Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.1.7 to 0.1.8

[gxydevbot]

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

• toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1

The workflow release number has been updated from 0.1.7 to 0.1.8.

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Assembly-Hifi-HiC-phasing-VGP4.ga_0

  Execution Problem:

  • Final state of invocation 72d990972d8a6c86 is [failed]. Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because step 7 requires a dataset created by step 6, but dataset entered a failed state.
  • Steps

    • Step 1: Pacbio Reads Collection:

      • step_state: scheduled

    • Step 2: HiC forward reads:

      • step_state: scheduled

    • Step 11: SAK input file:

      • step_state: scheduled

    • Step 12: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -f -s '/tmp/tmpo6gwntkw/files/5/2/5/dataset_525bd784-2f86-47c8-b243-5ca757a86691.dat' 'yeast_reads_sub1_fastq_gz.fa.gz' &&     cutadapt  -j=${GALAXY_SLOTS:-4}        -b 'Dummy-Adapter (do not use me)'='TGTAGGCC'   -b 'Dummy-Adapter (do not use me)'='TGTAGGCC'        --output='out1.fa.gz'  --error-rate=0.1 --times=1 --overlap=35    --action=trim --revcomp  --discard-trimmed           'yeast_reads_sub1_fastq_gz.fa.gz'  > report.txt

          Exit Code:

          • 1

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            adapter_options	{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"}
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_options	{"discard_cassava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": null, "pair_filter": "any"}
            library	{"__current_case__": 0, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 1, "adapter": "TGTAGGCC", "adapter_source_list": "builtin"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 1, "adapter": "TGTAGGCC", "adapter_source_list": "builtin"}, "single_noindels": false}], "front_adapters": []}, "type": "single"}
            output_selector	["report"]
            read_mod_options	{"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}

    • Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • grep -G -A 0 -B 0  -i -- "Haploid" '/tmp/tmpo6gwntkw/files/7/8/2/dataset_7828a74a-bd79-4b14-8f4f-742efe12d763.dat' | grep -v "^--$" > "/tmp/tmpo6gwntkw/job_working_directory/000/8/outputs/dataset_2ea232b0-7c15-42e8-b0b7-5d37ecc5f6da.dat"

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            case_sensitive	"-i"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            color	"NOCOLOR"
            dbkey	"?"
            invert	""
            lines_after	"0"
            lines_before	"0"
            regex_type	"-G"
            url_paste	"Haploid"

    • Step 14: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpo6gwntkw/job_working_directory/000/9/configs/tmpt89idwys' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpo6gwntkw/files/9/1/6/dataset_916c9f1b-bfe5-4a0d-853d-655fe6facc55.dat' '/tmp/tmpo6gwntkw/job_working_directory/000/9/outputs/dataset_2569ff89-a34b-43dc-a01b-7ee461aefc2f.dat'

          Exit Code:

          • 0

          Standard Output:

          • Computing 1 new columns with instructions ['c3*2;;']
            Computed new column values for 100.00% of 1 lines written.
            

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            ops	{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"}

    • Step 15: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comment	""
            dbkey	"?"
            export	false
            flat	false
            results	[{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}]
            saveLog	false
            title	""

    • Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpo6gwntkw/files/2/e/a/dataset_2ea232b0-7c15-42e8-b0b7-5d37ecc5f6da.dat' > '/tmp/tmpo6gwntkw/job_working_directory/000/11/outputs/dataset_01683cf3-6fcd-4a0f-85e3-d03486b06d6b.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}]

    • Step 17: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpo6gwntkw/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpo6gwntkw/files/2/5/6/dataset_2569ff89-a34b-43dc-a01b-7ee461aefc2f.dat' 'c7' T '/tmp/tmpo6gwntkw/job_working_directory/000/12/outputs/dataset_abad6900-ca4e-4f70-acbc-6b340abeee9e.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c7"
            dbkey	"?"
            delimiter	"T"

    • Step 18: Convert characters1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python /tmp/tmpo6gwntkw/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpo6gwntkw/files/0/1/6/dataset_01683cf3-6fcd-4a0f-85e3-d03486b06d6b.dat s /tmp/tmpo6gwntkw/job_working_directory/000/13/outputs/dataset_bf7598b5-f378-41a1-a6cd-28631390bf13.dat

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            condense	true
            convert_from	"s"
            dbkey	"?"
            strip	true

    • Step 19: Estimated homozygous read coverage:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 20: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpo6gwntkw/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpo6gwntkw/files/b/f/7/dataset_bf7598b5-f378-41a1-a6cd-28631390bf13.dat' 'c3' T '/tmp/tmpo6gwntkw/job_working_directory/000/15/outputs/dataset_2e909910-ebad-4621-8ff4-d705a7b41489.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c3"
            dbkey	"?"
            delimiter	"T"

    • Step 3: HiC reverse reads:

      • step_state: scheduled

    • Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastq.gz"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            advanced_options	{"__current_case__": 0, "advanced_selector": "blank"}
            assembly_options	{"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"}
            bins_out	false
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_bits	"32"
            hic_partition	{"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null}
            log_out	true
            mode	{"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}}
            ont_integration	{"__current_case__": 0, "ont_integration_selector": "blank"}
            purge_options	{"__current_case__": 0, "purge_selector": "blank"}
            scaffolding_options	{"__current_case__": 0, "scaffold_selector": "blank"}

    • Step 22: Estimated genome size:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 23: Raw Unitig Image:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fontsize	None
            height	"2000"
            lengths	false
            names	false
            nodewidth	"25.0"
            output_format	"png"
            width	None

    • Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 4: Genomescope Summary:

      • step_state: scheduled

    • Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 32: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"0f6c0188c3df11ee883b57abbd16a21f"
                chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"0f6c0188c3df11ee883b57abbd16a21f"
                chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"0f6c0188c3df11ee883b57abbd16a21f"
                chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"0f6c0188c3df11ee883b57abbd16a21f"
                chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"0f6c0188c3df11ee883b57abbd16a21f"
                chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 33: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"0f6c0189c3df11ee883b57abbd16a21f"
                chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"0f6c0189c3df11ee883b57abbd16a21f"
                chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"0f6c0189c3df11ee883b57abbd16a21f"
                chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"0f6c0189c3df11ee883b57abbd16a21f"
                chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"0f6c0189c3df11ee883b57abbd16a21f"
                chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 34: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 35: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 36: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap2\"}; {print}; "
            dbkey	"?"

    • Step 37: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap1\"}; {print}; "
            dbkey	"?"

    • Step 38: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 39: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image"]

    • Step 40: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            label	"output_merqury"
            mode	{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 42, "src": "hda"}]}, "assembly_02": {"values": [{"id": 41, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"}
            output_add_headers	true
            output_selector	["qv", "plots", "stats", "log"]

    • Step 5: Genomescope Model Parameters:

      • step_state: scheduled

    • Step 41: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image"]

    • Step 42: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2"
            dbkey	"?"
            delimiter	"T"

    • Step 43: Paste1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0f6c0187c3df11ee883b57abbd16a21f"
            chromInfo	"/tmp/tmpo6gwntkw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            delimiter	"T"

    • Step 6: Meryl Database:

      • step_state: scheduled

    • Step 7: Lineage:

      • step_state: scheduled

    • Step 8: Name for Haplotype 1:

      • step_state: scheduled

    • Step 9: Name for Haplotype 2:

      • step_state: scheduled

    • Step 10: Bits for bloom filter:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Final state of invocation 72d990972d8a6c86 is [failed]. Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 72d990972d8a6c86

    • history_state

      • error

    • invocation_id

      • 72d990972d8a6c86

    • invocation_state

      • failed

    • messages

      • [{'dependent_workflow_step_id': 5, 'hda_id': 'c8f0a2d523efb9e4', 'reason': 'dataset_failed', 'workflow_step_id': 6}]

    • workflow_id

      • b87659257bc8b532

[Delphine-L]

Sorry, I realised the latest version of cutadapt is not installed on .org and my workflow was reverted to an older version in my commit. I am working on it

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Assembly-Hifi-HiC-phasing-VGP4.ga_0

  Execution Problem:

  • Final state of invocation 77a2fc5390120f54 is [failed]. Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because step 7 requires a dataset created by step 6, but dataset entered a failed state.
  • Steps

    • Step 1: Pacbio Reads Collection:

      • step_state: scheduled

    • Step 2: HiC forward reads:

      • step_state: scheduled

    • Step 11: SAK input file:

      • step_state: scheduled

    • Step 12: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -f -s '/tmp/tmpwwvy9nke/files/3/f/d/dataset_3fd7e52e-c9c8-4e68-a98c-f1dafde38536.dat' 'yeast_reads_sub1_fastq_gz.fa.gz' &&     cutadapt  -j=${GALAXY_SLOTS:-4}        -b 'ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT'   -b 'ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT'        --output='out1.fa.gz'  --error-rate=0.1 --times=1 --overlap=35    --action=trim --revcomp  --discard-trimmed           'yeast_reads_sub1_fastq_gz.fa.gz'  > report.txt

          Exit Code:

          • 1

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            adapter_options	{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"}
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_options	{"discard_cassava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": null, "pair_filter": "any"}
            library	{"__current_case__": 0, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}], "front_adapters": []}, "type": "single"}
            output_selector	["report"]
            read_mod_options	{"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}

    • Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • grep -G -A 0 -B 0  -i -- "Haploid" '/tmp/tmpwwvy9nke/files/6/b/7/dataset_6b751769-a7f0-4add-885a-1875d3b08742.dat' | grep -v "^--$" > "/tmp/tmpwwvy9nke/job_working_directory/000/8/outputs/dataset_4a2c8d05-32fe-47ac-a24b-d643a4a1dc02.dat"

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            case_sensitive	"-i"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            color	"NOCOLOR"
            dbkey	"?"
            invert	""
            lines_after	"0"
            lines_before	"0"
            regex_type	"-G"
            url_paste	"Haploid"

    • Step 14: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpwwvy9nke/job_working_directory/000/9/configs/tmppobryhbh' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpwwvy9nke/files/0/9/6/dataset_096b12f2-f1fa-41a1-b6c6-40544768529b.dat' '/tmp/tmpwwvy9nke/job_working_directory/000/9/outputs/dataset_13303bb4-b5e3-4afd-81bf-8bec0ecf921f.dat'

          Exit Code:

          • 0

          Standard Output:

          • Computing 1 new columns with instructions ['c3*2;;']
            Computed new column values for 100.00% of 1 lines written.
            

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            ops	{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"}

    • Step 15: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comment	""
            dbkey	"?"
            export	false
            flat	false
            results	[{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}]
            saveLog	false
            title	""

    • Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpwwvy9nke/files/4/a/2/dataset_4a2c8d05-32fe-47ac-a24b-d643a4a1dc02.dat' > '/tmp/tmpwwvy9nke/job_working_directory/000/11/outputs/dataset_c4c21e6d-acb3-4ed9-8c2a-84ad60f2f36a.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}]

    • Step 17: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpwwvy9nke/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpwwvy9nke/files/1/3/3/dataset_13303bb4-b5e3-4afd-81bf-8bec0ecf921f.dat' 'c7' T '/tmp/tmpwwvy9nke/job_working_directory/000/12/outputs/dataset_b442a78b-8d5f-41d9-ab2a-9be87bfbe4dc.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c7"
            dbkey	"?"
            delimiter	"T"

    • Step 18: Convert characters1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python /tmp/tmpwwvy9nke/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpwwvy9nke/files/c/4/c/dataset_c4c21e6d-acb3-4ed9-8c2a-84ad60f2f36a.dat s /tmp/tmpwwvy9nke/job_working_directory/000/13/outputs/dataset_0e36279c-6816-46c0-a57d-e9485f6853ee.dat

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            condense	true
            convert_from	"s"
            dbkey	"?"
            strip	true

    • Step 19: Estimated homozygous read coverage:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 20: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpwwvy9nke/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpwwvy9nke/files/0/e/3/dataset_0e36279c-6816-46c0-a57d-e9485f6853ee.dat' 'c3' T '/tmp/tmpwwvy9nke/job_working_directory/000/15/outputs/dataset_def3f2b0-dee9-46bf-94b1-00b331110eb7.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c3"
            dbkey	"?"
            delimiter	"T"

    • Step 3: HiC reverse reads:

      • step_state: scheduled

    • Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastq.gz"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            advanced_options	{"__current_case__": 0, "advanced_selector": "blank"}
            assembly_options	{"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"}
            bins_out	false
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_bits	"32"
            hic_partition	{"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null}
            log_out	true
            mode	{"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}}
            ont_integration	{"__current_case__": 0, "ont_integration_selector": "blank"}
            purge_options	{"__current_case__": 0, "purge_selector": "blank"}
            scaffolding_options	{"__current_case__": 0, "scaffold_selector": "blank"}

    • Step 22: Estimated genome size:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 23: Raw Unitig Image:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fontsize	None
            height	"2000"
            lengths	false
            names	false
            nodewidth	"25.0"
            output_format	"png"
            width	None

    • Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 4: Genomescope Summary:

      • step_state: scheduled

    • Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 32: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"28c97f6ecc3311eeb668c16f269349c6"
                chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"28c97f6ecc3311eeb668c16f269349c6"
                chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"28c97f6ecc3311eeb668c16f269349c6"
                chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"28c97f6ecc3311eeb668c16f269349c6"
                chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"28c97f6ecc3311eeb668c16f269349c6"
                chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 33: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"28c97f6fcc3311eeb668c16f269349c6"
                chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"28c97f6fcc3311eeb668c16f269349c6"
                chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"28c97f6fcc3311eeb668c16f269349c6"
                chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"28c97f6fcc3311eeb668c16f269349c6"
                chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"28c97f6fcc3311eeb668c16f269349c6"
                chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 34: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 35: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 36: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap2\"}; {print}; "
            dbkey	"?"

    • Step 37: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap1\"}; {print}; "
            dbkey	"?"

    • Step 38: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 39: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image"]

    • Step 40: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            label	"output_merqury"
            mode	{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 42, "src": "hda"}]}, "assembly_02": {"values": [{"id": 41, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"}
            output_add_headers	true
            output_selector	["qv", "plots", "stats", "log", "hist"]

    • Step 5: Genomescope Model Parameters:

      • step_state: scheduled

    • Step 41: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image"]

    • Step 42: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2"
            dbkey	"?"
            delimiter	"T"

    • Step 43: Paste1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"28c97f6dcc3311eeb668c16f269349c6"
            chromInfo	"/tmp/tmpwwvy9nke/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            delimiter	"T"

    • Step 6: Meryl Database:

      • step_state: scheduled

    • Step 7: Lineage:

      • step_state: scheduled

    • Step 8: Name for Haplotype 1:

      • step_state: scheduled

    • Step 9: Name for Haplotype 2:

      • step_state: scheduled

    • Step 10: Bits for bloom filter:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Final state of invocation 77a2fc5390120f54 is [failed]. Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 77a2fc5390120f54

    • history_state

      • error

    • invocation_id

      • 77a2fc5390120f54

    • invocation_state

      • failed

    • messages

      • [{'dependent_workflow_step_id': 5, 'hda_id': '8d8241eb957d7bec', 'reason': 'dataset_failed', 'workflow_step_id': 6}]

    • workflow_id

      • 059691e645e706f3

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Assembly-Hifi-HiC-phasing-VGP4.ga_0

  Execution Problem:

  • Final state of invocation 157f4eaf06cc1341 is [failed]. Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because step 7 requires a dataset created by step 6, but dataset entered a failed state.
  • Steps

    • Step 1: Pacbio Reads Collection:

      • step_state: scheduled

    • Step 2: HiC forward reads:

      • step_state: scheduled

    • Step 11: SAK input file:

      • step_state: scheduled

    • Step 12: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -f -s '/tmp/tmpcrf0t8sz/files/e/9/e/dataset_e9eefd28-c112-408a-a53e-e737a8d939ef.dat' 'yeast_reads_sub1_fastq_gz.fa.gz' &&     cutadapt  -j=${GALAXY_SLOTS:-4}        -b 'ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT'   -b 'ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT'        --output='out1.fa.gz'  --error-rate=0.1 --times=1 --overlap=35    --action=trim --revcomp  --discard-trimmed           'yeast_reads_sub1_fastq_gz.fa.gz'  > report.txt

          Exit Code:

          • 1

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            adapter_options	{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"}
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_options	{"discard_cassava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": null, "pair_filter": "any"}
            library	{"__current_case__": 0, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}], "front_adapters": []}, "type": "single"}
            output_selector	["report"]
            read_mod_options	{"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}

    • Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • grep -G -A 0 -B 0  -i -- "Haploid" '/tmp/tmpcrf0t8sz/files/2/0/6/dataset_206b05be-8409-43f7-b9b3-9b2993725181.dat' | grep -v "^--$" > "/tmp/tmpcrf0t8sz/job_working_directory/000/8/outputs/dataset_91d70f24-e8e4-4c37-9c8f-c2b0671ed76b.dat"

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            case_sensitive	"-i"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            color	"NOCOLOR"
            dbkey	"?"
            invert	""
            lines_after	"0"
            lines_before	"0"
            regex_type	"-G"
            url_paste	"Haploid"

    • Step 14: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpcrf0t8sz/job_working_directory/000/9/configs/tmpefc34tqi' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpcrf0t8sz/files/a/5/f/dataset_a5fe6af1-5819-4acf-add2-6c0f8032f944.dat' '/tmp/tmpcrf0t8sz/job_working_directory/000/9/outputs/dataset_7efe36c0-fc27-4f82-a161-c084a1eafb01.dat'

          Exit Code:

          • 0

          Standard Output:

          • Computing 1 new columns with instructions ['c3*2;;']
            Computed new column values for 100.00% of 1 lines written.
            

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            ops	{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"}

    • Step 15: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comment	""
            dbkey	"?"
            export	false
            flat	false
            results	[{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}]
            saveLog	false
            title	""

    • Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpcrf0t8sz/files/9/1/d/dataset_91d70f24-e8e4-4c37-9c8f-c2b0671ed76b.dat' > '/tmp/tmpcrf0t8sz/job_working_directory/000/11/outputs/dataset_4d308d0e-4a6f-4a9e-b011-1432e1226bbd.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}]

    • Step 17: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpcrf0t8sz/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpcrf0t8sz/files/7/e/f/dataset_7efe36c0-fc27-4f82-a161-c084a1eafb01.dat' 'c7' T '/tmp/tmpcrf0t8sz/job_working_directory/000/12/outputs/dataset_2bc163ae-ee50-4365-a903-86b0791aec1b.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c7"
            dbkey	"?"
            delimiter	"T"

    • Step 18: Convert characters1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python /tmp/tmpcrf0t8sz/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpcrf0t8sz/files/4/d/3/dataset_4d308d0e-4a6f-4a9e-b011-1432e1226bbd.dat s /tmp/tmpcrf0t8sz/job_working_directory/000/13/outputs/dataset_c8f8e1b8-c13b-4530-9233-b82b439b49a8.dat

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            condense	true
            convert_from	"s"
            dbkey	"?"
            strip	true

    • Step 19: Estimated homozygous read coverage:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 20: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpcrf0t8sz/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpcrf0t8sz/files/c/8/f/dataset_c8f8e1b8-c13b-4530-9233-b82b439b49a8.dat' 'c3' T '/tmp/tmpcrf0t8sz/job_working_directory/000/15/outputs/dataset_34bef53b-4750-4621-b184-15308b9d328b.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c3"
            dbkey	"?"
            delimiter	"T"

    • Step 3: HiC reverse reads:

      • step_state: scheduled

    • Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastq.gz"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            advanced_options	{"__current_case__": 0, "advanced_selector": "blank"}
            assembly_options	{"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"}
            bins_out	false
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_bits	"32"
            hic_partition	{"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null}
            log_out	true
            mode	{"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}}
            ont_integration	{"__current_case__": 0, "ont_integration_selector": "blank"}
            purge_options	{"__current_case__": 0, "purge_selector": "blank"}
            scaffolding_options	{"__current_case__": 0, "scaffold_selector": "blank"}

    • Step 22: Estimated genome size:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 23: Raw Unitig Image:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fontsize	None
            height	"2000"
            lengths	false
            names	false
            nodewidth	"25.0"
            output_format	"png"
            width	None

    • Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 4: Genomescope Summary:

      • step_state: scheduled

    • Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 32: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"c8451ddad00411eebbebf70c0d22cd3e"
                chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"c8451ddad00411eebbebf70c0d22cd3e"
                chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"c8451ddad00411eebbebf70c0d22cd3e"
                chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"c8451ddad00411eebbebf70c0d22cd3e"
                chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"c8451ddad00411eebbebf70c0d22cd3e"
                chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 33: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"c8451ddbd00411eebbebf70c0d22cd3e"
                chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"c8451ddbd00411eebbebf70c0d22cd3e"
                chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"c8451ddbd00411eebbebf70c0d22cd3e"
                chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"c8451ddbd00411eebbebf70c0d22cd3e"
                chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"c8451ddbd00411eebbebf70c0d22cd3e"
                chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 34: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 35: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 36: Unlabelled step:

      • step_state: new

    • Step 37: Unlabelled step:

      • step_state: new

    • Step 38: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 39: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image"]

    • Step 40: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            label	"output_merqury"
            mode	{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 42, "src": "hda"}]}, "assembly_02": {"values": [{"id": 41, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"}
            output_add_headers	true
            output_selector	["qv", "plots", "stats", "log", "hist"]

    • Step 5: Genomescope Model Parameters:

      • step_state: scheduled

    • Step 41: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c8451dd9d00411eebbebf70c0d22cd3e"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpcrf0t8sz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image"]

    • Step 42: Unlabelled step:

      • step_state: new

    • Step 43: Unlabelled step:

      • step_state: new

    • Step 6: Meryl Database:

      • step_state: scheduled

    • Step 7: Lineage:

      • step_state: scheduled

    • Step 8: Name for Haplotype 1:

      • step_state: scheduled

    • Step 9: Name for Haplotype 2:

      • step_state: scheduled

    • Step 10: Bits for bloom filter:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Final state of invocation 157f4eaf06cc1341 is [failed]. Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 157f4eaf06cc1341

    • history_state

      • error

    • invocation_id

      • 157f4eaf06cc1341

    • invocation_state

      • failed

    • messages

      • [{'dependent_workflow_step_id': 5, 'hda_id': 'bff72287ac86d524', 'reason': 'dataset_failed', 'workflow_step_id': 6}]

    • workflow_id

      • 8a887079e075cca4

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Assembly-Hifi-HiC-phasing-VGP4.ga_0

  Execution Problem:

  • Final state of invocation 95dcd73a684910f7 is [failed]. Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because step 7 requires a dataset created by step 6, but dataset entered a failed state.
  • Steps

    • Step 1: Pacbio Reads Collection:

      • step_state: scheduled

    • Step 2: HiC forward reads:

      • step_state: scheduled

    • Step 11: SAK input file:

      • step_state: scheduled

    • Step 12: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -f -s '/tmp/tmpkvztv0l3/files/d/5/9/dataset_d5934517-81a4-4b61-9fe6-bfa479ea02a0.dat' 'yeast_reads_sub1_fastq_gz.fa.gz' &&     cutadapt  -j=${GALAXY_SLOTS:-4}        -b 'ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT'   -b 'ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT'        --output='out1.fa.gz'  --error-rate=0.1 --times=1 --overlap=35    --action=trim --revcomp  --discard-trimmed           'yeast_reads_sub1_fastq_gz.fa.gz'  > report.txt

          Exit Code:

          • 1

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            adapter_options	{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"}
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_options	{"discard_cassava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": null, "pair_filter": "any"}
            library	{"__current_case__": 0, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}], "front_adapters": []}, "type": "single"}
            output_selector	["report"]
            read_mod_options	{"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}

    • Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • grep -G -A 0 -B 0  -i -- "Haploid" '/tmp/tmpkvztv0l3/files/8/a/3/dataset_8a339ccc-9ea6-45cf-92cf-8d1b68782c8e.dat' | grep -v "^--$" > "/tmp/tmpkvztv0l3/job_working_directory/000/8/outputs/dataset_87659334-f210-437e-ba07-3b59468d1b3a.dat"

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            case_sensitive	"-i"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            color	"NOCOLOR"
            dbkey	"?"
            invert	""
            lines_after	"0"
            lines_before	"0"
            regex_type	"-G"
            url_paste	"Haploid"

    • Step 14: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpkvztv0l3/job_working_directory/000/9/configs/tmp9ay0epf2' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpkvztv0l3/files/0/0/4/dataset_0047fb2e-2ea5-4223-8550-8f3401dc07e2.dat' '/tmp/tmpkvztv0l3/job_working_directory/000/9/outputs/dataset_6c053eeb-4e20-485d-bd87-ea989891df3f.dat'

          Exit Code:

          • 0

          Standard Output:

          • Computing 1 new columns with instructions ['c3*2;;']
            Computed new column values for 100.00% of 1 lines written.
            

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            ops	{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"}

    • Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpkvztv0l3/files/8/7/6/dataset_87659334-f210-437e-ba07-3b59468d1b3a.dat' > '/tmp/tmpkvztv0l3/job_working_directory/000/10/outputs/dataset_5f142d51-1fd2-4af7-a854-24ee22611cad.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}]

    • Step 16: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpkvztv0l3/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpkvztv0l3/files/6/c/0/dataset_6c053eeb-4e20-485d-bd87-ea989891df3f.dat' 'c7' T '/tmp/tmpkvztv0l3/job_working_directory/000/11/outputs/dataset_0a155601-9f25-4a7e-acb7-40563a53437e.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c7"
            dbkey	"?"
            delimiter	"T"

    • Step 17: Convert characters1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python /tmp/tmpkvztv0l3/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpkvztv0l3/files/5/f/1/dataset_5f142d51-1fd2-4af7-a854-24ee22611cad.dat s /tmp/tmpkvztv0l3/job_working_directory/000/12/outputs/dataset_f8b5e088-9c44-4f8d-ac89-8745b68a7e45.dat

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            condense	true
            convert_from	"s"
            dbkey	"?"
            strip	true

    • Step 18: Estimated homozygous read coverage:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 19: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpkvztv0l3/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpkvztv0l3/files/f/8/b/dataset_f8b5e088-9c44-4f8d-ac89-8745b68a7e45.dat' 'c3' T '/tmp/tmpkvztv0l3/job_working_directory/000/14/outputs/dataset_f8e24eba-0d37-490d-b92a-65b4dee9277f.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c3"
            dbkey	"?"
            delimiter	"T"

    • Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastq.gz"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            advanced_options	{"__current_case__": 0, "advanced_selector": "blank"}
            assembly_options	{"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"}
            bins_out	false
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_bits	"32"
            hic_partition	{"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null}
            log_out	true
            mode	{"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}}
            ont_integration	{"__current_case__": 0, "ont_integration_selector": "blank"}
            purge_options	{"__current_case__": 0, "purge_selector": "blank"}
            scaffolding_options	{"__current_case__": 0, "scaffold_selector": "blank"}

    • Step 3: HiC reverse reads:

      • step_state: scheduled

    • Step 21: Estimated genome size:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 22: Raw Unitig Image:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fontsize	None
            height	"2000"
            lengths	false
            names	false
            nodewidth	"25.0"
            output_format	"png"
            width	None

    • Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 4: Genomescope Summary:

      • step_state: scheduled

    • Step 31: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"d3f5f5a6d0e411ee97612be80548e94a"
                chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"d3f5f5a6d0e411ee97612be80548e94a"
                chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"d3f5f5a6d0e411ee97612be80548e94a"
                chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"d3f5f5a6d0e411ee97612be80548e94a"
                chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"d3f5f5a6d0e411ee97612be80548e94a"
                chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 32: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"d3f5f5a7d0e411ee97612be80548e94a"
                chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"d3f5f5a7d0e411ee97612be80548e94a"
                chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"d3f5f5a7d0e411ee97612be80548e94a"
                chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"d3f5f5a7d0e411ee97612be80548e94a"
                chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"d3f5f5a7d0e411ee97612be80548e94a"
                chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 33: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 34: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 35: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap2\"}; {print}; "
            dbkey	"?"

    • Step 36: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap1\"}; {print}; "
            dbkey	"?"

    • Step 37: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 38: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image"]

    • Step 39: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            label	"output_merqury"
            mode	{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 43, "src": "hda"}]}, "assembly_02": {"values": [{"id": 42, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"}
            output_add_headers	true
            output_selector	["qv", "plots", "stats", "log", "hist"]

    • Step 40: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image"]

    • Step 5: Genomescope Model Parameters:

      • step_state: scheduled

    • Step 41: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2"
            dbkey	"?"
            delimiter	"T"

    • Step 42: Paste1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d3f5f5a5d0e411ee97612be80548e94a"
            chromInfo	"/tmp/tmpkvztv0l3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            delimiter	"T"

    • Step 6: Meryl Database:

      • step_state: scheduled

    • Step 7: Lineage:

      • step_state: scheduled

    • Step 8: Name for Haplotype 1:

      • step_state: scheduled

    • Step 9: Name for Haplotype 2:

      • step_state: scheduled

    • Step 10: Bits for bloom filter:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Final state of invocation 95dcd73a684910f7 is [failed]. Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 95dcd73a684910f7

    • history_state

      • error

    • invocation_id

      • 95dcd73a684910f7

    • invocation_state

      • failed

    • messages

      • [{'dependent_workflow_step_id': 5, 'hda_id': '6d12c8e505e6a2f9', 'reason': 'dataset_failed', 'workflow_step_id': 6}]

    • workflow_id

      • cb1d0ccc89a3152f

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Assembly-Hifi-HiC-phasing-VGP4.ga_0

  Execution Problem:

  • Final state of invocation ffe750b2e2f60c69 is [failed]. Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because step 7 requires a dataset created by step 6, but dataset entered a failed state.
  • Steps

    • Step 1: Pacbio Reads Collection:

      • step_state: scheduled

    • Step 2: HiC forward reads:

      • step_state: scheduled

    • Step 11: SAK input file:

      • step_state: scheduled

    • Step 12: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -f -s '/tmp/tmpu6txpr6h/files/f/b/0/dataset_fb0ff12a-dc81-4093-bf53-87a8ff8e86d8.dat' 'yeast_reads_sub1_fastq_gz.fa.gz' &&     cutadapt  -j=${GALAXY_SLOTS:-4}  --json stats.json       -b 'ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT'   -b 'ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT'        --output='out1.fa.gz'  --error-rate=0.1 --times=1 --overlap=35    --action=trim --revcomp  --discard-trimmed           'yeast_reads_sub1_fastq_gz.fa.gz'  > report.txt

          Exit Code:

          • 1

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            adapter_options	{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"}
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_options	{"discard_cassava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": null, "pair_filter": "any"}
            library	{"__current_case__": 0, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}], "front_adapters": []}, "type": "single"}
            output_selector	["report", "json_stats"]
            read_mod_options	{"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}

    • Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • grep -G -A 0 -B 0  -i -- "Haploid" '/tmp/tmpu6txpr6h/files/e/b/d/dataset_ebd678d4-b17e-41b1-b64a-63f2af4a903e.dat' | grep -v "^--$" > "/tmp/tmpu6txpr6h/job_working_directory/000/8/outputs/dataset_4e124611-3dbc-4bfe-986f-1d55499d2b84.dat"

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            case_sensitive	"-i"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            color	"NOCOLOR"
            dbkey	"?"
            invert	""
            lines_after	"0"
            lines_before	"0"
            regex_type	"-G"
            url_paste	"Haploid"

    • Step 14: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpu6txpr6h/job_working_directory/000/9/configs/tmp1zrs9jc0' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpu6txpr6h/files/0/1/2/dataset_012fa81f-49bf-42dd-a8d1-87209ce04010.dat' '/tmp/tmpu6txpr6h/job_working_directory/000/9/outputs/dataset_d0da3cd0-bf54-4441-9b5c-15503c5a910b.dat'

          Exit Code:

          • 0

          Standard Output:

          • Computing 1 new columns with instructions ['c3*2;;']
            Computed new column values for 100.00% of 1 lines written.
            

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            ops	{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"}

    • Step 15: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comment	""
            dbkey	"?"
            export	false
            flat	false
            results	[{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}]
            saveLog	false
            title	""

    • Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpu6txpr6h/files/4/e/1/dataset_4e124611-3dbc-4bfe-986f-1d55499d2b84.dat' > '/tmp/tmpu6txpr6h/job_working_directory/000/11/outputs/dataset_3ff89ed9-da87-4b18-a234-1ab4d51687f3.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}]

    • Step 17: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpu6txpr6h/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpu6txpr6h/files/d/0/d/dataset_d0da3cd0-bf54-4441-9b5c-15503c5a910b.dat' 'c7' T '/tmp/tmpu6txpr6h/job_working_directory/000/12/outputs/dataset_8ea60090-8fb9-4422-b0d1-35309a2b833e.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c7"
            dbkey	"?"
            delimiter	"T"

    • Step 18: Convert characters1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python /tmp/tmpu6txpr6h/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpu6txpr6h/files/3/f/f/dataset_3ff89ed9-da87-4b18-a234-1ab4d51687f3.dat s /tmp/tmpu6txpr6h/job_working_directory/000/13/outputs/dataset_b18ce60d-91fc-4157-8a2d-55cc712b1b92.dat

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            condense	true
            convert_from	"s"
            dbkey	"?"
            strip	true

    • Step 19: Estimated homozygous read coverage:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 20: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpu6txpr6h/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpu6txpr6h/files/b/1/8/dataset_b18ce60d-91fc-4157-8a2d-55cc712b1b92.dat' 'c3' T '/tmp/tmpu6txpr6h/job_working_directory/000/15/outputs/dataset_47a37a90-b705-4ca0-b935-706e43fae0aa.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c3"
            dbkey	"?"
            delimiter	"T"

    • Step 3: HiC reverse reads:

      • step_state: scheduled

    • Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastq.gz"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            advanced_options	{"__current_case__": 0, "advanced_selector": "blank"}
            assembly_options	{"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"}
            bins_out	false
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_bits	"32"
            hic_partition	{"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null}
            log_out	true
            mode	{"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}}
            ont_integration	{"__current_case__": 0, "ont_integration_selector": "blank"}
            purge_options	{"__current_case__": 0, "purge_selector": "blank"}
            scaffolding_options	{"__current_case__": 0, "scaffold_selector": "blank"}

    • Step 22: Estimated genome size:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 23: Raw Unitig Image:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fontsize	None
            height	"2000"
            lengths	false
            names	false
            nodewidth	"25.0"
            output_format	"png"
            width	None

    • Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 4: Genomescope Summary:

      • step_state: scheduled

    • Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 32: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"7df62502dfc311eea0f2cd99d810c2b1"
                chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"7df62502dfc311eea0f2cd99d810c2b1"
                chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"7df62502dfc311eea0f2cd99d810c2b1"
                chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"7df62502dfc311eea0f2cd99d810c2b1"
                chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"7df62502dfc311eea0f2cd99d810c2b1"
                chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 33: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"7df62503dfc311eea0f2cd99d810c2b1"
                chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"7df62503dfc311eea0f2cd99d810c2b1"
                chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"7df62503dfc311eea0f2cd99d810c2b1"
                chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"7df62503dfc311eea0f2cd99d810c2b1"
                chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"7df62503dfc311eea0f2cd99d810c2b1"
                chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 34: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 35: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 36: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap2\"}; {print}; "
            dbkey	"?"

    • Step 37: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap1\"}; {print}; "
            dbkey	"?"

    • Step 38: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 39: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image", "gff"]

    • Step 40: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            label	"output_merqury"
            mode	{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 43, "src": "hda"}]}, "assembly_02": {"values": [{"id": 42, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"}
            output_add_headers	true
            output_selector	["qv", "plots", "stats", "log", "hist"]

    • Step 5: Genomescope Model Parameters:

      • step_state: scheduled

    • Step 41: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image", "gff"]

    • Step 42: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2"
            dbkey	"?"
            delimiter	"T"

    • Step 43: Paste1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"7df62501dfc311eea0f2cd99d810c2b1"
            chromInfo	"/tmp/tmpu6txpr6h/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            delimiter	"T"

    • Step 6: Meryl Database:

      • step_state: scheduled

    • Step 7: Lineage:

      • step_state: scheduled

    • Step 8: Name for Haplotype 1:

      • step_state: scheduled

    • Step 9: Name for Haplotype 2:

      • step_state: scheduled

    • Step 10: Bits for bloom filter:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Final state of invocation ffe750b2e2f60c69 is [failed]. Failed to run workflow, at least one job is in [error] state.

    • history_id

      • ffe750b2e2f60c69

    • history_state

      • error

    • invocation_id

      • ffe750b2e2f60c69

    • invocation_state

      • failed

    • messages

      • [{'dependent_workflow_step_id': 5, 'hda_id': 'b5462d5aeb29522f', 'reason': 'dataset_failed', 'workflow_step_id': 6}]

    • workflow_id

      • 48e38aa800761a65

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Assembly-Hifi-HiC-phasing-VGP4.ga_0

  Execution Problem:

  • Final state of invocation b3d1fa322a0affe2 is [failed]. Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because step 7 requires a dataset created by step 6, but dataset entered a failed state.
  • Steps

    • Step 1: Pacbio Reads Collection:

      • step_state: scheduled

    • Step 2: HiC forward reads:

      • step_state: scheduled

    • Step 11: SAK input file:

      • step_state: scheduled

    • Step 12: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -f -s '/tmp/tmppydclwsg/files/e/7/9/dataset_e7969fc4-b2b0-45e3-a844-9ef08f0c235e.dat' 'yeast_reads_sub1_fastq_gz.fa.gz' &&     cutadapt  -j=${GALAXY_SLOTS:-4}        -b 'ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT'   -b 'ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT'        --output='out1.fa.gz'  --error-rate=0.1 --times=1 --overlap=35    --action=trim --revcomp  --discard-trimmed           'yeast_reads_sub1_fastq_gz.fa.gz'  > report.txt

          Exit Code:

          • 1

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            adapter_options	{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"}
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_options	{"discard_cassava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": null, "pair_filter": "any"}
            library	{"__current_case__": 0, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}], "front_adapters": []}, "type": "single"}
            output_selector	["report"]
            read_mod_options	{"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}

    • Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • grep -G -A 0 -B 0  -i -- "Haploid" '/tmp/tmppydclwsg/files/5/2/9/dataset_52947b1d-1fe9-434b-b65d-cf4cf209bed0.dat' | grep -v "^--$" > "/tmp/tmppydclwsg/job_working_directory/000/8/outputs/dataset_2f47a1f5-35d0-4957-8ceb-d36e61b2b914.dat"

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            case_sensitive	"-i"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            color	"NOCOLOR"
            dbkey	"?"
            invert	""
            lines_after	"0"
            lines_before	"0"
            regex_type	"-G"
            url_paste	"Haploid"

    • Step 14: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmppydclwsg/job_working_directory/000/9/configs/tmpd8rbwfkv' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmppydclwsg/files/2/7/b/dataset_27b476d9-a856-4a1a-953c-ef35f7801f0b.dat' '/tmp/tmppydclwsg/job_working_directory/000/9/outputs/dataset_195e6b15-a697-4c95-8235-a43394fd737e.dat'

          Exit Code:

          • 0

          Standard Output:

          • Computing 1 new columns with instructions ['c3*2;;']
            Computed new column values for 100.00% of 1 lines written.
            

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            ops	{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"}

    • Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmppydclwsg/files/2/f/4/dataset_2f47a1f5-35d0-4957-8ceb-d36e61b2b914.dat' > '/tmp/tmppydclwsg/job_working_directory/000/10/outputs/dataset_aa0134ed-18ca-4499-ac63-9cdb12df2561.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}]

    • Step 16: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmppydclwsg/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmppydclwsg/files/1/9/5/dataset_195e6b15-a697-4c95-8235-a43394fd737e.dat' 'c7' T '/tmp/tmppydclwsg/job_working_directory/000/11/outputs/dataset_c920e079-8d5a-4bc7-a8e9-47b6e5724def.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c7"
            dbkey	"?"
            delimiter	"T"

    • Step 17: Convert characters1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python /tmp/tmppydclwsg/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmppydclwsg/files/a/a/0/dataset_aa0134ed-18ca-4499-ac63-9cdb12df2561.dat s /tmp/tmppydclwsg/job_working_directory/000/12/outputs/dataset_e62633ee-45c1-4894-88d6-3a969eb03b8e.dat

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            condense	true
            convert_from	"s"
            dbkey	"?"
            strip	true

    • Step 18: Estimated homozygous read coverage:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 19: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmppydclwsg/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmppydclwsg/files/e/6/2/dataset_e62633ee-45c1-4894-88d6-3a969eb03b8e.dat' 'c3' T '/tmp/tmppydclwsg/job_working_directory/000/14/outputs/dataset_86125217-7a4a-4fe7-8184-e369cae86da4.dat'

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c3"
            dbkey	"?"
            delimiter	"T"

    • Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastq.gz"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            advanced_options	{"__current_case__": 0, "advanced_selector": "blank"}
            assembly_options	{"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"}
            bins_out	false
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_bits	"32"
            hic_partition	{"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null}
            log_out	true
            mode	{"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}}
            ont_integration	{"__current_case__": 0, "ont_integration_selector": "blank"}
            purge_options	{"__current_case__": 0, "purge_selector": "blank"}
            scaffolding_options	{"__current_case__": 0, "scaffold_selector": "blank"}

    • Step 3: HiC reverse reads:

      • step_state: scheduled

    • Step 21: Estimated genome size:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 22: Raw Unitig Image:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fontsize	None
            height	"2000"
            lengths	false
            names	false
            nodewidth	"25.0"
            output_format	"png"
            width	None

    • Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 4: Genomescope Summary:

      • step_state: scheduled

    • Step 31: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"ab1f18f4dfc311ee866a2965546b1d9a"
                chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"ab1f18f4dfc311ee866a2965546b1d9a"
                chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"ab1f18f4dfc311ee866a2965546b1d9a"
                chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"ab1f18f4dfc311ee866a2965546b1d9a"
                chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"ab1f18f4dfc311ee866a2965546b1d9a"
                chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 32: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"ab1f18f5dfc311ee866a2965546b1d9a"
                chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"ab1f18f5dfc311ee866a2965546b1d9a"
                chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"ab1f18f5dfc311ee866a2965546b1d9a"
                chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"ab1f18f5dfc311ee866a2965546b1d9a"
                chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"ab1f18f5dfc311ee866a2965546b1d9a"
                chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 33: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 34: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 35: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap2\"}; {print}; "
            dbkey	"?"

    • Step 36: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap1\"}; {print}; "
            dbkey	"?"

    • Step 37: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 38: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image"]

    • Step 39: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            label	"output_merqury"
            mode	{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 41, "src": "hda"}]}, "assembly_02": {"values": [{"id": 40, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"}
            output_add_headers	true
            output_selector	["qv", "plots", "stats", "log", "hist"]

    • Step 40: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image"]

    • Step 5: Genomescope Model Parameters:

      • step_state: scheduled

    • Step 41: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2"
            dbkey	"?"
            delimiter	"T"

    • Step 42: Paste1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"ab1f18f3dfc311ee866a2965546b1d9a"
            chromInfo	"/tmp/tmppydclwsg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            delimiter	"T"

    • Step 6: Meryl Database:

      • step_state: scheduled

    • Step 7: Lineage:

      • step_state: scheduled

    • Step 8: Name for Haplotype 1:

      • step_state: scheduled

    • Step 9: Name for Haplotype 2:

      • step_state: scheduled

    • Step 10: Bits for bloom filter:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Final state of invocation b3d1fa322a0affe2 is [failed]. Failed to run workflow, at least one job is in [error] state.

    • history_id

      • b3d1fa322a0affe2

    • history_state

      • error

    • invocation_id

      • b3d1fa322a0affe2

    • invocation_state

      • failed

    • messages

      • [{'dependent_workflow_step_id': 5, 'hda_id': '02f94e20a1d98131', 'reason': 'dataset_failed', 'workflow_step_id': 6}]

    • workflow_id

      • 617b9ab15b0a5c9a

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Assembly-Hifi-HiC-phasing-VGP4.ga_0

  Execution Problem:

  • Final state of invocation c5c6f1fcfe042a9d is [failed]. Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because step 7 requires a dataset created by step 6, but dataset entered a failed state.
  • Steps

    • Step 1: Pacbio Reads Collection:

      • step_state: scheduled

    • Step 2: HiC forward reads:

      • step_state: scheduled

    • Step 11: SAK input file:

      • step_state: scheduled

    • Step 12: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -f -s '/tmp/tmpoon_v71b/files/a/d/1/dataset_ad10a0b2-757f-4688-9a61-fd63af492efe.dat' 'yeast_reads_sub1_fastq_gz.fa.gz' &&     cutadapt  -j=${GALAXY_SLOTS:-4}  --json stats.json       -b 'ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT'   -b 'ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT'        --output='out1.fa.gz'  --error-rate=0.1 --times=1 --overlap=35    --action=trim --revcomp  --discard-trimmed           'yeast_reads_sub1_fastq_gz.fa.gz'  > report.txt

          Exit Code:

          • 1

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            adapter_options	{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"}
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_options	{"discard_cassava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": null, "pair_filter": "any"}
            library	{"__current_case__": 0, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}], "front_adapters": []}, "type": "single"}
            output_selector	["report", "json_stats"]
            read_mod_options	{"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}

    • Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • grep -G -A 0 -B 0  -i -- 'Haploid' '/tmp/tmpoon_v71b/files/b/8/a/dataset_b8ab6a91-efbe-4691-99ad-0fb3fef10a3e.dat' | grep -v "^--$" > '/tmp/tmpoon_v71b/job_working_directory/000/8/outputs/dataset_2bc81ea4-5ec6-426d-8d12-0fc5ee58ad11.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            case_sensitive	"-i"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            color	"NOCOLOR"
            dbkey	"?"
            invert	""
            lines_after	"0"
            lines_before	"0"
            regex_type	"-G"
            url_paste	"Haploid"

    • Step 14: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpoon_v71b/job_working_directory/000/9/configs/tmpumhruc5g' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpoon_v71b/files/2/7/5/dataset_27556d24-9dae-44c0-8811-84d488fc9c9c.dat' '/tmp/tmpoon_v71b/job_working_directory/000/9/outputs/dataset_30c1a30a-aaff-43f5-b1f1-9aee64557668.dat'

          Exit Code:

          • 0

          Standard Output:

          • Computing 1 new columns with instructions ['c3*2;;']
            Computed new column values for 100.00% of 1 lines written.
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            ops	{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"}

    • Step 15: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comment	""
            dbkey	"?"
            export	false
            flat	false
            results	[{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}]
            saveLog	false
            title	""

    • Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpoon_v71b/files/2/b/c/dataset_2bc81ea4-5ec6-426d-8d12-0fc5ee58ad11.dat' > '/tmp/tmpoon_v71b/job_working_directory/000/11/outputs/dataset_21314c8c-4c25-43c8-b175-bd1c78d1b33e.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}]

    • Step 17: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpoon_v71b/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpoon_v71b/files/3/0/c/dataset_30c1a30a-aaff-43f5-b1f1-9aee64557668.dat' 'c7' T '/tmp/tmpoon_v71b/job_working_directory/000/12/outputs/dataset_620d0c8c-006b-4744-874b-7462e9480a53.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c7"
            dbkey	"?"
            delimiter	"T"

    • Step 18: Convert characters1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python /tmp/tmpoon_v71b/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpoon_v71b/files/2/1/3/dataset_21314c8c-4c25-43c8-b175-bd1c78d1b33e.dat s /tmp/tmpoon_v71b/job_working_directory/000/13/outputs/dataset_4cb0c5c9-bc0f-423c-9b24-28b6ccdf75ee.dat

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            condense	true
            convert_from	"s"
            dbkey	"?"
            strip	true

    • Step 19: Estimated homozygous read coverage:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 20: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpoon_v71b/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpoon_v71b/files/4/c/b/dataset_4cb0c5c9-bc0f-423c-9b24-28b6ccdf75ee.dat' 'c3' T '/tmp/tmpoon_v71b/job_working_directory/000/15/outputs/dataset_022064c3-e8cd-40e0-8ce3-57e95beb0782.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c3"
            dbkey	"?"
            delimiter	"T"

    • Step 3: HiC reverse reads:

      • step_state: scheduled

    • Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastq.gz"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            advanced_options	{"__current_case__": 0, "advanced_selector": "blank"}
            assembly_options	{"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"}
            bins_out	false
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_bits	"32"
            hic_partition	{"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null}
            log_out	true
            mode	{"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}}
            ont_integration	{"__current_case__": 0, "ont_integration_selector": "blank"}
            purge_options	{"__current_case__": 0, "purge_selector": "blank"}
            scaffolding_options	{"__current_case__": 0, "scaffold_selector": "blank"}

    • Step 22: Estimated genome size:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 23: Raw Unitig Image:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fontsize	None
            height	"2000"
            lengths	false
            names	false
            nodewidth	"25.0"
            output_format	"png"
            width	None

    • Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 4: Genomescope Summary:

      • step_state: scheduled

    • Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 32: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"0d92aad5e1fa11eea59651e56d4fa232"
                chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"0d92aad5e1fa11eea59651e56d4fa232"
                chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"0d92aad5e1fa11eea59651e56d4fa232"
                chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"0d92aad5e1fa11eea59651e56d4fa232"
                chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"0d92aad5e1fa11eea59651e56d4fa232"
                chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 33: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"0d92aad6e1fa11eea59651e56d4fa232"
                chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"0d92aad6e1fa11eea59651e56d4fa232"
                chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"0d92aad6e1fa11eea59651e56d4fa232"
                chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"0d92aad6e1fa11eea59651e56d4fa232"
                chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"0d92aad6e1fa11eea59651e56d4fa232"
                chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 34: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 35: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 36: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap2\"}; {print}; "
            dbkey	"?"

    • Step 37: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap1\"}; {print}; "
            dbkey	"?"

    • Step 38: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 39: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image", "gff"]

    • Step 40: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            label	"output_merqury"
            mode	{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 43, "src": "hda"}]}, "assembly_02": {"values": [{"id": 42, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"}
            output_add_headers	true
            output_selector	["qv", "plots", "stats", "log", "hist"]

    • Step 5: Genomescope Model Parameters:

      • step_state: scheduled

    • Step 41: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image", "gff"]

    • Step 42: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2"
            dbkey	"?"
            delimiter	"T"

    • Step 43: Paste1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"0d92aad4e1fa11eea59651e56d4fa232"
            chromInfo	"/tmp/tmpoon_v71b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            delimiter	"T"

    • Step 6: Meryl Database:

      • step_state: scheduled

    • Step 7: Lineage:

      • step_state: scheduled

    • Step 8: Name for Haplotype 1:

      • step_state: scheduled

    • Step 9: Name for Haplotype 2:

      • step_state: scheduled

    • Step 10: Bits for bloom filter:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Final state of invocation c5c6f1fcfe042a9d is [failed]. Failed to run workflow, at least one job is in [error] state.

    • history_id

      • c5c6f1fcfe042a9d

    • history_state

      • error

    • invocation_id

      • c5c6f1fcfe042a9d

    • invocation_state

      • failed

    • messages

      • [{'dependent_workflow_step_id': 5, 'hda_id': '509b6f9d4e71010e', 'reason': 'dataset_failed', 'workflow_step_id': 6}]

    • workflow_id

      • f03033af3f367c22

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Assembly-Hifi-HiC-phasing-VGP4.ga_0

  Execution Problem:

  • Final state of invocation b8c504e790b945ee is [failed]. Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because step 7 requires a dataset created by step 6, but dataset entered a failed state.
  • Steps

    • Step 1: Pacbio Reads Collection:

      • step_state: scheduled

    • Step 2: HiC forward reads:

      • step_state: scheduled

    • Step 11: SAK input file:

      • step_state: scheduled

    • Step 12: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -f -s '/tmp/tmpi8i0xjhs/files/f/c/9/dataset_fc9f3e80-2d12-4133-8aec-c413b4990e13.dat' 'yeast_reads_sub1_fastq_gz.fa.gz' &&     cutadapt  -j=${GALAXY_SLOTS:-4}  --json stats.json       -b 'ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT'   -b 'ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT'        --output='out1.fa.gz'  --error-rate=0.1 --times=1 --overlap=35    --action=trim --revcomp  --discard-trimmed           'yeast_reads_sub1_fastq_gz.fa.gz'  > report.txt

          Exit Code:

          • 1

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            adapter_options	{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"}
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_options	{"discard_cassava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "minimum_length": null, "pair_filter": "any"}
            library	{"__current_case__": 0, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}], "front_adapters": []}, "type": "single"}
            output_selector	["report", "json_stats"]
            read_mod_options	{"cut": "0", "length_tag": "", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "rename": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": false, "zero_cap": false}

    • Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • grep -G -A 0 -B 0  -i -- 'Haploid' '/tmp/tmpi8i0xjhs/files/c/a/2/dataset_ca2f081e-bb2f-4178-8f29-de8bdae0ce3f.dat' | grep -v "^--$" > '/tmp/tmpi8i0xjhs/job_working_directory/000/8/outputs/dataset_26dbccbc-3bcf-4a2c-96a7-cf29c78a0a53.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            case_sensitive	"-i"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            color	"NOCOLOR"
            dbkey	"?"
            invert	""
            lines_after	"0"
            lines_before	"0"
            regex_type	"-G"
            url_paste	"Haploid"

    • Step 14: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/6595517c2dd8/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpi8i0xjhs/job_working_directory/000/9/configs/tmpl0sp7ixx' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpi8i0xjhs/files/3/9/8/dataset_398a03e6-8a2a-478b-a24c-f315164b75ca.dat' '/tmp/tmpi8i0xjhs/job_working_directory/000/9/outputs/dataset_a3c2102d-d08c-4ba5-abf2-85a6dece9aa8.dat'

          Exit Code:

          • 0

          Standard Output:

          • Computing 1 new columns with instructions ['c3*2;;']
            Computed new column values for 100.00% of 1 lines written.
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            ops	{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"}

    • Step 15: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comment	""
            dbkey	"?"
            export	false
            flat	false
            results	[{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 3, "src": "hdca"}]}, "software": "cutadapt"}}]
            saveLog	false
            title	""

    • Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/bp//g' -e 's/,//g' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpi8i0xjhs/files/2/6/d/dataset_26dbccbc-3bcf-4a2c-96a7-cf29c78a0a53.dat' > '/tmp/tmpi8i0xjhs/job_working_directory/000/11/outputs/dataset_7313d9a8-ca15-4dc5-81c1-b8d070392c06.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "bp", "replace_pattern": ""}, {"__index__": 1, "find_pattern": ",", "replace_pattern": ""}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2"}]

    • Step 17: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpi8i0xjhs/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpi8i0xjhs/files/a/3/c/dataset_a3c2102d-d08c-4ba5-abf2-85a6dece9aa8.dat' 'c7' T '/tmp/tmpi8i0xjhs/job_working_directory/000/12/outputs/dataset_0c1fffa0-05bf-4d11-8d3f-b08e9ca641ee.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c7"
            dbkey	"?"
            delimiter	"T"

    • Step 18: Convert characters1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python /tmp/tmpi8i0xjhs/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmpi8i0xjhs/files/7/3/1/dataset_7313d9a8-ca15-4dc5-81c1-b8d070392c06.dat s /tmp/tmpi8i0xjhs/job_working_directory/000/13/outputs/dataset_743df84e-ffd6-4868-b131-f6f10e75b9ef.dat

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            condense	true
            convert_from	"s"
            dbkey	"?"
            strip	true

    • Step 19: Estimated homozygous read coverage:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 20: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpi8i0xjhs/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpi8i0xjhs/files/7/4/3/dataset_743df84e-ffd6-4868-b131-f6f10e75b9ef.dat' 'c3' T '/tmp/tmpi8i0xjhs/job_working_directory/000/15/outputs/dataset_d67a82f7-f02d-409b-9204-7dfb498aad02.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c3"
            dbkey	"?"
            delimiter	"T"

    • Step 3: HiC reverse reads:

      • step_state: scheduled

    • Step 21: toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastq.gz"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            advanced_options	{"__current_case__": 0, "advanced_selector": "blank"}
            assembly_options	{"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"}
            bins_out	false
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_bits	"32"
            hic_partition	{"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 1, "src": "hda"}]}, "h2": {"values": [{"id": 2, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null}
            log_out	true
            mode	{"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 2, "src": "hdca"}]}}
            ont_integration	{"__current_case__": 0, "ont_integration_selector": "blank"}
            purge_options	{"__current_case__": 0, "purge_selector": "blank"}
            scaffolding_options	{"__current_case__": 0, "scaffold_selector": "blank"}

    • Step 22: Estimated genome size:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 23: Raw Unitig Image:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fontsize	None
            height	"2000"
            lengths	false
            names	false
            nodewidth	"25.0"
            output_format	"png"
            width	None

    • Step 24: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 26: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 28: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 4: Genomescope Summary:

      • step_state: scheduled

    • Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 32: Data Prep Hap2:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"557ca45de86311ee908b317db63fc5b3"
                chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"557ca45de86311ee908b317db63fc5b3"
                chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"557ca45de86311ee908b317db63fc5b3"
                chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"557ca45de86311ee908b317db63fc5b3"
                chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"557ca45de86311ee908b317db63fc5b3"
                chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 33: Data Prep Hap1:

      • step_state: new

      • Subworkflow Steps

        • Step 1: gfa_stats:

          • step_state: scheduled

        • Step 2: sort1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"557ca45ee86311ee908b317db63fc5b3"
                chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                column	"2"
                column_set	[]
                dbkey	"?"
                header_lines	"0"
                order	"DESC"
                style	"num"

        • Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"557ca45ee86311ee908b317db63fc5b3"
                chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                code	"{total += $2; $3 = total}1"
                dbkey	"?"

        • Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"557ca45ee86311ee908b317db63fc5b3"
                chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                grouping	""
                header_in	false
                header_out	false
                ignore_case	false
                narm	false
                need_sort	false
                operations	[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]
                print_full_line	false

        • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"557ca45ee86311ee908b317db63fc5b3"
                chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                exp	"1"
                iterate	"yes"

        • Step 6: param_value_from_file:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is paused

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"tabular"
                __workflow_invocation_uuid__	"557ca45ee86311ee908b317db63fc5b3"
                chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                param_type	"integer"
                remove_newlines	true

        • Step 7: Unlabelled step:

          • step_state: new

        • Step 8: Unlabelled step:

          • step_state: new

    • Step 34: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 35: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"s/_path//g"
            dbkey	"?"

    • Step 36: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap2\"}; {print}; "
            dbkey	"?"

    • Step 37: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN{print \"Metric\\thap1\"}; {print}; "
            dbkey	"?"

    • Step 38: Plot Data:

      • step_state: new

      • Subworkflow Steps

    • Step 39: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image", "gff"]

    • Step 40: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            label	"output_merqury"
            mode	{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 43, "src": "hda"}]}, "assembly_02": {"values": [{"id": 42, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"}
            output_add_headers	true
            output_selector	["qv", "plots", "stats", "log", "hist"]

    • Step 5: Genomescope Model Parameters:

      • step_state: scheduled

    • Step 41: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "miniprot": false, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 1, "selector": "download"}
            outputs	["short_summary", "missing", "image", "gff"]

    • Step 42: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2"
            dbkey	"?"
            delimiter	"T"

    • Step 43: Paste1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"557ca45ce86311ee908b317db63fc5b3"
            chromInfo	"/tmp/tmpi8i0xjhs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            delimiter	"T"

    • Step 6: Meryl Database:

      • step_state: scheduled

    • Step 7: Lineage:

      • step_state: scheduled

    • Step 8: Name for Haplotype 1:

      • step_state: scheduled

    • Step 9: Name for Haplotype 2:

      • step_state: scheduled

    • Step 10: Bits for bloom filter:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Final state of invocation b8c504e790b945ee is [failed]. Failed to run workflow, at least one job is in [error] state.

    • history_id

      • b8c504e790b945ee

    • history_state

      • error

    • invocation_id

      • b8c504e790b945ee

    • invocation_state

      • failed

    • messages

      • [{'dependent_workflow_step_id': 5, 'hda_id': '6f75fd5d9bdf6b19', 'reason': 'dataset_failed', 'workflow_step_id': 6}]

    • workflow_id

      • 70d0dca2ad4f2ac7