Add PHI toolkit

[bernt-matthias]

Wondering if there is an easier way to filter a FASTA collection by number of sequences (remove every element containing less than 2 sequences) ..

TODO:

• use same test assertions as in PHI TK report tool

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

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ PHI-Toolkit.ga_0

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Input Dataset Collection:

      • step_state: scheduled

    • Step 2: Set number of genomes for filter:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "2", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 11: Unlabelled step:

      • step_state: new

    • Step 12: Unlabelled step:

      • step_state: new

    • Step 13: Unlabelled step:

      • step_state: new

    • Step 14: Unlabelled step:

      • step_state: new

    • Step 15: Unlabelled step:

      • step_state: new

    • Step 16: Unlabelled step:

      • step_state: new

    • Step 17: Unlabelled step:

      • step_state: new

    • Step 3: toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • mkdir input_dir && ln -s '/tmp/tmp3ub897g_/files/9/7/5/dataset_975735c7-49fc-4aef-8334-1d06b7725c36.dat' 'input_dir/NC_021184.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/6/a/7/dataset_6a7e19c4-e892-49ef-90c6-22b8fd3403ad.dat' 'input_dir/NC_019936.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/4/4/e/dataset_44ed7b54-8083-404a-920a-a2d4bb2044c3.dat' 'input_dir/NC_019904.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/a/d/0/dataset_ad08cf08-c912-4662-8003-f53806e1b925.dat' 'input_dir/NC_019897.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/e/8/b/dataset_e8ba7c4a-bc15-46b9-84b5-f4c99483d1ea.dat' 'input_dir/NC_018515.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/0/6/f/dataset_06fe3ae6-357a-4f47-ad08-3724bfe53f2b.dat' 'input_dir/NC_018068.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/e/1/4/dataset_e1473661-98e5-45e8-8f54-c96c5ec608b9.dat' 'input_dir/NC_018014.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/2/b/5/dataset_2b55fb91-bae4-42a5-a163-37bea274c8ec.dat' 'input_dir/NC_017095.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/3/6/b/dataset_36b4ca3f-3279-41fa-94db-9ed232bd1189.dat' 'input_dir/NC_017033.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/5/3/7/dataset_53742bf9-decd-4436-aa88-ac8bd2ece65e.dat' 'input_dir/NC_015761.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/1/0/e/dataset_10ea4989-70c6-4aaf-9bfc-51335bb5bf61.dat' 'input_dir/NC_014364.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/c/9/6/dataset_c965affe-42cc-4965-8ab4-0028346c8b9a.dat' 'input_dir/NC_014363.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/b/c/c/dataset_bcc6bd02-6e2c-42da-81b2-75304de28caf.dat' 'input_dir/NC_014212.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/f/0/8/dataset_f08dd5e9-b0cc-479f-938f-414612bf25da.dat' 'input_dir/NC_014211.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/e/1/8/dataset_e18da9a4-3d23-4c08-b1a9-ecaed7499588.dat' 'input_dir/NC_014168.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/8/9/d/dataset_89dbce43-bfb8-4ba3-b935-b06cd1136486.dat' 'input_dir/NC_014008.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/0/4/6/dataset_0464041b-8ba0-415e-9ee4-693f6c3a66e0.dat' 'input_dir/NC_012982.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/3/8/c/dataset_38cab97e-59bb-494a-8814-f5d4e285436b.dat' 'input_dir/NC_009012.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/e/e/c/dataset_eec04662-8263-46e8-b964-22a21a51b49a.dat' 'input_dir/NC_008261.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/c/b/c/dataset_cbcc34cf-3057-4fb5-9aa6-31fc35bf504c.dat' 'input_dir/NC_003450.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/9/7/4/dataset_974bb1dc-b5df-46a2-beb2-ee1e2baeeae6.dat' 'input_dir/NC_002737.fasta.dat' && ln -s '/tmp/tmp3ub897g_/files/b/7/5/dataset_b75db64b-b151-4ae9-bb38-1eee1fb7694e.dat' 'input_dir/NC_000913.fasta.dat' && checkm2 predict --input input_dir   -x .dat --threads "${GALAXY_SLOTS:-1}" --database_path '/cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd' --output-directory output

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"1.0.2"
            dbkey	"?"
            genes	false
            model	""
            ttable	None

    • Step 4: toolshed.g2.bx.psu.edu/repos/ufz/genomad_end_to_end/genomad_end_to_end/1.11.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 2:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 3:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 4:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 5:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 6:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 7:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 8:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 9:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 10:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 11:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 12:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 13:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 14:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 15:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 16:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 17:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 18:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 19:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 20:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 21:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 22:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

    • Step 5: toolshed.g2.bx.psu.edu/repos/rplanel/defense_finder/defense_finder/2.0.1+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 2:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 3:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 4:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 5:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 6:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 7:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 8:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 9:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 10:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 11:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 12:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 13:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 14:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 15:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 16:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 17:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 18:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 19:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 20:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 21:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 22:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

    • Step 6: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.4.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"82c3ef065cb611f0b8940022480b0d2d"
            advanced	{"force": false, "min_af": "0.65", "min_perc_aa": "10", "output_process_log": false}
            chromInfo	"/tmp/tmp3ub897g_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            gtdbtk_db	"full_database_release_220_downloaded_2024-10-19"

    • Step 7: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 8: Unlabelled step:

      • step_state: new

    • Step 9: Unlabelled step:

      • step_state: new

    • Step 10: Unlabelled step:

      • step_state: new
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • 96bc5d92be274cd6

    • history_state

      • ok

    • invocation_id

      • 96bc5d92be274cd6

    • invocation_state

      • failed

    • workflow_id

      • 110896a00597b1a0

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ PHI-Toolkit.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '11' (Host contigs) is not optional and no input provided.","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ PHI-Toolkit.ga_0

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Host contigs:

      • step_state: scheduled

    • Step 2: GTDB-Tk database:

      • step_state: scheduled

    • Step 11: Unlabelled step:

      • step_state: new

    • Step 12: Unlabelled step:

      • step_state: new

    • Step 13: Unlabelled step:

      • step_state: new

    • Step 14: Unlabelled step:

      • step_state: new

    • Step 15: Unlabelled step:

      • step_state: new

    • Step 16: Unlabelled step:

      • step_state: new

    • Step 17: Unlabelled step:

      • step_state: new

    • Step 18: Unlabelled step:

      • step_state: new

    • Step 3: Set number of genomes for filter:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "2", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • mkdir input_dir && ln -s '/tmp/tmp16c455h1/files/6/f/e/dataset_6fe73613-106f-4655-bd34-17343b1f579a.dat' 'input_dir/NC_021184.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/a/9/3/dataset_a93867e0-c425-4b61-9ac3-3bf3229cd85d.dat' 'input_dir/NC_019936.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/b/3/3/dataset_b33183c2-432f-40af-a61f-2d4ac0072be1.dat' 'input_dir/NC_019904.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/4/9/a/dataset_49a66070-f77a-4268-949a-75068ab2f57b.dat' 'input_dir/NC_019897.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/4/e/1/dataset_4e1b90c6-084c-4d27-acf9-0fcefecd9b4d.dat' 'input_dir/NC_018515.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/c/4/9/dataset_c4924d6a-5dad-48d7-b138-b8316c9d7889.dat' 'input_dir/NC_018068.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/5/b/5/dataset_5b51ef01-d531-47d0-88e2-6e26e630f77f.dat' 'input_dir/NC_018014.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/6/6/1/dataset_6614162b-6d9d-4b1a-8902-d32288e97282.dat' 'input_dir/NC_017095.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/e/5/7/dataset_e57aef8c-a167-4e68-89e4-0c55ab412827.dat' 'input_dir/NC_017033.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/d/4/a/dataset_d4a68419-e8c5-4a40-ae0e-0966c1fec1d1.dat' 'input_dir/NC_015761.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/7/1/7/dataset_7176a9c4-58ee-4923-9fb5-83199d67a152.dat' 'input_dir/NC_014364.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/b/5/6/dataset_b56c9fb7-0027-4326-b75a-cb8ae571d5a5.dat' 'input_dir/NC_014363.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/d/4/9/dataset_d491ea4b-260a-476e-9599-e3aa42d4b6e4.dat' 'input_dir/NC_014212.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/3/3/4/dataset_334f79b5-b370-4177-81cb-02df886cff9d.dat' 'input_dir/NC_014211.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/d/e/a/dataset_dea4a99f-2650-4436-a79d-e57938668b9e.dat' 'input_dir/NC_014168.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/a/c/0/dataset_ac01ac42-7d2c-457c-a647-30747ce87018.dat' 'input_dir/NC_014008.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/2/f/c/dataset_2fcd964e-e235-4630-881e-df6413abb963.dat' 'input_dir/NC_012982.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/4/5/9/dataset_4597789e-4759-4db3-89e2-f89123dfd5d0.dat' 'input_dir/NC_009012.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/3/a/6/dataset_3a6e8ec3-fd4d-4935-bf3f-054b07a7bcd8.dat' 'input_dir/NC_008261.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/5/2/6/dataset_52600b57-c1ac-4312-8647-b54173029e78.dat' 'input_dir/NC_003450.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/5/2/5/dataset_525b986a-41b5-4ce0-8e49-0f69ab81fedf.dat' 'input_dir/NC_002737.fasta.dat' && ln -s '/tmp/tmp16c455h1/files/8/a/6/dataset_8a6dee0b-aff2-4867-a172-d76018fd2acf.dat' 'input_dir/NC_000913.fasta.dat' && checkm2 predict --input input_dir   -x .dat --threads "${GALAXY_SLOTS:-1}" --database_path '/cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd' --output-directory output

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"1.0.2"
            dbkey	"?"
            genes	false
            model	""
            ttable	None

    • Step 5: toolshed.g2.bx.psu.edu/repos/ufz/genomad_end_to_end/genomad_end_to_end/1.11.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 2:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 3:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 4:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 5:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 6:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 7:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 8:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 9:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 10:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 11:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 12:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 13:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 14:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 15:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 16:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 17:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 18:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 19:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 20:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 21:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 22:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

    • Step 6: toolshed.g2.bx.psu.edu/repos/rplanel/defense_finder/defense_finder/2.0.1+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 2:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 3:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 4:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 5:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 6:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 7:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 8:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 9:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 10:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 11:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 12:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 13:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 14:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 15:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 16:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 17:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 18:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 19:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 20:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 21:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 22:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

    • Step 7: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.4.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"5ea8e7845cbb11f0b894000d3a62b9ca"
            advanced	{"force": false, "min_af": "0.65", "min_perc_aa": "10", "output_process_log": false}
            chromInfo	"/tmp/tmp16c455h1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            gtdbtk_db	"Full Database - Release 220 (2024-10-19)"

    • Step 8: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 9: Unlabelled step:

      • step_state: new

    • Step 10: Unlabelled step:

      • step_state: new
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • 23fb5df36b250bb3

    • history_state

      • ok

    • invocation_id

      • 23fb5df36b250bb3

    • invocation_state

      • failed

    • workflow_id

      • 878535936693cd04

[mvdbeek]

genomad_end_to_end

do we need reference data for this ?

[bernt-matthias]

Almost all tools in this workflow need reference data. Seems that currently the following reference data is missing:

• genomad_end_to_end needs v1.9 of the reference data. seems not installed on org
• checkv v1.5 is needed
• vibrant v1.2.1

Oddly I can not find the checkv tool on org.

[mvdbeek]

Almost all tools in this workflow need reference data. Seems that currently the following reference data is missing:

• genomad_end_to_end needs v1.9 of the reference data. seems not installed on org
• checkv v1.5 is needed
• vibrant v1.2.1

Oddly I can not find the checkv tool on org.

Why's that odd ? But also https://usegalaxy.org/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fufz%2Fcheckv_end_to_end%2Fcheckv_end_to_end%2F1.0.3%2Bgalaxy0&version=latest ?

[mvdbeek]

The reference data is also not on usegalaxy.eu, where we usually copy it from. Do you have some links handy I could use ?

[bernt-matthias]

Why's that odd ?

Searching with checkv gives no results.

Do you have some links handy I could use ?

All should have data_managers. Should I open a PR to get them installed?

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ PHI-Toolkit.ga_0

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Host contigs:

      • step_state: scheduled

    • Step 2: GTDB-Tk database:

      • step_state: scheduled

    • Step 11: Unlabelled step:

      • step_state: new

    • Step 12: Unlabelled step:

      • step_state: new

    • Step 13: Unlabelled step:

      • step_state: new

    • Step 14: Unlabelled step:

      • step_state: new

    • Step 15: Unlabelled step:

      • step_state: new

    • Step 16: Unlabelled step:

      • step_state: new

    • Step 17: Unlabelled step:

      • step_state: new

    • Step 18: Unlabelled step:

      • step_state: new

    • Step 19: Unlabelled step:

      • step_state: new

    • Step 3: Agree with genomad license:

      • step_state: scheduled

    • Step 4: Set number of genomes for filter:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "2", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 5: toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • mkdir input_dir && ln -s '/tmp/tmph2ms_n4t/files/a/0/a/dataset_a0a7fd9a-d169-4efa-a022-b9993cf1cc4f.dat' 'input_dir/NC_021184.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/0/5/8/dataset_0580a55a-caf8-4421-9b64-4a93f729d184.dat' 'input_dir/NC_019936.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/2/d/3/dataset_2d38c145-982e-499a-8ade-0c8de23480ce.dat' 'input_dir/NC_019904.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/6/3/2/dataset_6324749e-145f-4186-9e83-12d4deb3105e.dat' 'input_dir/NC_019897.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/4/1/0/dataset_410ffdb5-14f5-438f-8223-b94f9d6eaf4d.dat' 'input_dir/NC_018515.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/d/7/9/dataset_d79402f6-feb5-49de-ae3e-1c073b7135fa.dat' 'input_dir/NC_018068.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/1/3/6/dataset_1360c1ca-effe-4b3e-97be-74244bdbc756.dat' 'input_dir/NC_018014.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/8/7/7/dataset_8770ff67-c8e6-4a8e-8479-0671826c5a22.dat' 'input_dir/NC_017095.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/a/8/3/dataset_a83a9bfa-32a0-4145-b42a-8099caf10e3b.dat' 'input_dir/NC_017033.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/b/8/8/dataset_b88c7847-c3f8-4bba-a772-33947618aee2.dat' 'input_dir/NC_015761.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/7/c/5/dataset_7c5a953d-932f-4f82-94a5-145004accdea.dat' 'input_dir/NC_014364.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/1/e/d/dataset_1eda79f5-cc1f-4fc2-b8d1-28f5de3e247b.dat' 'input_dir/NC_014363.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/d/b/7/dataset_db7912df-afb9-439c-a426-ee13148a325a.dat' 'input_dir/NC_014212.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/9/5/d/dataset_95d7234d-c17e-47ba-8e2d-b047e629c6fa.dat' 'input_dir/NC_014211.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/8/5/8/dataset_858a0fe5-df30-4522-a4d9-dcf80033de62.dat' 'input_dir/NC_014168.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/6/7/1/dataset_671b73ee-ca4e-42e3-8d55-6e842b2ef161.dat' 'input_dir/NC_014008.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/c/e/7/dataset_ce76a0ed-68e6-4761-9e6c-301cf2832fd0.dat' 'input_dir/NC_012982.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/a/a/d/dataset_aad523b0-ebd1-450c-b40c-5d294b58f947.dat' 'input_dir/NC_009012.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/f/5/7/dataset_f57faa9f-0b0e-43a5-875a-475a33d2607a.dat' 'input_dir/NC_008261.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/a/0/e/dataset_a0ec4909-f9d0-4fa3-aa24-aec2eca8bace.dat' 'input_dir/NC_003450.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/b/e/1/dataset_be1fce61-c7ea-424d-ba0d-589f0d48d2e5.dat' 'input_dir/NC_002737.fasta.dat' && ln -s '/tmp/tmph2ms_n4t/files/e/f/1/dataset_ef1b956e-a4dd-4cd0-bba8-6fe15a1367b8.dat' 'input_dir/NC_000913.fasta.dat' && checkm2 predict --input input_dir   -x .dat --threads "${GALAXY_SLOTS:-1}" --database_path '/cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd' --output-directory output

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"1.0.2"
            dbkey	"?"
            genes	false
            model	""
            ttable	None

    • Step 6: toolshed.g2.bx.psu.edu/repos/rplanel/defense_finder/defense_finder/2.0.1+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 2:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 3:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 4:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 5:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 6:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 7:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 8:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 9:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 10:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 11:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 12:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 13:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 14:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 15:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 16:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 17:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 18:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 19:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 20:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 21:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 22:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

    • Step 7: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.4.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            advanced	{"force": false, "min_af": "0.65", "min_perc_aa": "10", "output_process_log": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            gtdbtk_db	"Full Database - Release 220 (2024-10-19)"

    • Step 8: toolshed.g2.bx.psu.edu/repos/ufz/genomad_end_to_end/genomad_end_to_end/1.11.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 2:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 3:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 4:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 5:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 6:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 7:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 8:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 9:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 10:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 11:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 12:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 13:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 14:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 15:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 16:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 17:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 18:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 19:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 20:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 21:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 22:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"3b9b79c863fa11f08b81000d3a5599da"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmph2ms_n4t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

    • Step 9: Unlabelled step:

      • step_state: new

    • Step 10: Unlabelled step:

      • step_state: new

      • Subworkflow Steps
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • 574c516178e1ab1d

    • history_state

      • ok

    • invocation_id

      • 574c516178e1ab1d

    • invocation_state

      • failed

    • workflow_id

      • 13fafe75ada04076

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ PHI-Toolkit.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/ufz/phi_toolkit_report/phi_toolkit_report/0.2.0+galaxy0 (version 0.1.0+galaxy0)","err_code":0}
    

[bernt-matthias]

Missing reference data:

• checkv
• iphop
• vibrant

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ PHI-Toolkit.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/ufz/phi_toolkit_report/phi_toolkit_report/0.2.0+galaxy0 (version 0.1.0+galaxy0)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ PHI-Toolkit.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/ufz/phi_toolkit_report/phi_toolkit_report/0.2.0+galaxy0 (version 0.1.0+galaxy0)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ PHI-Toolkit.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/ufz/phi_toolkit_report/phi_toolkit_report/0.2.0+galaxy0 (version 0.1.0+galaxy0)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ PHI-Toolkit.ga_0

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because step 9 requires a dataset collection created by step 7, but dataset collection entered a failed state.
  • Steps

    • Step 1: Host contigs:

      • step_state: scheduled

    • Step 2: GTDB-Tk database:

      • step_state: scheduled

    • Step 11: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 12: Unlabelled step:

      • step_state: new

    • Step 13: Unlabelled step:

      • step_state: new

    • Step 14: Unlabelled step:

      • step_state: new

    • Step 15: Unlabelled step:

      • step_state: new

    • Step 16: Unlabelled step:

      • step_state: new

    • Step 17: Unlabelled step:

      • step_state: new

    • Step 18: Unlabelled step:

      • step_state: new

    • Step 19: Unlabelled step:

      • step_state: new

    • Step 3: Agree with genomad license:

      • step_state: scheduled

    • Step 4: Set number of genomes for filter:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "2", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 5: toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • mkdir input_dir && ln -s '/tmp/tmp1h1ev9pa/files/3/1/b/dataset_31b2d17e-f81f-4d24-996c-0d03c031696b.dat' 'input_dir/NC_021184.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/a/f/a/dataset_afabf307-2439-4a06-9633-483969688edf.dat' 'input_dir/NC_019936.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/5/2/c/dataset_52c4cccc-7dee-4f0a-a0ae-18d35e87244b.dat' 'input_dir/NC_019904.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/8/e/e/dataset_8ee31938-dd4f-4e3e-93b4-d49e6d5453a8.dat' 'input_dir/NC_019897.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/7/c/0/dataset_7c0f1acc-c9fb-42b1-ab88-23a805a35da7.dat' 'input_dir/NC_018515.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/b/8/7/dataset_b8791d29-7c08-48e9-83a8-6c7f3edc230a.dat' 'input_dir/NC_018068.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/0/b/c/dataset_0bcd0156-b7e3-4708-b01f-41da8ec3268d.dat' 'input_dir/NC_018014.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/7/6/6/dataset_7660e47e-7858-45b1-b557-b5470e6251a1.dat' 'input_dir/NC_017095.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/4/e/5/dataset_4e583833-d5c3-4249-bdfe-174b500583bc.dat' 'input_dir/NC_017033.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/4/e/a/dataset_4eaa24e6-7056-4c27-9235-f0d4d5e883df.dat' 'input_dir/NC_015761.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/7/f/5/dataset_7f5bc1ea-2d2f-4820-a1bc-5ebaec10cf78.dat' 'input_dir/NC_014364.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/4/c/0/dataset_4c01f34b-964b-46d3-b967-cdcdee212762.dat' 'input_dir/NC_014363.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/e/e/7/dataset_ee74df26-4ed3-4f7a-bd6d-ab48386fbe57.dat' 'input_dir/NC_014212.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/1/3/3/dataset_1338df9d-389c-4fc8-83e2-2c848afcf885.dat' 'input_dir/NC_014211.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/6/b/3/dataset_6b30277c-ada8-4518-9acf-d9a5836476f0.dat' 'input_dir/NC_014168.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/6/6/d/dataset_66dd962a-018f-4463-ae74-fd31a066b070.dat' 'input_dir/NC_014008.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/5/6/7/dataset_5672e1df-83f4-4d40-be43-b3fec3811479.dat' 'input_dir/NC_012982.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/c/7/f/dataset_c7f9c61a-ba4d-4d8c-9d3b-c057189bb148.dat' 'input_dir/NC_009012.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/0/d/2/dataset_0d2d837f-3cfd-4a04-bc7b-22e0d4b9a69c.dat' 'input_dir/NC_008261.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/4/7/2/dataset_47237f38-89a7-4dc5-8046-275116f35811.dat' 'input_dir/NC_003450.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/f/9/9/dataset_f9953074-ccde-4fe3-877c-eca0a9fc8b48.dat' 'input_dir/NC_002737.fasta.dat' && ln -s '/tmp/tmp1h1ev9pa/files/8/1/3/dataset_8132ac78-2964-45ae-be47-bc1fffaebbae.dat' 'input_dir/NC_000913.fasta.dat' && checkm2 predict --input input_dir   -x .dat --threads "${GALAXY_SLOTS:-1}" --database_path '/cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd' --output-directory output

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"1.0.2"
            dbkey	"?"
            genes	false
            model	""
            ttable	None

    • Step 6: toolshed.g2.bx.psu.edu/repos/rplanel/defense_finder/defense_finder/2.0.1+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 2:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 3:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 4:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 5:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 6:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 7:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 8:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 9:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 10:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 11:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 12:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 13:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 14:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 15:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 16:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 17:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 18:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 19:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 20:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 21:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

        • Job 22:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            antidefensefinder	false
            antidefensefinder_only	false
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	"0.4"
            db_type	"ordered_replicon"
            dbkey	"?"
            models	"defense-finder-models_2.0.2"
            no_cut_ga	false
            preserve_raw	false

    • Step 7: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.4.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            advanced	{"force": false, "min_af": "0.65", "min_perc_aa": "10", "output_process_log": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            gtdbtk_db	"Full Database - Release 220 (2024-10-19)"

    • Step 8: toolshed.g2.bx.psu.edu/repos/ufz/genomad_end_to_end/genomad_end_to_end/1.11.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 2:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 3:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 4:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 5:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 6:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 7:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 8:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 9:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 10:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 11:

          • Job state is queued

          Command Line:

          • ln -s '/tmp/tmp1h1ev9pa/files/3/1/b/dataset_31b2d17e-f81f-4d24-996c-0d03c031696b.dat' sequence.fa && mkdir output/ && genomad end-to-end --conservative --threads ${GALAXY_SLOTS:-4}      --sensitivity 4.2 --splits 0   --composition auto  sequence.fa output/ '/cvmfs/data.galaxyproject.org/byhand/genomad_databases/1.9'

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 12:

          • Job state is queued

          Command Line:

          • ln -s '/tmp/tmp1h1ev9pa/files/a/f/a/dataset_afabf307-2439-4a06-9633-483969688edf.dat' sequence.fa && mkdir output/ && genomad end-to-end --conservative --threads ${GALAXY_SLOTS:-4}      --sensitivity 4.2 --splits 0   --composition auto  sequence.fa output/ '/cvmfs/data.galaxyproject.org/byhand/genomad_databases/1.9'

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 13:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 14:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 15:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 16:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 17:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 18:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 19:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 20:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 21:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

        • Job 22:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            DATABASE	"1.9"
            __input_ext	"input"
            __workflow_invocation_uuid__	"faef3868a36b11f0a35e7ced8d4c92a2"
            annotation	{"full_ictv_lineage": false, "lenient_taxonomy": false, "sensitivity": "4.2", "splits": "0"}
            basic	{"disable_find_proviruses": true, "disable_nn_classification": true, "enable_score_calibration": false}
            chromInfo	"/tmp/tmp1h1ev9pa/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_cond	{"__current_case__": 0, "filtering_preset": "--conservative"}
            license	true
            provirus	{"skip_integrase_identification": false, "skip_trna_identification": false}
            score	{"composition": "auto", "force_auto": false}

    • Step 9: Unlabelled step:

      • step_state: new

    • Step 10: Unlabelled step:

      • step_state: new
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • 5bd59b483bed5571

    • history_state

      • queued

    • invocation_id

      • 5bd59b483bed5571

    • invocation_state

      • failed

    • messages

      • [{'dependent_workflow_step_id': 6, 'hdca_id': 'c3d4838b931fc7d2', 'reason': 'collection_failed', 'workflow_step_id': 8}]

    • workflow_id

      • 701743eee2689fad