Updating workflows/variant-calling/haploid-variant-calling-wgs-pe from 0.1 to 0.2 #587

gxydevbot · 2024-11-04T05:11:52Z

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/fastp/fastp/0.23.2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18
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/1.20+galaxy3
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/devteam/picard/picard_MarkDuplicates/2.18.2.2 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0
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/1.24.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0

The workflow release number has been updated from 0.1 to 0.2.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

github-actions · 2024-11-04T05:25:09Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ WGS-PE-variant-calling-in-haploid-system.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: Annotation GTF:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq viterbi --ref 'reference.fa'  --defqual 2 --out tmp.bam '/tmp/tmprsgjhw6k/files/4/1/4/dataset_414cf091-fae9-4c6a-bd70-e5e128f751e7.dat' &&  samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmprsgjhw6k/job_working_directory/000/20/outputs/dataset_a23283d2-66a5-4346-b41a-6fe604d49140.dat' tmp.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"}`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq viterbi --ref 'reference.fa'  --defqual 2 --out tmp.bam '/tmp/tmprsgjhw6k/files/3/9/f/dataset_39fcddb1-619b-418c-aa8e-8a1756f41fb4.dat' &&  samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmprsgjhw6k/job_working_directory/000/21/outputs/dataset_4addbe06-522b-43ae-8624-f5b59c083199.dat' tmp.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  ln -s '/tmp/tmprsgjhw6k/files/a/2/3/dataset_a23283d2-66a5-4346-b41a-6fe604d49140.dat' reads.bam && ln -s -f '/tmp/tmprsgjhw6k/files/_metadata_files/5/3/2/metadata_532e6e30-686a-416b-8008-01030c7a13e1.dat' reads.bam.bai &&   lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose  --ref 'reference.fa' --out variants.vcf --call-indels   --min-cov 10 --max-depth 1000000  --min-bq 20 --min-alt-bq 20    --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0  --sig 0.01 --bonf dynamic   reads.bam 2>&1  || (tool_exit_code=$? && cat "$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit $tool_exit_code)  && echo set_lofreq_standard

Exit Code:

```
0
```

Standard Output:

INFO [2024-11-04 05:23:28,346]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 10 --max-depth 1000000 --min-bq 20 --min-alt-bq 20 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam

INFO [2024-11-04 05:23:28,374]: Adding 19 commands to mp-pool
Checking the headers and starting positions of 19 files
Number of substitution tests performed: 189
Number of indel tests performed: 21
INFO [2024-11-04 05:23:32,058]: Executing lofreq filter -i /tmp/tmprsgjhw6k/tmp/lofreq2_call_parallel_6ah89gq/concat.vcf.gz -o variants.vcf --snvqual-thresh 43 --indelqual-thresh 33

set_lofreq_standard

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
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": "20", "min_bq": "20"}, "coverage": {"max_depth": "1000000", "min_cov": "10"}, "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/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 2, "bonf": "dynamic", "filter_type": "set_lofreq_standard", "others": "", "sig": "0.01"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  ln -s '/tmp/tmprsgjhw6k/files/4/a/d/dataset_4addbe06-522b-43ae-8624-f5b59c083199.dat' reads.bam && ln -s -f '/tmp/tmprsgjhw6k/files/_metadata_files/a/2/5/metadata_a2596e11-673c-47d0-81ef-99015af089a4.dat' reads.bam.bai &&   lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose  --ref 'reference.fa' --out variants.vcf --call-indels   --min-cov 10 --max-depth 1000000  --min-bq 20 --min-alt-bq 20    --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0  --sig 0.01 --bonf dynamic   reads.bam 2>&1  || (tool_exit_code=$? && cat "$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit $tool_exit_code)  && echo set_lofreq_standard

Exit Code:

```
0
```

Standard Output:

INFO [2024-11-04 05:23:28,342]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 10 --max-depth 1000000 --min-bq 20 --min-alt-bq 20 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam

INFO [2024-11-04 05:23:28,372]: Adding 19 commands to mp-pool
Checking the headers and starting positions of 19 files
Number of substitution tests performed: 189
Number of indel tests performed: 20
INFO [2024-11-04 05:23:32,237]: Executing lofreq filter -i /tmp/tmprsgjhw6k/tmp/lofreq2_call_parallellxshxa5k/concat.vcf.gz -o variants.vcf --snvqual-thresh 43 --indelqual-thresh 33

set_lofreq_standard

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
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": "20", "min_bq": "20"}, "coverage": {"max_depth": "1000000", "min_cov": "10"}, "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/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 2, "bonf": "dynamic", "filter_type": "set_lofreq_standard", "others": "", "sig": "0.01"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmprsgjhw6k/job_working_directory/000/24/configs/tmpuy09tbmz' '/tmp/tmprsgjhw6k/files/6/e/d/dataset_6edcf9ec-c0dc-48b0-9a35-fae64b8f1806.dat' > '/tmp/tmprsgjhw6k/job_working_directory/000/24/outputs/dataset_9194ee81-fd89-4f43-835d-6382959a4ba8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
chromInfo	`"/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^#/ { print; next } ($4 ~ /^[ACGT]$/ && $5 ~ /^[ACGT]$/) { print }"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmprsgjhw6k/job_working_directory/000/25/configs/tmpgb4n6s_7' '/tmp/tmprsgjhw6k/files/0/8/b/dataset_08bc1284-9ad7-41ef-b0f8-38a44d94b922.dat' > '/tmp/tmprsgjhw6k/job_working_directory/000/25/outputs/dataset_0aef1599-8d00-46b4-b279-c0c11d1eb558.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
chromInfo	`"/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^#/ { print; next } ($4 ~ /^[ACGT]$/ && $5 ~ /^[ACGT]$/) { print }"`
dbkey	`"?"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmprsgjhw6k/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"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 15, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Job 2:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmprsgjhw6k/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"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 15, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
chromInfo	`"/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
empty_text	`"."`
extract	`"CHROM POS FILTER REF ALT DP AF DP4 SB EFF[].IMPACT EFF[].FUNCLASS EFF[].EFFECT EFF[].GENE EFF[].CODON EFF[].AA EFF[*].TRID"`
one_effect_per_line	`true`
separator	`""`

Job 2:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
chromInfo	`"/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
empty_text	`"."`
extract	`"CHROM POS FILTER REF ALT DP AF DP4 SB EFF[].IMPACT EFF[].FUNCLASS EFF[].EFFECT EFF[].GENE EFF[].CODON EFF[].AA EFF[*].TRID"`
one_effect_per_line	`true`
separator	`""`

Step 16: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
chromInfo	`"/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 0, "add_name": true, "place_name": "same_multiple"}`
one_header	`true`

Step 3: Genome fasta:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmprsgjhw6k/files/8/2/5/dataset_8250b76f-78c8-4834-accb-30c5d5747bc6.dat' 'ERR018930.fastqsanger.gz' && ln -sf '/tmp/tmprsgjhw6k/files/8/d/3/dataset_8d3f8427-6300-4aa9-aa20-deb1ab128523.dat' 'ERR018930_R2.fastqsanger.gz' &&  cp '/tmp/tmprsgjhw6k/job_working_directory/000/7/configs/tmp6s_591_1' galaxy.json &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR018930.fastqsanger.gz'   -i 'ERR018930.fastqsanger.gz'   -I 'ERR018930_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmprsgjhw6k/job_working_directory/000/7/outputs/dataset_09699904-aedd-4004-9aeb-6bf22d2296e2.dat' && mv second.fastqsanger.gz '/tmp/tmprsgjhw6k/job_working_directory/000/7/outputs/dataset_1984aff0-89ca-4528-abdd-205d9eee3f03.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 7337
total bases: 555502
Q20 bases: 496161(89.3176%)
Q30 bases: 321585(57.8909%)

Read2 before filtering:
total reads: 7337
total bases: 555512
Q20 bases: 501389(90.2571%)
Q30 bases: 309357(55.6886%)

Read1 after filtering:
total reads: 7337
total bases: 555502
Q20 bases: 496161(89.3176%)
Q30 bases: 321585(57.8909%)

Read2 after filtering:
total reads: 7337
total bases: 555512
Q20 bases: 501389(90.2571%)
Q30 bases: 309357(55.6886%)

Filtering result:
reads passed filter: 14674
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 0
bases trimmed due to adapters: 0

Duplication rate: 0.0408886%

Insert size peak (evaluated by paired-end reads): 108

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for ERR018930.fastqsanger.gz -i ERR018930.fastqsanger.gz -I ERR018930_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz 
fastp v0.23.4, time used: 1 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
chromInfo	`"/tmp/tmprsgjhw6k/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}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Job 2:

Job state is ok

Command Line:

ln -sf '/tmp/tmprsgjhw6k/files/5/3/b/dataset_53be5bb6-10ae-46d7-a9b4-bebe9e7a6ac2.dat' 'ERR1035492.fastqsanger.gz' && ln -sf '/tmp/tmprsgjhw6k/files/a/8/e/dataset_a8e85b43-d213-441a-a5dc-acdc1ea5df54.dat' 'ERR1035492_R2.fastqsanger.gz' &&  cp '/tmp/tmprsgjhw6k/job_working_directory/000/8/configs/tmpdkopod5b' galaxy.json &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR1035492.fastqsanger.gz'   -i 'ERR1035492.fastqsanger.gz'   -I 'ERR1035492_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmprsgjhw6k/job_working_directory/000/8/outputs/dataset_f8f18331-4568-4a28-9b70-354a4e4a2bc0.dat' && mv second.fastqsanger.gz '/tmp/tmprsgjhw6k/job_working_directory/000/8/outputs/dataset_a3b64c44-3692-4a26-9f59-e48022458c52.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 6031
total bases: 602346
Q20 bases: 585185(97.151%)
Q30 bases: 549984(91.307%)

Read2 before filtering:
total reads: 6031
total bases: 602346
Q20 bases: 576449(95.7006%)
Q30 bases: 529319(87.8762%)

Read1 after filtering:
total reads: 6031
total bases: 602346
Q20 bases: 585185(97.151%)
Q30 bases: 549984(91.307%)

Read2 after filtering:
total reads: 6031
total bases: 602346
Q20 bases: 576449(95.7006%)
Q30 bases: 529319(87.8762%)

Filtering result:
reads passed filter: 12062
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 0
bases trimmed due to adapters: 0

Duplication rate: 0.381363%

Insert size peak (evaluated by paired-end reads): 165

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for ERR1035492.fastqsanger.gz -i ERR1035492.fastqsanger.gz -I ERR1035492_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz 
fastp v0.23.4, time used: 1 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
chromInfo	`"/tmp/tmprsgjhw6k/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}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 4, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p '/tmp/tmprsgjhw6k/job_working_directory/000/9/outputs/dataset_96dfaed8-9bc3-458d-8724-9924245b846e_files/snpeff_db' && mkdir -p snpeff_output/'snpeff_db' &&  ln -s '/tmp/tmprsgjhw6k/files/8/7/f/dataset_87f491bf-e94b-481e-8bfd-bba8dc4681d2.dat' 'snpeff_output/snpeff_db/sequences.fa.gz' && ln -s '/tmp/tmprsgjhw6k/files/6/0/5/dataset_6055fbce-5604-4838-8b19-b422f8c5cd19.dat' 'snpeff_output/snpeff_db/genes.gtf' &&  snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m build -noCheckCds -noCheckProtein -v -configOption 'snpeff_db'.genome='snpeff_db' -configOption 'snpeff_db'.codonTable='Standard' -gtf22 -dataDir "$(pwd)/snpeff_output" 'snpeff_db' && mv snpeff_output/'snpeff_db'/*.bin '/tmp/tmprsgjhw6k/job_working_directory/000/9/outputs/dataset_96dfaed8-9bc3-458d-8724-9924245b846e_files/snpeff_db' && echo 'snpeff_db.genome : snpeff_db' >> '/tmp/tmprsgjhw6k/job_working_directory/000/9/outputs/dataset_96dfaed8-9bc3-458d-8724-9924245b846e_files'/snpEff.config && echo 'snpeff_db.codonTable : Standard' >> '/tmp/tmprsgjhw6k/job_working_directory/000/9/outputs/dataset_96dfaed8-9bc3-458d-8724-9924245b846e_files'/snpEff.config

Exit Code:

```
0
```

Standard Error:

00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'snpeff_db'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'snpeff_db'
00:00:00 Reading config file: /tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'snpeff_db'
00:00:01 done
00:00:01 Reading GTF22 data file  : '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/genes.gtf'
00:00:01 Reading file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/genes.gtf'
....................................................................................................
		10000	....................................................................................................
		20000	..............................................00:00:03 
	Total: 24693 markers added.
00:00:03 Create exons from CDS (if needed): 
00:00:03 Exons created for 1466 transcripts.
00:00:03 Deleting redundant exons (if needed): 
.
		0	............................................00:00:03 	Total transcripts with deleted exons: 4424
00:00:03 Collapsing zero length introns (if needed): 
00:00:04 	Total collapsed transcripts: 0
00:00:04 	Reading sequences   :
00:00:04 	FASTA file: '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/genomes/snpeff_db.fa' not found.
00:00:04 	Reading FASTA file: '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequences.fa'
00:00:04 		Reading sequence 'NC_009906.1', length: 830022
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (174 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (381 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009907.1', length: 755035
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (158 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (394 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009908.2', length: 1011127
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (218 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (578 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009909.1', length: 876622
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (203 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (548 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009910.1', length: 1370936
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (312 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (806 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009911.1', length: 1033388
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (241 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (634 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009912.1', length: 1497819
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (343 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (901 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009913.1', length: 1678596
00:00:04 		Adding genomic sequences to genes: 
00:00:05 	Done (368 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (945 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NC_009914.1', length: 1923364
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (430 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (1173 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NC_009915.1', length: 1419739
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (317 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (753 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NC_009916.1', length: 2067354
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (444 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (1225 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NC_009917.1', length: 3004884
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (676 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (1795 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NC_009918.1', length: 2031768
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (442 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (1178 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NC_009919.1', length: 3120417
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (682 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (1662 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852640.1', length: 1000
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852639.1', length: 995
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852638.1', length: 877
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852637.1', length: 585
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852636.1', length: 1026
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852635.1', length: 900
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852634.1', length: 759
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852633.1', length: 1551
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852632.1', length: 563
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852631.1', length: 748
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852630.1', length: 1037
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852629.1', length: 416
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852628.1', length: 769
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852627.1', length: 1184
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852626.1', length: 900
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852625.1', length: 1255
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852624.1', length: 1294
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852623.1', length: 927
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852622.1', length: 664
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852621.1', length: 883
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852620.1', length: 1143
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852619.1', length: 652
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852618.1', length: 1396
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852617.1', length: 2007
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852616.1', length: 648
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852615.1', length: 2179
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852614.1', length: 786
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852613.1', length: 736
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852612.1', length: 1033
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852611.1', length: 2123
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852610.1', length: 3939
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852609.1', length: 1375
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (1 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (2 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852608.1', length: 1001
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852607.1', length: 908
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852606.1', length: 1938
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852605.1', length: 879
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852604.1', length: 3240
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852603.1', length: 803
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852602.1', length: 535
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852601.1', length: 1041
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852600.1', length: 877
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852599.1', length: 1281
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852598.1', length: 1004
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852597.1', length: 992
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852596.1', length: 1431
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852595.1', length: 1034
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852594.1', length: 785
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852593.1', length: 936
00:00:06 		Adding genomic sequences to genes: 
00:00:06 	Done (0 sequences added).
00:00:06 		Adding genomic sequences to exons: 
00:00:06 	Done (0 sequences added, 0 ignored).
00:00:06 		Reading sequence 'NW_001852592.1', length: 952
00:00:06 		Adding genomic sequences to genes:
..
d
#		'NW_001851052.1'	723	Standard
#		'NW_001851247.1'	723	Standard
#		'NW_001850604.1'	722	Standard
#		'NW_001851896.1'	722	Standard
#		'NW_001852533.1'	722	Standard
#		'NW_001850697.1'	721	Standard
#		'NW_001852332.1'	721	Standard
#		'NW_001850827.1'	720	Standard
#		'NW_001850835.1'	720	Standard
#		'NW_001850932.1'	720	Standard
#		'NW_001851438.1'	720	Standard
#		'NW_001851764.1'	720	Standard
#		'NW_001851031.1'	719	Standard
#		'NW_001851731.1'	719	Standard
#		'NW_001851442.1'	718	Standard
#		'NW_001850386.1'	717	Standard
#		'NW_001852233.1'	717	Standard
#		'NW_001850575.1'	716	Standard
#		'NW_001851005.1'	716	Standard
#		'NW_001850407.1'	715	Standard
#		'NW_001850696.1'	715	Standard
#		'NW_001850996.1'	715	Standard
#		'NW_001850658.1'	714	Standard
#		'NW_001850883.1'	714	Standard
#		'NW_001851045.1'	714	Standard
#		'NW_001851251.1'	714	Standard
#		'NW_001850065.1'	713	Standard
#		'NW_001850479.1'	713	Standard
#		'NW_001850629.1'	713	Standard
#		'NW_001850754.1'	712	Standard
#		'NW_001850759.1'	711	Standard
#		'NW_001850945.1'	711	Standard
#		'NW_001851278.1'	711	Standard
#		'NW_001850412.1'	709	Standard
#		'NW_001851865.1'	709	Standard
#		'NW_001850487.1'	708	Standard
#		'NW_001850480.1'	707	Standard
#		'NW_001850645.1'	705	Standard
#		'NW_001850859.1'	705	Standard
#		'NW_001851893.1'	705	Standard
#		'NW_001850749.1'	704	Standard
#		'NW_001851858.1'	703	Standard
#		'NW_001852190.1'	703	Standard
#		'NW_001850876.1'	702	Standard
#		'NW_001851524.1'	701	Standard
#		'NW_001850359.1'	700	Standard
#		'NW_001850753.1'	700	Standard
#		'NW_001851060.1'	700	Standard
#		'NW_001851908.1'	700	Standard
#		'NW_001850450.1'	699	Standard
#		'NW_001850602.1'	699	Standard
#		'NW_001851328.1'	698	Standard
#		'NW_001852308.1'	698	Standard
#		'NW_001851545.1'	696	Standard
#		'NW_001850699.1'	695	Standard
#		'NW_001851015.1'	695	Standard
#		'NW_001852340.1'	695	Standard
#		'NW_001850418.1'	693	Standard
#		'NW_001850686.1'	693	Standard
#		'NW_001850989.1'	693	Standard
#		'NW_001851933.1'	693	Standard
#		'NW_001851946.1'	693	Standard
#		'NW_001852141.1'	693	Standard
#		'NW_001850504.1'	692	Standard
#		'NW_001850632.1'	692	Standard
#		'NW_001852009.1'	692	Standard
#		'NW_001852071.1'	692	Standard
#		'NW_001850349.1'	691	Standard
#		'NW_001850825.1'	691	Standard
#		'NW_001851785.1'	691	Standard
#		'NW_001850649.1'	690	Standard
#		'NW_001851121.1'	690	Standard
#		'NW_001852499.1'	690	Standard
#		'NW_001850411.1'	688	Standard
#		'NW_001850533.1'	688	Standard
#		'NW_001852537.1'	687	Standard
#		'NW_001850096.1'	686	Standard
#		'NW_001850957.1'	686	Standard
#		'NW_001852305.1'	686	Standard
#		'NW_001850460.1'	685	Standard
#		'NW_001851222.1'	685	Standard
#		'NW_001851940.1'	685	Standard
#		'NW_001850334.1'	684	Standard
#		'NW_001850454.1'	684	Standard
#		'NW_001850942.1'	684	Standard
#		'NW_001850374.1'	682	Standard
#		'NW_001850492.1'	681	Standard
#		'NW_001850494.1'	681	Standard
#		'NW_001850975.1'	681	Standard
#		'NW_001850398.1'	680	Standard
#		'NW_001851640.1'	679	Standard
#		'NW_001852294.1'	679	Standard
#		'NW_001851769.1'	678	Standard
#		'NW_001850338.1'	677	Standard
#		'NW_001850419.1'	677	Standard
#		'NW_001851887.1'	677	Standard
#		'NW_001850100.1'	676	Standard
#		'NW_001850512.1'	676	Standard
#		'NW_001851745.1'	676	Standard
#		'NW_001850524.1'	675	Standard
#		'NW_001851245.1'	673	Standard
#		'NW_001852350.1'	673	Standard
#		'NW_001850586.1'	672	Standard
#		'NW_001850776.1'	672	Standard
#		'NW_001852395.1'	672	Standard
#		'NW_001851038.1'	671	Standard
#		'NW_001850867.1'	670	Standard
#		'NW_001851275.1'	670	Standard
#		'NW_001851936.1'	670	Standard
#		'NW_001850718.1'	668	Standard
#		'NW_001850862.1'	668	Standard
#		'NW_001851172.1'	668	Standard
#		'NW_001852353.1'	668	Standard
#		'NW_001850375.1'	667	Standard
#		'NW_001850636.1'	667	Standard
#		'NW_001852182.1'	667	Standard
#		'NW_001852426.1'	667	Standard
#		'NW_001850433.1'	664	Standard
#		'NW_001852622.1'	664	Standard
#		'NW_001850067.1'	663	Standard
#		'NW_001850491.1'	663	Standard
#		'NW_001849929.1'	661	Standard
#		'NW_001850748.1'	660	Standard
#		'NW_001851017.1'	660	Standard
#		'NW_001851932.1'	660	Standard
#		'NW_001850514.1'	658	Standard
#		'NW_001851679.1'	658	Standard
#		'NW_001851715.1'	656	Standard
#		'NW_001849982.1'	655	Standard
#		'NW_001852377.1'	655	Standard
#		'NW_001851939.1'	654	Standard
#		'NW_001852173.1'	654	Standard
#		'NW_001851501.1'	653	Standard
#		'NW_001852619.1'	652	Standard
#		'NW_001850901.1'	651	Standard
#		'NW_001850757.1'	648	Standard
#		'NW_001852616.1'	648	Standard
#		'NW_001850101.1'	646	Standard
#		'NW_001850875.1'	646	Standard
#		'NW_001852161.1'	645	Standard
#		'NW_001852025.1'	644	Standard
#		'NW_001851266.1'	643	Standard
#		'NW_001850370.1'	641	Standard
#		'NW_001852379.1'	640	Standard
#		'NW_001851298.1'	639	Standard
#		'NW_001851657.1'	639	Standard
#		'NW_001850455.1'	638	Standard
#		'NW_001852145.1'	638	Standard
#		'NW_001850477.1'	636	Standard
#		'NW_001850400.1'	634	Standard
#		'NW_001850443.1'	634	Standard
#		'NW_001850515.1'	633	Standard
#		'NW_001851387.1'	632	Standard
#		'NW_001851851.1'	632	Standard
#		'NW_001850560.1'	630	Standard
#		'NW_001850761.1'	630	Standard
#		'NW_001850368.1'	629	Standard
#		'NW_001851888.1'	629	Standard
#		'NW_001852297.1'	629	Standard
#		'NW_001850500.1'	628	Standard
#		'NW_001850499.1'	626	Standard
#		'NW_001850908.1'	626	Standard
#		'NW_001850371.1'	625	Standard
#		'NW_001850986.1'	625	Standard
#		'NW_001850336.1'	624	Standard
#		'NW_001850687.1'	624	Standard
#		'NW_001852365.1'	624	Standard
#		'NW_001852266.1'	623	Standard
#		'NW_001852378.1'	621	Standard
#		'NW_001850518.1'	620	Standard
#		'NW_001850849.1'	620	Standard
#		'NW_001851945.1'	620	Standard
#		'NW_001851891.1'	619	Standard
#		'NW_001851458.1'	618	Standard
#		'NW_001850830.1'	615	Standard
#		'NW_001850935.1'	614	Standard
#		'NW_001852111.1'	614	Standard
#		'NW_001850506.1'	613	Standard
#		'NW_001850674.1'	612	Standard
#		'NW_001850725.1'	609	Standard
#		'NW_001850501.1'	608	Standard
#		'NW_001850800.1'	606	Standard
#		'NW_001850874.1'	606	Standard
#		'NW_001851789.1'	603	Standard
#		'NW_001852326.1'	603	Standard
#		'NW_001851294.1'	601	Standard
#		'NW_001851186.1'	598	Standard
#		'NW_001851832.1'	598	Standard
#		'NW_001852296.1'	597	Standard
#		'NW_001850824.1'	594	Standard
#		'NW_001851830.1'	594	Standard
#		'NW_001851753.1'	593	Standard
#		'NW_001850000.1'	592	Standard
#		'NW_001850498.1'	590	Standard
#		'NW_001851290.1'	587	Standard
#		'NW_001851090.1'	585	Standard
#		'NW_001852637.1'	585	Standard
#		'NW_001850643.1'	583	Standard
#		'NW_001850401.1'	582	Standard
#		'NW_001850594.1'	582	Standard
#		'NW_001852116.1'	581	Standard
#		'NW_001850554.1'	579	Standard
#		'NW_001851024.1'	579	Standard
#		'NW_001850816.1'	578	Standard
#		'NW_001850822.1'	576	Standard
#		'NW_001850509.1'	575	Standard
#		'NW_001850635.1'	575	Standard
#		'NW_001850929.1'	575	Standard
#		'NW_001850369.1'	574	Standard
#		'NW_001850493.1'	574	Standard
#		'NW_001850395.1'	571	Standard
#		'NW_001851505.1'	570	Standard
#		'NW_001851631.1'	570	Standard
#		'NW_001850713.1'	565	Standard
#		'NW_001851809.1'	564	Standard
#		'NW_001850061.1'	563	Standard
#		'NW_001852632.1'	563	Standard
#		'NW_001851161.1'	562	Standard
#		'NW_001850765.1'	559	Standard
#		'NW_001850895.1'	558	Standard
#		'NW_001850978.1'	557	Standard
#		'NW_001850431.1'	551	Standard
#		'NW_001850709.1'	551	Standard
#		'NW_001850611.1'	550	Standard
#		'NW_001851035.1'	544	Standard
#		'NW_001850364.1'	543	Standard
#		'NW_001850701.1'	543	Standard
#		'NW_001850855.1'	539	Standard
#		'NW_001850597.1'	535	Standard
#		'NW_001852602.1'	535	Standard
#		'NW_001850655.1'	533	Standard
#		'NW_001852156.1'	531	Standard
#		'NW_001852269.1'	531	Standard
#		'NW_001850857.1'	529	Standard
#		'NW_001850333.1'	528	Standard
#		'NW_001850777.1'	526	Standard
#		'NW_001851162.1'	525	Standard
#		'NW_001851082.1'	522	Standard
#		'NW_001852486.1'	522	Standard
#		'NW_001852281.1'	521	Standard
#		'NW_001850666.1'	520	Standard
#		'NW_001850967.1'	518	Standard
#		'NW_001851126.1'	516	Standard
#		'NW_001850940.1'	515	Standard
#		'NW_001850796.1'	510	Standard
#		'NW_001850770.1'	508	Standard
#		'NW_001850871.1'	506	Standard
#		'NW_001851101.1'	495	Standard
#		'NW_001850814.1'	493	Standard
#		'NW_001850789.1'	491	Standard
#		'NW_001850928.1'	491	Standard
#		'NW_001850601.1'	488	Standard
#		'NW_001850841.1'	488	Standard
#		'NW_001850682.1'	485	Standard
#		'NW_001850663.1'	482	Standard
#		'NW_001852030.1'	480	Standard
#		'NW_001850376.1'	478	Standard
#		'NW_001850730.1'	478	Standard
#		'NW_001850614.1'	477	Standard
#		'NW_001850468.1'	475	Standard
#		'NW_001851859.1'	471	Standard
#		'NW_001851435.1'	468	Standard
#		'NW_001851845.1'	463	Standard
#		'NW_001850609.1'	461	Standard
#		'NW_001851377.1'	458	Standard
#		'NW_001850771.1'	456	Standard
#		'NW_001851274.1'	456	Standard
#		'NW_001850894.1'	455	Standard
#		'NW_001852355.1'	455	Standard
#		'NW_001852529.1'	454	Standard
#		'NW_001852035.1'	451	Standard
#		'NW_001850745.1'	447	Standard
#		'NW_001851895.1'	446	Standard
#		'NW_001852246.1'	446	Standard
#		'NW_001850952.1'	445	Standard
#		'NW_001850330.1'	441	Standard
#		'NW_001850705.1'	440	Standard
#		'NW_001850097.1'	438	Standard
#		'NW_001850537.1'	428	Standard
#		'NW_001850766.1'	428	Standard
#		'NW_001850406.1'	427	Standard
#		'NW_001850094.1'	426	Standard
#		'NW_001852530.1'	424	Standard
#		'NW_001850608.1'	419	Standard
#		'NW_001851375.1'	419	Standard
#		'NW_001851154.1'	417	Standard
#		'NW_001852055.1'	416	Standard
#		'NW_001852629.1'	416	Standard
#		'NW_001850671.1'	415	Standard
#		'NW_001852047.1'	412	Standard
#		'NW_001852202.1'	412	Standard
#		'NW_001852390.1'	411	Standard
#		'NW_001850898.1'	409	Standard
#		'NW_001850979.1'	409	Standard
#		'NW_001850920.1'	406	Standard
#		'NW_001850768.1'	403	Standard
#		'NW_001850782.1'	403	Standard
#		'NW_001850839.1'	401	Standard
#		'NW_001850783.1'	400	Standard
#		'NW_001850731.1'	398	Standard
#		'NW_001851261.1'	396	Standard
#		'NW_001850517.1'	393	Standard
#		'NW_001850931.1'	393	Standard
#		'NW_001850907.1'	390	Standard
#		'NW_001852391.1'	387	Standard
#		'NW_001850740.1'	386	Standard
#		'NW_001850956.1'	385	Standard
#		'NW_001850742.1'	384	Standard
#		'NW_001852125.1'	384	Standard
#		'NW_001850870.1'	382	Standard
#		'NW_001851899.1'	382	Standard
#		'NW_001850872.1'	380	Standard
#		'NW_001850739.1'	378	Standard
#		'NW_001851953.1'	378	Standard
#		'NW_001850598.1'	376	Standard
#		'NW_001851206.1'	376	Standard
#		'NW_001850831.1'	375	Standard
#		'NW_001850606.1'	374	Standard
#		'NW_001850747.1'	373	Standard
#		'NW_001850798.1'	372	Standard
#		'NW_001851053.1'	371	Standard
#		'NW_001850662.1'	370	Standard
#		'NW_001850969.1'	368	Standard
#		'NW_001850779.1'	367	Standard
#		'NW_001850919.1'	367	Standard
#		'NW_001850792.1'	366	Standard
#		'NW_001851975.1'	365	Standard
#		'NW_001850906.1'	364	Standard
#		'NW_001850853.1'	360	Standard
#		'NW_001850845.1'	359	Standard
#		'NW_001850780.1'	357	Standard
#		'NW_001852109.1'	356	Standard
#		'NW_001850954.1'	352	Standard
#		'NW_001852431.1'	352	Standard
#		'NW_001850772.1'	350	Standard
#		'NW_001851165.1'	350	Standard
#		'NW_001850600.1'	348	Standard
#		'NW_001850767.1'	347	Standard
#		'NW_001850923.1'	346	Standard
#		'NW_001850391.1'	344	Standard
#		'NW_001851284.1'	340	Standard
#		'NW_001851394.1'	338	Standard
#		'NW_001850781.1'	337	Standard
#		'NW_001851768.1'	337	Standard
#		'NW_001850763.1'	335	Standard
#		'NW_001850961.1'	332	Standard
#		'NW_001851861.1'	326	Standard
#		'NW_001851062.1'	318	Standard
#		'NW_001849951.1'	317	Standard
#		'NW_001850619.1'	315	Standard
#		'NW_001850842.1'	315	Standard
#		'NW_001851371.1'	313	Standard
#		'NW_001850860.1'	311	Standard
#		'NW_001850973.1'	311	Standard
#		'NW_001852103.1'	311	Standard
#		'NW_001850647.1'	310	Standard
#		'NW_001850762.1'	309	Standard
#		'NW_001851355.1'	308	Standard
#		'NW_001850850.1'	305	Standard
#		'NW_001851562.1'	305	Standard
#		'NW_001852189.1'	305	Standard
#		'NW_001850573.1'	304	Standard
#		'NW_001851986.1'	302	Standard
#		'NW_001852034.1'	300	Standard
#		'NW_001851255.1'	299	Standard
#		'NW_001850925.1'	297	Standard
#		'NW_001850424.1'	296	Standard
#		'NW_001850769.1'	296	Standard
#		'NW_001852496.1'	294	Standard
#		'NW_001850627.1'	293	Standard
#		'NW_001850795.1'	293	Standard
#		'NW_001851790.1'	292	Standard
#		'NW_001850755.1'	290	Standard
#		'NW_001850764.1'	290	Standard
#		'NW_001850793.1'	289	Standard
#		'NW_001852489.1'	284	Standard
#		'NW_001850735.1'	283	Standard
#		'NW_001851003.1'	283	Standard
#		'NW_001850807.1'	280	Standard
#		'NW_001850637.1'	272	Standard
#		'NW_001850703.1'	269	Standard
#		'NW_001851910.1'	267	Standard
#		'NW_001851178.1'	266	Standard
#		'NW_001850522.1'	265	Standard
#		'NW_001850959.1'	265	Standard
#		'NW_001852249.1'	262	Standard
#		'NW_001850465.1'	261	Standard
#		'NW_001850787.1'	260	Standard
#		'NW_001851429.1'	259	Standard
#		'NW_001850832.1'	255	Standard
#		'NW_001850656.1'	254	Standard
#		'NW_001850716.1'	252	Standard
#		'NW_001852069.1'	252	Standard
#		'NW_001851909.1'	251	Standard
#		'NW_001851999.1'	251	Standard
#		'NW_001850596.1'	250	Standard
#		'NW_001850854.1'	250	Standard
#		'NW_001852157.1'	250	Standard
#		'NW_001850720.1'	248	Standard
#		'NW_001850684.1'	244	Standard
#		'NW_001851920.1'	244	Standard
#		'NW_001851136.1'	243	Standard
#		'NW_001850852.1'	242	Standard
#		'NW_001850829.1'	241	Standard
#		'NW_001851952.1'	235	Standard
#		'NW_001850773.1'	234	Standard
#		'NW_001850823.1'	233	Standard
#		'NW_001851848.1'	233	Standard
#		'NW_001852108.1'	232	Standard
#		'NW_001850916.1'	230	Standard
#		'NW_001851743.1'	228	Standard
#		'NW_001850679.1'	226	Standard
#		'NW_001850971.1'	225	Standard
#		'NW_001851780.1'	225	Standard
#		'NW_001850634.1'	224	Standard
#		'NW_001850621.1'	223	Standard
#		'NW_001851970.1'	223	Standard
#		'NW_001851989.1'	223	Standard
#		'NW_001850702.1'	221	Standard
#		'NW_001852238.1'	221	Standard
#		'NW_001850803.1'	220	Standard
#		'NW_001851796.1'	220	Standard
#		'NW_001851311.1'	218	Standard
#		'NW_001851048.1'	217	Standard
#		'NW_001850977.1'	216	Standard
#		'NW_001850727.1'	215	Standard
#		'NW_001851238.1'	215	Standard
#		'NW_001850926.1'	213	Standard
#		'NW_001850924.1'	209	Standard
#		'NW_001852215.1'	209	Standard
#		'NW_001850861.1'	207	Standard
#		'NW_001851231.1'	200	Standard
#		'NW_001851799.1'	200	Standard
#-----------------------------------------------

00:00:12 Caracterizing exons by splicing (stage 1) : 
.............
00:00:12 Caracterizing exons by splicing (stage 2) : 
.............00:00:12 done.
00:00:12 [Optional] Rare amino acid annotations
WARNING_FILE_NOT_FOUND: Rare Amino Acid analysis: Cannot read protein sequence file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/protein.fa', nothing done.
00:00:12 Saving database
00:00:16 Saving sequences for chromosome 'NC_009914.1' to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009914.1.bin'
00:00:16 Saving sequences for chromosome 'NC_009916.1' to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009916.1.bin'
00:00:16 Saving sequences for chromosome 'NC_009917.1' to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009917.1.bin'
00:00:17 Saving sequences for chromosome 'NC_009918.1' to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009918.1.bin'
00:00:17 Saving sequences for chromosome 'NC_009919.1' to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009919.1.bin'
00:00:17 Saving sequences for small chromosmes to file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.bin'
00:00:19 [Optional] Reading regulation elements: GFF
WARNING_FILE_NOT_FOUND: Cannot read optional regulation file '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/regulation.gff', nothing done.
00:00:19 [Optional] Reading regulation elements: BED 
00:00:19 Cannot find optional regulation dir '/tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/regulation.bed/', nothing done.
00:00:19 [Optional] Reading motifs: GFF
WARNING_FILE_NOT_FOUND: Cannot open PWMs file /tmp/tmprsgjhw6k/job_working_directory/000/9/working/snpeff_output/snpeff_db/pwms.bin. Nothing done
00:00:19 Done
00:00:19 Done.

Standard Output:

..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
chromInfo	`"/tmp/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"snpeff_db"`
input_type	`{"__current_case__": 2, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_type_selector": "gtf", "reference_source": {"__current_case__": 1, "input_fasta": {"values": [{"id": 2, "src": "hda"}]}, "reference_source_selector": "history"}}`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1     -T '30' -h '5'    -Y   -q                           -R '@RG\tID:ERR018930\tSM:ERR018930\tPL:ILLUMINA\tLB:ERR018930'   'localref.fa' '/tmp/tmprsgjhw6k/files/0/9/6/dataset_09699904-aedd-4004-9aeb-6bf22d2296e2.dat' '/tmp/tmprsgjhw6k/files/1/9/8/dataset_1984aff0-89ca-4528-abdd-205d9eee3f03.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmprsgjhw6k/job_working_directory/000/11/outputs/dataset_29853fdd-ba77-48b7-a51d-2b8a7e675bad.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.16 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=54027382, availableWord=15801372
[BWTIncConstructFromPacked] 10 iterations done. 26064326 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 48149798 characters processed.
[bwt_gen] Finished constructing BWT in 23 iterations.
[bwa_index] 11.76 seconds elapse.
[bwa_index] Update BWT... 0.14 sec
[bwa_index] Pack forward-only FASTA... 0.10 sec
[bwa_index] Construct SA from BWT and Occ... 5.91 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 18.690 sec; CPU: 18.074 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (207, 242, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (33, 468)
[M::mem_pestat] mean and std.dev: (253.94, 65.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 555)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -t 1 -v 1 -T 30 -h 5 -Y -q -R @RG\tID:ERR018930\tSM:ERR018930\tPL:ILLUMINA\tLB:ERR018930 localref.fa /tmp/tmprsgjhw6k/files/0/9/6/dataset_09699904-aedd-4004-9aeb-6bf22d2296e2.dat /tmp/tmprsgjhw6k/files/1/9/8/dataset_1984aff0-89ca-4528-abdd-205d9eee3f03.dat
[main] Real time: 1.141 sec; CPU: 1.099 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
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/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 7, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 16, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"CN": null, "DS": null, "DT": null, "FO": null, "KS": null, "PG": null, "PI": null, "PL": "ILLUMINA", "PU": null, "__current_case__": 1, "read_group_id_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_lb_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "set"}`

Job 2:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmprsgjhw6k/files/5/c/3/dataset_5c3da7ae-9435-4e71-8061-78be0b529853.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1     -T '30' -h '5'    -Y   -q                           -R '@RG\tID:ERR1035492\tSM:ERR1035492\tPL:ILLUMINA\tLB:ERR1035492'   'localref.fa' '/tmp/tmprsgjhw6k/files/f/8/f/dataset_f8f18331-4568-4a28-9b70-354a4e4a2bc0.dat' '/tmp/tmprsgjhw6k/files/a/3/b/dataset_a3b64c44-3692-4a26-9f59-e48022458c52.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmprsgjhw6k/job_working_directory/000/12/outputs/dataset_de9f1abb-e8ec-4e9b-8531-1d576b3e553e.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.17 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=54027382, availableWord=15801372
[BWTIncConstructFromPacked] 10 iterations done. 26064326 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 48149798 characters processed.
[bwt_gen] Finished constructing BWT in 23 iterations.
[bwa_index] 11.71 seconds elapse.
[bwa_index] Update BWT... 0.15 sec
[bwa_index] Pack forward-only FASTA... 0.10 sec
[bwa_index] Construct SA from BWT and Occ... 5.80 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 18.396 sec; CPU: 17.937 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (185, 232, 297)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 521)
[M::mem_pestat] mean and std.dev: (246.23, 81.16)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 633)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -t 1 -v 1 -T 30 -h 5 -Y -q -R @RG\tID:ERR1035492\tSM:ERR1035492\tPL:ILLUMINA\tLB:ERR1035492 localref.fa /tmp/tmprsgjhw6k/files/f/8/f/dataset_f8f18331-4568-4a28-9b70-354a4e4a2bc0.dat /tmp/tmprsgjhw6k/files/a/3/b/dataset_a3b64c44-3692-4a26-9f59-e48022458c52.dat
[main] Real time: 0.945 sec; CPU: 0.928 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
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/tmprsgjhw6k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 8, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 16, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"CN": null, "DS": null, "DT": null, "FO": null, "KS": null, "PG": null, "PI": null, "PL": "ILLUMINA", "PU": null, "__current_case__": 1, "read_group_id_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_lb_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "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 ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmprsgjhw6k/files/2/9/8/dataset_29853fdd-ba77-48b7-a51d-2b8a7e675bad.dat' infile && ln -s '/tmp/tmprsgjhw6k/files/_metadata_files/b/f/0/metadata_bf01b080-1ec4-4f9d-b9fd-c179bb007ef5.dat' infile.bai &&               samtools view -@ $addthreads -b  -f 3 -F 0 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmprsgjhw6k/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"}}}

Job 2:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmprsgjhw6k/files/d/e/9/dataset_de9f1abb-e8ec-4e9b-8531-1d576b3e553e.dat' infile && ln -s '/tmp/tmprsgjhw6k/files/_metadata_files/7/3/c/metadata_73ce6f52-c356-447e-959d-a6d443ba0032.dat' infile.bai &&               samtools view -@ $addthreads -b  -f 3 -F 0 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmprsgjhw6k/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/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmprsgjhw6k/files/b/1/f/dataset_b1f6b30f-63df-4ae4-85b6-70f842176a71.dat' infile && ln -s '/tmp/tmprsgjhw6k/files/_metadata_files/f/1/3/metadata_f13a1cbe-205a-4a1c-9c6a-3aa6f8ba65b3.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmprsgjhw6k/job_working_directory/000/15/outputs/dataset_5ffd484f-96ba-4c1c-af93-bca99926f7c2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmprsgjhw6k/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`

Job 2:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmprsgjhw6k/files/6/4/6/dataset_6467edee-3a30-4ff4-aad6-ecd6c02da19b.dat' infile && ln -s '/tmp/tmprsgjhw6k/files/_metadata_files/8/3/e/metadata_83e07677-0d79-4441-891b-8b6d7d840f4e.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmprsgjhw6k/job_working_directory/000/16/outputs/dataset_00151697-aa08-45dc-a945-a8930f87a869.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmprsgjhw6k/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 9: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&   ln -sf '/tmp/tmprsgjhw6k/files/b/1/f/dataset_b1f6b30f-63df-4ae4-85b6-70f842176a71.dat' 'ERR018930' &&  picard MarkDuplicates  --INPUT 'ERR018930' --OUTPUT '/tmp/tmprsgjhw6k/job_working_directory/000/17/outputs/dataset_414cf091-fae9-4c6a-bd70-e5e128f751e7.dat'  --METRICS_FILE '/tmp/tmprsgjhw6k/job_working_directory/000/17/outputs/dataset_3616d219-d8fa-4153-aa5c-498ea936e5d1.dat'  --REMOVE_DUPLICATES 'true' --ASSUME_SORTED 'true'  --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES  --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100'   --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmprsgjhw6k/tmp
Nov 04, 2024 5:23:01 AM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmprsgjhw6k/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"`

Job 2:

Job state is ok

Command Line:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&   ln -sf '/tmp/tmprsgjhw6k/files/6/4/6/dataset_6467edee-3a30-4ff4-aad6-ecd6c02da19b.dat' 'ERR1035492' &&  picard MarkDuplicates  --INPUT 'ERR1035492' --OUTPUT '/tmp/tmprsgjhw6k/job_working_directory/000/18/outputs/dataset_39fcddb1-619b-418c-aa8e-8a1756f41fb4.dat'  --METRICS_FILE '/tmp/tmprsgjhw6k/job_working_directory/000/18/outputs/dataset_04c86bd6-57cc-4204-b620-2cf2e68dd790.dat'  --REMOVE_DUPLICATES 'true' --ASSUME_SORTED 'true'  --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES  --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100'   --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmprsgjhw6k/tmp
Nov 04, 2024 5:23:01 AM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmprsgjhw6k/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 10: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmprsgjhw6k/files/3/c/7/dataset_3c7835f2-2669-44ab-a34a-819e7863c5df.dat' 'multiqc_WDir/fastp_0/ERR018930fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/ERR018930fastp.json' || die "'report_title' or 'report_title' not found in the file" &&    ln -s '/tmp/tmprsgjhw6k/files/e/b/5/dataset_eb59d284-024a-4a6f-827f-31d8f8f38191.dat' 'multiqc_WDir/fastp_0/ERR1035492fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/ERR1035492fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/samtools_1 &&    mkdir 'multiqc_WDir/samtools_1/stats_0' &&      grep -q 'This file was produced by samtools stats' /tmp/tmprsgjhw6k/files/5/f/f/dataset_5ffd484f-96ba-4c1c-af93-bca99926f7c2.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'ERR018930'" && ln -s '/tmp/tmprsgjhw6k/files/5/f/f/dataset_5ffd484f-96ba-4c1c-af93-bca99926f7c2.dat' 'multiqc_WDir/samtools_1/stats_0/ERR018930'  &&    grep -q 'This file was produced by samtools stats' /tmp/tmprsgjhw6k/files/0/0/1/dataset_00151697-aa08-45dc-a945-a8930f87a869.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'ERR1035492'" && ln -s '/tmp/tmprsgjhw6k/files/0/0/1/dataset_00151697-aa08-45dc-a945-a8930f87a869.dat' 'multiqc_WDir/samtools_1/stats_0/ERR1035492'  &&    mkdir multiqc_WDir/picard_2 &&      mkdir 'multiqc_WDir/picard_2/markdups_0' &&    grep -q 'MarkDuplicates' /tmp/tmprsgjhw6k/files/3/6/1/dataset_3616d219-d8fa-4153-aa5c-498ea936e5d1.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'ERR018930'" && ln -s '/tmp/tmprsgjhw6k/files/3/6/1/dataset_3616d219-d8fa-4153-aa5c-498ea936e5d1.dat' 'multiqc_WDir/picard_2/markdups_0/ERR018930'  &&    grep -q 'MarkDuplicates' /tmp/tmprsgjhw6k/files/0/4/c/dataset_04c86bd6-57cc-4204-b620-2cf2e68dd790.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'ERR1035492'" && ln -s '/tmp/tmprsgjhw6k/files/0/4/c/dataset_04c86bd6-57cc-4204-b620-2cf2e68dd790.dat' 'multiqc_WDir/picard_2/markdups_0/ERR1035492'  &&     multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9ff130dc9a6c11efb160c573a96f40c7"`
chromInfo	`"/tmp/tmprsgjhw6k/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": 7, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 8, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - ccb3e58f5d9b49d5
- history_state
  - error
- invocation_id
  - ccb3e58f5d9b49d5
- invocation_state
  - scheduled
- workflow_id
  - ccb3e58f5d9b49d5

…m 0.1 to 0.2

gxydevbot · 2024-11-18T05:45:31Z

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

github-actions · 2024-11-18T05:55:24Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ WGS-PE-variant-calling-in-haploid-system.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: Annotation GTF:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp6rx0w62v/files/4/b/e/dataset_4bec5fbf-4d03-4114-ac85-e6dff7a4965a.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq viterbi --ref 'reference.fa'  --defqual 2 --out tmp.bam '/tmp/tmp6rx0w62v/files/c/b/c/dataset_cbc886bd-1a70-4d2b-9584-084dc7e0cc86.dat' &&  samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmp6rx0w62v/job_working_directory/000/20/outputs/dataset_34b068a0-7330-4015-8685-b0ccd4857dd7.dat' tmp.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"}`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp6rx0w62v/files/4/b/e/dataset_4bec5fbf-4d03-4114-ac85-e6dff7a4965a.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq viterbi --ref 'reference.fa'  --defqual 2 --out tmp.bam '/tmp/tmp6rx0w62v/files/a/2/4/dataset_a24f7cc3-0aee-4d2e-b79f-6d91c55f9d16.dat' &&  samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmp6rx0w62v/job_working_directory/000/21/outputs/dataset_685dfa07-80d4-4829-a421-e435f204d986.dat' tmp.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp6rx0w62v/files/4/b/e/dataset_4bec5fbf-4d03-4114-ac85-e6dff7a4965a.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  ln -s '/tmp/tmp6rx0w62v/files/3/4/b/dataset_34b068a0-7330-4015-8685-b0ccd4857dd7.dat' reads.bam && ln -s -f '/tmp/tmp6rx0w62v/files/_metadata_files/4/e/8/metadata_4e889fb7-434e-4ec9-8287-b345e7128a92.dat' reads.bam.bai &&   lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose  --ref 'reference.fa' --out variants.vcf --call-indels   --min-cov 10 --max-depth 1000000  --min-bq 20 --min-alt-bq 20    --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0  --sig 0.01 --bonf dynamic   reads.bam 2>&1  || (tool_exit_code=$? && cat "$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit $tool_exit_code)  && echo set_lofreq_standard

Exit Code:

```
0
```

Standard Output:

INFO [2024-11-18 05:53:54,991]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 10 --max-depth 1000000 --min-bq 20 --min-alt-bq 20 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam

INFO [2024-11-18 05:53:55,020]: Adding 19 commands to mp-pool
Checking the headers and starting positions of 19 files
Number of substitution tests performed: 189
Number of indel tests performed: 21
INFO [2024-11-18 05:53:58,264]: Executing lofreq filter -i /tmp/tmp6rx0w62v/tmp/lofreq2_call_parallelhhxsbg4k/concat.vcf.gz -o variants.vcf --snvqual-thresh 43 --indelqual-thresh 33

set_lofreq_standard

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
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": "20", "min_bq": "20"}, "coverage": {"max_depth": "1000000", "min_cov": "10"}, "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/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 2, "bonf": "dynamic", "filter_type": "set_lofreq_standard", "others": "", "sig": "0.01"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmp6rx0w62v/files/4/b/e/dataset_4bec5fbf-4d03-4114-ac85-e6dff7a4965a.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  ln -s '/tmp/tmp6rx0w62v/files/6/8/5/dataset_685dfa07-80d4-4829-a421-e435f204d986.dat' reads.bam && ln -s -f '/tmp/tmp6rx0w62v/files/_metadata_files/1/d/4/metadata_1d4284dc-db57-4bcd-9d47-98d3ee59d365.dat' reads.bam.bai &&   lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose  --ref 'reference.fa' --out variants.vcf --call-indels   --min-cov 10 --max-depth 1000000  --min-bq 20 --min-alt-bq 20    --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0  --sig 0.01 --bonf dynamic   reads.bam 2>&1  || (tool_exit_code=$? && cat "$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit $tool_exit_code)  && echo set_lofreq_standard

Exit Code:

```
0
```

Standard Output:

INFO [2024-11-18 05:53:55,031]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 10 --max-depth 1000000 --min-bq 20 --min-alt-bq 20 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam

INFO [2024-11-18 05:53:55,068]: Adding 19 commands to mp-pool
Checking the headers and starting positions of 19 files
Number of substitution tests performed: 189
Number of indel tests performed: 20
INFO [2024-11-18 05:53:58,853]: Executing lofreq filter -i /tmp/tmp6rx0w62v/tmp/lofreq2_call_paralleliecyjoxs/concat.vcf.gz -o variants.vcf --snvqual-thresh 43 --indelqual-thresh 33

set_lofreq_standard

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
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": "20", "min_bq": "20"}, "coverage": {"max_depth": "1000000", "min_cov": "10"}, "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/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 2, "bonf": "dynamic", "filter_type": "set_lofreq_standard", "others": "", "sig": "0.01"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 16, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp6rx0w62v/job_working_directory/000/24/configs/tmpkjmfbs1r' '/tmp/tmp6rx0w62v/files/7/f/9/dataset_7f9a1fa8-3788-43ea-adbd-3778ca6c643a.dat' > '/tmp/tmp6rx0w62v/job_working_directory/000/24/outputs/dataset_8b3e3154-fed9-4afb-a779-09122c4e7f47.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
chromInfo	`"/tmp/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^#/ { print; next } ($4 ~ /^[ACGT]$/ && $5 ~ /^[ACGT]$/) { print }"`
dbkey	`"?"`

Job 2:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp6rx0w62v/job_working_directory/000/25/configs/tmpkox16jep' '/tmp/tmp6rx0w62v/files/0/b/2/dataset_0b24a3c1-5d46-40c5-9076-8c043651dbe9.dat' > '/tmp/tmp6rx0w62v/job_working_directory/000/25/outputs/dataset_4cfad86a-7e25-44b5-aaa9-fecccd4e9fc8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
chromInfo	`"/tmp/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^#/ { print; next } ($4 ~ /^[ACGT]$/ && $5 ~ /^[ACGT]$/) { print }"`
dbkey	`"?"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmp6rx0w62v/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"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 15, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Job 2:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmp6rx0w62v/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"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 15, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
chromInfo	`"/tmp/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
empty_text	`"."`
extract	`"CHROM POS FILTER REF ALT DP AF DP4 SB EFF[].IMPACT EFF[].FUNCLASS EFF[].EFFECT EFF[].GENE EFF[].CODON EFF[].AA EFF[*].TRID"`
one_effect_per_line	`true`
separator	`""`

Job 2:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
chromInfo	`"/tmp/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
empty_text	`"."`
extract	`"CHROM POS FILTER REF ALT DP AF DP4 SB EFF[].IMPACT EFF[].FUNCLASS EFF[].EFFECT EFF[].GENE EFF[].CODON EFF[].AA EFF[*].TRID"`
one_effect_per_line	`true`
separator	`""`

Step 16: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
chromInfo	`"/tmp/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 0, "add_name": true, "place_name": "same_multiple"}`
one_header	`true`

Step 3: Genome fasta:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmp6rx0w62v/files/3/f/b/dataset_3fb141c9-c84b-4f08-b48c-4b45a968e5c0.dat' 'ERR018930.fastqsanger.gz' && ln -sf '/tmp/tmp6rx0w62v/files/a/8/b/dataset_a8bf2372-c51d-4600-bb69-111d6cf593b8.dat' 'ERR018930_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR018930.fastqsanger.gz'  -i 'ERR018930.fastqsanger.gz'   -I 'ERR018930_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmp6rx0w62v/job_working_directory/000/7/outputs/dataset_fd47c808-1e72-4f18-b269-89fa028e0614.dat' && mv second.fastqsanger.gz '/tmp/tmp6rx0w62v/job_working_directory/000/7/outputs/dataset_280793fd-086f-453e-8d98-d437cd012d57.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 7337
total bases: 555502
Q20 bases: 496161(89.3176%)
Q30 bases: 321585(57.8909%)

Read2 before filtering:
total reads: 7337
total bases: 555512
Q20 bases: 501389(90.2571%)
Q30 bases: 309357(55.6886%)

Read1 after filtering:
total reads: 7337
total bases: 555502
Q20 bases: 496161(89.3176%)
Q30 bases: 321585(57.8909%)

Read2 after filtering:
total reads: 7337
total bases: 555512
Q20 bases: 501389(90.2571%)
Q30 bases: 309357(55.6886%)

Filtering result:
reads passed filter: 14674
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 0
bases trimmed due to adapters: 0

Duplication rate: 0.0408886%

Insert size peak (evaluated by paired-end reads): 108

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for ERR018930.fastqsanger.gz -i ERR018930.fastqsanger.gz -I ERR018930_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz 
fastp v0.24.0, time used: 0 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
chromInfo	`"/tmp/tmp6rx0w62v/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}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Job 2:

Job state is ok

Command Line:

ln -sf '/tmp/tmp6rx0w62v/files/a/0/c/dataset_a0c6f0d9-8214-4eb5-a132-e0d5a19c1985.dat' 'ERR1035492.fastqsanger.gz' && ln -sf '/tmp/tmp6rx0w62v/files/3/6/2/dataset_36222c0d-e824-412f-922e-f55c6013fc0a.dat' 'ERR1035492_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR1035492.fastqsanger.gz'  -i 'ERR1035492.fastqsanger.gz'   -I 'ERR1035492_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmp6rx0w62v/job_working_directory/000/8/outputs/dataset_86b134f8-208e-498a-bf15-3b17c3fd0633.dat' && mv second.fastqsanger.gz '/tmp/tmp6rx0w62v/job_working_directory/000/8/outputs/dataset_82eb4cc6-2ff0-422d-bc95-b96f260f94ab.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 6031
total bases: 602346
Q20 bases: 585185(97.151%)
Q30 bases: 549984(91.307%)

Read2 before filtering:
total reads: 6031
total bases: 602346
Q20 bases: 576449(95.7006%)
Q30 bases: 529319(87.8762%)

Read1 after filtering:
total reads: 6031
total bases: 602346
Q20 bases: 585185(97.151%)
Q30 bases: 549984(91.307%)

Read2 after filtering:
total reads: 6031
total bases: 602346
Q20 bases: 576449(95.7006%)
Q30 bases: 529319(87.8762%)

Filtering result:
reads passed filter: 12062
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 0
bases trimmed due to adapters: 0

Duplication rate: 0.381363%

Insert size peak (evaluated by paired-end reads): 165

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for ERR1035492.fastqsanger.gz -i ERR1035492.fastqsanger.gz -I ERR1035492_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz 
fastp v0.24.0, time used: 1 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
chromInfo	`"/tmp/tmp6rx0w62v/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}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 4, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p '/tmp/tmp6rx0w62v/job_working_directory/000/9/outputs/dataset_b7dac99a-be6a-41ed-8cf7-c07585403bf4_files/snpeff_db' && mkdir -p snpeff_output/'snpeff_db' &&  ln -s '/tmp/tmp6rx0w62v/files/f/d/8/dataset_fd8c4d49-5f28-4ae9-be15-c7444951457f.dat' 'snpeff_output/snpeff_db/sequences.fa.gz' && ln -s '/tmp/tmp6rx0w62v/files/1/4/0/dataset_140619e3-d19f-4561-9517-7e490ce9e1bb.dat' 'snpeff_output/snpeff_db/genes.gtf' &&  snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m build -noCheckCds -noCheckProtein -v -configOption 'snpeff_db'.genome='snpeff_db' -configOption 'snpeff_db'.codonTable='Standard' -gtf22 -dataDir "$(pwd)/snpeff_output" 'snpeff_db' && mv snpeff_output/'snpeff_db'/*.bin '/tmp/tmp6rx0w62v/job_working_directory/000/9/outputs/dataset_b7dac99a-be6a-41ed-8cf7-c07585403bf4_files/snpeff_db' && echo 'snpeff_db.genome : snpeff_db' >> '/tmp/tmp6rx0w62v/job_working_directory/000/9/outputs/dataset_b7dac99a-be6a-41ed-8cf7-c07585403bf4_files'/snpEff.config && echo 'snpeff_db.codonTable : Standard' >> '/tmp/tmp6rx0w62v/job_working_directory/000/9/outputs/dataset_b7dac99a-be6a-41ed-8cf7-c07585403bf4_files'/snpEff.config

Exit Code:

```
0
```

Standard Error:

00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'snpeff_db'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'snpeff_db'
00:00:00 Reading config file: /tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'snpeff_db'
00:00:01 done
00:00:01 Reading GTF22 data file  : '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/genes.gtf'
00:00:01 Reading file '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/genes.gtf'
....................................................................................................
		10000	....................................................................................................
		20000	..............................................00:00:03 
	Total: 24693 markers added.
00:00:03 Create exons from CDS (if needed): 
00:00:03 Exons created for 1466 transcripts.
00:00:03 Deleting redundant exons (if needed): 
.
		0	............................................00:00:03 	Total transcripts with deleted exons: 4424
00:00:03 Collapsing zero length introns (if needed): 
00:00:03 	Total collapsed transcripts: 0
00:00:03 	Reading sequences   :
00:00:03 	FASTA file: '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/genomes/snpeff_db.fa' not found.
00:00:03 	Reading FASTA file: '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequences.fa'
00:00:03 		Reading sequence 'NC_009906.1', length: 830022
00:00:03 		Adding genomic sequences to genes: 
00:00:03 	Done (174 sequences added).
00:00:03 		Adding genomic sequences to exons: 
00:00:03 	Done (381 sequences added, 0 ignored).
00:00:03 		Reading sequence 'NC_009907.1', length: 755035
00:00:03 		Adding genomic sequences to genes: 
00:00:03 	Done (158 sequences added).
00:00:03 		Adding genomic sequences to exons: 
00:00:04 	Done (394 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009908.2', length: 1011127
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (218 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (578 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009909.1', length: 876622
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (203 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (548 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009910.1', length: 1370936
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (312 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (806 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009911.1', length: 1033388
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (241 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (634 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009912.1', length: 1497819
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (343 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (901 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009913.1', length: 1678596
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (368 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (945 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009914.1', length: 1923364
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (430 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (1173 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009915.1', length: 1419739
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (317 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:04 	Done (753 sequences added, 0 ignored).
00:00:04 		Reading sequence 'NC_009916.1', length: 2067354
00:00:04 		Adding genomic sequences to genes: 
00:00:04 	Done (444 sequences added).
00:00:04 		Adding genomic sequences to exons: 
00:00:05 	Done (1225 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NC_009917.1', length: 3004884
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (676 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (1795 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NC_009918.1', length: 2031768
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (442 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (1178 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NC_009919.1', length: 3120417
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (682 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (1662 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852640.1', length: 1000
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852639.1', length: 995
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852638.1', length: 877
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852637.1', length: 585
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852636.1', length: 1026
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852635.1', length: 900
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852634.1', length: 759
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852633.1', length: 1551
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852632.1', length: 563
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852631.1', length: 748
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852630.1', length: 1037
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852629.1', length: 416
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852628.1', length: 769
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852627.1', length: 1184
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852626.1', length: 900
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852625.1', length: 1255
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852624.1', length: 1294
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852623.1', length: 927
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852622.1', length: 664
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852621.1', length: 883
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852620.1', length: 1143
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852619.1', length: 652
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852618.1', length: 1396
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852617.1', length: 2007
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852616.1', length: 648
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852615.1', length: 2179
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852614.1', length: 786
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852613.1', length: 736
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852612.1', length: 1033
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852611.1', length: 2123
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852610.1', length: 3939
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852609.1', length: 1375
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (1 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (2 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852608.1', length: 1001
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852607.1', length: 908
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852606.1', length: 1938
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852605.1', length: 879
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852604.1', length: 3240
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852603.1', length: 803
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852602.1', length: 535
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852601.1', length: 1041
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852600.1', length: 877
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852599.1', length: 1281
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852598.1', length: 1004
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852597.1', length: 992
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852596.1', length: 1431
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852595.1', length: 1034
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852594.1', length: 785
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852593.1', length: 936
00:00:05 		Adding genomic sequences to genes: 
00:00:05 	Done (0 sequences added).
00:00:05 		Adding genomic sequences to exons: 
00:00:05 	Done (0 sequences added, 0 ignored).
00:00:05 		Reading sequence 'NW_001852592.1', length: 952
00:00:05 		Adding genomic sequences to genes:
..
d
#		'NW_001851052.1'	723	Standard
#		'NW_001851247.1'	723	Standard
#		'NW_001850604.1'	722	Standard
#		'NW_001851896.1'	722	Standard
#		'NW_001852533.1'	722	Standard
#		'NW_001850697.1'	721	Standard
#		'NW_001852332.1'	721	Standard
#		'NW_001850827.1'	720	Standard
#		'NW_001850835.1'	720	Standard
#		'NW_001850932.1'	720	Standard
#		'NW_001851438.1'	720	Standard
#		'NW_001851764.1'	720	Standard
#		'NW_001851031.1'	719	Standard
#		'NW_001851731.1'	719	Standard
#		'NW_001851442.1'	718	Standard
#		'NW_001850386.1'	717	Standard
#		'NW_001852233.1'	717	Standard
#		'NW_001850575.1'	716	Standard
#		'NW_001851005.1'	716	Standard
#		'NW_001850407.1'	715	Standard
#		'NW_001850696.1'	715	Standard
#		'NW_001850996.1'	715	Standard
#		'NW_001850658.1'	714	Standard
#		'NW_001850883.1'	714	Standard
#		'NW_001851045.1'	714	Standard
#		'NW_001851251.1'	714	Standard
#		'NW_001850065.1'	713	Standard
#		'NW_001850479.1'	713	Standard
#		'NW_001850629.1'	713	Standard
#		'NW_001850754.1'	712	Standard
#		'NW_001850759.1'	711	Standard
#		'NW_001850945.1'	711	Standard
#		'NW_001851278.1'	711	Standard
#		'NW_001850412.1'	709	Standard
#		'NW_001851865.1'	709	Standard
#		'NW_001850487.1'	708	Standard
#		'NW_001850480.1'	707	Standard
#		'NW_001850645.1'	705	Standard
#		'NW_001850859.1'	705	Standard
#		'NW_001851893.1'	705	Standard
#		'NW_001850749.1'	704	Standard
#		'NW_001851858.1'	703	Standard
#		'NW_001852190.1'	703	Standard
#		'NW_001850876.1'	702	Standard
#		'NW_001851524.1'	701	Standard
#		'NW_001850359.1'	700	Standard
#		'NW_001850753.1'	700	Standard
#		'NW_001851060.1'	700	Standard
#		'NW_001851908.1'	700	Standard
#		'NW_001850450.1'	699	Standard
#		'NW_001850602.1'	699	Standard
#		'NW_001851328.1'	698	Standard
#		'NW_001852308.1'	698	Standard
#		'NW_001851545.1'	696	Standard
#		'NW_001850699.1'	695	Standard
#		'NW_001851015.1'	695	Standard
#		'NW_001852340.1'	695	Standard
#		'NW_001850418.1'	693	Standard
#		'NW_001850686.1'	693	Standard
#		'NW_001850989.1'	693	Standard
#		'NW_001851933.1'	693	Standard
#		'NW_001851946.1'	693	Standard
#		'NW_001852141.1'	693	Standard
#		'NW_001850504.1'	692	Standard
#		'NW_001850632.1'	692	Standard
#		'NW_001852009.1'	692	Standard
#		'NW_001852071.1'	692	Standard
#		'NW_001850349.1'	691	Standard
#		'NW_001850825.1'	691	Standard
#		'NW_001851785.1'	691	Standard
#		'NW_001850649.1'	690	Standard
#		'NW_001851121.1'	690	Standard
#		'NW_001852499.1'	690	Standard
#		'NW_001850411.1'	688	Standard
#		'NW_001850533.1'	688	Standard
#		'NW_001852537.1'	687	Standard
#		'NW_001850096.1'	686	Standard
#		'NW_001850957.1'	686	Standard
#		'NW_001852305.1'	686	Standard
#		'NW_001850460.1'	685	Standard
#		'NW_001851222.1'	685	Standard
#		'NW_001851940.1'	685	Standard
#		'NW_001850334.1'	684	Standard
#		'NW_001850454.1'	684	Standard
#		'NW_001850942.1'	684	Standard
#		'NW_001850374.1'	682	Standard
#		'NW_001850492.1'	681	Standard
#		'NW_001850494.1'	681	Standard
#		'NW_001850975.1'	681	Standard
#		'NW_001850398.1'	680	Standard
#		'NW_001851640.1'	679	Standard
#		'NW_001852294.1'	679	Standard
#		'NW_001851769.1'	678	Standard
#		'NW_001850338.1'	677	Standard
#		'NW_001850419.1'	677	Standard
#		'NW_001851887.1'	677	Standard
#		'NW_001850100.1'	676	Standard
#		'NW_001850512.1'	676	Standard
#		'NW_001851745.1'	676	Standard
#		'NW_001850524.1'	675	Standard
#		'NW_001851245.1'	673	Standard
#		'NW_001852350.1'	673	Standard
#		'NW_001850586.1'	672	Standard
#		'NW_001850776.1'	672	Standard
#		'NW_001852395.1'	672	Standard
#		'NW_001851038.1'	671	Standard
#		'NW_001850867.1'	670	Standard
#		'NW_001851275.1'	670	Standard
#		'NW_001851936.1'	670	Standard
#		'NW_001850718.1'	668	Standard
#		'NW_001850862.1'	668	Standard
#		'NW_001851172.1'	668	Standard
#		'NW_001852353.1'	668	Standard
#		'NW_001850375.1'	667	Standard
#		'NW_001850636.1'	667	Standard
#		'NW_001852182.1'	667	Standard
#		'NW_001852426.1'	667	Standard
#		'NW_001850433.1'	664	Standard
#		'NW_001852622.1'	664	Standard
#		'NW_001850067.1'	663	Standard
#		'NW_001850491.1'	663	Standard
#		'NW_001849929.1'	661	Standard
#		'NW_001850748.1'	660	Standard
#		'NW_001851017.1'	660	Standard
#		'NW_001851932.1'	660	Standard
#		'NW_001850514.1'	658	Standard
#		'NW_001851679.1'	658	Standard
#		'NW_001851715.1'	656	Standard
#		'NW_001849982.1'	655	Standard
#		'NW_001852377.1'	655	Standard
#		'NW_001851939.1'	654	Standard
#		'NW_001852173.1'	654	Standard
#		'NW_001851501.1'	653	Standard
#		'NW_001852619.1'	652	Standard
#		'NW_001850901.1'	651	Standard
#		'NW_001850757.1'	648	Standard
#		'NW_001852616.1'	648	Standard
#		'NW_001850101.1'	646	Standard
#		'NW_001850875.1'	646	Standard
#		'NW_001852161.1'	645	Standard
#		'NW_001852025.1'	644	Standard
#		'NW_001851266.1'	643	Standard
#		'NW_001850370.1'	641	Standard
#		'NW_001852379.1'	640	Standard
#		'NW_001851298.1'	639	Standard
#		'NW_001851657.1'	639	Standard
#		'NW_001850455.1'	638	Standard
#		'NW_001852145.1'	638	Standard
#		'NW_001850477.1'	636	Standard
#		'NW_001850400.1'	634	Standard
#		'NW_001850443.1'	634	Standard
#		'NW_001850515.1'	633	Standard
#		'NW_001851387.1'	632	Standard
#		'NW_001851851.1'	632	Standard
#		'NW_001850560.1'	630	Standard
#		'NW_001850761.1'	630	Standard
#		'NW_001850368.1'	629	Standard
#		'NW_001851888.1'	629	Standard
#		'NW_001852297.1'	629	Standard
#		'NW_001850500.1'	628	Standard
#		'NW_001850499.1'	626	Standard
#		'NW_001850908.1'	626	Standard
#		'NW_001850371.1'	625	Standard
#		'NW_001850986.1'	625	Standard
#		'NW_001850336.1'	624	Standard
#		'NW_001850687.1'	624	Standard
#		'NW_001852365.1'	624	Standard
#		'NW_001852266.1'	623	Standard
#		'NW_001852378.1'	621	Standard
#		'NW_001850518.1'	620	Standard
#		'NW_001850849.1'	620	Standard
#		'NW_001851945.1'	620	Standard
#		'NW_001851891.1'	619	Standard
#		'NW_001851458.1'	618	Standard
#		'NW_001850830.1'	615	Standard
#		'NW_001850935.1'	614	Standard
#		'NW_001852111.1'	614	Standard
#		'NW_001850506.1'	613	Standard
#		'NW_001850674.1'	612	Standard
#		'NW_001850725.1'	609	Standard
#		'NW_001850501.1'	608	Standard
#		'NW_001850800.1'	606	Standard
#		'NW_001850874.1'	606	Standard
#		'NW_001851789.1'	603	Standard
#		'NW_001852326.1'	603	Standard
#		'NW_001851294.1'	601	Standard
#		'NW_001851186.1'	598	Standard
#		'NW_001851832.1'	598	Standard
#		'NW_001852296.1'	597	Standard
#		'NW_001850824.1'	594	Standard
#		'NW_001851830.1'	594	Standard
#		'NW_001851753.1'	593	Standard
#		'NW_001850000.1'	592	Standard
#		'NW_001850498.1'	590	Standard
#		'NW_001851290.1'	587	Standard
#		'NW_001851090.1'	585	Standard
#		'NW_001852637.1'	585	Standard
#		'NW_001850643.1'	583	Standard
#		'NW_001850401.1'	582	Standard
#		'NW_001850594.1'	582	Standard
#		'NW_001852116.1'	581	Standard
#		'NW_001850554.1'	579	Standard
#		'NW_001851024.1'	579	Standard
#		'NW_001850816.1'	578	Standard
#		'NW_001850822.1'	576	Standard
#		'NW_001850509.1'	575	Standard
#		'NW_001850635.1'	575	Standard
#		'NW_001850929.1'	575	Standard
#		'NW_001850369.1'	574	Standard
#		'NW_001850493.1'	574	Standard
#		'NW_001850395.1'	571	Standard
#		'NW_001851505.1'	570	Standard
#		'NW_001851631.1'	570	Standard
#		'NW_001850713.1'	565	Standard
#		'NW_001851809.1'	564	Standard
#		'NW_001850061.1'	563	Standard
#		'NW_001852632.1'	563	Standard
#		'NW_001851161.1'	562	Standard
#		'NW_001850765.1'	559	Standard
#		'NW_001850895.1'	558	Standard
#		'NW_001850978.1'	557	Standard
#		'NW_001850431.1'	551	Standard
#		'NW_001850709.1'	551	Standard
#		'NW_001850611.1'	550	Standard
#		'NW_001851035.1'	544	Standard
#		'NW_001850364.1'	543	Standard
#		'NW_001850701.1'	543	Standard
#		'NW_001850855.1'	539	Standard
#		'NW_001850597.1'	535	Standard
#		'NW_001852602.1'	535	Standard
#		'NW_001850655.1'	533	Standard
#		'NW_001852156.1'	531	Standard
#		'NW_001852269.1'	531	Standard
#		'NW_001850857.1'	529	Standard
#		'NW_001850333.1'	528	Standard
#		'NW_001850777.1'	526	Standard
#		'NW_001851162.1'	525	Standard
#		'NW_001851082.1'	522	Standard
#		'NW_001852486.1'	522	Standard
#		'NW_001852281.1'	521	Standard
#		'NW_001850666.1'	520	Standard
#		'NW_001850967.1'	518	Standard
#		'NW_001851126.1'	516	Standard
#		'NW_001850940.1'	515	Standard
#		'NW_001850796.1'	510	Standard
#		'NW_001850770.1'	508	Standard
#		'NW_001850871.1'	506	Standard
#		'NW_001851101.1'	495	Standard
#		'NW_001850814.1'	493	Standard
#		'NW_001850789.1'	491	Standard
#		'NW_001850928.1'	491	Standard
#		'NW_001850601.1'	488	Standard
#		'NW_001850841.1'	488	Standard
#		'NW_001850682.1'	485	Standard
#		'NW_001850663.1'	482	Standard
#		'NW_001852030.1'	480	Standard
#		'NW_001850376.1'	478	Standard
#		'NW_001850730.1'	478	Standard
#		'NW_001850614.1'	477	Standard
#		'NW_001850468.1'	475	Standard
#		'NW_001851859.1'	471	Standard
#		'NW_001851435.1'	468	Standard
#		'NW_001851845.1'	463	Standard
#		'NW_001850609.1'	461	Standard
#		'NW_001851377.1'	458	Standard
#		'NW_001850771.1'	456	Standard
#		'NW_001851274.1'	456	Standard
#		'NW_001850894.1'	455	Standard
#		'NW_001852355.1'	455	Standard
#		'NW_001852529.1'	454	Standard
#		'NW_001852035.1'	451	Standard
#		'NW_001850745.1'	447	Standard
#		'NW_001851895.1'	446	Standard
#		'NW_001852246.1'	446	Standard
#		'NW_001850952.1'	445	Standard
#		'NW_001850330.1'	441	Standard
#		'NW_001850705.1'	440	Standard
#		'NW_001850097.1'	438	Standard
#		'NW_001850537.1'	428	Standard
#		'NW_001850766.1'	428	Standard
#		'NW_001850406.1'	427	Standard
#		'NW_001850094.1'	426	Standard
#		'NW_001852530.1'	424	Standard
#		'NW_001850608.1'	419	Standard
#		'NW_001851375.1'	419	Standard
#		'NW_001851154.1'	417	Standard
#		'NW_001852055.1'	416	Standard
#		'NW_001852629.1'	416	Standard
#		'NW_001850671.1'	415	Standard
#		'NW_001852047.1'	412	Standard
#		'NW_001852202.1'	412	Standard
#		'NW_001852390.1'	411	Standard
#		'NW_001850898.1'	409	Standard
#		'NW_001850979.1'	409	Standard
#		'NW_001850920.1'	406	Standard
#		'NW_001850768.1'	403	Standard
#		'NW_001850782.1'	403	Standard
#		'NW_001850839.1'	401	Standard
#		'NW_001850783.1'	400	Standard
#		'NW_001850731.1'	398	Standard
#		'NW_001851261.1'	396	Standard
#		'NW_001850517.1'	393	Standard
#		'NW_001850931.1'	393	Standard
#		'NW_001850907.1'	390	Standard
#		'NW_001852391.1'	387	Standard
#		'NW_001850740.1'	386	Standard
#		'NW_001850956.1'	385	Standard
#		'NW_001850742.1'	384	Standard
#		'NW_001852125.1'	384	Standard
#		'NW_001850870.1'	382	Standard
#		'NW_001851899.1'	382	Standard
#		'NW_001850872.1'	380	Standard
#		'NW_001850739.1'	378	Standard
#		'NW_001851953.1'	378	Standard
#		'NW_001850598.1'	376	Standard
#		'NW_001851206.1'	376	Standard
#		'NW_001850831.1'	375	Standard
#		'NW_001850606.1'	374	Standard
#		'NW_001850747.1'	373	Standard
#		'NW_001850798.1'	372	Standard
#		'NW_001851053.1'	371	Standard
#		'NW_001850662.1'	370	Standard
#		'NW_001850969.1'	368	Standard
#		'NW_001850779.1'	367	Standard
#		'NW_001850919.1'	367	Standard
#		'NW_001850792.1'	366	Standard
#		'NW_001851975.1'	365	Standard
#		'NW_001850906.1'	364	Standard
#		'NW_001850853.1'	360	Standard
#		'NW_001850845.1'	359	Standard
#		'NW_001850780.1'	357	Standard
#		'NW_001852109.1'	356	Standard
#		'NW_001850954.1'	352	Standard
#		'NW_001852431.1'	352	Standard
#		'NW_001850772.1'	350	Standard
#		'NW_001851165.1'	350	Standard
#		'NW_001850600.1'	348	Standard
#		'NW_001850767.1'	347	Standard
#		'NW_001850923.1'	346	Standard
#		'NW_001850391.1'	344	Standard
#		'NW_001851284.1'	340	Standard
#		'NW_001851394.1'	338	Standard
#		'NW_001850781.1'	337	Standard
#		'NW_001851768.1'	337	Standard
#		'NW_001850763.1'	335	Standard
#		'NW_001850961.1'	332	Standard
#		'NW_001851861.1'	326	Standard
#		'NW_001851062.1'	318	Standard
#		'NW_001849951.1'	317	Standard
#		'NW_001850619.1'	315	Standard
#		'NW_001850842.1'	315	Standard
#		'NW_001851371.1'	313	Standard
#		'NW_001850860.1'	311	Standard
#		'NW_001850973.1'	311	Standard
#		'NW_001852103.1'	311	Standard
#		'NW_001850647.1'	310	Standard
#		'NW_001850762.1'	309	Standard
#		'NW_001851355.1'	308	Standard
#		'NW_001850850.1'	305	Standard
#		'NW_001851562.1'	305	Standard
#		'NW_001852189.1'	305	Standard
#		'NW_001850573.1'	304	Standard
#		'NW_001851986.1'	302	Standard
#		'NW_001852034.1'	300	Standard
#		'NW_001851255.1'	299	Standard
#		'NW_001850925.1'	297	Standard
#		'NW_001850424.1'	296	Standard
#		'NW_001850769.1'	296	Standard
#		'NW_001852496.1'	294	Standard
#		'NW_001850627.1'	293	Standard
#		'NW_001850795.1'	293	Standard
#		'NW_001851790.1'	292	Standard
#		'NW_001850755.1'	290	Standard
#		'NW_001850764.1'	290	Standard
#		'NW_001850793.1'	289	Standard
#		'NW_001852489.1'	284	Standard
#		'NW_001850735.1'	283	Standard
#		'NW_001851003.1'	283	Standard
#		'NW_001850807.1'	280	Standard
#		'NW_001850637.1'	272	Standard
#		'NW_001850703.1'	269	Standard
#		'NW_001851910.1'	267	Standard
#		'NW_001851178.1'	266	Standard
#		'NW_001850522.1'	265	Standard
#		'NW_001850959.1'	265	Standard
#		'NW_001852249.1'	262	Standard
#		'NW_001850465.1'	261	Standard
#		'NW_001850787.1'	260	Standard
#		'NW_001851429.1'	259	Standard
#		'NW_001850832.1'	255	Standard
#		'NW_001850656.1'	254	Standard
#		'NW_001850716.1'	252	Standard
#		'NW_001852069.1'	252	Standard
#		'NW_001851909.1'	251	Standard
#		'NW_001851999.1'	251	Standard
#		'NW_001850596.1'	250	Standard
#		'NW_001850854.1'	250	Standard
#		'NW_001852157.1'	250	Standard
#		'NW_001850720.1'	248	Standard
#		'NW_001850684.1'	244	Standard
#		'NW_001851920.1'	244	Standard
#		'NW_001851136.1'	243	Standard
#		'NW_001850852.1'	242	Standard
#		'NW_001850829.1'	241	Standard
#		'NW_001851952.1'	235	Standard
#		'NW_001850773.1'	234	Standard
#		'NW_001850823.1'	233	Standard
#		'NW_001851848.1'	233	Standard
#		'NW_001852108.1'	232	Standard
#		'NW_001850916.1'	230	Standard
#		'NW_001851743.1'	228	Standard
#		'NW_001850679.1'	226	Standard
#		'NW_001850971.1'	225	Standard
#		'NW_001851780.1'	225	Standard
#		'NW_001850634.1'	224	Standard
#		'NW_001850621.1'	223	Standard
#		'NW_001851970.1'	223	Standard
#		'NW_001851989.1'	223	Standard
#		'NW_001850702.1'	221	Standard
#		'NW_001852238.1'	221	Standard
#		'NW_001850803.1'	220	Standard
#		'NW_001851796.1'	220	Standard
#		'NW_001851311.1'	218	Standard
#		'NW_001851048.1'	217	Standard
#		'NW_001850977.1'	216	Standard
#		'NW_001850727.1'	215	Standard
#		'NW_001851238.1'	215	Standard
#		'NW_001850926.1'	213	Standard
#		'NW_001850924.1'	209	Standard
#		'NW_001852215.1'	209	Standard
#		'NW_001850861.1'	207	Standard
#		'NW_001851231.1'	200	Standard
#		'NW_001851799.1'	200	Standard
#-----------------------------------------------

00:00:10 Caracterizing exons by splicing (stage 1) : 
.............
00:00:10 Caracterizing exons by splicing (stage 2) : 
.............00:00:10 done.
00:00:10 [Optional] Rare amino acid annotations
WARNING_FILE_NOT_FOUND: Rare Amino Acid analysis: Cannot read protein sequence file '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/protein.fa', nothing done.
00:00:10 Saving database
00:00:14 Saving sequences for chromosome 'NC_009914.1' to file '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009914.1.bin'
00:00:15 Saving sequences for chromosome 'NC_009916.1' to file '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009916.1.bin'
00:00:15 Saving sequences for chromosome 'NC_009917.1' to file '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009917.1.bin'
00:00:15 Saving sequences for chromosome 'NC_009918.1' to file '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009918.1.bin'
00:00:16 Saving sequences for chromosome 'NC_009919.1' to file '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.NC_009919.1.bin'
00:00:16 Saving sequences for small chromosmes to file '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/sequence.bin'
00:00:17 [Optional] Reading regulation elements: GFF
WARNING_FILE_NOT_FOUND: Cannot read optional regulation file '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/regulation.gff', nothing done.
00:00:17 [Optional] Reading regulation elements: BED 
00:00:17 Cannot find optional regulation dir '/tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/regulation.bed/', nothing done.
00:00:17 [Optional] Reading motifs: GFF
WARNING_FILE_NOT_FOUND: Cannot open PWMs file /tmp/tmp6rx0w62v/job_working_directory/000/9/working/snpeff_output/snpeff_db/pwms.bin. Nothing done
00:00:17 Done
00:00:17 Done.

Standard Output:

..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
chromInfo	`"/tmp/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"snpeff_db"`
input_type	`{"__current_case__": 2, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_type_selector": "gtf", "reference_source": {"__current_case__": 1, "input_fasta": {"values": [{"id": 2, "src": "hda"}]}, "reference_source_selector": "history"}}`

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

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp6rx0w62v/files/4/b/e/dataset_4bec5fbf-4d03-4114-ac85-e6dff7a4965a.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1     -T '30' -h '5'    -Y   -q                           -R '@RG\tID:ERR018930\tSM:ERR018930\tPL:ILLUMINA\tLB:ERR018930'   'localref.fa' '/tmp/tmp6rx0w62v/files/f/d/4/dataset_fd47c808-1e72-4f18-b269-89fa028e0614.dat' '/tmp/tmp6rx0w62v/files/2/8/0/dataset_280793fd-086f-453e-8d98-d437cd012d57.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp6rx0w62v/job_working_directory/000/11/outputs/dataset_e714f609-e174-4a71-a9ef-5a1d4d66d58a.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.18 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=54027382, availableWord=15801372
[BWTIncConstructFromPacked] 10 iterations done. 26064326 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 48149798 characters processed.
[bwt_gen] Finished constructing BWT in 23 iterations.
[bwa_index] 10.47 seconds elapse.
[bwa_index] Update BWT... 0.13 sec
[bwa_index] Pack forward-only FASTA... 0.12 sec
[bwa_index] Construct SA from BWT and Occ... 5.14 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 16.599 sec; CPU: 16.045 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (207, 242, 294)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (33, 468)
[M::mem_pestat] mean and std.dev: (253.94, 65.92)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 555)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -t 1 -v 1 -T 30 -h 5 -Y -q -R @RG\tID:ERR018930\tSM:ERR018930\tPL:ILLUMINA\tLB:ERR018930 localref.fa /tmp/tmp6rx0w62v/files/f/d/4/dataset_fd47c808-1e72-4f18-b269-89fa028e0614.dat /tmp/tmp6rx0w62v/files/2/8/0/dataset_280793fd-086f-453e-8d98-d437cd012d57.dat
[main] Real time: 1.213 sec; CPU: 1.139 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
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/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 7, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 16, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"CN": null, "DS": null, "DT": null, "FO": null, "KS": null, "PG": null, "PI": null, "PL": "ILLUMINA", "PU": null, "__current_case__": 1, "read_group_id_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_lb_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "set"}`

Job 2:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmp6rx0w62v/files/4/b/e/dataset_4bec5fbf-4d03-4114-ac85-e6dff7a4965a.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1     -T '30' -h '5'    -Y   -q                           -R '@RG\tID:ERR1035492\tSM:ERR1035492\tPL:ILLUMINA\tLB:ERR1035492'   'localref.fa' '/tmp/tmp6rx0w62v/files/8/6/b/dataset_86b134f8-208e-498a-bf15-3b17c3fd0633.dat' '/tmp/tmp6rx0w62v/files/8/2/e/dataset_82eb4cc6-2ff0-422d-bc95-b96f260f94ab.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp6rx0w62v/job_working_directory/000/12/outputs/dataset_74215ee8-8841-491e-93ea-b76c1abe0237.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.17 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=54027382, availableWord=15801372
[BWTIncConstructFromPacked] 10 iterations done. 26064326 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 48149798 characters processed.
[bwt_gen] Finished constructing BWT in 23 iterations.
[bwa_index] 10.55 seconds elapse.
[bwa_index] Update BWT... 0.16 sec
[bwa_index] Pack forward-only FASTA... 0.12 sec
[bwa_index] Construct SA from BWT and Occ... 5.01 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 16.424 sec; CPU: 16.014 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (185, 232, 297)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 521)
[M::mem_pestat] mean and std.dev: (246.23, 81.16)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 633)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -t 1 -v 1 -T 30 -h 5 -Y -q -R @RG\tID:ERR1035492\tSM:ERR1035492\tPL:ILLUMINA\tLB:ERR1035492 localref.fa /tmp/tmp6rx0w62v/files/8/6/b/dataset_86b134f8-208e-498a-bf15-3b17c3fd0633.dat /tmp/tmp6rx0w62v/files/8/2/e/dataset_82eb4cc6-2ff0-422d-bc95-b96f260f94ab.dat
[main] Real time: 1.058 sec; CPU: 1.043 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
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/tmp6rx0w62v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 8, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 16, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"CN": null, "DS": null, "DT": null, "FO": null, "KS": null, "PG": null, "PI": null, "PL": "ILLUMINA", "PU": null, "__current_case__": 1, "read_group_id_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_lb_conditional": {"__current_case__": 0, "do_auto_name": true}, "read_group_sm_conditional": {"__current_case__": 0, "do_auto_name": true}, "rg_selector": "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 ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmp6rx0w62v/files/e/7/1/dataset_e714f609-e174-4a71-a9ef-5a1d4d66d58a.dat' infile && ln -s '/tmp/tmp6rx0w62v/files/_metadata_files/6/a/2/metadata_6a211519-8548-4170-b3f5-16ac8d37c34d.dat' infile.bai &&               samtools view -@ $addthreads -b  -f 3 -F 0 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp6rx0w62v/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"}}}

Job 2:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmp6rx0w62v/files/7/4/2/dataset_74215ee8-8841-491e-93ea-b76c1abe0237.dat' infile && ln -s '/tmp/tmp6rx0w62v/files/_metadata_files/5/e/8/metadata_5e8b3ea9-ef54-48a9-9e20-ae893a9d707d.dat' infile.bai &&               samtools view -@ $addthreads -b  -f 3 -F 0 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp6rx0w62v/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/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmp6rx0w62v/files/9/a/a/dataset_9aa0458d-04ba-431d-a971-dc17f1e83d4b.dat' infile && ln -s '/tmp/tmp6rx0w62v/files/_metadata_files/3/d/8/metadata_3d854a5d-e3a0-4203-81d4-d64fe4b9554b.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmp6rx0w62v/job_working_directory/000/15/outputs/dataset_0492aa02-32c7-4a3b-a469-458b63c89f16.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp6rx0w62v/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`

Job 2:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmp6rx0w62v/files/2/e/6/dataset_2e6b31c3-5877-4b3b-9671-868e0cca5c30.dat' infile && ln -s '/tmp/tmp6rx0w62v/files/_metadata_files/b/7/5/metadata_b751c5f7-b115-4d0e-a422-0ef534994adc.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmp6rx0w62v/job_working_directory/000/16/outputs/dataset_5957a528-c430-4bb0-821b-33280a26f2fb.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp6rx0w62v/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 9: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&   ln -sf '/tmp/tmp6rx0w62v/files/9/a/a/dataset_9aa0458d-04ba-431d-a971-dc17f1e83d4b.dat' 'ERR018930' &&  picard MarkDuplicates  --INPUT 'ERR018930' --OUTPUT '/tmp/tmp6rx0w62v/job_working_directory/000/17/outputs/dataset_cbc886bd-1a70-4d2b-9584-084dc7e0cc86.dat'  --METRICS_FILE '/tmp/tmp6rx0w62v/job_working_directory/000/17/outputs/dataset_7473c0ed-8066-4885-b28e-ca217c3bdfce.dat'  --REMOVE_DUPLICATES 'true' --ASSUME_SORTED 'true'  --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES  --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100'   --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmp6rx0w62v/tmp
Nov 18, 2024 5:53:29 AM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmp6rx0w62v/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"`

Job 2:

Job state is ok

Command Line:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&   ln -sf '/tmp/tmp6rx0w62v/files/2/e/6/dataset_2e6b31c3-5877-4b3b-9671-868e0cca5c30.dat' 'ERR1035492' &&  picard MarkDuplicates  --INPUT 'ERR1035492' --OUTPUT '/tmp/tmp6rx0w62v/job_working_directory/000/18/outputs/dataset_a24f7cc3-0aee-4d2e-b79f-6d91c55f9d16.dat'  --METRICS_FILE '/tmp/tmp6rx0w62v/job_working_directory/000/18/outputs/dataset_42d915dd-450e-4058-9bf1-a76b022e2d39.dat'  --REMOVE_DUPLICATES 'true' --ASSUME_SORTED 'true'  --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES  --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100'   --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmp6rx0w62v/tmp
Nov 18, 2024 5:53:29 AM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmp6rx0w62v/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 10: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmp6rx0w62v/files/a/2/a/dataset_a2aaab2c-03a9-464d-889d-bc020a9209cf.dat' 'multiqc_WDir/fastp_0/ERR018930fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/ERR018930fastp.json' || die "'report_title' or 'report_title' not found in the file" &&    ln -s '/tmp/tmp6rx0w62v/files/7/7/b/dataset_77b94b2b-af0b-4986-ac05-85173e13c91a.dat' 'multiqc_WDir/fastp_0/ERR1035492fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/ERR1035492fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/samtools_1 &&    mkdir 'multiqc_WDir/samtools_1/stats_0' &&      grep -q 'This file was produced by samtools stats' /tmp/tmp6rx0w62v/files/0/4/9/dataset_0492aa02-32c7-4a3b-a469-458b63c89f16.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'ERR018930'" && ln -s '/tmp/tmp6rx0w62v/files/0/4/9/dataset_0492aa02-32c7-4a3b-a469-458b63c89f16.dat' 'multiqc_WDir/samtools_1/stats_0/ERR018930'  &&    grep -q 'This file was produced by samtools stats' /tmp/tmp6rx0w62v/files/5/9/5/dataset_5957a528-c430-4bb0-821b-33280a26f2fb.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'ERR1035492'" && ln -s '/tmp/tmp6rx0w62v/files/5/9/5/dataset_5957a528-c430-4bb0-821b-33280a26f2fb.dat' 'multiqc_WDir/samtools_1/stats_0/ERR1035492'  &&    mkdir multiqc_WDir/picard_2 &&      mkdir 'multiqc_WDir/picard_2/markdups_0' &&    grep -q 'MarkDuplicates' /tmp/tmp6rx0w62v/files/7/4/7/dataset_7473c0ed-8066-4885-b28e-ca217c3bdfce.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'ERR018930'" && ln -s '/tmp/tmp6rx0w62v/files/7/4/7/dataset_7473c0ed-8066-4885-b28e-ca217c3bdfce.dat' 'multiqc_WDir/picard_2/markdups_0/ERR018930'  &&    grep -q 'MarkDuplicates' /tmp/tmp6rx0w62v/files/4/2/d/dataset_42d915dd-450e-4058-9bf1-a76b022e2d39.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'ERR1035492'" && ln -s '/tmp/tmp6rx0w62v/files/4/2/d/dataset_42d915dd-450e-4058-9bf1-a76b022e2d39.dat' 'multiqc_WDir/picard_2/markdups_0/ERR1035492'  &&     multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3681ad38a57111ef8aa0d3db8825cf66"`
chromInfo	`"/tmp/tmp6rx0w62v/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": 7, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 8, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - a700d6499d5cc463
- history_state
  - error
- invocation_id
  - a700d6499d5cc463
- invocation_state
  - scheduled
- workflow_id
  - a700d6499d5cc463

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

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gxydevbot changed the title ~~Updating workflows/variant-calling/haploid-variant-calling-wgs-pe from 0.1 to 0.2~~ Updating workflows/variant-calling/haploid-variant-calling-wgs-pe from 0.1 to 0.2 Nov 18, 2024

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Updating workflows/variant-calling/haploid-variant-calling-wgs-pe from 0.1 to 0.2 #587

Updating workflows/variant-calling/haploid-variant-calling-wgs-pe from 0.1 to 0.2 #587

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Updating workflows/variant-calling/haploid-variant-calling-wgs-pe from 0.1 to 0.2 #587

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Updating workflows/variant-calling/haploid-variant-calling-wgs-pe from 0.1 to 0.2 #587

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