ('')

Workflow invocation details

Invocation Messages

Steps

Step 1: BUSCO lineage:
- step_state: scheduled
Step 2: Genome sequence:
- step_state: scheduled

Step 11: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp03c70u6q/files/b/7/6/dataset_b7691ba6-7071-4f82-acab-06892e51c5f3.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp03c70u6q/job_working_directory/000/10/outputs/dataset_b4e0c31d-3e20-46f4-b5e3-2047994f4797.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp03c70u6q/files/0/d/f/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.dat' 2>&1 | tail -n +3 >> '/tmp/tmp03c70u6q/job_working_directory/000/10/outputs/dataset_b4e0c31d-3e20-46f4-b5e3-2047994f4797.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp03c70u6q/job_working_directory/000/10/outputs/dataset_b4e0c31d-3e20-46f4-b5e3-2047994f4797.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp03c70u6q/job_working_directory/000/10/outputs/dataset_fb442674-5023-4c5e-a8fc-9e5e2567b800.dat'

Exit Code:

```
0
```

Standard Error:

�[0;33m15:41:58 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m15:41:59 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m15:41:59 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m15:41:59 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m15:41:59 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m15:41:59 [stats]�[0m�[0;35m A total of 860 transcripts populated.�[0m
�[0;33m15:42:00 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m15:42:00 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m15:42:00 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m15:42:00 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m15:42:00 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m15:42:00 [__init__]�[0m�[0;35m platform is linux2�[0m
�[0;33m15:42:00 [__init__]�[0m�[0;35m loaded modules: ['numpy.core.info', 'Bio.SeqIO.UniprotIO', 'jcvi.apps.base', 'ctypes.os', 'Bio.os', 'runpy', 'gc', 'distutils.sysconfig', 'matplotlib.cbook._backports', 'Bio._py3k.urllib2', 'logging.weakref', 'base64', 'jcvi.utils', 'jcvi.apps.signal', 'unittest.sys', 'numpy.core.umath', 'string', 'Bio.SeqIO.InsdcIO', 'numpy.lib.arraysetops', '_elementtree', 'xml.etree.warnings', 'xml.etree.sys', 'Bio.SeqUtils.binascii', 'json.encoder', 'Bio.SeqIO.QualityIO', 'numpy.core.machar', 'jcvi.formats.collections', 'unittest.StringIO', 'unittest.types', 'jcvi.apps.threading', 'numpy.ma.extras', 'numpy.fft.fftpack_lite', 'matplotlib.cbook', 'dis', 'zlib', 'logging.threading', 'jcvi.annotation', 'Bio.SeqIO.Bio', '_json', 'Bio.GenBank.warnings', 'matplotlib.cbook.warnings', 'pyparsing', 'matplotlib.cbook.textwrap', 'abc', 'numpy._globals', 'numpy.lib.npyio', 'xml.sax.io', 'Bio._py3k.sys', 'Bio.SeqIO.sys', 'numpy.fft.helper', 'matplotlib.rcsetup', 'optparse', 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�[0;33m15:42:00 [font_manager]�[0m�[0;35m generated new fontManager�[0m
�[0;33m15:42:00 [__init__]�[0m�[0;35m backend agg version v2.2�[0m
�[0;33m15:42:00 [stats]�[0m�[0;35m Parsing files in `Exon_Length`..�[0m
Exon_Length/input.txt: Min=2 Max=14154 N=1899 Mean=646.007898894 SD=928.667351336 Median=267.0 Sum=1226769
�[0;33m15:42:00 [base]�[0m�[0;35m Rscript /tmp/tmp03c70u6q/tmp/tmpnXc4ja�[0m
Warning message:
Removed 428 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 428 rows containing non-finite values (stat_bin). 
�[0;33m15:42:04 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
Intron_Length/input.txt: Min=4 Max=6176 N=1039 Mean=113.739172281 SD=294.202696254 Median=60.0 Sum=118175
�[0;33m15:42:04 [base]�[0m�[0;35m Rscript /tmp/tmp03c70u6q/tmp/tmp9M4WTv�[0m
Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
�[0;33m15:42:08 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=42 Max=14154 N=860 Mean=1426.4755814 SD=1121.67919619 Median=1123.5 Sum=1226769
�[0;33m15:42:08 [base]�[0m�[0;35m Rscript /tmp/tmp03c70u6q/tmp/tmphgOUPZ�[0m
Warning message:
Removed 28 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 28 rows containing non-finite values (stat_bin). 
�[0;33m15:42:12 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=860 Mean=2.20813953488 SD=1.72456365336 Median=2.0 Sum=1899
�[0;33m15:42:12 [base]�[0m�[0;35m Rscript /tmp/tmp03c70u6q/tmp/tmpJx5zsJ�[0m
Saving 7 x 7 in image

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"976add4aff5311ef8d450022482371a3"`
chromInfo	`"/tmp/tmp03c70u6q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 12: Map annotation ids:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmp03c70u6q/files/b/7/6/dataset_b7691ba6-7071-4f82-acab-06892e51c5f3.dat' '/tmp/tmp03c70u6q/job_working_directory/000/11/outputs/dataset_abd92058-0610-46f5-876d-caae44fc01ee.dat' && maker_map_ids --prefix '' --justify 6 '/tmp/tmp03c70u6q/files/b/7/6/dataset_b7691ba6-7071-4f82-acab-06892e51c5f3.dat' > '/tmp/tmp03c70u6q/job_working_directory/000/11/outputs/dataset_a58d7380-ee7f-4788-8f6c-0859ed9448b6.dat' && map_gff_ids '/tmp/tmp03c70u6q/job_working_directory/000/11/outputs/dataset_a58d7380-ee7f-4788-8f6c-0859ed9448b6.dat' '/tmp/tmp03c70u6q/job_working_directory/000/11/outputs/dataset_abd92058-0610-46f5-876d-caae44fc01ee.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"976add4aff5311ef8d450022482371a3"`
chromInfo	`"/tmp/tmp03c70u6q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
justify	`"6"`
prefix	`None`

Step 13: BUSCO on the predicted protein sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp03c70u6q/files/b/2/f/dataset_b2f15a6c-e5ff-4f5f-a16c-f0680421d3ac.dat' --mode 'tran' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2025-03-12 15:50:10 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-03-12 15:41:54 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/12/2025 15:41:54 *****
2025-03-12 15:41:54 INFO:	Configuring BUSCO with local environment
2025-03-12 15:41:54 INFO:	Running transcriptome mode
2025-03-12 15:41:54 INFO:	Input file is /tmp/tmp03c70u6q/files/b/2/f/dataset_b2f15a6c-e5ff-4f5f-a16c-f0680421d3ac.dat
2025-03-12 15:41:54 WARNING:	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-12 15:41:54 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-12 15:41:54 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2025-03-12 15:41:54 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-12 15:41:54 INFO:	Running 1 job(s) on metaeuk, starting at 03/12/2025 15:41:54
2025-03-12 15:44:29 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-12 15:44:29 INFO:	***** Run HMMER on gene sequences *****
2025-03-12 15:44:30 INFO:	Running 758 job(s) on hmmsearch, starting at 03/12/2025 15:44:30
2025-03-12 15:44:48 INFO:	[hmmsearch]	76 of 758 task(s) completed
2025-03-12 15:44:55 INFO:	[hmmsearch]	152 of 758 task(s) completed
2025-03-12 15:45:02 INFO:	[hmmsearch]	228 of 758 task(s) completed
2025-03-12 15:45:09 INFO:	[hmmsearch]	304 of 758 task(s) completed
2025-03-12 15:45:16 INFO:	[hmmsearch]	379 of 758 task(s) completed
2025-03-12 15:45:22 INFO:	[hmmsearch]	455 of 758 task(s) completed
2025-03-12 15:45:29 INFO:	[hmmsearch]	531 of 758 task(s) completed
2025-03-12 15:45:35 INFO:	[hmmsearch]	607 of 758 task(s) completed
2025-03-12 15:45:42 INFO:	[hmmsearch]	683 of 758 task(s) completed
2025-03-12 15:45:50 INFO:	[hmmsearch]	758 of 758 task(s) completed
2025-03-12 15:45:50 INFO:	140 exons in total
2025-03-12 15:45:50 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2025-03-12 15:46:10 INFO:	Running 1 job(s) on metaeuk, starting at 03/12/2025 15:46:10
2025-03-12 15:49:55 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-12 15:49:55 INFO:	***** Run HMMER on gene sequences *****
2025-03-12 15:49:55 INFO:	Running 630 job(s) on hmmsearch, starting at 03/12/2025 15:49:55
2025-03-12 15:49:56 INFO:	[hmmsearch]	63 of 630 task(s) completed
2025-03-12 15:49:57 INFO:	[hmmsearch]	126 of 630 task(s) completed
2025-03-12 15:49:58 INFO:	[hmmsearch]	189 of 630 task(s) completed
2025-03-12 15:50:00 INFO:	[hmmsearch]	252 of 630 task(s) completed
2025-03-12 15:50:00 INFO:	[hmmsearch]	315 of 630 task(s) completed
2025-03-12 15:50:02 INFO:	[hmmsearch]	378 of 630 task(s) completed
2025-03-12 15:50:02 INFO:	[hmmsearch]	441 of 630 task(s) completed
2025-03-12 15:50:03 INFO:	[hmmsearch]	504 of 630 task(s) completed
2025-03-12 15:50:04 INFO:	[hmmsearch]	567 of 630 task(s) completed
2025-03-12 15:50:05 INFO:	[hmmsearch]	630 of 630 task(s) completed
2025-03-12 15:50:06 INFO:	1 candidate overlapping regions found
2025-03-12 15:50:06 INFO:	143 exons in total
2025-03-12 15:50:06 INFO:	Results:	C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758	   

2025-03-12 15:50:07 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758      |
    |128    Complete BUSCOs (C)                        |
    |127    Complete and single-copy BUSCOs (S)        |
    |1    Complete and duplicated BUSCOs (D)           |
    |11    Fragmented BUSCOs (F)                       |
    |619    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2025-03-12 15:50:07 INFO:	BUSCO analysis done with WARNING(s). Total running time: 492 seconds

***** Summary of warnings: *****
2025-03-12 15:41:54 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-12 15:41:54 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-12 15:41:54 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2025-03-12 15:50:07 INFO:	Results written in /tmp/tmp03c70u6q/job_working_directory/000/12/working/busco_galaxy
2025-03-12 15:50:07 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-03-12 15:50:07 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 64
drwxr-xr-x 5 1001 118  4096 Mar 12 15:41 busco_sequences
-rw-r--r-- 1 1001 118 36524 Mar 12 15:50 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Mar 12 15:45 hmmer_output
drwxr-xr-x 4 1001 118  4096 Mar 12 15:50 metaeuk_output
-rw-r--r-- 1 1001 118  8066 Mar 12 15:50 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2395 Mar 12 15:50 short_summary.json
-rw-r--r-- 1 1001 118   761 Mar 12 15:50 short_summary.txt
2025-03-12 15:50:07 INFO:	****************** Start plot generation at 03/12/2025 15:50:07 ******************
2025-03-12 15:50:07 INFO:	Load data ...
2025-03-12 15:50:07 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2025-03-12 15:50:07 INFO:	Generate the R code ...
2025-03-12 15:50:07 INFO:	Run the R code ...
2025-03-12 15:50:10 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-03-12 15:50:10 INFO:	Plot generation done. Total running time: 2.264319896697998 seconds
2025-03-12 15:50:10 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"976add4aff5311ef8d450022482371a3"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
chromInfo	`"/tmp/tmp03c70u6q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 14: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmp03c70u6q/job_working_directory/000/13/outputs/dataset_600c7072-bbf0-42e7-abeb-f6a7590fdffc_files &&  cp /tmp/tmp03c70u6q/job_working_directory/000/13/configs/tmpbpja58vq /tmp/tmp03c70u6q/job_working_directory/000/13/outputs/dataset_600c7072-bbf0-42e7-abeb-f6a7590fdffc_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp03c70u6q/job_working_directory/000/13/outputs/dataset_600c7072-bbf0-42e7-abeb-f6a7590fdffc_files /tmp/tmp03c70u6q/job_working_directory/000/13/configs/tmpbpja58vq &&  cp /tmp/tmp03c70u6q/job_working_directory/000/13/outputs/dataset_600c7072-bbf0-42e7-abeb-f6a7590fdffc_files/index.html /tmp/tmp03c70u6q/job_working_directory/000/13/outputs/dataset_600c7072-bbf0-42e7-abeb-f6a7590fdffc.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Maker annotation / Map annotation ids on data 12: renamed GFF
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"976add4aff5311ef8d450022482371a3"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp03c70u6q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Maker annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 18, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 3: Genome assembly:
- step_state: scheduled
Step 4: Protein sequences:
- step_state: scheduled
Step 5: Augustus training:
- step_state: scheduled
Step 6: SNAP training:
- step_state: scheduled

**Step 7: Fasta Statistics **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmp03c70u6q/files/0/d/f/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.dat' --stats_output '/tmp/tmp03c70u6q/job_working_directory/000/6/outputs/dataset_37a342ff-c909-4fb5-8c39-5ccc43ba4e3f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"976add4aff5311ef8d450022482371a3"`
chromInfo	`"/tmp/tmp03c70u6q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 8: BUSCO on the genome sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp03c70u6q/files/0/d/f/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

/tmp/tmp03c70u6q/job_working_directory/000/7/tool_script.sh: line 23:    11 Killed                  busco --in '/tmp/tmp03c70u6q/files/0/d/f/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5 --lineage_dataset 'fungi_odb10' --miniprot

Standard Output:

2025-03-12 15:07:41 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/12/2025 15:07:41 *****
2025-03-12 15:07:41 INFO:	Configuring BUSCO with local environment
2025-03-12 15:07:41 INFO:	Running genome mode
2025-03-12 15:07:43 INFO:	Input file is /tmp/tmp03c70u6q/files/0/d/f/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.dat
2025-03-12 15:07:43 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2025-03-12 15:07:43 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2025-03-12 15:07:43 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-12 15:07:43 INFO:	Running 1 job(s) on bbtools, starting at 03/12/2025 15:07:43
2025-03-12 15:07:44 INFO:	[bbtools]	1 of 1 task(s) completed
2025-03-12 15:07:44 INFO:	Running 1 job(s) on miniprot_index, starting at 03/12/2025 15:07:44
2025-03-12 15:07:45 INFO:	[miniprot_index]	1 of 1 task(s) completed
2025-03-12 15:07:45 INFO:	Running 1 job(s) on miniprot_align, starting at 03/12/2025 15:07:45
2025-03-12 15:25:25 INFO:	[miniprot_align]	1 of 1 task(s) completed

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"976add4aff5311ef8d450022482371a3"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmp03c70u6q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 9: Maker:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

RM_PATH=$(which RepeatMasker) && if [ -z "$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH ($PATH)" >&2 ; exit 1 ; fi &&  LIBDIR=$(dirname "$RM_PATH")/../share/RepeatMasker/Libraries &&  export LIBDIR &&  maker -CTL  &&  cp '/tmp/tmp03c70u6q/job_working_directory/000/8/configs/tmpywpd2wfy' maker_opts.ctl  &&    cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&  mkdir -p 'augustus_dir/species/' &&  tar -C 'augustus_dir/species/' -xzvf '/tmp/tmp03c70u6q/files/4/3/f/dataset_43f31f37-9da4-4b52-9eb6-9eeb6c74b591.dat' > /dev/null &&  export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&  MPI_CMD="" && if [ "$MAKER_MPI" == "1" ]; then MPI_CMD="mpiexec -n ${GALAXY_SLOTS:-4}"; fi &&  ${MPI_CMD} maker --ignore_nfs_tmp  maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null  &&  gff3_merge -d *.maker.output/*_master_datastore_index.log -o '/tmp/tmp03c70u6q/job_working_directory/000/8/outputs/dataset_97d37b5c-f84d-40bf-9eb0-eafd304619d0.dat'  &&  awk '{if ($2 == "maker" || $1 ~ /^#/) {print}}' '/tmp/tmp03c70u6q/job_working_directory/000/8/outputs/dataset_97d37b5c-f84d-40bf-9eb0-eafd304619d0.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmp03c70u6q/job_working_directory/000/8/outputs/dataset_b7691ba6-7071-4f82-acab-06892e51c5f3.dat'  &&  awk '{if ($2 != "maker") {print}}' '/tmp/tmp03c70u6q/job_working_directory/000/8/outputs/dataset_97d37b5c-f84d-40bf-9eb0-eafd304619d0.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmp03c70u6q/job_working_directory/000/8/outputs/dataset_9b4c88ef-d323-4dbe-985a-490d4785c9d4.dat'

Exit Code:

```
0
```

Standard Error:

Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore

To access files for individual sequences use the datastore index:
/tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: NC_003421.2
Length: 2452883
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.1.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.2.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.3.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.4.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.5.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.6.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.7.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.8.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.9.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.10.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.11.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.12.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.13.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.14.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.15.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.16.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.17.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.18.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmp03c70u6q/tmp/maker_TMz7Fe; /usr/local/bin/RepeatMasker /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.19.human.rb -species human -dir /tmp/tmp03c70u6q/job_working_directory/000/8/working/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.maker.output/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -----
..
f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/130_0.2303936-2305953.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/130_0.2303936-2305953.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/130_0.2303936-2305953.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/130_0.2303936-2305953.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/131_0.2317785-2319394.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/131_0.2317785-2319394.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/131_0.2317785-2319394.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/131_0.2317785-2319394.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/131_0.2317785-2319394.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/131_0.2317785-2319394.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/132_0.2326855-2328897.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/132_0.2326855-2328897.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/132_0.2326855-2328897.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/132_0.2326855-2328897.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/132_0.2326855-2328897.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/132_0.2326855-2328897.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/133_0.2329261-2334928.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/133_0.2329261-2334928.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/133_0.2329261-2334928.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/133_0.2329261-2334928.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/133_0.2329261-2334928.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/133_0.2329261-2334928.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/134_0.2341240-2344143.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/134_0.2341240-2344143.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/134_0.2341240-2344143.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/134_0.2341240-2344143.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/134_0.2341240-2344143.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/134_0.2341240-2344143.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/135_0.2349164-2354609.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/135_0.2349164-2354609.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/135_0.2349164-2354609.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/135_0.2349164-2354609.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/135_0.2349164-2354609.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/135_0.2349164-2354609.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/136_0.2366363-2370156.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/136_0.2366363-2370156.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/136_0.2366363-2370156.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/136_0.2366363-2370156.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/136_0.2366363-2370156.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/136_0.2366363-2370156.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/137_0.2373919-2380223.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/137_0.2373919-2380223.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/137_0.2373919-2380223.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/137_0.2373919-2380223.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/137_0.2373919-2380223.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/137_0.2373919-2380223.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/138_0.2381056-2382231.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/138_0.2381056-2382231.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/138_0.2381056-2382231.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/138_0.2381056-2382231.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/138_0.2381056-2382231.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/138_0.2381056-2382231.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/139_0.2384415-2388063.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/139_0.2384415-2388063.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/139_0.2384415-2388063.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/139_0.2384415-2388063.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/139_0.2384415-2388063.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/139_0.2384415-2388063.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/140_0.2388096-2391775.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/140_0.2388096-2391775.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/140_0.2388096-2391775.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/140_0.2388096-2391775.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/140_0.2388096-2391775.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/140_0.2388096-2391775.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/141_0.2407535-2408933.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/141_0.2407535-2408933.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/141_0.2407535-2408933.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/141_0.2407535-2408933.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/141_0.2407535-2408933.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/141_0.2407535-2408933.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp03c70u6q/files/2/5/b/dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat -xdef /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/142_0.2428734-2431724.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.xdef.snap  /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/142_0.2428734-2431724.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/142_0.2428734-2431724.dataset_25bc308f-2aea-45c9-a611-ca3510ef64a7.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/142_0.2428734-2431724.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp03c70u6q/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/142_0.2428734-2431724.local.auto_annotator.augustus.fasta > /tmp/tmp03c70u6q/tmp/maker_TMz7Fe/0/142_0.2428734-2431724.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output


Maker is now finished!!!

Standard Output:

Start_time: 1741792079
End_time:   1741794087
Elapsed:    2008

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"976add4aff5311ef8d450022482371a3"`
abinitio_gene_prediction	`{"aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 4, "src": "hda"}]}}, "snaphmm": {"values": [{"id": 5, "src": "hda"}]}, "unmask": false}`
advanced	`{"AED_threshold": "1.0", "alt_peptide": "C", "alt_splice": false, "always_complete": false, "correct_est_fusion": false, "fix_nucleotides": false, "keep_preds": "0.0", "map_forward": false, "max_dna_len": "100000", "min_contig": "1", "min_protein": "0", "other_gff": null, "pred_flank": "200", "pred_stats": false, "single_exon": {"__current_case__": 0, "single_exon": "0"}, "split_hit": "10000"}`
chromInfo	`"/tmp/tmp03c70u6q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
est_evidences	`{"altest": null, "altest_gff": null, "est": {"values": [{"id": 2, "src": "hda"}]}, "est2genome": false, "est_gff": null}`
gene_prediction	`{"model_gff": null, "pred_gff": null, "snoscan_rrna": null, "trna": false}`
license_agreement	`true`
organism_type	`"eukaryotic"`
protein_evidences	`{"protein": {"values": [{"id": 3, "src": "hda"}]}, "protein2genome": false, "protein_gff": null}`
reannotation	`{"__current_case__": 0, "reannotate": "no"}`
repeat_masking	`{"repeat_source": {"__current_case__": 0, "softmask": true, "source_type": "dfam", "species_source": {"__current_case__": 0, "species_from_list": "yes", "species_list": "human"}}}`

Step 10: GFFRead:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp03c70u6q/files/0/d/f/dataset_0df7a1a0-5d95-4e70-abcf-64b2b451e48f.dat' genomeref.fa &&  gffread '/tmp/tmp03c70u6q/files/b/7/6/dataset_b7691ba6-7071-4f82-acab-06892e51c5f3.dat' -g genomeref.fa      -w exons.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"976add4aff5311ef8d450022482371a3"`
chr_replace	`None`
chromInfo	`"/tmp/tmp03c70u6q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-w exons.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Other invocation details
- history_id
  - 755b74b555fe1e55
- history_state
  - ok
- invocation_id
  - 755b74b555fe1e55
- invocation_state
  - scheduled
- workflow_id
  - 755b74b555fe1e55

github-actions · 2025-03-17T11:38:30Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

Problems:

Output with path /tmp/tmppgzc1ef3/Fasta Statistics on data 1 summary stats__a9da3df9-d415-4ba7-8bd4-eeeee7240c33 different than expected
Expected 32+-0 lines in the output found 30

Workflow invocation details

Invocation Messages

Steps

Step 1: BUSCO lineage:
- step_state: scheduled
Step 2: Genome sequence:
- step_state: scheduled

Step 11: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpcxqpfl9y/files/e/b/d/dataset_ebd0a7f6-160d-426f-aa7e-ae1ca00bb19e.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpcxqpfl9y/job_working_directory/000/10/outputs/dataset_a3179ce5-bb95-46f7-a3f1-866bd033628f.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpcxqpfl9y/files/a/2/f/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.dat' 2>&1 | tail -n +3 >> '/tmp/tmpcxqpfl9y/job_working_directory/000/10/outputs/dataset_a3179ce5-bb95-46f7-a3f1-866bd033628f.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpcxqpfl9y/job_working_directory/000/10/outputs/dataset_a3179ce5-bb95-46f7-a3f1-866bd033628f.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpcxqpfl9y/job_working_directory/000/10/outputs/dataset_b73d72d6-6d04-44c1-9fae-48f2d53d4fe4.dat'

Exit Code:

```
0
```

Standard Error:

�[0;33m11:27:09 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m11:27:10 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m11:27:10 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m11:27:10 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m11:27:10 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m11:27:10 [stats]�[0m�[0;35m A total of 860 transcripts populated.�[0m
�[0;33m11:27:11 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m11:27:11 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m11:27:11 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m11:27:11 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m11:27:11 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m11:27:11 [__init__]�[0m�[0;35m platform is linux2�[0m
�[0;33m11:27:11 [__init__]�[0m�[0;35m loaded modules: ['numpy.core.info', 'Bio.SeqIO.UniprotIO', 'jcvi.apps.base', 'ctypes.os', 'Bio.os', 'runpy', 'gc', 'distutils.sysconfig', 'matplotlib.cbook._backports', 'Bio._py3k.urllib2', 'logging.weakref', 'base64', 'jcvi.utils', 'jcvi.apps.signal', 'unittest.sys', 'numpy.core.umath', 'string', 'Bio.SeqIO.InsdcIO', 'numpy.lib.arraysetops', '_elementtree', 'xml.etree.warnings', 'xml.etree.sys', 'Bio.SeqUtils.binascii', 'json.encoder', 'Bio.SeqIO.QualityIO', 'numpy.core.machar', 'jcvi.formats.collections', 'unittest.StringIO', 'unittest.types', 'jcvi.apps.threading', 'numpy.ma.extras', 'numpy.fft.fftpack_lite', 'matplotlib.cbook', 'dis', 'zlib', 'logging.threading', 'jcvi.annotation', 'Bio.SeqIO.Bio', '_json', 'Bio.GenBank.warnings', 'matplotlib.cbook.warnings', 'pyparsing', 'matplotlib.cbook.textwrap', 'abc', 'numpy._globals', 'numpy.lib.npyio', 'xml.sax.io', 'Bio._py3k.sys', 'Bio.SeqIO.sys', 'numpy.fft.helper', 'matplotlib.rcsetup', 'optparse', 'unittest.suite', '_ctypes', 'xml.etree', 'json.scanner', 'codecs', 'Bio.collections', 'numpy.os', 'jcvi.annotation.jcvi', 'mkl_fft._numpy_fft', 'StringIO', 'Bio.Alphabet.IUPAC', 'weakref', 'numpy.core._internal', 'distutils.sys', 'numpy.lib.arraypad', 'pprint', 'Bio.SeqIO.math', 'Bio.warnings', 'jcvi.apps.httplib', 'sqlite3.dbapi2', 'select', 'ctypes._ctypes', '_heapq', 'six.moves.urllib', 'numpy.lib.financial', 'Bio.Align.Generic', 'binascii', 'jcvi.formats.sizes', 'unittest.loader', 'unittest.fnmatch', 'numpy.polynomial.chebyshev', '_functools', 'cPickle', 'numpy.polynomial.hermite_e', 'jcvi.apps.urllib', 'jcvi', 'numpy.testing.utils', 'jcvi.graphics.histogram', 'jcvi.utils.UserDict', 'numpy.core.fromnumeric', 'unicodedata', 'numpy.ctypeslib', 'matplotlib._version', '_ast', 'jcvi.utils.range', 'encodings.aliases', 'Bio.SeqIO.SeqXmlIO', 'fnmatch', 'sre_parse', 'pickle', 'Bio.SeqIO.AceIO', 'numpy.random.warnings', 'xml.sax.types', 'jcvi.utils.itertools', 'logging.cStringIO', 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�[0;33m11:27:12 [__init__]�[0m�[0;35m backend agg version v2.2�[0m
�[0;33m11:27:12 [stats]�[0m�[0;35m Parsing files in `Exon_Length`..�[0m
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�[0;33m11:27:12 [base]�[0m�[0;35m Rscript /tmp/tmpcxqpfl9y/tmp/tmp_fWl1x�[0m
Warning message:
Removed 428 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 428 rows containing non-finite values (stat_bin). 
�[0;33m11:27:14 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
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�[0;33m11:27:14 [base]�[0m�[0;35m Rscript /tmp/tmpcxqpfl9y/tmp/tmpQKs4wf�[0m
Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
�[0;33m11:27:17 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=42 Max=14154 N=860 Mean=1426.56976744 SD=1122.09033277 Median=1123.5 Sum=1226850
�[0;33m11:27:17 [base]�[0m�[0;35m Rscript /tmp/tmpcxqpfl9y/tmp/tmpT8Febf�[0m
Warning message:
Removed 29 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 29 rows containing non-finite values (stat_bin). 
�[0;33m11:27:20 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=860 Mean=2.20930232558 SD=1.73819124827 Median=2.0 Sum=1900
�[0;33m11:27:20 [base]�[0m�[0;35m Rscript /tmp/tmpcxqpfl9y/tmp/tmpzxKX3p�[0m
Saving 7 x 7 in image

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c7ad78f0031d11f08d45000d3a548ffa"`
chromInfo	`"/tmp/tmpcxqpfl9y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 12: Map annotation ids:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpcxqpfl9y/files/e/b/d/dataset_ebd0a7f6-160d-426f-aa7e-ae1ca00bb19e.dat' '/tmp/tmpcxqpfl9y/job_working_directory/000/11/outputs/dataset_cb408996-fa25-45d4-a9b0-b6159ce20cb0.dat' && maker_map_ids --prefix '' --justify 6 '/tmp/tmpcxqpfl9y/files/e/b/d/dataset_ebd0a7f6-160d-426f-aa7e-ae1ca00bb19e.dat' > '/tmp/tmpcxqpfl9y/job_working_directory/000/11/outputs/dataset_6bfcbff8-7c35-4f70-85e3-c3d59bbfea6d.dat' && map_gff_ids '/tmp/tmpcxqpfl9y/job_working_directory/000/11/outputs/dataset_6bfcbff8-7c35-4f70-85e3-c3d59bbfea6d.dat' '/tmp/tmpcxqpfl9y/job_working_directory/000/11/outputs/dataset_cb408996-fa25-45d4-a9b0-b6159ce20cb0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c7ad78f0031d11f08d45000d3a548ffa"`
chromInfo	`"/tmp/tmpcxqpfl9y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
justify	`"6"`
prefix	`None`

Step 13: BUSCO on the predicted protein sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpcxqpfl9y/files/e/c/9/dataset_ec9fa2bd-eb58-4a86-80eb-c5ed93b6fcbe.dat' --mode 'tran' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2025-03-17 11:37:08 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-03-17 11:26:38 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/17/2025 11:26:38 *****
2025-03-17 11:26:38 INFO:	Configuring BUSCO with local environment
2025-03-17 11:26:38 INFO:	Running transcriptome mode
2025-03-17 11:26:38 INFO:	Input file is /tmp/tmpcxqpfl9y/files/e/c/9/dataset_ec9fa2bd-eb58-4a86-80eb-c5ed93b6fcbe.dat
2025-03-17 11:26:38 WARNING:	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-17 11:26:38 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-17 11:26:38 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2025-03-17 11:26:38 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-17 11:26:38 INFO:	Running 1 job(s) on metaeuk, starting at 03/17/2025 11:26:38
2025-03-17 11:31:25 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-17 11:31:25 INFO:	***** Run HMMER on gene sequences *****
2025-03-17 11:31:25 INFO:	Running 758 job(s) on hmmsearch, starting at 03/17/2025 11:31:25
2025-03-17 11:31:33 INFO:	[hmmsearch]	76 of 758 task(s) completed
2025-03-17 11:31:38 INFO:	[hmmsearch]	152 of 758 task(s) completed
2025-03-17 11:31:45 INFO:	[hmmsearch]	228 of 758 task(s) completed
2025-03-17 11:31:52 INFO:	[hmmsearch]	304 of 758 task(s) completed
2025-03-17 11:31:58 INFO:	[hmmsearch]	379 of 758 task(s) completed
2025-03-17 11:32:04 INFO:	[hmmsearch]	455 of 758 task(s) completed
2025-03-17 11:32:10 INFO:	[hmmsearch]	531 of 758 task(s) completed
2025-03-17 11:32:17 INFO:	[hmmsearch]	607 of 758 task(s) completed
2025-03-17 11:32:26 INFO:	[hmmsearch]	683 of 758 task(s) completed
2025-03-17 11:32:35 INFO:	[hmmsearch]	758 of 758 task(s) completed
2025-03-17 11:32:35 INFO:	142 exons in total
2025-03-17 11:32:35 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2025-03-17 11:32:55 INFO:	Running 1 job(s) on metaeuk, starting at 03/17/2025 11:32:55
2025-03-17 11:36:53 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-17 11:36:53 INFO:	***** Run HMMER on gene sequences *****
2025-03-17 11:36:53 INFO:	Running 630 job(s) on hmmsearch, starting at 03/17/2025 11:36:53
2025-03-17 11:36:55 INFO:	[hmmsearch]	63 of 630 task(s) completed
2025-03-17 11:36:56 INFO:	[hmmsearch]	126 of 630 task(s) completed
2025-03-17 11:36:57 INFO:	[hmmsearch]	189 of 630 task(s) completed
2025-03-17 11:36:59 INFO:	[hmmsearch]	252 of 630 task(s) completed
2025-03-17 11:36:59 INFO:	[hmmsearch]	315 of 630 task(s) completed
2025-03-17 11:37:01 INFO:	[hmmsearch]	378 of 630 task(s) completed
2025-03-17 11:37:02 INFO:	[hmmsearch]	441 of 630 task(s) completed
2025-03-17 11:37:03 INFO:	[hmmsearch]	504 of 630 task(s) completed
2025-03-17 11:37:03 INFO:	[hmmsearch]	567 of 630 task(s) completed
2025-03-17 11:37:05 INFO:	[hmmsearch]	630 of 630 task(s) completed
2025-03-17 11:37:05 INFO:	1 candidate overlapping regions found
2025-03-17 11:37:05 INFO:	145 exons in total
2025-03-17 11:37:05 INFO:	Results:	C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758	   

2025-03-17 11:37:05 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758      |
    |128    Complete BUSCOs (C)                        |
    |127    Complete and single-copy BUSCOs (S)        |
    |1    Complete and duplicated BUSCOs (D)           |
    |11    Fragmented BUSCOs (F)                       |
    |619    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2025-03-17 11:37:05 INFO:	BUSCO analysis done with WARNING(s). Total running time: 627 seconds

***** Summary of warnings: *****
2025-03-17 11:26:38 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-17 11:26:38 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-17 11:26:38 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2025-03-17 11:37:05 INFO:	Results written in /tmp/tmpcxqpfl9y/job_working_directory/000/12/working/busco_galaxy
2025-03-17 11:37:05 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-03-17 11:37:05 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 64
drwxr-xr-x 5 1001 118  4096 Mar 17 11:26 busco_sequences
-rw-r--r-- 1 1001 118 36554 Mar 17 11:37 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Mar 17 11:32 hmmer_output
drwxr-xr-x 4 1001 118  4096 Mar 17 11:37 metaeuk_output
-rw-r--r-- 1 1001 118  8066 Mar 17 11:37 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2395 Mar 17 11:37 short_summary.json
-rw-r--r-- 1 1001 118   761 Mar 17 11:37 short_summary.txt
2025-03-17 11:37:06 INFO:	****************** Start plot generation at 03/17/2025 11:37:06 ******************
2025-03-17 11:37:06 INFO:	Load data ...
2025-03-17 11:37:06 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2025-03-17 11:37:06 INFO:	Generate the R code ...
2025-03-17 11:37:06 INFO:	Run the R code ...
2025-03-17 11:37:08 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-03-17 11:37:08 INFO:	Plot generation done. Total running time: 2.288506031036377 seconds
2025-03-17 11:37:08 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c7ad78f0031d11f08d45000d3a548ffa"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
chromInfo	`"/tmp/tmpcxqpfl9y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 14: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmpcxqpfl9y/job_working_directory/000/13/outputs/dataset_bce899ae-b5ea-425f-b933-e749d79d26fc_files &&  cp /tmp/tmpcxqpfl9y/job_working_directory/000/13/configs/tmpxwm1ha53 /tmp/tmpcxqpfl9y/job_working_directory/000/13/outputs/dataset_bce899ae-b5ea-425f-b933-e749d79d26fc_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpcxqpfl9y/job_working_directory/000/13/outputs/dataset_bce899ae-b5ea-425f-b933-e749d79d26fc_files /tmp/tmpcxqpfl9y/job_working_directory/000/13/configs/tmpxwm1ha53 &&  cp /tmp/tmpcxqpfl9y/job_working_directory/000/13/outputs/dataset_bce899ae-b5ea-425f-b933-e749d79d26fc_files/index.html /tmp/tmpcxqpfl9y/job_working_directory/000/13/outputs/dataset_bce899ae-b5ea-425f-b933-e749d79d26fc.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Maker annotation / Map annotation ids on data 12: renamed GFF
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"c7ad78f0031d11f08d45000d3a548ffa"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpcxqpfl9y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Maker annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 18, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 3: Genome assembly:
- step_state: scheduled
Step 4: Protein sequences:
- step_state: scheduled
Step 5: Augustus training:
- step_state: scheduled
Step 6: SNAP training:
- step_state: scheduled

**Step 7: Fasta Statistics **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmpcxqpfl9y/files/a/2/f/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.dat' --stats_output '/tmp/tmpcxqpfl9y/job_working_directory/000/6/outputs/dataset_a9da3df9-d415-4ba7-8bd4-eeeee7240c33.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c7ad78f0031d11f08d45000d3a548ffa"`
chromInfo	`"/tmp/tmpcxqpfl9y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 8: BUSCO on the genome sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpcxqpfl9y/files/a/2/f/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2025-03-17 11:10:22 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-03-17 10:52:50 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/17/2025 10:52:50 *****
2025-03-17 10:52:50 INFO:	Configuring BUSCO with local environment
2025-03-17 10:52:50 INFO:	Running genome mode
2025-03-17 10:52:54 INFO:	Input file is /tmp/tmpcxqpfl9y/files/a/2/f/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.dat
2025-03-17 10:52:55 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-17 10:52:55 INFO:	Running 1 job(s) on bbtools, starting at 03/17/2025 10:52:55
2025-03-17 10:52:56 INFO:	[bbtools]	1 of 1 task(s) completed
2025-03-17 10:52:56 INFO:	Running 1 job(s) on makeblastdb, starting at 03/17/2025 10:52:56
2025-03-17 10:52:56 INFO:	Creating BLAST database with input file
2025-03-17 10:52:57 INFO:	[makeblastdb]	1 of 1 task(s) completed
2025-03-17 10:52:57 INFO:	Running a BLAST search for BUSCOs against created database
2025-03-17 10:52:57 INFO:	Running 1 job(s) on tblastn, starting at 03/17/2025 10:52:57
2025-03-17 10:53:09 INFO:	[tblastn]	1 of 1 task(s) completed
2025-03-17 10:53:09 INFO:	Running Augustus gene predictor on BLAST search results.
2025-03-17 10:53:09 INFO:	Running Augustus prediction using aspergillus_nidulans as species:
2025-03-17 10:53:09 INFO:	Running 233 job(s) on augustus, starting at 03/17/2025 10:53:09
2025-03-17 10:54:24 INFO:	[augustus]	24 of 233 task(s) completed
2025-03-17 10:55:03 INFO:	[augustus]	47 of 233 task(s) completed
2025-03-17 10:55:42 INFO:	[augustus]	70 of 233 task(s) completed
2025-03-17 10:56:18 INFO:	[augustus]	94 of 233 task(s) completed
2025-03-17 10:56:53 INFO:	[augustus]	117 of 233 task(s) completed
2025-03-17 10:57:25 INFO:	[augustus]	140 of 233 task(s) completed
2025-03-17 10:57:56 INFO:	[augustus]	164 of 233 task(s) completed
2025-03-17 10:58:26 INFO:	[augustus]	187 of 233 task(s) completed
2025-03-17 10:58:57 INFO:	[augustus]	210 of 233 task(s) completed
2025-03-17 10:59:25 INFO:	[augustus]	233 of 233 task(s) completed
2025-03-17 10:59:25 INFO:	Extracting predicted proteins...
2025-03-17 10:59:25 INFO:	***** Run HMMER on gene sequences *****
2025-03-17 10:59:26 INFO:	Running 152 job(s) on hmmsearch, starting at 03/17/2025 10:59:26
2025-03-17 10:59:28 INFO:	[hmmsearch]	16 of 152 task(s) completed
2025-03-17 10:59:30 INFO:	[hmmsearch]	31 of 152 task(s) completed
2025-03-17 10:59:32 INFO:	[hmmsearch]	46 of 152 task(s) completed
2025-03-17 10:59:33 INFO:	[hmmsearch]	61 of 152 task(s) completed
2025-03-17 10:59:35 INFO:	[hmmsearch]	76 of 152 task(s) completed
2025-03-17 10:59:37 INFO:	[hmmsearch]	92 of 152 task(s) completed
2025-03-17 10:59:39 INFO:	[hmmsearch]	107 of 152 task(s) completed
2025-03-17 10:59:40 INFO:	[hmmsearch]	122 of 152 task(s) completed
2025-03-17 10:59:42 INFO:	[hmmsearch]	137 of 152 task(s) completed
2025-03-17 10:59:45 INFO:	[hmmsearch]	152 of 152 task(s) completed
2025-03-17 10:59:45 INFO:	0 exons in total
2025-03-17 10:59:45 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2025-03-17 10:59:45 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2025-03-17 10:59:46 INFO:	Running a BLAST search for BUSCOs against created database
2025-03-17 10:59:46 INFO:	Running 1 job(s) on tblastn, starting at 03/17/2025 10:59:46
2025-03-17 11:01:17 INFO:	[tblastn]	1 of 1 task(s) completed
2025-03-17 11:01:17 INFO:	Converting predicted genes to short genbank files
2025-03-17 11:01:17 INFO:	Running 66 job(s) on gff2gbSmallDNA.pl, starting at 03/17/2025 11:01:17
2025-03-17 11:01:17 INFO:	[gff2gbSmallDNA.pl]	7 of 66 task(s) completed
2025-03-17 11:01:17 INFO:	[gff2gbSmallDNA.pl]	14 of 66 task(s) completed
2025-03-17 11:01:18 INFO:	[gff2gbSmallDNA.pl]	20 of 66 task(s) completed
2025-03-17 11:01:18 INFO:	[gff2gbSmallDNA.pl]	27 of 66 task(s) completed
2025-03-17 11:01:18 INFO:	[gff2gbSmallDNA.pl]	33 of 66 task(s) completed
2025-03-17 11:01:18 INFO:	[gff2gbSmallDNA.pl]	40 of 66 task(s) completed
2025-03-17 11:01:18 INFO:	[gff2gbSmallDNA.pl]	47 of 66 task(s) completed
2025-03-17 11:01:19 INFO:	[gff2gbSmallDNA.pl]	53 of 66 task(s) completed
2025-03-17 11:01:19 INFO:	[gff2gbSmallDNA.pl]	60 of 66 task(s) completed
2025-03-17 11:01:19 INFO:	[gff2gbSmallDNA.pl]	66 of 66 task(s) completed
2025-03-17 11:01:19 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2025-03-17 11:01:19 INFO:	Running 1 job(s) on new_species.pl, starting at 03/17/2025 11:01:19
2025-03-17 11:01:19 INFO:	[new_species.pl]	1 of 1 task(s) completed
2025-03-17 11:01:19 INFO:	Running 1 job(s) on etraining, starting at 03/17/2025 11:01:19
2025-03-17 11:01:20 INFO:	[etraining]	1 of 1 task(s) completed
2025-03-17 11:01:20 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 692
2025-03-17 11:01:20 INFO:	Running Augustus gene predictor on BLAST search results.
2025-03-17 11:01:20 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2025-03-17 11:01:20 INFO:	Running 234 job(s) on augustus, starting at 03/17/2025 11:01:20
2025-03-17 11:03:53 INFO:	[augustus]	24 of 234 task(s) completed
2025-03-17 11:04:46 INFO:	[augustus]	47 of 234 task(s) completed
2025-03-17 11:05:26 INFO:	[augustus]	71 of 234 task(s) completed
2025-03-17 11:06:13 INFO:	[augustus]	94 of 234 task(s) completed
2025-03-17 11:06:49 INFO:	[augustus]	117 of 234 task(s) completed
2025-03-17 11:07:28 INFO:	[augustus]	141 of 234 task(s) completed
2025-03-17 11:08:05 INFO:	[augustus]	164 of 234 task(s) completed
2025-03-17 11:08:44 INFO:	[augustus]	188 of 234 task(s) completed
2025-03-17 11:09:18 INFO:	[augustus]	211 of 234 task(s) completed
2025-03-17 11:09:52 INFO:	[augustus]	234 of 234 task(s) completed
2025-03-17 11:09:52 INFO:	Extracting predicted proteins...
2025-03-17 11:09:52 INFO:	***** Run HMMER on gene sequences *****
2025-03-17 11:09:52 INFO:	Running 230 job(s) on hmmsearch, starting at 03/17/2025 11:09:52
2025-03-17 11:09:55 INFO:	[hmmsearch]	23 of 230 task(s) completed
2025-03-17 11:09:57 INFO:	[hmmsearch]	46 of 230 task(s) completed
2025-03-17 11:10:00 INFO:	[hmmsearch]	69 of 230 task(s) completed
2025-03-17 11:10:03 INFO:	[hmmsearch]	92 of 230 task(s) completed
2025-03-17 11:10:05 INFO:	[hmmsearch]	115 of 230 task(s) completed
2025-03-17 11:10:09 INFO:	[hmmsearch]	138 of 230 task(s) completed
2025-03-17 11:10:11 INFO:	[hmmsearch]	161 of 230 task(s) completed
2025-03-17 11:10:13 INFO:	[hmmsearch]	184 of 230 task(s) completed
2025-03-17 11:10:17 INFO:	[hmmsearch]	207 of 230 task(s) completed
2025-03-17 11:10:19 INFO:	[hmmsearch]	230 of 230 task(s) completed
2025-03-17 11:10:19 INFO:	0 exons in total
2025-03-17 11:10:19 INFO:	Results:	C:11.6%[S:11.6%,D:0.0%],F:2.2%,M:86.2%,n:758	   

2025-03-17 11:10:19 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:11.6%[S:11.6%,D:0.0%],F:2.2%,M:86.2%,n:758      |
    |88    Complete BUSCOs (C)                         |
    |88    Complete and single-copy BUSCOs (S)         |
    |0    Complete and duplicated BUSCOs (D)           |
    |17    Fragmented BUSCOs (F)                       |
    |653    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2025-03-17 11:10:19 INFO:	BUSCO analysis done. Total running time: 1046 seconds
2025-03-17 11:10:19 INFO:	Results written in /tmp/tmpcxqpfl9y/job_working_directory/000/7/working/busco_galaxy
2025-03-17 11:10:19 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-03-17 11:10:19 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 64
drwxr-xr-x 8 1001 118  4096 Mar 17 11:10 augustus_output
drwxr-xr-x 3 1001 118  4096 Mar 17 11:01 blast_output
drwxr-xr-x 5 1001 118  4096 Mar 17 10:52 busco_sequences
-rw-r--r-- 1 1001 118 28598 Mar 17 11:10 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Mar 17 10:59 hmmer_output
-rw-r--r-- 1 1001 118  8505 Mar 17 11:10 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  3171 Mar 17 11:10 short_summary.json
-rw-r--r-- 1 1001 118  1060 Mar 17 11:10 short_summary.txt
2025-03-17 11:10:20 INFO:	****************** Start plot generation at 03/17/2025 11:10:20 ******************
2025-03-17 11:10:20 INFO:	Load data ...
2025-03-17 11:10:20 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2025-03-17 11:10:20 INFO:	Generate the R code ...
2025-03-17 11:10:20 INFO:	Run the R code ...
2025-03-17 11:10:22 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-03-17 11:10:22 INFO:	Plot generation done. Total running time: 2.175921678543091 seconds
2025-03-17 11:10:22 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c7ad78f0031d11f08d45000d3a548ffa"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmpcxqpfl9y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 9: Maker:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

RM_PATH=$(which RepeatMasker) && if [ -z "$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH ($PATH)" >&2 ; exit 1 ; fi &&  LIBDIR=$(dirname "$RM_PATH")/../share/RepeatMasker/Libraries &&  export LIBDIR &&  maker -CTL  &&  cp '/tmp/tmpcxqpfl9y/job_working_directory/000/8/configs/tmpfp68a7ym' maker_opts.ctl  &&    cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&  mkdir -p 'augustus_dir/species/' &&  tar -C 'augustus_dir/species/' -xzvf '/tmp/tmpcxqpfl9y/files/5/3/6/dataset_5369bd61-4430-4327-8e37-7c8b85ba8a94.dat' > /dev/null &&  export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&  MPI_CMD="" && if [ "$MAKER_MPI" == "1" ]; then MPI_CMD="mpiexec -n ${GALAXY_SLOTS:-4}"; fi &&  ${MPI_CMD} maker --ignore_nfs_tmp  maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null  &&  gff3_merge -d *.maker.output/*_master_datastore_index.log -o '/tmp/tmpcxqpfl9y/job_working_directory/000/8/outputs/dataset_4c1b6ea9-8bbf-4288-bd3a-c11694c9efad.dat'  &&  awk '{if ($2 == "maker" || $1 ~ /^#/) {print}}' '/tmp/tmpcxqpfl9y/job_working_directory/000/8/outputs/dataset_4c1b6ea9-8bbf-4288-bd3a-c11694c9efad.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmpcxqpfl9y/job_working_directory/000/8/outputs/dataset_ebd0a7f6-160d-426f-aa7e-ae1ca00bb19e.dat'  &&  awk '{if ($2 != "maker") {print}}' '/tmp/tmpcxqpfl9y/job_working_directory/000/8/outputs/dataset_4c1b6ea9-8bbf-4288-bd3a-c11694c9efad.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmpcxqpfl9y/job_working_directory/000/8/outputs/dataset_355c45c8-2944-48d9-af20-9705d528f2a7.dat'

Exit Code:

```
0
```

Standard Error:

Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore

To access files for individual sequences use the datastore index:
/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: NC_003421.2
Length: 2452883
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.1.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.2.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.3.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.4.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.5.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.6.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.7.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.8.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.9.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.10.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.11.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.12.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.13.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.14.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.15.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.16.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.17.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.18.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpcxqpfl9y/tmp/maker_loZJZY; /usr/local/bin/RepeatMasker /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.19.human.rb -species human -dir /tmp/tmpcxqpfl9y/job_working_directory/000/8/working/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.maker.output/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -----
..
3-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/130_0.2303936-2305953.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/130_0.2303936-2305953.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/130_0.2303936-2305953.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/130_0.2303936-2305953.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/131_0.2317785-2319394.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/131_0.2317785-2319394.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/131_0.2317785-2319394.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/131_0.2317785-2319394.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/131_0.2317785-2319394.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/131_0.2317785-2319394.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/132_0.2326855-2328897.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/132_0.2326855-2328897.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/132_0.2326855-2328897.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/132_0.2326855-2328897.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/132_0.2326855-2328897.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/132_0.2326855-2328897.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/133_0.2329261-2334928.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/133_0.2329261-2334928.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/133_0.2329261-2334928.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/133_0.2329261-2334928.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/133_0.2329261-2334928.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/133_0.2329261-2334928.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/134_0.2341240-2344143.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/134_0.2341240-2344143.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/134_0.2341240-2344143.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/134_0.2341240-2344143.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/134_0.2341240-2344143.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/134_0.2341240-2344143.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/135_0.2349164-2354609.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/135_0.2349164-2354609.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/135_0.2349164-2354609.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/135_0.2349164-2354609.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/135_0.2349164-2354609.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/135_0.2349164-2354609.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/136_0.2366363-2370156.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/136_0.2366363-2370156.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/136_0.2366363-2370156.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/136_0.2366363-2370156.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/136_0.2366363-2370156.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/136_0.2366363-2370156.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/137_0.2373919-2380223.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/137_0.2373919-2380223.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/137_0.2373919-2380223.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/137_0.2373919-2380223.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/137_0.2373919-2380223.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/137_0.2373919-2380223.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/138_0.2381056-2382231.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/138_0.2381056-2382231.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/138_0.2381056-2382231.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/138_0.2381056-2382231.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/138_0.2381056-2382231.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/138_0.2381056-2382231.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/139_0.2384415-2388063.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/139_0.2384415-2388063.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/139_0.2384415-2388063.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/139_0.2384415-2388063.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/139_0.2384415-2388063.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/139_0.2384415-2388063.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/140_0.2388096-2391775.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/140_0.2388096-2391775.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/140_0.2388096-2391775.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/140_0.2388096-2391775.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/140_0.2388096-2391775.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/140_0.2388096-2391775.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/141_0.2407535-2408933.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/141_0.2407535-2408933.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/141_0.2407535-2408933.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/141_0.2407535-2408933.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/141_0.2407535-2408933.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/141_0.2407535-2408933.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpcxqpfl9y/files/8/6/c/dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat -xdef /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/142_0.2428734-2431724.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.xdef.snap  /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/142_0.2428734-2431724.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/142_0.2428734-2431724.dataset_86c36193-db41-4cbc-9794-6770b5c14b0e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/142_0.2428734-2431724.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpcxqpfl9y/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/142_0.2428734-2431724.local.auto_annotator.augustus.fasta > /tmp/tmpcxqpfl9y/tmp/maker_loZJZY/0/142_0.2428734-2431724.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output


Maker is now finished!!!

Standard Output:

Start_time: 1742208784
End_time:   1742210777
Elapsed:    1993

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c7ad78f0031d11f08d45000d3a548ffa"`
abinitio_gene_prediction	`{"aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 4, "src": "hda"}]}}, "snaphmm": {"values": [{"id": 5, "src": "hda"}]}, "unmask": false}`
advanced	`{"AED_threshold": "1.0", "alt_peptide": "C", "alt_splice": false, "always_complete": false, "correct_est_fusion": false, "fix_nucleotides": false, "keep_preds": "0.0", "map_forward": false, "max_dna_len": "100000", "min_contig": "1", "min_protein": "0", "other_gff": null, "pred_flank": "200", "pred_stats": false, "single_exon": {"__current_case__": 0, "single_exon": "0"}, "split_hit": "10000"}`
chromInfo	`"/tmp/tmpcxqpfl9y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
est_evidences	`{"altest": null, "altest_gff": null, "est": {"values": [{"id": 2, "src": "hda"}]}, "est2genome": false, "est_gff": null}`
gene_prediction	`{"model_gff": null, "pred_gff": null, "snoscan_rrna": null, "trna": false}`
license_agreement	`true`
organism_type	`"eukaryotic"`
protein_evidences	`{"protein": {"values": [{"id": 3, "src": "hda"}]}, "protein2genome": false, "protein_gff": null}`
reannotation	`{"__current_case__": 0, "reannotate": "no"}`
repeat_masking	`{"repeat_source": {"__current_case__": 0, "softmask": true, "source_type": "dfam", "species_source": {"__current_case__": 0, "species_from_list": "yes", "species_list": "human"}}}`

Step 10: GFFRead:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpcxqpfl9y/files/a/2/f/dataset_a2f3eb09-90b0-426e-852e-9c4afdab57d3.dat' genomeref.fa &&  gffread '/tmp/tmpcxqpfl9y/files/e/b/d/dataset_ebd0a7f6-160d-426f-aa7e-ae1ca00bb19e.dat' -g genomeref.fa      -w exons.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c7ad78f0031d11f08d45000d3a548ffa"`
chr_replace	`None`
chromInfo	`"/tmp/tmpcxqpfl9y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-w exons.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Other invocation details
- history_id
  - 677c3a591e71568e
- history_state
  - ok
- invocation_id
  - 677c3a591e71568e
- invocation_state
  - scheduled
- workflow_id
  - 677c3a591e71568e

github-actions · 2025-03-17T13:40:01Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Genome_annotation_with_maker_short.ga_0

Problems:

Output with path /tmp/tmpiqxf06ix/Maker on data 4, data 5, and others evidences__5ab2d90a-30c1-41b7-8415-0eb73fc7239e different than expected
Expected 76072+-10 lines in the output found 76060

Workflow invocation details

Invocation Messages

Steps

Step 1: BUSCO lineage:
- step_state: scheduled
Step 2: Genome sequence:
- step_state: scheduled

Step 11: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpqm5gzq1j/files/0/d/f/dataset_0df6b4c1-8024-4e73-a0fb-56e91906fda0.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpqm5gzq1j/job_working_directory/000/10/outputs/dataset_9c3ba785-dfe2-40c4-8cf2-6d01f4f82f86.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpqm5gzq1j/files/b/4/f/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.dat' 2>&1 | tail -n +3 >> '/tmp/tmpqm5gzq1j/job_working_directory/000/10/outputs/dataset_9c3ba785-dfe2-40c4-8cf2-6d01f4f82f86.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpqm5gzq1j/job_working_directory/000/10/outputs/dataset_9c3ba785-dfe2-40c4-8cf2-6d01f4f82f86.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpqm5gzq1j/job_working_directory/000/10/outputs/dataset_02e1e7c5-00b7-472e-9e6e-3c346dc5ace8.dat'

Exit Code:

```
0
```

Standard Error:

�[0;33m13:30:56 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m13:30:57 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m13:30:57 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m13:30:57 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m13:30:57 [base]�[0m�[0;35m Imported 860 records from `transcript.sizes`.�[0m
�[0;33m13:30:57 [stats]�[0m�[0;35m A total of 860 transcripts populated.�[0m
�[0;33m13:30:58 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m13:30:58 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m13:30:58 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m13:30:58 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m13:30:58 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m13:30:58 [__init__]�[0m�[0;35m platform is linux2�[0m
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'numpy.core.getlimits', '_sysconfigdata', 'Bio.SeqIO.SffIO', 'numpy.fft', 'numpy.random.numpy', 'logging.time', 'Bio.GenBank.collections', 'jcvi.formats.gff', 'numpy.lib.function_base', 'logging.warnings', 'mimetools', 'xml.sax', 'Bio._py3k.cStringIO', 'logging.codecs', 'numpy.compat.py3k', 'Bio.Data.CodonTable', 'numpy.polynomial._polybase', 'numpy.polynomial.hermite', 'contextlib', 'numpy.polynomial.polynomial', 'grp', 'numpy.core.defchararray', 'gettext', '_abcoll', 'Bio.SeqFeature', 'xml.sax._exceptions', 'genericpath', 'stat', 'urllib2', 'unittest.signals', 'backports.functools_lru_cache', 'ctypes.ctypes', 'numpy.lib.format', 'numpy.testing.nosetester', 'xml.dom', 'time', 'jcvi.apps.socket', 'jcvi.annotation.os', 'Bio.Sequencing.Ace']�[0m
�[0;33m13:30:58 [__init__]�[0m�[0;35m CACHEDIR=/tmp/tmpqm5gzq1j/tmp/matplotlib-cCTo8d�[0m
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�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono-Oblique.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSans-Oblique.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansDisplay.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmr10.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizFourSymReg.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizTwoSymReg.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizThreeSymBol.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralBolIta.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmtt10.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizTwoSymBol.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneral.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmmi10.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizOneSymBol.ttf�[0m
�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmb10.ttf�[0m
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�[0;33m13:30:58 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmss10.ttf�[0m
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�[0;33m13:31:06 [base]�[0m�[0;35m Rscript /tmp/tmpqm5gzq1j/tmp/tmp1V20eF�[0m
Warning message:
Removed 29 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 29 rows containing non-finite values (stat_bin). 
�[0;33m13:31:08 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=860 Mean=2.21046511628 SD=1.73771629537 Median=2.0 Sum=1901
�[0;33m13:31:08 [base]�[0m�[0;35m Rscript /tmp/tmpqm5gzq1j/tmp/tmpXOgGXT�[0m
Saving 7 x 7 in image

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"24104ada032f11f08d457c1e52258e31"`
chromInfo	`"/tmp/tmpqm5gzq1j/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 12: Map annotation ids:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpqm5gzq1j/files/0/d/f/dataset_0df6b4c1-8024-4e73-a0fb-56e91906fda0.dat' '/tmp/tmpqm5gzq1j/job_working_directory/000/11/outputs/dataset_13fb18c5-535f-4d26-bd14-a9ef28769eea.dat' && maker_map_ids --prefix '' --justify 6 '/tmp/tmpqm5gzq1j/files/0/d/f/dataset_0df6b4c1-8024-4e73-a0fb-56e91906fda0.dat' > '/tmp/tmpqm5gzq1j/job_working_directory/000/11/outputs/dataset_efcf54d4-d865-450b-a558-96951e668cf9.dat' && map_gff_ids '/tmp/tmpqm5gzq1j/job_working_directory/000/11/outputs/dataset_efcf54d4-d865-450b-a558-96951e668cf9.dat' '/tmp/tmpqm5gzq1j/job_working_directory/000/11/outputs/dataset_13fb18c5-535f-4d26-bd14-a9ef28769eea.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"24104ada032f11f08d457c1e52258e31"`
chromInfo	`"/tmp/tmpqm5gzq1j/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
justify	`"6"`
prefix	`None`

Step 13: BUSCO on the predicted protein sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpqm5gzq1j/files/a/5/c/dataset_a5c1b192-87b0-4fa0-855d-d3f202a41c14.dat' --mode 'tran' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2025-03-17 13:38:37 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-03-17 13:30:34 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/17/2025 13:30:34 *****
2025-03-17 13:30:34 INFO:	Configuring BUSCO with local environment
2025-03-17 13:30:34 INFO:	Running transcriptome mode
2025-03-17 13:30:34 INFO:	Input file is /tmp/tmpqm5gzq1j/files/a/5/c/dataset_a5c1b192-87b0-4fa0-855d-d3f202a41c14.dat
2025-03-17 13:30:34 WARNING:	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-17 13:30:34 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-17 13:30:34 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2025-03-17 13:30:34 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-17 13:30:34 INFO:	Running 1 job(s) on metaeuk, starting at 03/17/2025 13:30:34
2025-03-17 13:33:23 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-17 13:33:23 INFO:	***** Run HMMER on gene sequences *****
2025-03-17 13:33:23 INFO:	Running 758 job(s) on hmmsearch, starting at 03/17/2025 13:33:23
2025-03-17 13:33:30 INFO:	[hmmsearch]	76 of 758 task(s) completed
2025-03-17 13:33:33 INFO:	[hmmsearch]	152 of 758 task(s) completed
2025-03-17 13:33:38 INFO:	[hmmsearch]	228 of 758 task(s) completed
2025-03-17 13:33:43 INFO:	[hmmsearch]	304 of 758 task(s) completed
2025-03-17 13:33:47 INFO:	[hmmsearch]	379 of 758 task(s) completed
2025-03-17 13:33:52 INFO:	[hmmsearch]	455 of 758 task(s) completed
2025-03-17 13:33:56 INFO:	[hmmsearch]	531 of 758 task(s) completed
2025-03-17 13:34:00 INFO:	[hmmsearch]	607 of 758 task(s) completed
2025-03-17 13:34:06 INFO:	[hmmsearch]	683 of 758 task(s) completed
2025-03-17 13:34:11 INFO:	[hmmsearch]	758 of 758 task(s) completed
2025-03-17 13:34:11 INFO:	141 exons in total
2025-03-17 13:34:11 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2025-03-17 13:34:30 INFO:	Running 1 job(s) on metaeuk, starting at 03/17/2025 13:34:30
2025-03-17 13:38:23 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-03-17 13:38:23 INFO:	***** Run HMMER on gene sequences *****
2025-03-17 13:38:23 INFO:	Running 630 job(s) on hmmsearch, starting at 03/17/2025 13:38:23
2025-03-17 13:38:24 INFO:	[hmmsearch]	63 of 630 task(s) completed
2025-03-17 13:38:25 INFO:	[hmmsearch]	126 of 630 task(s) completed
2025-03-17 13:38:26 INFO:	[hmmsearch]	189 of 630 task(s) completed
2025-03-17 13:38:27 INFO:	[hmmsearch]	252 of 630 task(s) completed
2025-03-17 13:38:28 INFO:	[hmmsearch]	315 of 630 task(s) completed
2025-03-17 13:38:29 INFO:	[hmmsearch]	378 of 630 task(s) completed
2025-03-17 13:38:30 INFO:	[hmmsearch]	441 of 630 task(s) completed
2025-03-17 13:38:31 INFO:	[hmmsearch]	504 of 630 task(s) completed
2025-03-17 13:38:32 INFO:	[hmmsearch]	567 of 630 task(s) completed
2025-03-17 13:38:33 INFO:	[hmmsearch]	630 of 630 task(s) completed
2025-03-17 13:38:33 INFO:	1 candidate overlapping regions found
2025-03-17 13:38:33 INFO:	144 exons in total
2025-03-17 13:38:33 INFO:	Results:	C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758	   

2025-03-17 13:38:33 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758      |
    |128    Complete BUSCOs (C)                        |
    |127    Complete and single-copy BUSCOs (S)        |
    |1    Complete and duplicated BUSCOs (D)           |
    |11    Fragmented BUSCOs (F)                       |
    |619    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2025-03-17 13:38:33 INFO:	BUSCO analysis done with WARNING(s). Total running time: 479 seconds

***** Summary of warnings: *****
2025-03-17 13:30:34 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, euk_tran
2025-03-17 13:30:34 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2025-03-17 13:30:34 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2025-03-17 13:38:33 INFO:	Results written in /tmp/tmpqm5gzq1j/job_working_directory/000/12/working/busco_galaxy
2025-03-17 13:38:33 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-03-17 13:38:33 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 64
drwxr-xr-x 5 1001 118  4096 Mar 17 13:30 busco_sequences
-rw-r--r-- 1 1001 118 36509 Mar 17 13:38 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Mar 17 13:34 hmmer_output
drwxr-xr-x 4 1001 118  4096 Mar 17 13:38 metaeuk_output
-rw-r--r-- 1 1001 118  8066 Mar 17 13:38 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2395 Mar 17 13:38 short_summary.json
-rw-r--r-- 1 1001 118   761 Mar 17 13:38 short_summary.txt
2025-03-17 13:38:35 INFO:	****************** Start plot generation at 03/17/2025 13:38:35 ******************
2025-03-17 13:38:35 INFO:	Load data ...
2025-03-17 13:38:35 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2025-03-17 13:38:35 INFO:	Generate the R code ...
2025-03-17 13:38:35 INFO:	Run the R code ...
2025-03-17 13:38:37 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-03-17 13:38:37 INFO:	Plot generation done. Total running time: 2.1291134357452393 seconds
2025-03-17 13:38:37 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"24104ada032f11f08d457c1e52258e31"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
chromInfo	`"/tmp/tmpqm5gzq1j/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 14: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmpqm5gzq1j/job_working_directory/000/13/outputs/dataset_feffafa8-6214-496d-a40b-2ba71172ad85_files &&  cp /tmp/tmpqm5gzq1j/job_working_directory/000/13/configs/tmplyi58vbu /tmp/tmpqm5gzq1j/job_working_directory/000/13/outputs/dataset_feffafa8-6214-496d-a40b-2ba71172ad85_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpqm5gzq1j/job_working_directory/000/13/outputs/dataset_feffafa8-6214-496d-a40b-2ba71172ad85_files /tmp/tmpqm5gzq1j/job_working_directory/000/13/configs/tmplyi58vbu &&  cp /tmp/tmpqm5gzq1j/job_working_directory/000/13/outputs/dataset_feffafa8-6214-496d-a40b-2ba71172ad85_files/index.html /tmp/tmpqm5gzq1j/job_working_directory/000/13/outputs/dataset_feffafa8-6214-496d-a40b-2ba71172ad85.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Maker annotation / Map annotation ids on data 12: renamed GFF
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"24104ada032f11f08d457c1e52258e31"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpqm5gzq1j/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Maker annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 18, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 3: Genome assembly:
- step_state: scheduled
Step 4: Protein sequences:
- step_state: scheduled
Step 5: Augustus training:
- step_state: scheduled
Step 6: SNAP training:
- step_state: scheduled

**Step 7: Fasta Statistics **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmpqm5gzq1j/files/b/4/f/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.dat' --stats_output '/tmp/tmpqm5gzq1j/job_working_directory/000/6/outputs/dataset_0e21d67c-780f-43aa-add9-cb468f276136.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"24104ada032f11f08d457c1e52258e31"`
chromInfo	`"/tmp/tmpqm5gzq1j/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 8: BUSCO on the genome sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpqm5gzq1j/files/b/4/f/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'fungi_odb10'   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2025-03-17 13:14:08 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-03-17 12:57:18 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 03/17/2025 12:57:18 *****
2025-03-17 12:57:18 INFO:	Configuring BUSCO with local environment
2025-03-17 12:57:18 INFO:	Running genome mode
2025-03-17 12:57:20 INFO:	Input file is /tmp/tmpqm5gzq1j/files/b/4/f/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.dat
2025-03-17 12:57:21 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2025-03-17 12:57:21 INFO:	Running 1 job(s) on bbtools, starting at 03/17/2025 12:57:21
2025-03-17 12:57:22 INFO:	[bbtools]	1 of 1 task(s) completed
2025-03-17 12:57:22 INFO:	Running 1 job(s) on makeblastdb, starting at 03/17/2025 12:57:22
2025-03-17 12:57:22 INFO:	Creating BLAST database with input file
2025-03-17 12:57:22 INFO:	[makeblastdb]	1 of 1 task(s) completed
2025-03-17 12:57:22 INFO:	Running a BLAST search for BUSCOs against created database
2025-03-17 12:57:22 INFO:	Running 1 job(s) on tblastn, starting at 03/17/2025 12:57:22
2025-03-17 12:57:33 INFO:	[tblastn]	1 of 1 task(s) completed
2025-03-17 12:57:33 INFO:	Running Augustus gene predictor on BLAST search results.
2025-03-17 12:57:33 INFO:	Running Augustus prediction using aspergillus_nidulans as species:
2025-03-17 12:57:33 INFO:	Running 233 job(s) on augustus, starting at 03/17/2025 12:57:33
2025-03-17 12:58:47 INFO:	[augustus]	24 of 233 task(s) completed
2025-03-17 12:59:24 INFO:	[augustus]	47 of 233 task(s) completed
2025-03-17 13:00:02 INFO:	[augustus]	70 of 233 task(s) completed
2025-03-17 13:00:36 INFO:	[augustus]	94 of 233 task(s) completed
2025-03-17 13:01:10 INFO:	[augustus]	117 of 233 task(s) completed
2025-03-17 13:01:40 INFO:	[augustus]	140 of 233 task(s) completed
2025-03-17 13:02:11 INFO:	[augustus]	164 of 233 task(s) completed
2025-03-17 13:02:39 INFO:	[augustus]	187 of 233 task(s) completed
2025-03-17 13:03:09 INFO:	[augustus]	210 of 233 task(s) completed
2025-03-17 13:03:36 INFO:	[augustus]	233 of 233 task(s) completed
2025-03-17 13:03:36 INFO:	Extracting predicted proteins...
2025-03-17 13:03:36 INFO:	***** Run HMMER on gene sequences *****
2025-03-17 13:03:36 INFO:	Running 152 job(s) on hmmsearch, starting at 03/17/2025 13:03:36
2025-03-17 13:03:38 INFO:	[hmmsearch]	16 of 152 task(s) completed
2025-03-17 13:03:40 INFO:	[hmmsearch]	31 of 152 task(s) completed
2025-03-17 13:03:41 INFO:	[hmmsearch]	46 of 152 task(s) completed
2025-03-17 13:03:42 INFO:	[hmmsearch]	61 of 152 task(s) completed
2025-03-17 13:03:44 INFO:	[hmmsearch]	76 of 152 task(s) completed
2025-03-17 13:03:45 INFO:	[hmmsearch]	92 of 152 task(s) completed
2025-03-17 13:03:46 INFO:	[hmmsearch]	107 of 152 task(s) completed
2025-03-17 13:03:47 INFO:	[hmmsearch]	122 of 152 task(s) completed
2025-03-17 13:03:49 INFO:	[hmmsearch]	137 of 152 task(s) completed
2025-03-17 13:03:50 INFO:	[hmmsearch]	152 of 152 task(s) completed
2025-03-17 13:03:50 INFO:	0 exons in total
2025-03-17 13:03:50 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2025-03-17 13:03:50 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2025-03-17 13:03:51 INFO:	Running a BLAST search for BUSCOs against created database
2025-03-17 13:03:51 INFO:	Running 1 job(s) on tblastn, starting at 03/17/2025 13:03:51
2025-03-17 13:05:21 INFO:	[tblastn]	1 of 1 task(s) completed
2025-03-17 13:05:21 INFO:	Converting predicted genes to short genbank files
2025-03-17 13:05:21 INFO:	Running 66 job(s) on gff2gbSmallDNA.pl, starting at 03/17/2025 13:05:21
2025-03-17 13:05:22 INFO:	[gff2gbSmallDNA.pl]	7 of 66 task(s) completed
2025-03-17 13:05:22 INFO:	[gff2gbSmallDNA.pl]	14 of 66 task(s) completed
2025-03-17 13:05:22 INFO:	[gff2gbSmallDNA.pl]	20 of 66 task(s) completed
2025-03-17 13:05:22 INFO:	[gff2gbSmallDNA.pl]	27 of 66 task(s) completed
2025-03-17 13:05:23 INFO:	[gff2gbSmallDNA.pl]	33 of 66 task(s) completed
2025-03-17 13:05:23 INFO:	[gff2gbSmallDNA.pl]	40 of 66 task(s) completed
2025-03-17 13:05:23 INFO:	[gff2gbSmallDNA.pl]	47 of 66 task(s) completed
2025-03-17 13:05:23 INFO:	[gff2gbSmallDNA.pl]	53 of 66 task(s) completed
2025-03-17 13:05:23 INFO:	[gff2gbSmallDNA.pl]	60 of 66 task(s) completed
2025-03-17 13:05:24 INFO:	[gff2gbSmallDNA.pl]	66 of 66 task(s) completed
2025-03-17 13:05:24 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2025-03-17 13:05:24 INFO:	Running 1 job(s) on new_species.pl, starting at 03/17/2025 13:05:24
2025-03-17 13:05:24 INFO:	[new_species.pl]	1 of 1 task(s) completed
2025-03-17 13:05:24 INFO:	Running 1 job(s) on etraining, starting at 03/17/2025 13:05:24
2025-03-17 13:05:25 INFO:	[etraining]	1 of 1 task(s) completed
2025-03-17 13:05:25 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 692
2025-03-17 13:05:25 INFO:	Running Augustus gene predictor on BLAST search results.
2025-03-17 13:05:25 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2025-03-17 13:05:25 INFO:	Running 234 job(s) on augustus, starting at 03/17/2025 13:05:25
2025-03-17 13:07:58 INFO:	[augustus]	24 of 234 task(s) completed
2025-03-17 13:08:51 INFO:	[augustus]	47 of 234 task(s) completed
2025-03-17 13:09:31 INFO:	[augustus]	71 of 234 task(s) completed
2025-03-17 13:10:17 INFO:	[augustus]	94 of 234 task(s) completed
2025-03-17 13:10:54 INFO:	[augustus]	117 of 234 task(s) completed
2025-03-17 13:11:32 INFO:	[augustus]	141 of 234 task(s) completed
2025-03-17 13:12:07 INFO:	[augustus]	164 of 234 task(s) completed
2025-03-17 13:12:44 INFO:	[augustus]	188 of 234 task(s) completed
2025-03-17 13:13:17 INFO:	[augustus]	211 of 234 task(s) completed
2025-03-17 13:13:49 INFO:	[augustus]	234 of 234 task(s) completed
2025-03-17 13:13:49 INFO:	Extracting predicted proteins...
2025-03-17 13:13:49 INFO:	***** Run HMMER on gene sequences *****
2025-03-17 13:13:50 INFO:	Running 230 job(s) on hmmsearch, starting at 03/17/2025 13:13:50
2025-03-17 13:13:52 INFO:	[hmmsearch]	23 of 230 task(s) completed
2025-03-17 13:13:53 INFO:	[hmmsearch]	46 of 230 task(s) completed
2025-03-17 13:13:54 INFO:	[hmmsearch]	69 of 230 task(s) completed
2025-03-17 13:13:56 INFO:	[hmmsearch]	92 of 230 task(s) completed
2025-03-17 13:13:57 INFO:	[hmmsearch]	115 of 230 task(s) completed
2025-03-17 13:13:59 INFO:	[hmmsearch]	138 of 230 task(s) completed
2025-03-17 13:14:00 INFO:	[hmmsearch]	161 of 230 task(s) completed
2025-03-17 13:14:02 INFO:	[hmmsearch]	184 of 230 task(s) completed
2025-03-17 13:14:04 INFO:	[hmmsearch]	207 of 230 task(s) completed
2025-03-17 13:14:05 INFO:	[hmmsearch]	230 of 230 task(s) completed
2025-03-17 13:14:05 INFO:	0 exons in total
2025-03-17 13:14:05 INFO:	Results:	C:11.6%[S:11.6%,D:0.0%],F:2.2%,M:86.2%,n:758	   

2025-03-17 13:14:05 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:11.6%[S:11.6%,D:0.0%],F:2.2%,M:86.2%,n:758      |
    |88    Complete BUSCOs (C)                         |
    |88    Complete and single-copy BUSCOs (S)         |
    |0    Complete and duplicated BUSCOs (D)           |
    |17    Fragmented BUSCOs (F)                       |
    |653    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2025-03-17 13:14:05 INFO:	BUSCO analysis done. Total running time: 1005 seconds
2025-03-17 13:14:05 INFO:	Results written in /tmp/tmpqm5gzq1j/job_working_directory/000/7/working/busco_galaxy
2025-03-17 13:14:05 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-03-17 13:14:05 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 64
drwxr-xr-x 8 1001 118  4096 Mar 17 13:14 augustus_output
drwxr-xr-x 3 1001 118  4096 Mar 17 13:05 blast_output
drwxr-xr-x 5 1001 118  4096 Mar 17 12:57 busco_sequences
-rw-r--r-- 1 1001 118 28598 Mar 17 13:14 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Mar 17 13:03 hmmer_output
-rw-r--r-- 1 1001 118  8505 Mar 17 13:14 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  3171 Mar 17 13:14 short_summary.json
-rw-r--r-- 1 1001 118  1060 Mar 17 13:14 short_summary.txt
2025-03-17 13:14:06 INFO:	****************** Start plot generation at 03/17/2025 13:14:06 ******************
2025-03-17 13:14:06 INFO:	Load data ...
2025-03-17 13:14:06 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2025-03-17 13:14:06 INFO:	Generate the R code ...
2025-03-17 13:14:06 INFO:	Run the R code ...
2025-03-17 13:14:08 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-03-17 13:14:08 INFO:	Plot generation done. Total running time: 2.17374587059021 seconds
2025-03-17 13:14:08 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"24104ada032f11f08d457c1e52258e31"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmpqm5gzq1j/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 9: Maker:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

RM_PATH=$(which RepeatMasker) && if [ -z "$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH ($PATH)" >&2 ; exit 1 ; fi &&  LIBDIR=$(dirname "$RM_PATH")/../share/RepeatMasker/Libraries &&  export LIBDIR &&  maker -CTL  &&  cp '/tmp/tmpqm5gzq1j/job_working_directory/000/8/configs/tmpffmr6pjv' maker_opts.ctl  &&    cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&  mkdir -p 'augustus_dir/species/' &&  tar -C 'augustus_dir/species/' -xzvf '/tmp/tmpqm5gzq1j/files/8/8/b/dataset_88ba0e57-f6d8-4ca0-96aa-ed22a164bd6d.dat' > /dev/null &&  export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&  MPI_CMD="" && if [ "$MAKER_MPI" == "1" ]; then MPI_CMD="mpiexec -n ${GALAXY_SLOTS:-4}"; fi &&  ${MPI_CMD} maker --ignore_nfs_tmp  maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null  &&  gff3_merge -d *.maker.output/*_master_datastore_index.log -o '/tmp/tmpqm5gzq1j/job_working_directory/000/8/outputs/dataset_84443e29-6fce-49c3-b1c7-ff609f0acd04.dat'  &&  awk '{if ($2 == "maker" || $1 ~ /^#/) {print}}' '/tmp/tmpqm5gzq1j/job_working_directory/000/8/outputs/dataset_84443e29-6fce-49c3-b1c7-ff609f0acd04.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmpqm5gzq1j/job_working_directory/000/8/outputs/dataset_0df6b4c1-8024-4e73-a0fb-56e91906fda0.dat'  &&  awk '{if ($2 != "maker") {print}}' '/tmp/tmpqm5gzq1j/job_working_directory/000/8/outputs/dataset_84443e29-6fce-49c3-b1c7-ff609f0acd04.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmpqm5gzq1j/job_working_directory/000/8/outputs/dataset_5ab2d90a-30c1-41b7-8415-0eb73fc7239e.dat'

Exit Code:

```
0
```

Standard Error:

Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore

To access files for individual sequences use the datastore index:
/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: NC_003421.2
Length: 2452883
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.1.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.2.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.3.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.4.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.5.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.6.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.7.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.8.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.9.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.10.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.11.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.12.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.13.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.14.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.15.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.16.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.17.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.18.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t; /usr/local/bin/RepeatMasker /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1/NC_003421%2E2.19.human.rb -species human -dir /tmp/tmpqm5gzq1j/job_working_directory/000/8/working/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.maker.output/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -----
..
e-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/130_0.2303936-2305953.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/130_0.2303936-2305953.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/130_0.2303936-2305953.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/130_0.2303936-2305953.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/131_0.2317785-2319394.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/131_0.2317785-2319394.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/131_0.2317785-2319394.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/131_0.2317785-2319394.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/131_0.2317785-2319394.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/131_0.2317785-2319394.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/132_0.2326855-2328897.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/132_0.2326855-2328897.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/132_0.2326855-2328897.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/132_0.2326855-2328897.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/132_0.2326855-2328897.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/132_0.2326855-2328897.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/133_0.2329261-2334928.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/133_0.2329261-2334928.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/133_0.2329261-2334928.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/133_0.2329261-2334928.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/133_0.2329261-2334928.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/133_0.2329261-2334928.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/134_0.2341240-2344143.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/134_0.2341240-2344143.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/134_0.2341240-2344143.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/134_0.2341240-2344143.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/134_0.2341240-2344143.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/134_0.2341240-2344143.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/135_0.2349164-2354609.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/135_0.2349164-2354609.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/135_0.2349164-2354609.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/135_0.2349164-2354609.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/135_0.2349164-2354609.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/135_0.2349164-2354609.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/136_0.2366363-2370156.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/136_0.2366363-2370156.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/136_0.2366363-2370156.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/136_0.2366363-2370156.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/136_0.2366363-2370156.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/136_0.2366363-2370156.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/137_0.2373919-2380223.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/137_0.2373919-2380223.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/137_0.2373919-2380223.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/137_0.2373919-2380223.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/137_0.2373919-2380223.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/137_0.2373919-2380223.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/138_0.2381056-2382231.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/138_0.2381056-2382231.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/138_0.2381056-2382231.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/138_0.2381056-2382231.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/138_0.2381056-2382231.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/138_0.2381056-2382231.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/139_0.2384415-2388063.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/139_0.2384415-2388063.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/139_0.2384415-2388063.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/139_0.2384415-2388063.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/139_0.2384415-2388063.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/139_0.2384415-2388063.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/140_0.2388096-2391775.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/140_0.2388096-2391775.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/140_0.2388096-2391775.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/140_0.2388096-2391775.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/140_0.2388096-2391775.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/140_0.2388096-2391775.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/141_0.2407535-2408933.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/141_0.2407535-2408933.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/141_0.2407535-2408933.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/141_0.2407535-2408933.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/141_0.2407535-2408933.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/141_0.2407535-2408933.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmpqm5gzq1j/files/a/8/0/dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat -xdef /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/142_0.2428734-2431724.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.xdef.snap  /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/142_0.2428734-2431724.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/142_0.2428734-2431724.dataset_a80cadae-a37d-4352-b348-9a0a5791f0b6.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/142_0.2428734-2431724.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmpqm5gzq1j/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/142_0.2428734-2431724.local.auto_annotator.augustus.fasta > /tmp/tmpqm5gzq1j/tmp/maker_iOpk2t/0/142_0.2428734-2431724.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output


Maker is now finished!!!

Standard Output:

Start_time: 1742216241
End_time:   1742218214
Elapsed:    1973

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"24104ada032f11f08d457c1e52258e31"`
abinitio_gene_prediction	`{"aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 4, "src": "hda"}]}}, "snaphmm": {"values": [{"id": 5, "src": "hda"}]}, "unmask": false}`
advanced	`{"AED_threshold": "1.0", "alt_peptide": "C", "alt_splice": false, "always_complete": false, "correct_est_fusion": false, "fix_nucleotides": false, "keep_preds": "0.0", "map_forward": false, "max_dna_len": "100000", "min_contig": "1", "min_protein": "0", "other_gff": null, "pred_flank": "200", "pred_stats": false, "single_exon": {"__current_case__": 0, "single_exon": "0"}, "split_hit": "10000"}`
chromInfo	`"/tmp/tmpqm5gzq1j/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
est_evidences	`{"altest": null, "altest_gff": null, "est": {"values": [{"id": 2, "src": "hda"}]}, "est2genome": false, "est_gff": null}`
gene_prediction	`{"model_gff": null, "pred_gff": null, "snoscan_rrna": null, "trna": false}`
license_agreement	`true`
organism_type	`"eukaryotic"`
protein_evidences	`{"protein": {"values": [{"id": 3, "src": "hda"}]}, "protein2genome": false, "protein_gff": null}`
reannotation	`{"__current_case__": 0, "reannotate": "no"}`
repeat_masking	`{"repeat_source": {"__current_case__": 0, "softmask": true, "source_type": "dfam", "species_source": {"__current_case__": 0, "species_from_list": "yes", "species_list": "human"}}}`

Step 10: GFFRead:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpqm5gzq1j/files/b/4/f/dataset_b4fa9a31-0f16-4225-86ef-a9d3f9a2e39f.dat' genomeref.fa &&  gffread '/tmp/tmpqm5gzq1j/files/0/d/f/dataset_0df6b4c1-8024-4e73-a0fb-56e91906fda0.dat' -g genomeref.fa      -w exons.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"24104ada032f11f08d457c1e52258e31"`
chr_replace	`None`
chromInfo	`"/tmp/tmpqm5gzq1j/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-w exons.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Other invocation details
- history_id
  - 917f6f99020e6693
- history_state
  - ok
- invocation_id
  - 917f6f99020e6693
- invocation_state
  - scheduled
- workflow_id
  - 917f6f99020e6693

rlibouba · 2025-03-17T15:10:08Z

Hi @mvdbeek, thank you for your help and recommendation for my problem. I have corrected the last errors.

workflows/genome_annotation/annotation-maker/Genome_annotation_with_maker_short.ga

add workflow: annotation a genome with maker

1ce1f00

rlibouba marked this pull request as draft December 11, 2024 09:40

rlibouba changed the title ~~Add workflow: annotation a genome with Maker~~ Add workflow: genome annotation with Maker Dec 11, 2024

Merge branch 'galaxyproject:main' into add_wf_annotation_maker

60b9c0b

wm75 reviewed Dec 12, 2024

View reviewed changes

workflows/genome_annotation/annotation_maker/Genome_annotation_with_maker_short_tests.yml Outdated Show resolved Hide resolved

rlibouba added 2 commits December 17, 2024 15:10

some modification

356d164

error typo

364eb9f

correct error

89c0035

correct error

38d88ae

rlibouba and others added 2 commits December 18, 2024 12:03

correct error

e617648

Merge branch 'galaxyproject:main' into add_wf_annotation_maker

da361e7

Update Genome_annotation_with_maker_short_tests.yml

bc44bb9

rlibouba marked this pull request as ready for review January 15, 2025 09:56

bgruening closed this Jan 28, 2025

bgruening reopened this Jan 28, 2025

add BUSCO lineage & modifications

4d0a045

rlibouba and others added 2 commits March 10, 2025 15:22

fix lint

ba3f76c

Use text parameter value restriction

301dfee

Small modification

cc9e163

error test

3d63e86

change cached_db

cc72c4c

fix test error

2af1607

fiw test error

e8fecb3

fix error tests

e0b5275

rlibouba added 2 commits March 17, 2025 13:07

fix error tests

ea930b3

fix lint

a02add1

error test

0949218

mvdbeek reviewed Mar 17, 2025

View reviewed changes

workflows/genome_annotation/annotation-maker/Genome_annotation_with_maker_short.ga Show resolved Hide resolved

mvdbeek reviewed Mar 20, 2025

View reviewed changes

workflows/genome_annotation/annotation-maker/Genome_annotation_with_maker_short.ga Outdated Show resolved Hide resolved

add description

c2856ff

mvdbeek approved these changes Mar 20, 2025

View reviewed changes

mvdbeek enabled auto-merge March 20, 2025 15:00

mvdbeek merged commit c829730 into galaxyproject:main Mar 24, 2025
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Add workflow: genome annotation with Maker #631

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Add workflow: genome annotation with Maker #631

Add workflow: genome annotation with Maker #631

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