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Tissue Microarray Analysis #750

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@mvdbeek mvdbeek commented Mar 19, 2025

FOR CONTRIBUTOR:

  • I have read the Adding workflows guidelines
  • License permits unrestricted use (educational + commercial)
  • Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

  • .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
  • Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
  • In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
  • In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
  • In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
  • Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
  • Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
  • Changelog contains appropriate entries
  • Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

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Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 0
Failure 1
Skipped 0
Failed Tests
  • ❌ tissue-micro-array-analysis.ga_0

    Problems:

    • Output with path /tmp/tmpei_cnxuu/ASHLAR on data 1, data 11, and others__edf97046-bbcd-468f-b7a2-c19f2047afe8 different than expected
Output checksum [6a7d35708dbc284271837a36349ea21b86977ed8] does not match expected [376a88f5c00f5a7f721580885a433d907487ac69] (using hash algorithm sha1).

    • Output with path /tmp/tmplnzngiww/UNetCoreograph on data 12 TMA Map__554411ea-6a18-4086-b63a-5437b237647e different than expected
Output checksum [d272e32ed07db1be5a73a6ad0accc2fdbd91c25b] does not match expected [691ea536b89418fb047b8c8676ff790ee34c4a21] (using hash algorithm sha1).

    • Output with path /tmp/tmpxbs6jvp3/1__507ee8ed-8cc2-4336-a6ce-d781849ae578 different than expected
Output checksum [1b550b7799ad4828ee0d04efd5249e0a6c6899cc] does not match expected [fc22c8b243b37004c1c9387f4e4eec5095fb00dc] (using hash algorithm sha1).

    • Output with path /tmp/tmpn8dypmd3/1__7b6ccd9f-782a-412e-89ac-e5d300aca823 different than expected
Output checksum [bd5f9c8443ed05173793c64e0dda1375cda42aa1] does not match expected [b24c83ca1e507f844dd269100efdf0ed3d93eedd] (using hash algorithm sha1).

    • Output with path /tmp/tmpff0vuwx0/Convert image format on data 17__3bbb036f-43e2-43e4-bebf-de9a3131bc58 different than expected
Output checksum [3f696872d4b80190e49872bdabf72b1f26b60816] does not match expected [d3607799410b7f456567b07ad32b1c2925fb5926] (using hash algorithm sha1).

    • Output with path /tmp/tmp8ai2jg05/Rename OME-TIFF channels on data 1 and data 21__3441dbec-64a0-40bd-89f6-0948843537e8 different than expected
Output checksum [77450cebed302a2ee3ac674f640e7c0db27398cf] does not match expected [376a88f5c00f5a7f721580885a433d907487ac69] (using hash algorithm sha1).

    • Output with path /tmp/tmpytwdzfkw/Convert McMicro Output to Anndata on data 23__fef05ed3-78c4-44a9-8f04-9cf7ff396145 different than expected
Output checksum [8db6f09dd305d3b52b0ad34f0f2bfd85caab014d] does not match expected [0854881c334a6aff0cba56d88f096722543bad66] (using hash algorithm sha1).

    • Output with path /tmp/tmpgigs3qmu/Single Cell Phenotyping on data 2 and data 27__718cff60-4e7c-4b8a-acc2-083b0aae907c different than expected
Output checksum [105beeff7f5e9f8e7aa244ed7f61eb5c145a3050] does not match expected [437266f0f2da4f12459cddedeb57d8e31416ad45] (using hash algorithm sha1).

    • Output with path /tmp/tmp8i8qx5wh/Vitessce on data 29, data 19, and data 25__eb7125fa-b995-4334-a040-a611ba232cfc different than expected
Output checksum [82723a2116df494f87633c63d6e415157d9abdfd] does not match expected [f08e9f4a4151651fec019c504d3cc0e056956b71] (using hash algorithm sha1).

    Workflow invocation details

    • Invocation Messages

    • Steps

      • Step 1: Raw cycle images:

        • step_state: scheduled

      • Step 2: markers.csv:

        • step_state: scheduled

      • Step 11: Convert to Anndata:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/49c178651194/scimap_mcmicro_to_anndata/mcmicro_to_anndata.py' --inputs '/tmp/tmp_ttt6ywo/job_working_directory/000/13/configs/tmpdrjjg8qi' --outfile '/tmp/tmp_ttt6ywo/job_working_directory/000/13/outputs/dataset_fef05ed3-78c4-44a9-8f04-9cf7ff396145.dat'

            Exit Code:

            • 0

            Standard Output:

            • Running SCIMAP  2.1.0
Loading dataset_047d3947-aa99-4ec1-a602-44a2b766e60f.dat

            Traceback:

            • 

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
drop_markers
""

              

              
options
{"CellId": "CellID", "custom_imageid": "", "log": true, "min_cells": null, "random_sample": null, "remove_dna": false, "remove_string_from_name": "", "split": "X_centroid", "unique_CellId": false}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 12: Scimap phenotyping:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/88fca6e905be/scimap_phenotyping/scimap_phenotyping.py' --adata '/tmp/tmp_ttt6ywo/files/f/e/f/dataset_fef05ed3-78c4-44a9-8f04-9cf7ff396145.dat' --log --gating_workflow '/tmp/tmp_ttt6ywo/files/c/c/0/dataset_cc08582c-1e89-48ba-bc3e-eb15267ac0cf.dat' --gating_workflow_ext 'csv' --random_state '0' --output '/tmp/tmp_ttt6ywo/job_working_directory/000/14/outputs/dataset_718cff60-4e7c-4b8a-acc2-083b0aae907c.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              Running SCIMAP  2.1.0

 adata.raw.X will be log1p transformed 

GMM for ['dataset_047d3947-aa99-4ec1-a602-44a2b766e60f']
Categories (1, object): ['dataset_047d3947-aa99-4ec1-a602-44a2b766e60f']
Finding the optimal gate by GMM for DNA_7
Finding the optimal gate by GMM for CD11B
Finding the optimal gate by GMM for SMA
Finding the optimal gate by GMM for CD16
Finding the optimal gate by GMM for DNA_8
Finding the optimal gate by GMM for ECAD
Finding the optimal gate by GMM for FOXP3
Finding the optimal gate by GMM for NCAM
Scaling Image dataset_047d3947-aa99-4ec1-a602-44a2b766e60f
Scaling DNA_7
Scaling CD11B
Scaling SMA
Scaling CD16
Scaling DNA_8
Scaling ECAD
Scaling FOXP3
Scaling NCAM
Phenotyping Stroma
Phenotyping Epithelial
Phenotyping Immune
-- Subsetting Immune
Phenotyping Myeloid
Consolidating the phenotypes across all groups
phenotype
Epithelial    4119
Stroma        3549
Myeloid       3261
Unknown       1668
Immune        1475
Name: count, dtype: int64

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
log
true

              

              
manual_gates
None

              

              
random_state
"0"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 13: Create a Vitessce dashboard:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              MAX_MEM=${GALAXY_MEMORY_MB:-2000} && export BF_MAX_MEM="$(($MAX_MEM/2))m" && mkdir -p '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0' && ln -sf '/tmp/tmp_ttt6ywo/files/3/4/4/dataset_3441dbec-64a0-40bd-89f6-0948843537e8.dat' '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/image01.ome.tiff' && info=$(showinf -nopix -nometa -noflat -no-upgrade '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/image01.ome.tiff') && echo '>showinf -nopix -nometa -noflat -no-upgrade $image' && echo "$info\n" && masks_info=$(showinf -nopix -nometa -noflat -no-upgrade '/tmp/tmp_ttt6ywo/files/7/f/d/dataset_7fd9e39a-e760-40d2-bf06-5838710303c8.dat') && echo '>showinf -nopix -nometa -noflat -no-upgrade $masks' && echo "$masks_info\n" && masks_n_resolutions=$(echo "$masks_info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) && if [ -z $masks_n_resolutions ]; then n_resolutions=$(echo "$info" | grep '^\s*Resolutions\s*=' -m1 | cut -d'=' -f2 | xargs) && pyramid_scale=1 && if [ -z "$n_resolutions" ]; then echo "Warning: Failded to retrieve the number of pyramid resolutions. Set pyramid resolutions to 4 and scale to 2!"; n_resolutions=4; pyramid_scale=2; else echo "Found the number of pyramid resolutions: $n_resolutions"; if [ "$n_resolutions" -gt 1 ]; then sizeX0=$(echo "$info" | grep '^\s*sizeX\[0\]\s*=' -m1 | cut -d'=' -f2 | xargs) ; sizeX1=$(echo "$info" | grep '^\s*sizeX\[1\]\s*=' -m1 | cut -d'=' -f2 | xargs) ; if [ "$sizeX0" -gt 0 ] && [ "$sizeX1" -gt 0 ]; then pyramid_scale=$((($sizeX0 + $sizeX1 / 2 ) / $sizeX1)); echo "Calculate pyramid scale: $sizeX0 / $sizeX1 ~= $pyramid_scale."; else pyramid_scale=2; echo "Warning: Failed to calculate the pyramid scale; set it to 2!"; fi; fi; fi; tile_info=$(showinf -nopix -nometa -noflat -no-upgrade '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/image01.ome.tiff' | grep '^\s*Tile\ssize\s*=' -m1); tile_x=$(echo "$tile_info" | cut -d' ' -f4); tile_y=$(echo "$tile_info" | cut -d' ' -f6); convert_cmd="bfconvert -no-upgrade -pyramid-resolutions $n_resolutions -pyramid-scale $pyramid_scale -noflat -tilex $tile_x -tiley $tile_y '/tmp/tmp_ttt6ywo/files/7/f/d/dataset_7fd9e39a-e760-40d2-bf06-5838710303c8.dat' '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/masks01.ome.tiff'"; echo "\n>$convert_cmd"; eval $convert_cmd; masks_info_new=$(showinf -nopix -nometa -noflat -no-upgrade '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/masks01.ome.tiff'); echo "\n>showinf -nopix -nometa -noflat -no-upgrade '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/masks01.ome.tiff'"; echo "$masks_info_new\n"; else ln -sf '/tmp/tmp_ttt6ywo/files/7/f/d/dataset_7fd9e39a-e760-40d2-bf06-5838710303c8.dat' '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/masks01.ome.tiff'; fi && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/068da7f7cd83/vitessce_spatial/vitessce_spatial.py' --inputs '/tmp/tmp_ttt6ywo/job_working_directory/000/15/configs/tmpi4qg7jkv' --output '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files' --image '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/image01.ome.tiff' --offsets '/tmp/tmp_ttt6ywo/files/_metadata_files/7/b/4/metadata_7b408e06-971f-4d8e-ba7e-e994e94dbd72.dat' --masks '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/masks01.ome.tiff' --anndata '/tmp/tmp_ttt6ywo/files/7/1/8/dataset_718cff60-4e7c-4b8a-acc2-083b0aae907c.dat' && cp '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/068da7f7cd83/vitessce_spatial/index.html' '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc.dat'; echo "export var config = $(cat /tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/config.json)" >> '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/config.js'; cat '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/config.json' >> '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_d7b93aaa-1745-42ac-9425-e9a83b43abf6.dat';
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              >showinf -nopix -nometa -noflat -no-upgrade $image
Checking file format [OME-TIFF]
Initializing reader
OMETiffReader initializing /tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/image01.ome.tiff
Reading IFDs
Populating metadata
Initialization took 0.112s

Reading core metadata
filename = /tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/image01.ome.tiff
Series count = 1
Series #0 :
	Resolutions = 4
		sizeX[0] = 2508
		sizeX[1] = 1254
		sizeX[2] = 627
		sizeX[3] = 313
	Image count = 8
	RGB = false (1) 
	Interleaved = false
	Indexed = false (false color)
	Width = 2508
	Height = 2646
	SizeZ = 1
	SizeT = 1
	SizeC = 8
	Tile size = 512 x 512
	Thumbnail size = 121 x 128
	Endianness = intel (little)
	Dimension order = XYCZT (certain)
	Pixel type = uint16
	Valid bits per pixel = 16
	Metadata complete = true
	Thumbnail series = false

>showinf -nopix -nometa -noflat -no-upgrade $masks
Checking file format [Tagged Image File Format]
Initializing reader
TiffDelegateReader initializing /tmp/tmp_ttt6ywo/files/7/f/d/dataset_7fd9e39a-e760-40d2-bf06-5838710303c8.dat
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
Initialization took 0.137s

Reading core metadata
filename = /tmp/tmp_ttt6ywo/files/7/f/d/dataset_7fd9e39a-e760-40d2-bf06-5838710303c8.dat
Series count = 1
Series #0 :
	Image count = 1
	RGB = false (1) 
	Interleaved = false
	Indexed = false (false color)
	Width = 2508
	Height = 2646
	SizeZ = 1
	SizeT = 1
	SizeC = 1
	Tile size = 2508 x 2646
	Thumbnail size = 121 x 128
	Endianness = intel (little)
	Dimension order = XYCZT (certain)
	Pixel type = int32
	Valid bits per pixel = 32
	Metadata complete = true
	Thumbnail series = false

Found the number of pyramid resolutions: 4
Calculate pyramid scale: 2508 / 1254 ~= 2.

>bfconvert -no-upgrade -pyramid-resolutions 4 -pyramid-scale 2 -noflat -tilex 512 -tiley 512 '/tmp/tmp_ttt6ywo/files/7/f/d/dataset_7fd9e39a-e760-40d2-bf06-5838710303c8.dat' '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/masks01.ome.tiff'
/tmp/tmp_ttt6ywo/files/7/f/d/dataset_7fd9e39a-e760-40d2-bf06-5838710303c8.dat
TiffDelegateReader initializing /tmp/tmp_ttt6ywo/files/7/f/d/dataset_7fd9e39a-e760-40d2-bf06-5838710303c8.dat
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
[Tagged Image File Format] -> /tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/masks01.ome.tiff [OME-TIFF]
Tile size = 512 x 512
	Converted 1/1 planes (100%)
Tile size = 512 x 512
	Converted 1/1 planes (100%)
Tile size = 512 x 512
	Converted 1/1 planes (100%)
Tile size = 320 x 336
	Converted 1/1 planes (100%)
[done]
2.862s elapsed (50.5+387.5ms per plane, 968ms overhead)

>showinf -nopix -nometa -noflat -no-upgrade '/tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/masks01.ome.tiff'
Checking file format [OME-TIFF]
Initializing reader
OMETiffReader initializing /tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/masks01.ome.tiff
Reading IFDs
Populating metadata
Initialization took 0.104s

Reading core metadata
filename = /tmp/tmp_ttt6ywo/job_working_directory/000/15/outputs/dataset_eb7125fa-b995-4334-a040-a611ba232cfc_files/A/0/masks01.ome.tiff
Series count = 1
Series #0 :
	Resolutions = 4
		sizeX[0] = 2508
		sizeX[1] = 1254
		sizeX[2] = 627
		sizeX[3] = 313
	Image count = 1
	RGB = false (1) 
	Interleaved = false
	Indexed = false (false color)
	Width = 2508
	Height = 2646
	SizeZ = 1
	SizeT = 1
	SizeC = 1
	Tile size = 512 x 512
	Thumbnail size = 121 x 128
	Endianness = intel (little)
	Dimension order = XYCZT (certain)
	Pixel type = int32
	Valid bits per pixel = 32
	Metadata complete = true
	Thumbnail series = false


              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
do_phenotyping
{"__current_case__": 1, "anndata": {"values": [{"id": 14, "src": "dce"}]}, "phenotype_factory": {"__current_case__": 0, "phenotype_mode": "choices", "phenotypes": ["phenotype"]}, "phenotyping_choice": "add_h5ad", "scatterplot_embeddings": {"__current_case__": 0, "embedding": "umap", "options": {"knn": true, "n_neighbors": "30", "n_pcs": "10", "random_state": "0"}}}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 3: PhenotypeWorkflow:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 4: Illumination correction with Basic:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmp_ttt6ywo/files/5/3/e/dataset_53ea439a-5a66-4fb1-8bb9-07786f487920.dat' 'exemplar-001-cycle-07.ome.tiff' &&     if ! [ -x "$(which ImageJ)" ]; then ln -sf "$(which ImageJ-linux64)" "ImageJ"; export PATH="$PATH:$(pwd)/"; fi &&  BASIC_SCRIPT="" && if [ -f "/opt/fiji/imagej_basic_ashlar.py" ]; then export BASIC_SCRIPT="/opt/fiji/imagej_basic_ashlar.py"; else export BASIC_SCRIPT="/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/7ee5b6f7533e/basic_illumination/imagej_basic_ashlar.py"; fi &&  ImageJ --ij2 --headless --run $BASIC_SCRIPT   "filename='exemplar-001-cycle-07.ome.tiff',output_dir='.',experiment_name='output'";
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              OpenJDK 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Mar 19, 2025 8:51:35 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.

              

              • 

            

            Standard Output:
            

              

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OMETiffReader initializing exemplar-001-cycle-07.ome.tiff
Reading IFDs
Populating metadata



Processing channel 1/4...
===========================
Reading IFDs
Populating metadata
Compute spatial shading profiles...
Reweighting Iteration:1
Stop Criterion1  0.7237670853187328
Stop Criterion2  0.3479267311604723
Stop Criterion3  0.32547963283789005
Stop Criterion4  0.29393595194522004
Stop Criterion5  0.2626094537543461
Stop Criterion6  0.236263978445132
Stop Criterion7  0.21260488200470687
Stop Criterion8  0.18072720245069188
Stop Criterion9  0.1358723871159032
Stop Criterion10  0.09413198317233705
Stop Criterion11  0.06139677565279799
Stop Criterion12  0.038659911620879416
Stop Criterion13  0.02425396876589163
Stop Criterion14  0.015550318267246909
Stop Criterion15  0.00999537908741311
Stop Criterion16  0.00625833537439219
Stop Criterion17  0.003787136986360472
Stop Criterion18  0.002203256001992479
Stop Criterion19  0.0012646928848501957
Stop Criterion20  7.398321930514644E-4
Stop Criterion21  4.498666248083781E-4
Stop Criterion22  2.824581483896693E-4
Stop Criterion23  1.797069701524201E-4
Stop Criterion24  1.1340622552790771E-4
Stop Criterion25  7.37733601677205E-5
Stop Criterion26  4.782858070096793E-5
Stop Criterion27  3.0708517710206266E-5
Stop Criterion28  1.979652405415095E-5
Stop Criterion29  1.2711629428388742E-5
Stop Criterion30  8.230152417037178E-6
Stop Criterion31  5.218561503883828E-6
Stop Criterion32  3.3202927665365916E-6
Stop Criterion33  2.123878636281263E-6
Stop Criterion34  1.3786255315990336E-6
Stop Criterion35  8.846152320878804E-7
Reweighting Iteration:2
Stop Criterion1  0.7220809335985949
Stop Criterion2  0.3349210021289422
Stop Criterion3  0.2990679411087291
Stop Criterion4  0.2533877687846563
Stop Criterion5  0.20415955799881097
Stop Criterion6  0.16102430655162367
Stop Criterion7  0.12269216094837528
Stop Criterion8  0.09251127470777432
Stop Criterion9  0.06831206236644628
Stop Criterion10  0.049964977737517804
Stop Criterion11  0.035854407317382715
Stop Criterion12  0.025656001832040972
Stop Criterion13  0.018151905990311523
Stop Criterion14  0.012711277515116677
Stop Criterion15  0.008851570271736577
Stop Criterion16  0.006153221106709571
Stop Criterion17  0.004239454430571974
Stop Criterion18  0.0028990391283510585
Stop Criterion19  0.001999443343104988
Stop Criterion20  0.0013951463099972008
Stop Criterion21  0.0010051893134380133
Stop Criterion22  7.232201374656854E-4
Stop Criterion23  5.010723721481596E-4
Stop Criterion24  3.263915475360964E-4
Stop Criterion25  2.038742145272361E-4
Stop Criterion26  1.24131906364217E-4
Stop Criterion27  7.332443838850404E-5
Stop Criterion28  4.367826573039298E-5
Stop Criterion29  2.684569769155132E-5
Stop Criterion30  1.6673385034094978E-5
Stop Criterion31  1.0581242851124275E-5
Stop Criterion32  6.728650979696252E-6
Stop Criterion33  4.287675766672403E-6
Stop Criterion34  2.759721570306882E-6
Stop Criterion35  1.81152515149765E-6
Stop Criterion36  1.211454642743518E-6
Stop Criterion37  8.001552742253611E-7
Reweighting Iteration:3
Stop Criterion1  0.7212795465593611
Stop Criterion2  0.3315802173522141
Stop Criterion3  0.2937407295297951
Stop Criterion4  0.24711546998830772
Stop Criterion5  0.19790601236843014
Stop Criterion6  0.1561569672512293
Stop Criterion7  0.11836696256686309
Stop Criterion8  0.08833513132871271
Stop Criterion9  0.06481604922612756
Stop Criterion10  0.04727966379904183
Stop Criterion11  0.03394140871924927
Stop Criterion12  0.024360892475624025
Stop Criterion13  0.017293107171975172
Stop Criterion14  0.012166439485922439
Stop Criterion15  0.008494623096100147
Stop Criterion16  0.005895832454084787
Stop Criterion17  0.00405885943069697
Stop Criterion18  0.0028038884308911735
Stop Criterion19  0.0019520112543607532
Stop Criterion20  0.0013932705930686702
Stop Criterion21  0.001006801354863656
Stop Criterion22  7.230962268370507E-4
Stop Criterion23  5.051733125256513E-4
Stop Criterion24  3.3987943828625767E-4
Stop Criterion25  2.172815245345853E-4
Stop Criterion26  1.337184050783558E-4
Stop Criterion27  8.026303880594906E-5
Stop Criterion28  4.871449883616721E-5
Stop Criterion29  3.0080982606652E-5
Stop Criterion30  1.8903352329491593E-5
Stop Criterion31  1.1968799176903062E-5
Stop Criterion32  7.635211768899285E-6
Stop Criterion33  4.894242112824505E-6
Stop Criterion34  3.2056494670547914E-6
Stop Criterion35  2.158335403729524E-6
Stop Criterion36  1.4635476526734252E-6
Stop Criterion37  9.728772878800295E-7
Reweighting Iteration:4
Stop Criterion1  0.7210546324740597
Stop Criterion2  0.330586073955919
Stop Criterion3  0.2920239367454098
Stop Criterion4  0.24498404917448985
Stop Criterion5  0.19586696512209864
Stop Criterion6  0.15436744930517718
Stop Criterion7  0.11663273128594645
Stop Criterion8  0.08671935108372159
Stop Criterion9  0.0635206222566844
Stop Criterion10  0.04633606849322478
Stop Criterion11  0.03336864705979566
Stop Criterion12  0.02394883440442301
Stop Criterion13  0.017028855084164452
Stop Criterion14  0.012001912836323498
Stop Criterion15  0.008392807441572335
Stop Criterion16  0.005835062156855148
Stop Criterion17  0.004036085672579521
Stop Criterion18  0.0027981211213919236
Stop Criterion19  0.0019510396085183326
Stop Criterion20  0.0013912813782344688
Stop Criterion21  0.001006683443054068
Stop Criterion22  7.2339604790488E-4
Stop Criterion23  5.064378306695817E-4
Stop Criterion24  3.4176037447240386E-4
Stop Criterion25  2.200800712668998E-4
Stop Criterion26  1.3633908863816752E-4
Stop Criterion27  8.279662912340982E-5
Stop Criterion28  5.011992545976079E-5
Stop Criterion29  3.103371504572929E-5
Stop Criterion30  1.975238085560732E-5
Stop Criterion31  1.2678617427504478E-5
Stop Criterion32  8.035258954534731E-6
Stop Criterion33  5.0868408819904616E-6
Stop Criterion34  3.297453590106317E-6
Stop Criterion35  2.229892310169164E-6
Stop Criterion36  1.5349021972060712E-6
Stop Criterion37  1.0239020649300614E-6
Stop Criterion38  6.546602765567362E-7
Reweighting Iteration:5
Stop Criterion1  0.7209575246989496
Stop Criterion2  0.3300484646938468
Stop Criterion3  0.2911934225851583
Stop Criterion4  0.2439690283823731
Stop Criterion5  0.1948102010673965
Stop Criterion6  0.1534271185612789
Stop Criterion7  0.11573890150600555
Stop Criterion8  0.08594988770911194
Stop Criterion9  0.06294335306136437
Stop Criterion10  0.045855659724208124
Stop Criterion11  0.03302773563332642
Stop Criterion12  0.023744050317809625
Stop Criterion13  0.0169339536305764
Stop Criterion14  0.011918740600140164
Stop Criterion15  0.008342350537669069
Stop Criterion16  0.005812979474102632
Stop Criterion17  0.004026654431399881
Stop Criterion18  0.002803849600708367
Stop Criterion19  0.0019551465896893634
Stop Criterion20  0.0013972146003593852
Stop Criterion21  0.0010094634844667364
Stop Criterion22  7.238058271946413E-4
Stop Criterion23  5.079486867405099E-4
Stop Criterion24  3.440547514844041E-4
Stop Criterion25  2.2168694604722745E-4
Stop Criterion26  1.3679786081377874E-4
Stop Criterion27  8.278758813629323E-5
Stop Criterion28  5.048338816200862E-5
Stop Criterion29  3.150823744542287E-5
Stop Criterion30  2.0238236320259404E-5
Stop Criterion31  1.2859538554855209E-5
Stop Criterion32  8.09863635816984E-6
Stop Criterion33  5.100874725819114E-6
Stop Criterion34  3.3310360857996435E-6
Stop Criterion35  2.286595943104388E-6
Stop Criterion36  1.5767560016198907E-6
Stop Criterion37  1.0460315667826398E-6
Stop Criterion38  6.655779388239014E-7



Processing channel 2/4...
===========================
Reading IFDs
Populating metadata
Compute spatial shading profiles...
Reweighting Iteration:1
Stop Criterion1  0.4423799241875226
Stop Criterion2  0.2372178633245174
Stop Criterion3  0.22627280722240323
Stop Criterion4  0.2012322507835943
Stop Criterion5  0.17207039276712371
Stop Criterion6  0.14871669649357092
Stop Criterion7  0.13116131969854475
Stop Criterion8  0.11918606008883324
Stop Criterion9  0.1089601559491928
Stop Criterion10  0.09253524570555947
Stop Criterion11  0.068080330132032
Stop Criterion12  0.04470391469721303
Stop Criterion13  0.028284726716081263
Stop Criterion14  0.017671656522790926
Stop Criterion15  0.010678289362721582
Stop Criterion16  0.006230243002628107
Stop Criterion17  0.0035624069891578222
Stop Criterion18  0.002057049103616311
Stop Criterion19  0.0012112781960951144
Stop Criterion20  7.271988243789328E-4
Stop Criterion21  4.4275098815185044E-4
Stop Criterion22  2.732126228671104E-4
Stop Criterion23  1.6790471620874286E-4
Stop Criterion24  1.0457601430799875E-4
Stop Criterion25  6.579857545600054E-5
Stop Criterion26  4.314377482003961E-5
Stop Criterion27  2.8624793884674673E-5
Stop Criterion28  1.9337042622796468E-5
Stop Criterion29  1.285529423965208E-5
Stop Criterion30  8.643657177513327E-6
Stop Criterion31  5.917679127436841E-6
Stop Criterion32  3.983532749069094E-6
Stop Criterion33  2.641799108661195E-6
Stop Criterion34  1.7072435320477937E-6
Stop Criterion35  1.0942942952176409E-6
Stop Criterion36  6.810266986200522E-7
Reweighting Iteration:2
Stop Criterion1  0.42257990867803935
Stop Criterion2  0.18740402725593738
Stop Criterion3  0.16732216357115656
Stop Criterion4  0.151252514160056
Stop Criterion5  0.13613811067417078
Stop Criterion6  0.12233113679166843
Stop Criterion7  0.1067076257660518
Stop Criterion8  0.08882145122618654
Stop Criterion9  0.07042664876468192
Stop Criterion10  0.05450411257084611
Stop Criterion11  0.04186384956203349
Stop Criterion12  0.0314890820776625
Stop Criterion13  0.02273220283471806
Stop Criterion14  0.015714806232363935
Stop Criterion15  0.010640597389448307
Stop Criterion16  0.007074746782106462
Stop Criterion17  0.004665359399119968
Stop Criterion18  0.003055680254227488
Stop Criterion19  0.0019832008474083692
Stop Criterion20  0.001273962453982327
Stop Criterion21  8.141131637226073E-4
Stop Criterion22  5.168154470844637E-4
Stop Criterion23  3.3065912632888325E-4
Stop Criterion24  2.076356357312356E-4
Stop Criterion25  1.29019690923118E-4
Stop Criterion26  7.917025266302749E-5
Stop Criterion27  4.902307492029196E-5
Stop Criterion28  3.110716989417707E-5
Stop Criterion29  2.000107394012174E-5
Stop Criterion30  1.3351647829627844E-5
Stop Criterion31  9.140243586598838E-6
Stop Criterion32  6.1904904115647265E-6
Stop Criterion33  4.148557959212696E-6
Stop Criterion34  2.7307577413069856E-6
Stop Criterion35  1.775853852015066E-6
Stop Criterion36  1.1309293902180203E-6
Stop Criterion37  7.245358124349701E-7
Reweighting Iteration:3
Stop Criterion1  0.4195294521304906
Stop Criterion2  0.18279800608436983
Stop Criterion3  0.1634385581152382
Stop Criterion4  0.14735363477243607
Stop Criterion5  0.13269850248352863
Stop Criterion6  0.11895752426547404
Stop Criterion7  0.10254349715763814
Stop Criterion8  0.08471737717817229
Stop Criterion9  0.06695908214657657
Stop Criterion10  0.05211899864882223
Stop Criterion11  0.04011691151965093
Stop Criterion12  0.030022516291679454
Stop Criterion13  0.021506856395414317
Stop Criterion14  0.01490375676036718
Stop Criterion15  0.010047514970185613
Stop Criterion16  0.006717431406052016
Stop Criterion17  0.004485894519176218
Stop Criterion18  0.0029997511960213963
Stop Criterion19  0.0020002354458389334
Stop Criterion20  0.0013178914789555133
Stop Criterion21  8.521878189522363E-4
Stop Criterion22  5.537648034503049E-4
Stop Criterion23  3.577407448193152E-4
Stop Criterion24  2.2880410697815687E-4
Stop Criterion25  1.4192401494561954E-4
Stop Criterion26  8.652999699191287E-5
Stop Criterion27  5.2798899670277355E-5
Stop Criterion28  3.2685264861988844E-5
Stop Criterion29  2.0863190256967807E-5
Stop Criterion30  1.3769263358469457E-5
Stop Criterion31  9.290191950485955E-6
Stop Criterion32  6.331833949507299E-6
Stop Criterion33  4.235856370349216E-6
Stop Criterion34  2.790443358161982E-6
Stop Criterion35  1.814297142654861E-6
Stop Criterion36  1.1659571727755089E-6
Stop Criterion37  7.442772661241211E-7
Reweighting Iteration:4
Stop Criterion1  0.4186698081590988
Stop Criterion2  0.18155779442790274
Stop Criterion3  0.1622181941494189
Stop Criterion4  0.14613743566399923
Stop Criterion5  0.13156396846073143
Stop Criterion6  0.11777100197129914
Stop Criterion7  0.10127216591038243
Stop Criterion8  0.0835502168164857
Stop Criterion9  0.06613944840310958
Stop Criterion10  0.0517018464688895
Stop Criterion11  0.039846452464666955
Stop Criterion12  0.02987170940727564
Stop Criterion13  0.021376219899229346
Stop Criterion14  0.014797210366699707
Stop Criterion15  0.009953831169272558
Stop Criterion16  0.0066751537362799585
Stop Criterion17  0.004443971560632756
Stop Criterion18  0.0029750398425349343
Stop Criterion19  0.0019920311582981827
Stop Criterion20  0.0013209952924383764
Stop Criterion21  8.66493106146037E-4
Stop Criterion22  5.597460009552118E-4
Stop Criterion23  3.594646631725197E-4
Stop Criterion24  2.3011838600241202E-4
Stop Criterion25  1.4412437364302972E-4
Stop Criterion26  8.869672936583198E-5
Stop Criterion27  5.4610851830231576E-5
Stop Criterion28  3.35988565196006E-5
Stop Criterion29  2.1414305616232898E-5
Stop Criterion30  1.418861767174635E-5
Stop Criterion31  9.596139644030476E-6
Stop Criterion32  6.507424250817217E-6
Stop Criterion33  4.354139333356348E-6
Stop Criterion34  2.8476291053866863E-6
Stop Criterion35  1.847730181287584E-6
Stop Criterion36  1.1725952112616632E-6
Stop Criterion37  7.499354697413578E-7
Reweighting Iteration:5
Stop Criterion1  0.41832783410184093
Stop Criterion2  0.18111422034159008
Stop Criterion3  0.16168394608447553
Stop Criterion4  0.14561044281518976
Stop Criterion5  0.13108754893035623
Stop Criterion6  0.11728560346093593
Stop Criterion7  0.10074038790978622
Stop Criterion8  0.08305361093874736
Stop Criterion9  0.06583458538580224
Stop Criterion10  0.05153545351739017
Stop Criterion11  0.03976040429219308
Stop Criterion12  0.02982401067906478
Stop Criterion13  0.021368861328818593
Stop Criterion14  0.01478187979704329
Stop Criterion15  0.009924584606546903
Stop Criterion16  0.006653367437712419
Stop Criterion17  0.004434833322448793
Stop Criterion18  0.0029699195086823364
Stop Criterion19  0.0019876744441365145
Stop Criterion20  0.0013200187037610573
Stop Criterion21  8.681608608338584E-4
Stop Criterion22  5.608210886801141E-4
Stop Criterion23  3.6074937882387076E-4
Stop Criterion24  2.303212090810648E-4
Stop Criterion25  1.4449198873439312E-4
Stop Criterion26  8.845354324202279E-5
Stop Criterion27  5.504724831004072E-5
Stop Criterion28  3.417914015609913E-5
Stop Criterion29  2.1832665335071244E-5
Stop Criterion30  1.4433022671193142E-5
Stop Criterion31  9.679710410736057E-6
Stop Criterion32  6.499206318750645E-6
Stop Criterion33  4.291445751798643E-6
Stop Criterion34  2.8669076732136478E-6
Stop Criterion35  1.8869697630211743E-6
Stop Criterion36  1.2200253518763813E-6
Stop Criterion37  7.822645350098684E-7



Processing channel 3/4...
===========================
Reading IFDs
Populating metadata
Compute spatial shading profiles...
Reweighting Iteration:1
Stop Criterion1  0.6143746084661007
Stop Criterion2  0.3854607693655193
Stop Criterion3  0.3053217525746348
Stop Criterion4  0.2525816684882698
Stop Criterion5  0.20873827133574746
Stop Criterion6  0.17260204783802977
Stop Criterion7  0.14484733363796598
Stop Criterion8  0.12069010436935594
Stop Criterion9  0.09899111500878742
Stop Criterion10  0.07771007607472614
Stop Criterion11  0.058274814130533
Stop Criterion12  0.04195990795571857
Stop Criterion13  0.028660893174567346
Stop Criterion14  0.018021075590948062
Stop Criterion15  0.010603626819466194
Stop Criterion16  0.006122609169229356
Stop Criterion17  0.0035631430982639325
Stop Criterion18  0.0021299198952220663
Stop Criterion19  0.00129066541888925
Stop Criterion20  7.898291555843844E-4
Stop Criterion21  4.782435013301397E-4
Stop Criterion22  2.893837713186813E-4
Stop Criterion23  1.7809120783052594E-4
Stop Criterion24  1.1039605002636458E-4
Stop Criterion25  6.901940073601745E-5
Stop Criterion26  4.2847281880132135E-5
Stop Criterion27  2.6853616369432156E-5
Stop Criterion28  1.6963837820300994E-5
Stop Criterion29  1.1063065634398487E-5
Stop Criterion30  7.218202956473053E-6
Stop Criterion31  4.750031680334451E-6
Stop Criterion32  2.9843336020534093E-6
Stop Criterion33  1.9360820809578157E-6
Stop Criterion34  1.2620241998202487E-6
Stop Criterion35  8.147135133424535E-7
Reweighting Iteration:2
Stop Criterion1  0.48553249496549555
Stop Criterion2  0.2496151502890477
Stop Criterion3  0.21268526119626488
Stop Criterion4  0.17909641860370024
Stop Criterion5  0.1509526393844221
Stop Criterion6  0.12696567449036952
Stop Criterion7  0.10567581315110114
Stop Criterion8  0.08632134883659204
Stop Criterion9  0.06929349844125239
Stop Criterion10  0.05426596399425627
Stop Criterion11  0.042019216143390964
Stop Criterion12  0.03179220995729858
Stop Criterion13  0.023263533645729615
Stop Criterion14  0.016383653598359475
Stop Criterion15  0.011189655556860217
Stop Criterion16  0.007473167642266178
Stop Criterion17  0.004867467439904904
Stop Criterion18  0.003133661686118026
Stop Criterion19  0.001996503830871962
Stop Criterion20  0.0012790808736367518
Stop Criterion21  8.261347823077796E-4
Stop Criterion22  5.297046339762117E-4
Stop Criterion23  3.369585429570465E-4
Stop Criterion24  2.1390903126824017E-4
Stop Criterion25  1.347850558003631E-4
Stop Criterion26  8.54287249352612E-5
Stop Criterion27  5.427217110162213E-5
Stop Criterion28  3.382034779497455E-5
Stop Criterion29  2.1450734633200802E-5
Stop Criterion30  1.413071056480458E-5
Stop Criterion31  9.443581104859682E-6
Stop Criterion32  6.302786152136017E-6
Stop Criterion33  4.094801799635135E-6
Stop Criterion34  2.6726026796644738E-6
Stop Criterion35  1.7681255137888132E-6
Stop Criterion36  1.1630058460654578E-6
Stop Criterion37  7.685795907887224E-7
Reweighting Iteration:3
Stop Criterion1  0.47036478116871444
Stop Criterion2  0.23384811225719895
Stop Criterion3  0.1962002984791176
Stop Criterion4  0.16451573354030752
Stop Criterion5  0.13879230731232575
Stop Criterion6  0.11680514870830784
Stop Criterion7  0.09740639444451143
Stop Criterion8  0.07990434825157473
Stop Criterion9  0.0644930280414396
Stop Criterion10  0.05091603013593614
Stop Criterion11  0.03965216174009371
Stop Criterion12  0.03001013786137514
Stop Criterion13  0.02195374947271327
Stop Criterion14  0.015487283392928571
Stop Criterion15  0.010670237913498625
Stop Criterion16  0.007235426956401981
Stop Criterion17  0.004851066986401055
Stop Criterion18  0.0031916770581381995
Stop Criterion19  0.002073968477722429
Stop Criterion20  0.0013521165017255086
Stop Criterion21  8.923572102279155E-4
Stop Criterion22  5.850170073625438E-4
Stop Criterion23  3.733528201023707E-4
Stop Criterion24  2.3450385677367512E-4
Stop Criterion25  1.451312475212009E-4
Stop Criterion26  9.066993889444774E-5
Stop Criterion27  5.81081294241694E-5
Stop Criterion28  3.779259601435486E-5
Stop Criterion29  2.443841588674577E-5
Stop Criterion30  1.5771842247182363E-5
Stop Criterion31  1.027875487829346E-5
Stop Criterion32  6.780183868576396E-6
Stop Criterion33  4.499888597509919E-6
Stop Criterion34  3.005717196766989E-6
Stop Criterion35  2.0005071361623133E-6
Stop Criterion36  1.3246849043350255E-6
Stop Criterion37  8.468798035928767E-7
Reweighting Iteration:4
Stop Criterion1  0.46526698049719273
Stop Criterion2  0.22812517454085254
Stop Criterion3  0.1893418425509073
Stop Criterion4  0.15862018052172663
Stop Criterion5  0.13326325840155362
Stop Criterion6  0.11208930042048856
Stop Criterion7  0.09380786775461313
Stop Criterion8  0.07726530451435923
Stop Criterion9  0.06243020265695438
Stop Criterion10  0.04938282509578285
Stop Criterion11  0.03847230795859546
Stop Criterion12  0.02909568152504244
Stop Criterion13  0.02132542169273165
Stop Criterion14  0.015038924428616011
Stop Criterion15  0.010424050084913568
Stop Criterion16  0.007119931792441911
Stop Criterion17  0.004797663106540595
Stop Criterion18  0.0032049619825435943
Stop Criterion19  0.0020999680300047095
Stop Criterion20  0.0013916461987073224
Stop Criterion21  9.305658447854554E-4
Stop Criterion22  6.117944992323976E-4
Stop Criterion23  3.884972754084751E-4
Stop Criterion24  2.4148966923988877E-4
Stop Criterion25  1.50809721602422E-4
Stop Criterion26  9.392329766362392E-5
Stop Criterion27  5.968312845455812E-5
Stop Criterion28  3.775442248111427E-5
Stop Criterion29  2.4344544103588207E-5
Stop Criterion30  1.6175675431405745E-5
Stop Criterion31  1.0770828075577013E-5
Stop Criterion32  7.153103175653674E-6
Stop Criterion33  4.7442045575062264E-6
Stop Criterion34  3.136222734056682E-6
Stop Criterion35  2.0547203193421498E-6
Stop Criterion36  1.3621891633322432E-6
Stop Criterion37  8.919960367338608E-7
Reweighting Iteration:5
Stop Criterion1  0.4630265070759725
Stop Criterion2  0.22548719863656375
Stop Criterion3  0.18631865083173266
Stop Criterion4  0.15580718709446317
Stop Criterion5  0.13067354215075144
Stop Criterion6  0.109864151342739
Stop Criterion7  0.09201163753264692
Stop Criterion8  0.07572651324453929
Stop Criterion9  0.06123597079898749
Stop Criterion10  0.04854919562083764
Stop Criterion11  0.03784258267750899
Stop Criterion12  0.028718635636316207
Stop Criterion13  0.02105804498139881
Stop Criterion14  0.014880750651334275
Stop Criterion15  0.01031686782775736
Stop Criterion16  0.007073364559535135
Stop Criterion17  0.0047860262339558144
Stop Criterion18  0.0032046603447530683
Stop Criterion19  0.002116206468612548
Stop Criterion20  0.0014055684175590202
Stop Criterion21  9.462153723557071E-4
Stop Criterion22  6.228736788302825E-4
Stop Criterion23  3.9666063585787423E-4
Stop Criterion24  2.47755917609509E-4
Stop Criterion25  1.5326764078924605E-4
Stop Criterion26  9.544415977608429E-5
Stop Criterion27  6.0740853385345745E-5
Stop Criterion28  3.822358901338925E-5
Stop Criterion29  2.4300260931720517E-5
Stop Criterion30  1.6024853008656956E-5
Stop Criterion31  1.0797783431108478E-5
Stop Criterion32  7.332354715193716E-6
Stop Criterion33  4.865263153582115E-6
Stop Criterion34  3.2282012566648274E-6
Stop Criterion35  2.1447890750566013E-6
Stop Criterion36  1.4010587450869468E-6
Stop Criterion37  9.242017265843661E-7



Processing channel 4/4...
===========================
Reading IFDs
Populating metadata
Compute spatial shading profiles...
Reweighting Iteration:1
Stop Criterion1  0.4479681107537465
Stop Criterion2  0.3157140274179291
Stop Criterion3  0.2900613041211816
Stop Criterion4  0.25175532895968566
Stop Criterion5  0.205052396326697
Stop Criterion6  0.16420246506877698
Stop Criterion7  0.1325908655070602
Stop Criterion8  0.10744858287377103
Stop Criterion9  0.08502538697620358
Stop Criterion10  0.0647539420902654
Stop Criterion11  0.0477613548677605
Stop Criterion12  0.034154527072218485
Stop Criterion13  0.024385435672747653
Stop Criterion14  0.017212638115895646
Stop Criterion15  0.011672695273491497
Stop Criterion16  0.007368447917092527
Stop Criterion17  0.004391238886042392
Stop Criterion18  0.0026524628488264635
Stop Criterion19  0.0016231789325759994
Stop Criterion20  9.883975143657052E-4
Stop Criterion21  6.09177651693973E-4
Stop Criterion22  3.7587265363994395E-4
Stop Criterion23  2.2798311599199657E-4
Stop Criterion24  1.3822053987856117E-4
Stop Criterion25  8.344957151755916E-5
Stop Criterion26  5.1166823798376606E-5
Stop Criterion27  3.141041467238371E-5
Stop Criterion28  1.9731512100420125E-5
Stop Criterion29  1.2492437607593672E-5
Stop Criterion30  7.999494458623476E-6
Stop Criterion31  5.211122309262443E-6
Stop Criterion32  3.407519894038643E-6
Stop Criterion33  2.2857028299553833E-6
Stop Criterion34  1.5424941367192673E-6
Stop Criterion35  1.0077987705226751E-6
Stop Criterion36  6.400466573475565E-7
Reweighting Iteration:2
Stop Criterion1  0.39667091215538514
Stop Criterion2  0.2180325016261655
Stop Criterion3  0.1802859782211687
Stop Criterion4  0.1514867861676155
Stop Criterion5  0.1271979395699544
Stop Criterion6  0.10691834753528981
Stop Criterion7  0.08920264643188212
Stop Criterion8  0.07289026174851995
Stop Criterion9  0.05835682905816366
Stop Criterion10  0.045772125055313966
Stop Criterion11  0.035566659550500944
Stop Criterion12  0.027031189339687584
Stop Criterion13  0.020409720668363964
Stop Criterion14  0.015328405881716526
Stop Criterion15  0.011191528591540118
Stop Criterion16  0.007689793411153369
Stop Criterion17  0.005000960471005131
Stop Criterion18  0.003222778877849684
Stop Criterion19  0.0020580944417130254
Stop Criterion20  0.0012958132964206262
Stop Criterion21  8.36981699870311E-4
Stop Criterion22  5.393644509569901E-4
Stop Criterion23  3.408820239352478E-4
Stop Criterion24  2.105485529620046E-4
Stop Criterion25  1.2866870978098753E-4
Stop Criterion26  7.694189393163375E-5
Stop Criterion27  4.673729386979814E-5
Stop Criterion28  2.8738670567832088E-5
Stop Criterion29  1.8068539083103478E-5
Stop Criterion30  1.1490804397426156E-5
Stop Criterion31  7.740354003151058E-6
Stop Criterion32  5.328098247112567E-6
Stop Criterion33  3.653993074052531E-6
Stop Criterion34  2.4423207153618607E-6
Stop Criterion35  1.6028291866875239E-6
Stop Criterion36  1.036041187414067E-6
Stop Criterion37  6.745569348690806E-7
Reweighting Iteration:3
Stop Criterion1  0.37357934848266405
Stop Criterion2  0.19648855289784514
Stop Criterion3  0.1614666616252115
Stop Criterion4  0.1346069124729321
Stop Criterion5  0.11287699364585549
Stop Criterion6  0.09451702684230294
Stop Criterion7  0.07843142002914678
Stop Criterion8  0.06398882927665074
Stop Criterion9  0.051488745065421136
Stop Criterion10  0.04116716546466214
Stop Criterion11  0.032496208639963005
Stop Criterion12  0.025356406932499714
Stop Criterion13  0.019770971634502522
Stop Criterion14  0.015083235491123894
Stop Criterion15  0.01115315181608557
Stop Criterion16  0.007773535096091266
Stop Criterion17  0.005101749922952886
Stop Criterion18  0.003288826405577515
Stop Criterion19  0.0021093363989006402
Stop Criterion20  0.0013479866655417255
Stop Criterion21  8.734526164501817E-4
Stop Criterion22  5.658375456061792E-4
Stop Criterion23  3.6099786390981646E-4
Stop Criterion24  2.2396083096893566E-4
Stop Criterion25  1.3683257646866686E-4
Stop Criterion26  8.423698989016003E-5
Stop Criterion27  5.124967743443076E-5
Stop Criterion28  3.126294967000657E-5
Stop Criterion29  1.9723314216892947E-5
Stop Criterion30  1.307834424992461E-5
Stop Criterion31  8.888503517134966E-6
Stop Criterion32  6.133657594957294E-6
Stop Criterion33  4.1711386641742536E-6
Stop Criterion34  2.7814817715054915E-6
Stop Criterion35  1.8107733182409367E-6
Stop Criterion36  1.1803357401121006E-6
Stop Criterion37  7.5467409296394E-7
Reweighting Iteration:4
Stop Criterion1  0.36776349204577374
Stop Criterion2  0.1913852903656396
Stop Criterion3  0.1569493536621846
Stop Criterion4  0.13032212397201154
Stop Criterion5  0.10855782575136098
Stop Criterion6  0.09096451486205366
Stop Criterion7  0.07525494582905842
Stop Criterion8  0.06118219811738668
Stop Criterion9  0.04936112333852717
Stop Criterion10  0.039578798997880194
Stop Criterion11  0.031338472205287876
Stop Criterion12  0.024737319708623386
Stop Criterion13  0.019426767511477438
Stop Criterion14  0.014952518304746207
Stop Criterion15  0.011121846564328266
Stop Criterion16  0.007772095208578778
Stop Criterion17  0.005111153658929467
Stop Criterion18  0.003313518570189934
Stop Criterion19  0.0021474239398336613
Stop Criterion20  0.0013833072514135777
Stop Criterion21  9.032459014375629E-4
Stop Criterion22  5.855666695180038E-4
Stop Criterion23  3.704107815688485E-4
Stop Criterion24  2.3027578708795094E-4
Stop Criterion25  1.4129581933148603E-4
Stop Criterion26  8.673800423438192E-5
Stop Criterion27  5.3089735194553144E-5
Stop Criterion28  3.261372042784563E-5
Stop Criterion29  2.0933133958277906E-5
Stop Criterion30  1.3911669305840525E-5
Stop Criterion31  9.41502178365073E-6
Stop Criterion32  6.490855529399125E-6
Stop Criterion33  4.423407069587656E-6
Stop Criterion34  2.9476541905981745E-6
Stop Criterion35  1.92068253944716E-6
Stop Criterion36  1.2361367730918522E-6
Stop Criterion37  8.021253365415824E-7
Reweighting Iteration:5
Stop Criterion1  0.3656226558224595
Stop Criterion2  0.1895750099583647
Stop Criterion3  0.15524902025202852
Stop Criterion4  0.1287089037706085
Stop Criterion5  0.1069678227468498
Stop Criterion6  0.08966414667465859
Stop Criterion7  0.07413302426915272
Stop Criterion8  0.0602714169776661
Stop Criterion9  0.04857806028264819
Stop Criterion10  0.03899044737427765
Stop Criterion11  0.03093922980940134
Stop Criterion12  0.02452063785466279
Stop Criterion13  0.01931509632603819
Stop Criterion14  0.014891753568879819
Stop Criterion15  0.01110054487937095
Stop Criterion16  0.0077534173021152905
Stop Criterion17  0.005115629850185271
Stop Criterion18  0.003324944328610618
Stop Criterion19  0.0021529569090019754
Stop Criterion20  0.0013920838581615185
Stop Criterion21  9.118593867105161E-4
Stop Criterion22  5.920488479805264E-4
Stop Criterion23  3.75602753881049E-4
Stop Criterion24  2.3520389405278595E-4
Stop Criterion25  1.4471927021479457E-4
Stop Criterion26  8.880131563674456E-5
Stop Criterion27  5.40430654175866E-5
Stop Criterion28  3.3192205657096906E-5
Stop Criterion29  2.1164151236388304E-5
Stop Criterion30  1.4164989693461548E-5
Stop Criterion31  9.829114390027E-6
Stop Criterion32  6.798895890198662E-6
Stop Criterion33  4.592073628091112E-6
Stop Criterion34  3.0514772475982946E-6
Stop Criterion35  1.984444222814624E-6
Stop Criterion36  1.2738122992072768E-6
Stop Criterion37  8.061668471345133E-7



Done!

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          • 

            Job 2:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmp_ttt6ywo/files/4/0/8/dataset_408a6437-a10a-45ce-9112-de53056c43d1.dat' 'exemplar-001-cycle-08.ome.tiff' &&     if ! [ -x "$(which ImageJ)" ]; then ln -sf "$(which ImageJ-linux64)" "ImageJ"; export PATH="$PATH:$(pwd)/"; fi &&  BASIC_SCRIPT="" && if [ -f "/opt/fiji/imagej_basic_ashlar.py" ]; then export BASIC_SCRIPT="/opt/fiji/imagej_basic_ashlar.py"; else export BASIC_SCRIPT="/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/7ee5b6f7533e/basic_illumination/imagej_basic_ashlar.py"; fi &&  ImageJ --ij2 --headless --run $BASIC_SCRIPT   "filename='exemplar-001-cycle-08.ome.tiff',output_dir='.',experiment_name='output'";
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              OpenJDK 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Mar 19, 2025 8:51:35 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.

              

              • 

            

            Standard Output:
            

              

            • 

              Loading images...
OMETiffReader initializing exemplar-001-cycle-08.ome.tiff
Reading IFDs
Populating metadata



Processing channel 1/4...
===========================
Reading IFDs
Populating metadata
Compute spatial shading profiles...
Reweighting Iteration:1
Stop Criterion1  0.7311467674531571
Stop Criterion2  0.33776917894318165
Stop Criterion3  0.3222797035332431
Stop Criterion4  0.29662524071964164
Stop Criterion5  0.26663031991846586
Stop Criterion6  0.23553419316112528
Stop Criterion7  0.21129360178399695
Stop Criterion8  0.18450607812989503
Stop Criterion9  0.141705137719022
Stop Criterion10  0.09706237952634814
Stop Criterion11  0.06251636131353143
Stop Criterion12  0.03901981468675839
Stop Criterion13  0.02420387752095631
Stop Criterion14  0.014991605132951344
Stop Criterion15  0.009272082524059895
Stop Criterion16  0.005694490341386539
Stop Criterion17  0.0035022830853647046
Stop Criterion18  0.002144940726928031
Stop Criterion19  0.0012671121576745326
Stop Criterion20  7.506209855810259E-4
Stop Criterion21  4.579307536342121E-4
Stop Criterion22  2.8589420944736963E-4
Stop Criterion23  1.8335433294605166E-4
Stop Criterion24  1.1658099788942293E-4
Stop Criterion25  7.356804025339338E-5
Stop Criterion26  4.6040518382638416E-5
Stop Criterion27  2.8796145486742682E-5
Stop Criterion28  1.8246394979814844E-5
Stop Criterion29  1.1739894759283322E-5
Stop Criterion30  7.507318663978098E-6
Stop Criterion31  4.848132473921191E-6
Stop Criterion32  3.164959440155004E-6
Stop Criterion33  2.023109685175598E-6
Stop Criterion34  1.2735293092785104E-6
Stop Criterion35  8.250942943061695E-7
Reweighting Iteration:2
Stop Criterion1  0.7297955678392262
Stop Criterion2  0.3263659841349978
Stop Criterion3  0.2968026367240697
Stop Criterion4  0.25908808788991705
Stop Criterion5  0.2152130082061819
Stop Criterion6  0.1705574954671425
Stop Criterion7  0.13193472683350385
Stop Criterion8  0.10195645492391146
Stop Criterion9  0.07852214343936147
Stop Criterion10  0.06005295212844348
Stop Criterion11  0.04504751828343006
Stop Criterion12  0.03325705560584478
Stop Criterion13  0.02242909957417891
Stop Criterion14  0.015283488759978897
Stop Criterion15  0.010203758466327692
Stop Criterion16  0.006716309410138964
Stop Criterion17  0.004367592869671251
Stop Criterion18  0.002871317000829027
Stop Criterion19  0.0019114695796925833
Stop Criterion20  0.0012945741850549637
Stop Criterion21  8.908299807440404E-4
Stop Criterion22  6.110374873627907E-4
Stop Criterion23  4.1379534151128415E-4
Stop Criterion24  2.762006186315205E-4
Stop Criterion25  1.791603930503736E-4
Stop Criterion26  1.1224746248631148E-4
Stop Criterion27  6.876099141441645E-5
Stop Criterion28  4.23547369021402E-5
Stop Criterion29  2.6098266502025183E-5
Stop Criterion30  1.6084706846504953E-5
Stop Criterion31  1.0010506801801122E-5
Stop Criterion32  6.391522757848879E-6
Stop Criterion33  4.122521128806993E-6
Stop Criterion34  2.6563580262012733E-6
Stop Criterion35  1.7287827842130043E-6
Stop Criterion36  1.1288123175018852E-6
Stop Criterion37  7.426926416645056E-7
Reweighting Iteration:3
Stop Criterion1  0.7293189389743933
Stop Criterion2  0.32348975026320104
Stop Criterion3  0.2921628307077374
Stop Criterion4  0.25338921654387003
Stop Criterion5  0.20940717821091737
Stop Criterion6  0.16391965377131715
Stop Criterion7  0.12462059829169746
Stop Criterion8  0.09491659743372083
Stop Criterion9  0.07248858757660281
Stop Criterion10  0.05498359340015898
Stop Criterion11  0.041193154376659574
Stop Criterion12  0.030404061127515446
Stop Criterion13  0.02072939904916756
Stop Criterion14  0.014203409909260329
Stop Criterion15  0.009605452907548237
Stop Criterion16  0.0063742857342783295
Stop Criterion17  0.004177655459209917
Stop Criterion18  0.002796199575752331
Stop Criterion19  0.001893887232255911
Stop Criterion20  0.0013027722560219653
Stop Criterion21  9.063761706859977E-4
Stop Criterion22  6.325462776213223E-4
Stop Criterion23  4.39372943167347E-4
Stop Criterion24  3.006772549253242E-4
Stop Criterion25  2.0110172198640683E-4
Stop Criterion26  1.3002494046164718E-4
Stop Criterion27  8.144113473932921E-5
Stop Criterion28  5.059807609339794E-5
Stop Criterion29  3.1473611830781895E-5
Stop Criterion30  1.9313053170971362E-5
Stop Criterion31  1.198577119002008E-5
Stop Criterion32  7.518182749990032E-6
Stop Criterion33  4.773799629951052E-6
Stop Criterion34  3.0993840733754288E-6
Stop Criterion35  2.053864127231708E-6
Stop Criterion36  1.3718931382455896E-6
Stop Criterion37  9.160531408845223E-7
Reweighting Iteration:4
Stop Criterion1  0.7289131159007839
Stop Criterion2  0.3214562545298726
Stop Criterion3  0.28914998626076543
Stop Criterion4  0.250503625169547
Stop Criterion5  0.20698206664267854
Stop Criterion6  0.16151791265617896
Stop Criterion7  0.12184244623026276
Stop Criterion8  0.0921017873899682
Stop Criterion9  0.06969732144805302
Stop Criterion10  0.052793324119530506
Stop Criterion11  0.03952316307499
Stop Criterion12  0.02768372326711728
Stop Criterion13  0.01943323440917947
Stop Criterion14  0.013483181290708112
Stop Criterion15  0.00922186905378811
Stop Criterion16  0.0062195299455286
Stop Criterion17  0.004162605959901103
Stop Criterion18  0.002816697496464745
Stop Criterion19  0.0019222649032498717
Stop Criterion20  0.0013345877598777154
Stop Criterion21  9.383869285917836E-4
Stop Criterion22  6.619259364397815E-4
Stop Criterion23  4.6246804233082163E-4
Stop Criterion24  3.165173178909594E-4
Stop Criterion25  2.114238875390695E-4
Stop Criterion26  1.3597745085222845E-4
Stop Criterion27  8.45946262277811E-5
Stop Criterion28  5.1417669450512846E-5
Stop Criterion29  3.146313947197865E-5
Stop Criterion30  1.940054659546145E-5
Stop Criterion31  1.2046436869867436E-5
Stop Criterion32  7.636426690868035E-6
Stop Criterion33  4.954815684327667E-6
Stop Criterion34  3.216708929787448E-6
Stop Criterion35  2.083192820866774E-6
Stop Criterion36  1.3897561891712644E-6
Stop Criterion37  9.391443876947838E-7
Reweighting Iteration:5
Stop Criterion1  0.7286216868407291
Stop Criterion2  0.3203584120311842
Stop Criterion3  0.2874178669882144
Stop Criterion4  0.24897236185340732
Stop Criterion5  0.20581903411408597
Stop Criterion6  0.16044776735948632
Stop Criterion7  0.12065676496848822
Stop Criterion8  0.09085982023868307
Stop Criterion9  0.06861502918618367
Stop Criterion10  0.05169825180420134
Stop Criterion11  0.037088604527958674
Stop Criterion12  0.02643127287516637
Stop Criterion13  0.018615349305546158
Stop Criterion14  0.01297629081639671
Stop Criterion15  0.008928796704339742
Stop Criterion16  0.006078840205963281
Stop Criterion17  0.004133824509310082
Stop Criterion18  0.002829551199840402
Stop Criterion19  0.0019398705695852358
Stop Criterion20  0.0013539989410121663
Stop Criterion21  9.571470339152504E-4
Stop Criterion22  6.742384828837762E-4
Stop Criterion23  4.698994981451631E-4
Stop Criterion24  3.220609735400747E-4
Stop Criterion25  2.1499687654495613E-4
Stop Criterion26  1.3713231703396607E-4
Stop Criterion27  8.439815130275647E-5
Stop Criterion28  5.1339249467655346E-5
Stop Criterion29  3.10589776306346E-5
Stop Criterion30  1.934675013651908E-5
Stop Criterion31  1.1989125900162843E-5
Stop Criterion32  7.562283998315536E-6
Stop Criterion33  4.83606181360968E-6
Stop Criterion34  3.1740973263387645E-6
Stop Criterion35  2.095177009997969E-6
Stop Criterion36  1.395591911583188E-6
Stop Criterion37  9.206244795421113E-7



Processing channel 2/4...
===========================
Reading IFDs
Populating metadata
Compute spatial shading profiles...
Reweighting Iteration:1
Stop Criterion1  0.4865266496737295
Stop Criterion2  0.26029423793291845
Stop Criterion3  0.24517424540864144
Stop Criterion4  0.22752888922323056
Stop Criterion5  0.20580693966086516
Stop Criterion6  0.1811321849077001
Stop Criterion7  0.15588522123045864
Stop Criterion8  0.1320906463189433
Stop Criterion9  0.10929110106629014
Stop Criterion10  0.08500137051574479
Stop Criterion11  0.06314606196289221
Stop Criterion12  0.04492015995201233
Stop Criterion13  0.029303498709037454
Stop Criterion14  0.017609016644959542
Stop Criterion15  0.010215639966116656
Stop Criterion16  0.005949299296553138
Stop Criterion17  0.003538631358361559
Stop Criterion18  0.002132144808103559
Stop Criterion19  0.001296992704053855
Stop Criterion20  7.926118018907942E-4
Stop Criterion21  4.826904447368808E-4
Stop Criterion22  2.946364314304115E-4
Stop Criterion23  1.8167028091906363E-4
Stop Criterion24  1.1447757025319949E-4
Stop Criterion25  7.113297617488361E-5
Stop Criterion26  4.390899098837903E-5
Stop Criterion27  2.827722092368468E-5
Stop Criterion28  1.8012991440658774E-5
Stop Criterion29  1.1737655735165246E-5
Stop Criterion30  7.867422385025183E-6
Stop Criterion31  5.1316910181152614E-6
Stop Criterion32  3.288197658180372E-6
Stop Criterion33  2.074230334069252E-6
Stop Criterion34  1.3708025988432613E-6
Stop Criterion35  8.993060349793785E-7
Reweighting Iteration:2
Stop Criterion1  0.48484941558659594
Stop Criterion2  0.25093618519217753
Stop Criterion3  0.223791613709165
Stop Criterion4  0.19416321741670584
Stop Criterion5  0.16719313792561566
Stop Criterion6  0.14160767759326714
Stop Criterion7  0.11695510808899592
Stop Criterion8  0.09485006690803513
Stop Criterion9  0.0754482145837962
Stop Criterion10  0.05888601548032168
Stop Criterion11  0.045274973456514475
Stop Criterion12  0.03349686259962536
Stop Criterion13  0.023864421638786736
Stop Criterion14  0.016545812109370596
Stop Criterion15  0.011188434927687679
Stop Criterion16  0.0075187861989681505
Stop Criterion17  0.004924663178656971
Stop Criterion18  0.0031747265779081307
Stop Criterion19  0.0020274587334744485
Stop Criterion20  0.001303516311557936
Stop Criterion21  8.431876296199574E-4
Stop Criterion22  5.465024084319674E-4
Stop Criterion23  3.512399222886652E-4
Stop Criterion24  2.261403039503943E-4
Stop Criterion25  1.4337422874807567E-4
Stop Criterion26  9.071975101047622E-5
Stop Criterion27  5.712933160259709E-5
Stop Criterion28  3.610520700308128E-5
Stop Criterion29  2.3464878824140577E-5
Stop Criterion30  1.5305476167669693E-5
Stop Criterion31  1.0111271646869245E-5
Stop Criterion32  6.6946079471242415E-6
Stop Criterion33  4.3635563172914E-6
Stop Criterion34  2.835431092039857E-6
Stop Criterion35  1.8165070819608728E-6
Stop Criterion36  1.2138221628845917E-6
Stop Criterion37  8.026340130825474E-7
Reweighting Iteration:3
Stop Criterion1  0.4839559381877759
Stop Criterion2  0.24632155305743095
Stop Criterion3  0.2159989471921455
Stop Criterion4  0.1868161668648299
Stop Criterion5  0.1600249039453469
Stop Criterion6  0.13457789137084306
Stop Criterion7  0.11091161576268863
Stop Criterion8  0.0900060965183252
Stop Criterion9  0.07134980418400431
Stop Criterion10  0.05599687186190798
Stop Criterion11  0.04281868004448292
Stop Criterion12  0.031672550143665046
Stop Criterion13  0.022662110724549888
Stop Criterion14  0.015763832949506826
Stop Criterion15  0.010813248491556775
Stop Criterion16  0.007393025351315308
Stop Criterion17  0.004936055758647839
Stop Criterion18  0.003244709170302696
Stop Criterion19  0.0021060078671209753
Stop Criterion20  0.001371750759199341
Stop Criterion21  8.965460035676285E-4
Stop Criterion22  5.896313633125184E-4
Stop Criterion23  3.8368243672561215E-4
Stop Criterion24  2.4540989733983783E-4
Stop Criterion25  1.557234483002533E-4
Stop Criterion26  9.799843072774287E-5
Stop Criterion27  6.163509625720684E-5
Stop Criterion28  3.889474921811792E-5
Stop Criterion29  2.531215611888283E-5
Stop Criterion30  1.659982262139424E-5
Stop Criterion31  1.0881671742869777E-5
Stop Criterion32  7.2075410294597836E-6
Stop Criterion33  4.7797481685138445E-6
Stop Criterion34  3.173302462964585E-6
Stop Criterion35  2.0803804194103746E-6
Stop Criterion36  1.3575382290317375E-6
Stop Criterion37  8.887595272658994E-7
Reweighting Iteration:4
Stop Criterion1  0.483523780432802
Stop Criterion2  0.2443017693837955
Stop Criterion3  0.2128364861120719
Stop Criterion4  0.18368488151640452
Stop Criterion5  0.1567174688330295
Stop Criterion6  0.13149604384697477
Stop Criterion7  0.10824869796597829
Stop Criterion8  0.08767973179760653
Stop Criterion9  0.06970360903316125
Stop Criterion10  0.054717517952857814
Stop Criterion11  0.04167051217800635
Stop Criterion12  0.030817481314079128
Stop Criterion13  0.022107393324692207
Stop Criterion14  0.015412430176155897
Stop Criterion15  0.01063840468773402
Stop Criterion16  0.007331654188932137
Stop Criterion17  0.0049144388393825185
Stop Criterion18  0.003251647623025965
Stop Criterion19  0.0021274708518179137
Stop Criterion20  0.0013893429804622294
Stop Criterion21  9.220920764066033E-4
Stop Criterion22  6.104058068977153E-4
Stop Criterion23  3.9398120486263067E-4
Stop Criterion24  2.5178539928927355E-4
Stop Criterion25  1.5880669975404407E-4
Stop Criterion26  1.003603223211902E-4
Stop Criterion27  6.348594134910242E-5
Stop Criterion28  4.034518765687167E-5
Stop Criterion29  2.5707190738472918E-5
Stop Criterion30  1.655038285006723E-5
Stop Criterion31  1.0984259190219948E-5
Stop Criterion32  7.384817923895117E-6
Stop Criterion33  4.997874352015931E-6
Stop Criterion34  3.3227972657550256E-6
Stop Criterion35  2.1806305092965136E-6
Stop Criterion36  1.4314424230618616E-6
Stop Criterion37  9.082008012333865E-7
Reweighting Iteration:5
Stop Criterion1  0.48328729953901717
Stop Criterion2  0.2433552949659248
Stop Criterion3  0.21139982721174863
Stop Criterion4  0.18207582401867056
Stop Criterion5  0.15502545027298398
Stop Criterion6  0.12995171485609772
Stop Criterion7  0.10682509031378179
Stop Criterion8  0.08653992645079668
Stop Criterion9  0.06888921909531903
Stop Criterion10  0.05409506278207824
Stop Criterion11  0.04116302451837585
Stop Criterion12  0.030405425827878287
Stop Criterion13  0.021842769803141295
Stop Criterion14  0.015270107999837518
Stop Criterion15  0.010547205524304729
Stop Criterion16  0.007249609717264817
Stop Criterion17  0.004885690808537772
Stop Criterion18  0.00324636697747817
Stop Criterion19  0.00213243905862437
Stop Criterion20  0.001401396811332506
Stop Criterion21  9.343884410458876E-4
Stop Criterion22  6.185265902176764E-4
Stop Criterion23  4.003926223146221E-4
Stop Criterion24  2.555189186262115E-4
Stop Criterion25  1.6158290070933056E-4
Stop Criterion26  1.018131100397077E-4
Stop Criterion27  6.442843260187534E-5
Stop Criterion28  4.0733519365982714E-5
Stop Criterion29  2.5932062455877626E-5
Stop Criterion30  1.7175537599067216E-5
Stop Criterion31  1.1497910950507993E-5
Stop Criterion32  7.69502917131467E-6
Stop Criterion33  5.116703873207261E-6
Stop Criterion34  3.3703192171986558E-6
Stop Criterion35  2.201077132566191E-6
Stop Criterion36  1.45175602190814E-6
Stop Criterion37  9.284669715781996E-7



Processing channel 3/4...
===========================
Reading IFDs
Populating metadata
Compute spatial shading profiles...
Reweighting Iteration:1
Stop Criterion1  0.3183155802482436
Stop Criterion2  0.25508270015259676
Stop Criterion3  0.24181561697822618
Stop Criterion4  0.20710593794275803
Stop Criterion5  0.16569070534018845
Stop Criterion6  0.13029801883837186
Stop Criterion7  0.10261000119664414
Stop Criterion8  0.08140602653968661
Stop Criterion9  0.06495122407707667
Stop Criterion10  0.05240036807244588
Stop Criterion11  0.04201861553459834
Stop Criterion12  0.033439278779752404
Stop Criterion13  0.026176237760181135
Stop Criterion14  0.01905174208161877
Stop Criterion15  0.012659891514915637
Stop Criterion16  0.007526405711628363
Stop Criterion17  0.00448578595442922
Stop Criterion18  0.0027157757886874054
Stop Criterion19  0.00165339443534272
Stop Criterion20  0.0010142113662110013
Stop Criterion21  6.262852135377893E-4
Stop Criterion22  3.797922093307641E-4
Stop Criterion23  2.2930626688053466E-4
Stop Criterion24  1.3999152115786186E-4
Stop Criterion25  8.425240145647823E-5
Stop Criterion26  5.132498663742397E-5
Stop Criterion27  3.1076061034934524E-5
Stop Criterion28  1.9023597645527455E-5
Stop Criterion29  1.2279973916451716E-5
Stop Criterion30  8.12336858624892E-6
Stop Criterion31  5.529574092453237E-6
Stop Criterion32  3.7038786849279555E-6
Stop Criterion33  2.4145203701565905E-6
Stop Criterion34  1.5637962444638586E-6
Stop Criterion35  1.0031820721633469E-6
Stop Criterion36  6.582803855845413E-7
Reweighting Iteration:2
Stop Criterion1  0.2489493841940968
Stop Criterion2  0.14051668280467278
Stop Criterion3  0.11487517356940194
Stop Criterion4  0.09526815709854752
Stop Criterion5  0.08117760285469365
Stop Criterion6  0.06826612899593923
Stop Criterion7  0.05798846413915349
Stop Criterion8  0.04985833290238125
Stop Criterion9  0.04328553875010868
Stop Criterion10  0.03746780941796625
Stop Criterion11  0.03237036241682846
Stop Criterion12  0.02718421125226338
Stop Criterion13  0.02149519608560517
Stop Criterion14  0.016175081927569328
Stop Criterion15  0.011484153392594777
Stop Criterion16  0.0077486641071353125
Stop Criterion17  0.005104125544009953
Stop Criterion18  0.0032553927239066796
Stop Criterion19  0.002033682854443319
Stop Criterion20  0.0012796993102290714
Stop Criterion21  8.178990454220706E-4
Stop Criterion22  5.18375664969136E-4
Stop Criterion23  3.1996397944394705E-4
Stop Criterion24  1.9782895449311537E-4
Stop Criterion25  1.2194178376305248E-4
Stop Criterion26  7.511879786504455E-5
Stop Criterion27  4.5934751535282944E-5
Stop Criterion28  2.88039020931857E-5
Stop Criterion29  1.8483701760123494E-5
Stop Criterion30  1.2300088655282818E-5
Stop Criterion31  8.394003100740113E-6
Stop Criterion32  5.859820495537591E-6
Stop Criterion33  3.974107321707534E-6
Stop Criterion34  2.638749654814634E-6
Stop Criterion35  1.7237433482488937E-6
Stop Criterion36  1.1224722922707697E-6
Stop Criterion37  7.184602197895808E-7
Reweighting Iteration:3
Stop Criterion1  0.24255077091047203
Stop Criterion2  0.13386525751786563
Stop Criterion3  0.10776619950881867
Stop Criterion4  0.0889034843897337
Stop Criterion5  0.07537950072875739
Stop Criterion6  0.06335585534847378
Stop Criterion7  0.05391044641882082
Stop Criterion8  0.04638018536574398
Stop Criterion9  0.040231612007856
Stop Criterion10  0.03533616680426666
Stop Criterion11  0.030969686295199195
Stop Criterion12  0.02605135074300367
Stop Criterion13  0.02070885471887212
Stop Criterion14  0.015599315199235046
Stop Criterion15  0.011065787653418391
Stop Criterion16  0.0076340208630102215
Stop Criterion17  0.005075269699760119
Stop Criterion18  0.0032859852980698856
Stop Criterion19  0.0020773753153772285
Stop Criterion20  0.001327993644659546
Stop Criterion21  8.557369520637417E-4
Stop Criterion22  5.482536008561914E-4
Stop Criterion23  3.408284679744916E-4
Stop Criterion24  2.1098485182387259E-4
Stop Criterion25  1.29451219111069E-4
Stop Criterion26  7.907649309587929E-5
Stop Criterion27  4.885667280760285E-5
Stop Criterion28  3.065042440294804E-5
Stop Criterion29  2.022032056797106E-5
Stop Criterion30  1.3794681611469676E-5
Stop Criterion31  9.593892654885949E-6
Stop Criterion32  6.5283820525609846E-6
Stop Criterion33  4.341079867711039E-6
Stop Criterion34  2.8628372151969537E-6
Stop Criterion35  1.8480164958086805E-6
Stop Criterion36  1.2116798595880643E-6
Stop Criterion37  7.801594635042186E-7
Reweighting Iteration:4
Stop Criterion1  0.2413648011894645
Stop Criterion2  0.13267073811697333
Stop Criterion3  0.10653492552300857
Stop Criterion4  0.08774739468233131
Stop Criterion5  0.07431833004811043
Stop Criterion6  0.06244942731015314
Stop Criterion7  0.053062699170304664
Stop Criterion8  0.045586404689172175
Stop Criterion9  0.03962291866856642
Stop Criterion10  0.03487660822737334
Stop Criterion11  0.030720407287424766
Stop Criterion12  0.02588641449648856
Stop Criterion13  0.020561632055988266
Stop Criterion14  0.015502363992821063
Stop Criterion15  0.011002806513039153
Stop Criterion16  0.0075903918763851295
Stop Criterion17  0.005060880030069755
Stop Criterion18  0.003271738283910359
Stop Criterion19  0.002080263633631578
Stop Criterion20  0.0013308790476171258
Stop Criterion21  8.618612308178808E-4
Stop Criterion22  5.550508038538863E-4
Stop Criterion23  3.4884706270570066E-4
Stop Criterion24  2.1644064143077948E-4
Stop Criterion25  1.3248185361652032E-4
Stop Criterion26  8.11260539717364E-5
Stop Criterion27  5.037569452944982E-5
Stop Criterion28  3.183492924474164E-5
Stop Criterion29  2.0778835235376037E-5
Stop Criterion30  1.4195453915378252E-5
Stop Criterion31  9.846104599499876E-6
Stop Criterion32  6.743971343143278E-6
Stop Criterion33  4.5405534833821916E-6
Stop Criterion34  2.9509006829470312E-6
Stop Criterion35  1.9231295543089922E-6
Stop Criterion36  1.244602761420872E-6
Stop Criterion37  8.046504833239618E-7
Reweighting Iteration:5
Stop Criterion1  0.24097384579585207
Stop Criterion2  0.13228771409235693
Stop Criterion3  0.10614984486714572
Stop Criterion4  0.08846059008406132
Stop Criterion5  0.07359254264029026
Stop Criterion6  0.06197334804797695
Stop Criterion7  0.05261748682118917
Stop Criterion8  0.045209155458155834
Stop Criterion9  0.03933295228026779
Stop Criterion10  0.03467550859579869
Stop Criterion11  0.030599103875269498
Stop Criterion12  0.02582541291340666
Stop Criterion13  0.020511766905421648
Stop Criterion14  0.015443403655392998
Stop Criterion15  0.010967017363327641
Stop Criterion16  0.007580383696581913
Stop Criterion17  0.005053645660818895
Stop Criterion18  0.0032683217340313585
Stop Criterion19  0.0020778099468504244
Stop Criterion20  0.0013319947063021303
Stop Criterion21  8.643089139711144E-4
Stop Criterion22  5.570370078016372E-4
Stop Criterion23  3.5166000958780424E-4
Stop Criterion24  2.1727873327933084E-4
Stop Criterion25  1.3452959712859422E-4
Stop Criterion26  8.255578521201021E-5
Stop Criterion27  5.0961477011320826E-5
Stop Criterion28  3.231938103538888E-5
Stop Criterion29  2.1268209347692563E-5
Stop Criterion30  1.4383446280564804E-5
Stop Criterion31  9.97850907008056E-6
Stop Criterion32  6.956368765435423E-6
Stop Criterion33  4.6491049233850225E-6
Stop Criterion34  3.008220485561713E-6
Stop Criterion35  1.942012349581826E-6
Stop Criterion36  1.2655494049056466E-6
Stop Criterion37  8.211791637313781E-7



Processing channel 4/4...
===========================
Reading IFDs
Populating metadata
Compute spatial shading profiles...
Reweighting Iteration:1
Stop Criterion1  0.0705778874584899
Stop Criterion2  0.044071660628088434
Stop Criterion3  0.04321581640483133
Stop Criterion4  0.04268506338167386
Stop Criterion5  0.04219950093796835
Stop Criterion6  0.04032633320605965
Stop Criterion7  0.03697343647807243
Stop Criterion8  0.03247415944812778
Stop Criterion9  0.02750606014420259
Stop Criterion10  0.022880968658372577
Stop Criterion11  0.019264432028272185
Stop Criterion12  0.016182734628598566
Stop Criterion13  0.013753042547239169
Stop Criterion14  0.011927052649340405
Stop Criterion15  0.01030971941646529
Stop Criterion16  0.008353631477710231
Stop Criterion17  0.006003160427203062
Stop Criterion18  0.0038385841290826325
Stop Criterion19  0.0023584739932476055
Stop Criterion20  0.0014462241676873272
Stop Criterion21  8.887597718753313E-4
Stop Criterion22  5.307129714546522E-4
Stop Criterion23  3.0857974874134406E-4
Stop Criterion24  1.8050812322601597E-4
Stop Criterion25  1.0860217413661556E-4
Stop Criterion26  6.676047861474977E-5
Stop Criterion27  4.076590440624891E-5
Stop Criterion28  2.5094740215772097E-5
Stop Criterion29  1.562312518425573E-5
Stop Criterion30  9.708374396597715E-6
Stop Criterion31  6.227196962823613E-6
Stop Criterion32  4.116364218194398E-6
Stop Criterion33  2.7879611956370105E-6
Stop Criterion34  1.8766479384295954E-6
Stop Criterion35  1.251974809644939E-6
Stop Criterion36  8.232345956397363E-7
Reweighting Iteration:2
Stop Criterion1  0.07050455978456739
Stop Criterion2  0.04164394033092374
Stop Criterion3  0.038024275389553344
Stop Criterion4  0.03431011171787284
Stop Criterion5  0.030632375869718332
Stop Criterion6  0.027315243667498667
Stop Criterion7  0.02429556302994335
Stop Criterion8  0.021705797230172918
Stop Criterion9  0.01910956190639723
Stop Criterion10  0.01676722228514393
Stop Criterion11  0.01478922885032007
Stop Criterion12  0.013152645714540903
Stop Criterion13  0.011822863770654621
Stop Criterion14  0.010718378987026511
Stop Criterion15  0.009541618677959367
Stop Criterion16  0.007724624825073011
Stop Criterion17  0.005651225963840381
Stop Criterion18  0.00377214692028812
Stop Criterion19  0.0024413382183045107
Stop Criterion20  0.0015503060061615658
Stop Criterion21  9.600336810804758E-4
Stop Criterion22  5.82401544838986E-4
Stop Criterion23  3.463097522987077E-4
Stop Criterion24  2.075889991335039E-4
Stop Criterion25  1.2577796638459083E-4
Stop Criterion26  7.768641965648033E-5
Stop Criterion27  4.845043643698146E-5
Stop Criterion28  3.0200696815518578E-5
Stop Criterion29  1.8770374820905082E-5
Stop Criterion30  1.1779678271005962E-5
Stop Criterion31  7.5570028623628005E-6
Stop Criterion32  5.052699346891213E-6
Stop Criterion33  3.370582975974743E-6
Stop Criterion34  2.2559757120049218E-6
Stop Criterion35  1.5049637679815057E-6
Stop Criterion36  1.022906771847144E-6
Stop Criterion37  6.860356439671056E-7
Reweighting Iteration:3
Stop Criterion1  0.07049728819122314
Stop Criterion2  0.041605927644230364
Stop Criterion3  0.03793293505918899
Stop Criterion4  0.03417991490324175
Stop Criterion5  0.030500957390151465
Stop Criterion6  0.027145131227822177
Stop Criterion7  0.024153877109430587
Stop Criterion8  0.021548621335147528
Stop Criterion9  0.01894825150112659
Stop Criterion10  0.016627756431530052
Stop Criterion11  0.014662640011554387
Stop Criterion12  0.013053931038885346
Stop Criterion13  0.011741323849520154
Stop Criterion14  0.01065761211390949
Stop Criterion15  0.009507635729565495
Stop Criterion16  0.007698858931352348
Stop Criterion17  0.005632875977550732
Stop Criterion18  0.0037632944718845227
Stop Criterion19  0.002438908673485372
Stop Criterion20  0.0015490743918493961
Stop Criterion21  9.582269841549666E-4
Stop Criterion22  5.81777399933494E-4
Stop Criterion23  3.473622831764757E-4
Stop Criterion24  2.091977336066952E-4
Stop Criterion25  1.2731737261693305E-4
Stop Criterion26  7.905971564012266E-5
Stop Criterion27  4.9299697270362614E-5
Stop Criterion28  3.0850994066009464E-5
Stop Criterion29  1.919077002855477E-5
Stop Criterion30  1.2042887927967707E-5
Stop Criterion31  7.934242350057952E-6
Stop Criterion32  5.207344542379494E-6
Stop Criterion33  3.4904149650426155E-6
Stop Criterion34  2.3596946381550027E-6
Stop Criterion35  1.6007078934575635E-6
Stop Criterion36  1.06827441532423E-6
Stop Criterion37  7.018393962893133E-7
Reweighting Iteration:4
Stop Criterion1  0.07049660704680122
Stop Criterion2  0.041601511411267764
Stop Criterion3  0.03792432230095763
Stop Criterion4  0.034166561806153004
Stop Criterion5  0.03048814290582057
Stop Criterion6  0.0271295855995751
Stop Criterion7  0.024139251808077383
Stop Criterion8  0.021531720685444296
Stop Criterion9  0.018930742086357248
Stop Criterion10  0.01661214263064778
Stop Criterion11  0.014647623453636328
Stop Criterion12  0.013042140962966426
Stop Criterion13  0.011730964273149104
Stop Criterion14  0.010649696154397087
Stop Criterion15  0.009503794532040564
Stop Criterion16  0.007695974742677192
Stop Criterion17  0.005630895779263013
Stop Criterion18  0.003762694675797251
Stop Criterion19  0.0024386607978424723
Stop Criterion20  0.001548765627953489
Stop Criterion21  9.579267460870678E-4
Stop Criterion22  5.816861123390775E-4
Stop Criterion23  3.4741554345439315E-4
Stop Criterion24  2.0937441368194131E-4
Stop Criterion25  1.274969561752709E-4
Stop Criterion26  7.915377971498245E-5
Stop Criterion27  4.94353328720936E-5
Stop Criterion28  3.113661508152643E-5
Stop Criterion29  1.9252017504975996E-5
Stop Criterion30  1.212927515789145E-5
Stop Criterion31  7.971110739758924E-6
Stop Criterion32  5.255856873052687E-6
Stop Criterion33  3.542238563910335E-6
Stop Criterion34  2.3929409244728593E-6
Stop Criterion35  1.6146468952503738E-6
Stop Criterion36  1.0707920417335094E-6
Stop Criterion37  7.129080388117749E-7
Reweighting Iteration:5
Stop Criterion1  0.07049649177794497
Stop Criterion2  0.04160076067963487
Stop Criterion3  0.03792292164169964
Stop Criterion4  0.03416394370270264
Stop Criterion5  0.03048609456447916
Stop Criterion6  0.027126980086357184
Stop Criterion7  0.02413646761828083
Stop Criterion8  0.021528569263706658
Stop Criterion9  0.018927535176627708
Stop Criterion10  0.016609347479882672
Stop Criterion11  0.014644876818237068
Stop Criterion12  0.013040092688359768
Stop Criterion13  0.011729054521671868
Stop Criterion14  0.01064820154360459
Stop Criterion15  0.009503095391724925
Stop Criterion16  0.007695425644812517
Stop Criterion17  0.005630556338052111
Stop Criterion18  0.0037627038621989664
Stop Criterion19  0.002438556678290036
Stop Criterion20  0.0015486645593287738
Stop Criterion21  9.578893721092252E-4
Stop Criterion22  5.816897781682345E-4
Stop Criterion23  3.47417355841746E-4
Stop Criterion24  2.0939227018937806E-4
Stop Criterion25  1.2752324768495877E-4
Stop Criterion26  7.916489160521913E-5
Stop Criterion27  4.948883644509169E-5
Stop Criterion28  3.119720651230016E-5
Stop Criterion29  1.9282835978042127E-5
Stop Criterion30  1.2134052302254724E-5
Stop Criterion31  7.973254580020904E-6
Stop Criterion32  5.267991021292113E-6
Stop Criterion33  3.5545577355516153E-6
Stop Criterion34  2.4108746617331104E-6
Stop Criterion35  1.6240583501301804E-6
Stop Criterion36  1.07558459521062E-6
Stop Criterion37  7.154178752016715E-7



Done!

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 5: Stitching and registration with Ashlar:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmp_ttt6ywo/files/3/0/2/dataset_3029b763-f80c-4f71-992e-62802b790406.dat' 'exemplar-001-cycle-07_dfp.ome.tiff' && ln -s '/tmp/tmp_ttt6ywo/files/8/7/c/dataset_87c9c94f-6c54-4cfb-9287-a9a70a8d5d80.dat' 'exemplar-001-cycle-08_dfp.ome.tiff' &&  ln -s '/tmp/tmp_ttt6ywo/files/6/a/4/dataset_6a45ab7b-76e6-47d9-a880-a180bf00623b.dat' 'exemplar-001-cycle-07_ffp.ome.tiff' && ln -s '/tmp/tmp_ttt6ywo/files/d/2/d/dataset_d2d40ce5-c65f-419d-ab6b-7e88bfe1d543.dat' 'exemplar-001-cycle-08_ffp.ome.tiff' &&  ashlar  '/tmp/tmp_ttt6ywo/files/5/3/e/dataset_53ea439a-5a66-4fb1-8bb9-07786f487920.dat' '/tmp/tmp_ttt6ywo/files/4/0/8/dataset_408a6437-a10a-45ce-9112-de53056c43d1.dat'  -m 30     -c 0     --ffp 'exemplar-001-cycle-07_ffp.ome.tiff' 'exemplar-001-cycle-08_ffp.ome.tiff'  --dfp 'exemplar-001-cycle-07_dfp.ome.tiff' 'exemplar-001-cycle-08_dfp.ome.tiff'     -o registered.ome.tif;  python3 '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/perssond/ashlar/0b8423c7ee3e/ashlar/rename_channels.py' --image registered.ome.tif --markers '/tmp/tmp_ttt6ywo/files/d/3/a/dataset_d3a3768b-b8b9-40cb-b8a5-eafc1257323b.dat';
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              WARNING: Stage coordinates' measurement unit is undefined; assuming μm.
WARNING: Stage coordinates' measurement unit is undefined; assuming μm.

              

              • 

            

            Standard Output:
            

              

            • 

              Stitching and registering input images
Cycle 0:
    reading /tmp/tmp_ttt6ywo/files/5/3/e/dataset_53ea439a-5a66-4fb1-8bb9-07786f487920.dat

    assembling thumbnail 1/6
    assembling thumbnail 2/6
    assembling thumbnail 3/6
    assembling thumbnail 4/6
    assembling thumbnail 5/6
    assembling thumbnail 6/6

    quantifying alignment error 10/90
    quantifying alignment error 20/90
    quantifying alignment error 30/90
    quantifying alignment error 40/90
    quantifying alignment error 50/90
    quantifying alignment error 60/90
    quantifying alignment error 70/90
    quantifying alignment error 80/90
    quantifying alignment error 90/90

    aligning edge 1/7
    aligning edge 2/7
    aligning edge 3/7
    aligning edge 4/7
    aligning edge 5/7
    aligning edge 6/7
    aligning edge 7/7
Cycle 1:
    reading /tmp/tmp_ttt6ywo/files/4/0/8/dataset_408a6437-a10a-45ce-9112-de53056c43d1.dat

    assembling thumbnail 1/6
    assembling thumbnail 2/6
    assembling thumbnail 3/6
    assembling thumbnail 4/6
    assembling thumbnail 5/6
    assembling thumbnail 6/6

    estimated cycle offset [y x] = [-1.0646154 -7.452307 ]

    aligning tile 1/6
    aligning tile 2/6
    aligning tile 3/6
    aligning tile 4/6
    aligning tile 5/6
    aligning tile 6/6

Merging tiles and writing to registered.ome.tif
Cycle 0:
    Channel 0:

        merging tile 1/6
        merging tile 2/6
        merging tile 3/6
        merging tile 4/6
        merging tile 5/6
        merging tile 6/6
    Channel 1:

        merging tile 1/6
        merging tile 2/6
        merging tile 3/6
        merging tile 4/6
        merging tile 5/6
        merging tile 6/6
    Channel 2:

        merging tile 1/6
        merging tile 2/6
        merging tile 3/6
        merging tile 4/6
        merging tile 5/6
        merging tile 6/6
    Channel 3:

        merging tile 1/6
        merging tile 2/6
        merging tile 3/6
        merging tile 4/6
        merging tile 5/6
        merging tile 6/6
Cycle 1:
    Channel 0:

        merging tile 1/6
        merging tile 2/6
        merging tile 3/6
        merging tile 4/6
        merging tile 5/6
        merging tile 6/6
    Channel 1:

        merging tile 1/6
        merging tile 2/6
        merging tile 3/6
        merging tile 4/6
        merging tile 5/6
        merging tile 6/6
    Channel 2:

        merging tile 1/6
        merging tile 2/6
        merging tile 3/6
        merging tile 4/6
        merging tile 5/6
        merging tile 6/6
    Channel 3:

        merging tile 1/6
        merging tile 2/6
        merging tile 3/6
        merging tile 4/6
        merging tile 5/6
        merging tile 6/6
Generating pyramid
    Level 1 (1255 x 1570)

        processing channel 1/8
        processing channel 2/8
        processing channel 3/8
        processing channel 4/8
        processing channel 5/8
        processing channel 6/8
        processing channel 7/8
        processing channel 8/8
    Level 2 (628 x 785)

        processing channel 1/8
        processing channel 2/8
        processing channel 3/8
        processing channel 4/8
        processing channel 5/8
        processing channel 6/8
        processing channel 7/8
        processing channel 8/8
Updated OME-TIFF metadata:
<?xml version='1.0' encoding='utf-8'?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd" UUID="urn:uuid:89ee4bba-049f-11f0-a3d0-0242ac110002" Creator="Ashlar v1.18.0"><Image ID="Image:0" Name="Image0"><Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint16" SizeX="2510" SizeY="3139" SizeC="8" SizeZ="1" SizeT="1" PhysicalSizeX="0.6499999761581421" PhysicalSizeXUnit="µm" PhysicalSizeY="0.6499999761581421" PhysicalSizeYUnit="µm"><Channel ID="Channel:0:0" SamplesPerPixel="1" Name="DNA_7"><LightPath /></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1" Name="CD11B"><LightPath /></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1" Name="SMA"><LightPath /></Channel><Channel ID="Channel:0:3" SamplesPerPixel="1" Name="CD16"><LightPath /></Channel><Channel ID="Channel:0:4" SamplesPerPixel="1" Name="DNA_8"><LightPath /></Channel><Channel ID="Channel:0:5" SamplesPerPixel="1" Name="ECAD"><LightPath /></Channel><Channel ID="Channel:0:6" SamplesPerPixel="1" Name="FOXP3"><LightPath /></Channel><Channel ID="Channel:0:7" SamplesPerPixel="1" Name="NCAM"><LightPath /></Channel><TiffData IFD="0" PlaneCount="8" /></Pixels></Image></OME>

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
adv
{"align_channel": "0", "filter_sigma": null, "flip_mosaic_x": false, "flip_mosaic_y": false, "stitch_alpha": null, "tile_size": null}

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
flip_x
false

              

              
flip_y
false

              

              
ldfp
{"values": [{"id": 2, "src": "hdca"}]}

              

              
lffp
{"values": [{"id": 3, "src": "hdca"}]}

              

              
lraw
{"values": [{"id": 1, "src": "hdca"}]}

              

              
max_shift
"30"

              

              
rename
{"__current_case__": 0, "decide": "do_rename", "markers_file": {"values": [{"id": 1, "src": "hda"}]}}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 6: TMA dearray with UNetCoreograph:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmp_ttt6ywo/files/e/d/f/dataset_edf97046-bbcd-468f-b7a2-c19f2047afe8.dat' 'image.ome.tiff' &&   UNET_PATH="" && if [ -f "/app/UNetCoreograph.py" ]; then export UNET_PATH="/app/UNetCoreograph.py"; else export UNET_PATH="/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/perssond/coreograph/ee92746d141a/coreograph/UNetCoreograph.py"; fi &&   python $UNET_PATH --imagePath 'image.ome.tiff' --downsampleFactor 5 --channel 0 --buffer 2.0 --sensitivity 0.3   --outputPath '.'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2025-03-19 08:54:06.857948: E tensorflow/stream_executor/cuda/cuda_driver.cc:318] failed call to cuInit: UNKNOWN ERROR (303)
/usr/local/lib/python3.6/dist-packages/skimage/transform/_warps.py:105: UserWarning: The default mode, 'constant', will be changed to 'reflect' in skimage 0.15.
  warn("The default mode, 'constant', will be changed to 'reflect' in "
/usr/local/lib/python3.6/dist-packages/skimage/transform/_warps.py:110: UserWarning: Anti-aliasing will be enabled by default in skimage 0.15 to avoid aliasing artifacts when down-sampling images.
  warn("Anti-aliasing will be enabled by default in skimage 0.15 to "
/usr/local/lib/python3.6/dist-packages/skimage/external/tifffile/tifffile.py:444: UserWarning: writing incompatible bigtiff ImageJ
  warnings.warn("writing incompatible bigtiff ImageJ")
/usr/local/lib/python3.6/dist-packages/skimage/io/_io.py:140: UserWarning: ./masks/1_mask.tif is a low contrast image
  warn('%s is a low contrast image' % fname)

              

              • 

            

            Standard Output:
            

              

            • 

              WARNING! IF USING FOR TISSUE SPLITTING, IT IS ADVISED TO SET --downsampleFactor TO HIGHER THAN DEFAULT OF 5
loading data
loading data
loading data
0.09
0.09
Model restored.
Inference...
TMA mode selected
1 cores detected!
Segmented core/tissue 1
Segmented all cores/tissues!

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
buffer
"2.0"

              

              
channel
"0"

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
cluster
false

              

              
dbkey
"?"

              

              
downsamplefactor
"5"

              

              
sensitivity
"0.3"

              

              
tissue
false

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 7: Nuclear segmentation:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              python /tmp/tmp_ttt6ywo/job_working_directory/000/9/configs/tmptxfbhh08
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2025-03-19 08:55:14.041516: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/lib/python3.8/dist-packages/cv2/../../lib64:
2025-03-19 08:55:14.041555: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
2025-03-19 08:55:20.299722: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/lib/python3.8/dist-packages/cv2/../../lib64:
2025-03-19 08:55:20.299773: W tensorflow/stream_executor/cuda/cuda_driver.cc:269] failed call to cuInit: UNKNOWN ERROR (303)
2025-03-19 08:55:20.299809: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (b26120a15f44): /proc/driver/nvidia/version does not exist
2025-03-19 08:55:20.300101: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.
WARNING:root:Found constant value array in batch 0 and channel 1. Normalizing as zeros.
2025-03-19 08:55:36.132620: W tensorflow/core/framework/cpu_allocator_impl.cc:82] Allocation of 67108864 exceeds 10% of free system memory.
2025-03-19 08:55:36.216663: W tensorflow/core/framework/cpu_allocator_impl.cc:82] Allocation of 67108864 exceeds 10% of free system memory.
2025-03-19 08:55:36.317116: W tensorflow/core/framework/cpu_allocator_impl.cc:82] Allocation of 67108864 exceeds 10% of free system memory.
2025-03-19 08:55:36.402862: W tensorflow/core/framework/cpu_allocator_impl.cc:82] Allocation of 67108864 exceeds 10% of free system memory.
2025-03-19 08:55:36.431012: W tensorflow/core/framework/cpu_allocator_impl.cc:82] Allocation of 134217728 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/deepcell_toolbox/deep_watershed.py:179: FutureWarning: `selem` is a deprecated argument name for `h_maxima`. It will be removed in version 1.0. Please use `footprint` instead.
  markers = h_maxima(image=maxima,
/tmp/tmp_ttt6ywo/job_working_directory/000/9/configs/tmptxfbhh08:56: DeprecationWarning: <tifffile.imsave> is deprecated. Use tifffile.imwrite
  tifffile.imsave("mask.tif", mask)

              

              • 

            

            Standard Output:
            

              

            • 

              Downloading data from https://deepcell-data.s3-us-west-1.amazonaws.com/saved-models/MultiplexSegmentation-9.tar.gz

   16384/96885295 [..............................] - ETA: 0s������������������������������������������������������������
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  180224/96885295 [..............................] - ETA: 1:48��������������������������������������������������������������
  409600/96885295 [..............................] - ETA: 1:03��������������������������������������������������������������
  843776/96885295 [..............................] - ETA: 38s �������������������������������������������������������������
 1712128/96885295 [..............................] - ETA: 22s�������������������������������������������������������������
 3457024/96885295 [>.............................] - ETA: 12s�������������������������������������������������������������
 6963200/96885295 [=>............................] - ETA: 6s ������������������������������������������������������������
 9879552/96885295 [==>...........................] - ETA: 5s������������������������������������������������������������
13336576/96885295 [===>..........................] - ETA: 4s������������������������������������������������������������
17170432/96885295 [====>.........................] - ETA: 3s������������������������������������������������������������
20758528/96885295 [=====>........................] - ETA: 2s������������������������������������������������������������
23265280/96885295 [======>.......................] - ETA: 2s������������������������������������������������������������
26591232/96885295 [=======>......................] - ETA: 2s������������������������������������������������������������
30162944/96885295 [========>.....................] - ETA: 2s������������������������������������������������������������
33734656/96885295 [=========>....................] - ETA: 2s������������������������������������������������������������
37601280/96885295 [==========>...................] - ETA: 1s������������������������������������������������������������
41156608/96885295 [===========>..................] - ETA: 1s������������������������������������������������������������
43876352/96885295 [============>.................] - ETA: 1s������������������������������������������������������������
47546368/96885295 [=============>................] - ETA: 1s������������������������������������������������������������
51249152/96885295 [==============>...............] - ETA: 1s������������������������������������������������������������
54919168/96885295 [================>.............] - ETA: 1s������������������������������������������������������������
58589184/96885295 [=================>............] - ETA: 1s������������������������������������������������������������
61325312/96885295 [=================>............] - ETA: 0s������������������������������������������������������������
64372736/96885295 [==================>...........] - ETA: 0s������������������������������������������������������������
67174400/96885295 [===================>..........] - ETA: 0s������������������������������������������������������������
71024640/96885295 [====================>.........] - ETA: 0s������������������������������������������������������������
74924032/96885295 [======================>.......] - ETA: 0s������������������������������������������������������������
78249984/96885295 [=======================>......] - ETA: 0s������������������������������������������������������������
82083840/96885295 [========================>.....] - ETA: 0s������������������������������������������������������������
85901312/96885295 [=========================>....] - ETA: 0s������������������������������������������������������������
88801280/96885295 [==========================>...] - ETA: 0s������������������������������������������������������������
91635712/96885295 [===========================>..] - ETA: 0s������������������������������������������������������������
95567872/96885295 [============================>.] - ETA: 0s������������������������������������������������������������
96886784/96885295 [==============================] - 2s 0us/step
����������������������������������������������������������������
96894976/96885295 [==============================] - 2s 0us/step

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
compartment_select
{"__current_case__": 0, "compartment": "nuclear", "nuclear_options": {"adv_options": {"fill_holes_threshold": "15", "interior_smooth": "2", "interior_threshold": "0.2", "maxima_smooth": "0", "radius": "1", "small_objects_threshold": "15"}, "maxima_threshold": "0.1", "pixel_expansion": null}}

              

              
dbkey
"?"

              

              
image_mpp
"0.65"

              

              
nuclear_channels
"0"

              

              
squeeze
true

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 8: Convert dearray images to OME-TIFF:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              bfconvert -tilex 512 -tiley 512 -pyramid-resolutions 4 -pyramid-scale 2  -noflat '/tmp/tmp_ttt6ywo/files/5/0/7/dataset_507ee8ed-8cc2-4336-a6ce-d781849ae578.dat' './res.ome.tiff' && mv './res.ome.tiff' ./result_image
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              /tmp/tmp_ttt6ywo/files/5/0/7/dataset_507ee8ed-8cc2-4336-a6ce-d781849ae578.dat
TiffDelegateReader initializing /tmp/tmp_ttt6ywo/files/5/0/7/dataset_507ee8ed-8cc2-4336-a6ce-d781849ae578.dat
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
[Tagged Image File Format] -> ./res.ome.tiff [OME-TIFF]
Tile size = 512 x 512
	Converted 2/8 planes (25%)
	Converted 6/8 planes (75%)
	Converted 8/8 planes (100%)
Tile size = 512 x 512
	Converted 7/8 planes (87%)
	Converted 8/8 planes (100%)
Tile size = 512 x 512
	Converted 8/8 planes (100%)
Tile size = 313 x 330
	Converted 8/8 planes (100%)
[done]
6.413s elapsed (23.21875+144.78125ms per plane, 779ms overhead)

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
bigtiff
false

              

              
channel_options
{"__current_case__": 0, "extract": "False"}

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
compression
"False"

              

              
crop_options
{"__current_case__": 0, "extract": "False"}

              

              
dbkey
"?"

              

              
noflat
true

              

              
out_format
"ome.tiff"

              

              
pyramid_options
{"__current_case__": 0, "generate": "True", "pyramid_resolutions": "4", "pyramid_scale": "2"}

              

              
range_options
{"__current_case__": 0, "extract": "False"}

              

              
series_options
{"__current_case__": 0, "extract": "False"}

              

              
tile_options
{"__current_case__": 1, "extract": "True", "tile_x": "512", "tile_y": "512"}

              

              
timepoint_options
{"__current_case__": 0, "extract": "False"}

              

              
z_options
{"__current_case__": 0, "extract": "False"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 9: Cell feature quantification with MC-Quant:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmp_ttt6ywo/files/5/0/7/dataset_507ee8ed-8cc2-4336-a6ce-d781849ae578.dat' 'input.ome.tiff' && ln -s '/tmp/tmp_ttt6ywo/files/7/f/d/dataset_7fd9e39a-e760-40d2-bf06-5838710303c8.dat' 'primary_mask.tiff' &&  mkdir './tool_out' &&  mcquant  --masks 'primary_mask.tiff'  --image 'input.ome.tiff' --output './tool_out'   --channel_names '/tmp/tmp_ttt6ywo/files/d/3/a/dataset_d3a3768b-b8b9-40cb-b8a5-eafc1257323b.dat' &&   mv tool_out/*primary_mask.csv primary_mask.csv
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              {'masks': ['primary_mask.tiff'], 'image': 'input.ome.tiff', 'channel_names': '/tmp/tmp_ttt6ywo/files/d/3/a/dataset_d3a3768b-b8b9-40cb-b8a5-eafc1257323b.dat', 'output': './tool_out', 'intensity_props': {'intensity_mean'}, 'mask_props': None}
Extracting single-cell data for input.ome.tiff...
Finished 0
Finished 1
Finished 2
Finished 3
Finished 4
Finished 5
Finished 6
Finished 7
Finished input

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
intensity_props
""

              

              
mask_props
""

              

              
supp_mask
None

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 10: Rename OME-TIFF channels:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cp '/tmp/tmp_ttt6ywo/files/3/b/b/dataset_3bbb036f-43e2-43e4-bebf-de9a3131bc58.dat' ./renamed_image.ome.tiff &&  ln -s '/tmp/tmp_ttt6ywo/files/d/3/a/dataset_d3a3768b-b8b9-40cb-b8a5-eafc1257323b.dat' ./channels.csv &&  python '/tmp/tmp_ttt6ywo/job_working_directory/000/12/configs/tmpfuj_w0ij'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              Channel 0 renamed to DNA_7
Channel 1 renamed to CD11B
Channel 2 renamed to SMA
Channel 3 renamed to CD16
Channel 4 renamed to DNA_8
Channel 5 renamed to ECAD
Channel 6 renamed to FOXP3
Channel 7 renamed to NCAM
Updated OME-TIFF metadata:
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd" UUID="urn:uuid:be361998-79ec-421d-a2f1-49397b426d5a" Creator="OME Bio-Formats 6.7.0">
  <Image ID="Image:0" Name="dataset_507ee8ed-8cc2-4336-a6ce-d781849ae578.dat">
    <AcquisitionDate>2025-03-19T08:54:11</AcquisitionDate>
    <Description/>
    <Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="2508" SizeY="2646" SizeZ="1" SizeC="8" SizeT="1">
      <Channel ID="Channel:0:0" Name="DNA_7" SamplesPerPixel="1" Color="65535">
        <LightPath/>
      </Channel>
      <Channel ID="Channel:0:1" Name="CD11B" SamplesPerPixel="1" Color="16711935">
        <LightPath/>
      </Channel>
      <Channel ID="Channel:0:2" Name="SMA" SamplesPerPixel="1" Color="-16711681">
        <LightPath/>
      </Channel>
      <Channel ID="Channel:0:3" Name="CD16" SamplesPerPixel="1" Color="-65281">
        <LightPath/>
      </Channel>
      <Channel ID="Channel:0:4" Name="DNA_8" SamplesPerPixel="1" Color="-8453889">
        <LightPath/>
      </Channel>
      <Channel ID="Channel:0:5" Name="ECAD" SamplesPerPixel="1" Color="16777215">
        <LightPath/>
      </Channel>
      <Channel ID="Channel:0:6" Name="FOXP3" SamplesPerPixel="1" Color="-1">
        <LightPath/>
      </Channel>
      <Channel ID="Channel:0:7" Name="NCAM" SamplesPerPixel="1" Color="-16776961">
        <LightPath/>
      </Channel>
      <TiffData IFD="0" FirstZ="0" FirstT="0" FirstC="0" PlaneCount="1">
        <UUID FileName="res.ome.tiff">urn:uuid:be361998-79ec-421d-a2f1-49397b426d5a</UUID>
      </TiffData>
      <TiffData IFD="1" FirstZ="0" FirstT="0" FirstC="1" PlaneCount="1">
        <UUID FileName="res.ome.tiff">urn:uuid:be361998-79ec-421d-a2f1-49397b426d5a</UUID>
      </TiffData>
      <TiffData IFD="2" FirstZ="0" FirstT="0" FirstC="2" PlaneCount="1">
        <UUID FileName="res.ome.tiff">urn:uuid:be361998-79ec-421d-a2f1-49397b426d5a</UUID>
      </TiffData>
      <TiffData IFD="3" FirstZ="0" FirstT="0" FirstC="3" PlaneCount="1">
        <UUID FileName="res.ome.tiff">urn:uuid:be361998-79ec-421d-a2f1-49397b426d5a</UUID>
      </TiffData>
      <TiffData IFD="4" FirstZ="0" FirstT="0" FirstC="4" PlaneCount="1">
        <UUID FileName="res.ome.tiff">urn:uuid:be361998-79ec-421d-a2f1-49397b426d5a</UUID>
      </TiffData>
      <TiffData IFD="5" FirstZ="0" FirstT="0" FirstC="5" PlaneCount="1">
        <UUID FileName="res.ome.tiff">urn:uuid:be361998-79ec-421d-a2f1-49397b426d5a</UUID>
      </TiffData>
      <TiffData IFD="6" FirstZ="0" FirstT="0" FirstC="6" PlaneCount="1">
        <UUID FileName="res.ome.tiff">urn:uuid:be361998-79ec-421d-a2f1-49397b426d5a</UUID>
      </TiffData>
      <TiffData IFD="7" FirstZ="0" FirstT="0" FirstC="7" PlaneCount="1">
        <UUID FileName="res.ome.tiff">urn:uuid:be361998-79ec-421d-a2f1-49397b426d5a</UUID>
      </TiffData>
    </Pixels>
  </Image>
  <StructuredAnnotations>
    <XMLAnnotation ID="Annotation:0" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>hyperstack</Key>
          <Value>true</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:1" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>DateTime</Key>
          <Value>2025:03:19 08:54:11</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:2" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>MetaDataPhotometricInterpretation</Key>
          <Value>Monochrome</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:3" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>NewSubfileType</Key>
          <Value>0</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:4" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>SamplesPerPixel</Key>
          <Value>1</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:5" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>NumberOfChannels</Key>
          <Value>1</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:6" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>ImageJ</Key>
          <Value>1.11a</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:7" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>ImageWidth</Key>
          <Value>2508</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:8" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>PhotometricInterpretation</Key>
          <Value>BlackIsZero</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:9" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>Software</Key>
          <Value>tifffile.py</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:10" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>Compression</Key>
          <Value>Uncompressed</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:11" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>MetaMorph</Key>
          <Value>no</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:12" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>SampleFormat</Key>
          <Value>unsigned integer</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:13" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>BitsPerSample</Key>
          <Value>16</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:14" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>ImageLength</Key>
          <Value>2646</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <XMLAnnotation ID="Annotation:15" Namespace="openmicroscopy.org/OriginalMetadata">
      <Value>
        <OriginalMetadata>
          <Key>Color mode</Key>
          <Value>grayscale</Value>
        </OriginalMetadata>
      </Value>
    </XMLAnnotation>
    <MapAnnotation ID="Annotation:Resolution:0" Namespace="openmicroscopy.org/PyramidResolution">
      <Value>
        <M K="1">1254 1323</M>
        <M K="2">627 661</M>
        <M K="3">313 330</M>
      </Value>
    </MapAnnotation>
  </StructuredAnnotations>
</OME>

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"53ad9966049f11f08a577c1e52430338"

              

              
chromInfo
"/tmp/tmp_ttt6ywo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      
 
      

      • 

    • 

      Other invocation details

        

      • 

        history_id
        

          

        • 0c61d4b6f10a99f9
          • 

        

        • 

      • 

        history_state
        

          

        • ok
          • 

        

        • 

      • 

        invocation_id
        

          

        • 0c61d4b6f10a99f9
          • 

        

        • 

      • 

        invocation_state
        

          

        • scheduled
          • 

        

        • 

      • 

        workflow_id
        

          

        • 0c61d4b6f10a99f9
          • 

        

        • 

      

      

      • 

    
  
    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    
















  
  

    

      

  




      

    


    

      

              

  
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