Updating workflows/variant-calling/generic-variant-calling-wgs-pe from 0.1.1 to 0.1.2 #310

gxydevbot · 2023-11-28T01:46:46Z

Hello! This is an automated update of the following workflow: workflows/variant-calling/generic-variant-calling-wgs-pe. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1

The workflow release number has been updated from 0.1.1 to 0.1.2.

github-actions · 2024-03-05T21:41:42Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`false`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpz4c4n4id/files/7/d/9/dataset_7d908bfb-60a4-4d5b-8cca-711b00fc6485.dat' 'ERR3485802.fastq.gz' && ln -sf '/tmp/tmpz4c4n4id/files/5/6/f/dataset_56feda9e-76e3-4092-83fc-7c3af0900fb1.dat' 'ERR3485802_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastq.gz'   -i 'ERR3485802.fastq.gz' -o first.fastq.gz  -I 'ERR3485802_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                                          &&  mv first.fastq.gz '/tmp/tmpz4c4n4id/job_working_directory/000/4/outputs/dataset_c5823120-23f5-4e3c-9a86-e323f6b92114.dat' && mv second.fastq.gz '/tmp/tmpz4c4n4id/job_working_directory/000/4/outputs/dataset_eedb4b3f-888a-4a9b-94be-53f2eb6e6182.dat'

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1252, in prepare
    tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/evaluation.py", line 140, in set_compute_environment
    self._validate_incoming(incoming)
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/evaluation.py", line 283, in _validate_incoming
    visit_input_values(self.tool.inputs, incoming, validate_inputs)
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 208, in visit_input_values
    visit_input_values(
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 224, in visit_input_values
    callback_helper(
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 159, in callback_helper
    new_value = callback(**args)
                ^^^^^^^^^^^^^^^^
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/evaluation.py", line 280, in validate_inputs
    value = input.from_json(value, request_context, context)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/parameters/basic.py", line 2125, in from_json
    raise ParameterValueError("specify a dataset of the required format / build for parameter", self.name)
galaxy.tools.parameters.basic.ParameterValueError: parameter 'input': specify a dataset of the required format / build for parameter

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 28042ee027c0dd35
- history_state
  - error
- invocation_id
  - 28042ee027c0dd35
- invocation_state
  - scheduled
- workflow_id
  - 28042ee027c0dd35

github-actions · 2024-06-28T12:34:58Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`false`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpfssbqaga/files/5/d/7/dataset_5d7f8f65-aab6-43ee-ab13-5a3bb2db3f08.dat' 'ERR3485802.fastq.gz' && ln -sf '/tmp/tmpfssbqaga/files/4/7/8/dataset_478e2043-630b-4ce3-98f1-7ad29f5575c7.dat' 'ERR3485802_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastq.gz'   -i 'ERR3485802.fastq.gz' -o first.fastq.gz  -I 'ERR3485802_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                                          &&  mv first.fastq.gz '/tmp/tmpfssbqaga/job_working_directory/000/4/outputs/dataset_9672ad49-fdb6-41c3-9783-88ba91d60bb5.dat' && mv second.fastq.gz '/tmp/tmpfssbqaga/job_working_directory/000/4/outputs/dataset_6436c89c-73af-437a-8d25-e59d9f7491d6.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 6d1903d2a7697dff
- history_state
  - error
- invocation_id
  - 6d1903d2a7697dff
- invocation_state
  - scheduled
- workflow_id
  - 6d1903d2a7697dff

gxydevbot · 2024-09-23T14:55:43Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-23T15:18:06Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpzlky_v4l/files/1/8/8/dataset_188e7349-c305-4172-8054-fdbd5e8cb3e3.dat' 'ERR3485802.fastq.gz' && ln -sf '/tmp/tmpzlky_v4l/files/4/8/a/dataset_48a90d04-02c1-4211-a892-4f753a5521c0.dat' 'ERR3485802_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastq.gz'   -i 'ERR3485802.fastq.gz' -o first.fastq.gz  -I 'ERR3485802_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmpzlky_v4l/job_working_directory/000/4/outputs/dataset_464ccfaf-9e86-4d49-a2bb-7d08e2b66aee.dat' && mv second.fastq.gz '/tmp/tmpzlky_v4l/job_working_directory/000/4/outputs/dataset_4bd7be6f-be15-486a-a72d-0595b22f6498.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 8d215961e677b8ba
- history_state
  - error
- invocation_id
  - 8d215961e677b8ba
- invocation_state
  - scheduled
- workflow_id
  - 8d215961e677b8ba

…m 0.1.1 to 0.1.2

gxydevbot · 2024-09-24T14:31:14Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-24T14:40:04Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpv1gad90b/files/8/d/7/dataset_8d703642-fdfc-4d03-8fc3-7f112a5db3ad.dat' 'ERR3485802.fastq.gz' && ln -sf '/tmp/tmpv1gad90b/files/2/f/c/dataset_2fcc3bbb-84bf-4110-b851-27454cb22253.dat' 'ERR3485802_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastq.gz'   -i 'ERR3485802.fastq.gz' -o first.fastq.gz  -I 'ERR3485802_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmpv1gad90b/job_working_directory/000/4/outputs/dataset_cfa7c789-6609-4254-b069-66ee469dccc3.dat' && mv second.fastq.gz '/tmp/tmpv1gad90b/job_working_directory/000/4/outputs/dataset_5e778c48-66e3-43a6-a1cf-6c57556f6aa1.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - eaeec6be92929b42
- history_state
  - error
- invocation_id
  - eaeec6be92929b42
- invocation_state
  - scheduled
- workflow_id
  - eaeec6be92929b42

gxydevbot changed the title ~~Updating workflows/variant-calling/generic-variant-calling-wgs-pe from 0.1.1 to 0.1.2~~ Updating workflows/variant-calling/generic-variant-calling-wgs-pe from 0.1.1 to 0.1.2 Mar 5, 2024

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from 4fd752a to efa4703 Compare September 23, 2024 14:55

Updating workflows/variant-calling/generic-variant-calling-wgs-pe fro…

7c636a0

…m 0.1.1 to 0.1.2

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from efa4703 to 7c636a0 Compare September 24, 2024 14:31

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Updating workflows/variant-calling/generic-variant-calling-wgs-pe from 0.1.1 to 0.1.2 #310

Updating workflows/variant-calling/generic-variant-calling-wgs-pe from 0.1.1 to 0.1.2 #310

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

Updating workflows/variant-calling/generic-variant-calling-wgs-pe from 0.1.1 to 0.1.2 #310

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Updating workflows/variant-calling/generic-variant-calling-wgs-pe from 0.1.1 to 0.1.2 #310

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Workflow invocation details

github-actions bot commented Jun 28, 2024

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Workflow invocation details

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