Updating workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling from 0.2.4 to 0.2.5

Open gxydevbot opened this issue 2 years ago • 35 comments

Hello! This is an automated update of the following workflow: workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/samtools_view/samtools_view/1.13+galaxy2 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.3 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/2.18.2.3 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2

The workflow release number has been updated from 0.2.4 to 0.2.5.

Nov 27 '23 23:11 gxydevbot

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

Sep 23 '24 14:09 gxydevbot

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

❌ pe-wgs-variation.ga_0

Problems:

Output with path /tmp/tmp73y5aois/Final (SnpEff-)annotated variants__c24a33bc-2e2a-468e-933d-192eac5208a0 different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/test-data/final_snpeff_annotated_variants.vcf v. /tmp/tmp0nsstpf1final_snpeff_annotated_variants.vcf )
--- local_file
+++ history_data
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.0
-##fileDate=20210221
-##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /tmp/lofreq2_call_parallelxh3mih1k/0.vcf.gz reads.bam 
+##fileDate=20240923
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /tmp/tmpqzv4nshl/tmp/lofreq2_call_paralleljay8oa8u/0.vcf.gz reads.bam 
 ##reference=reference.fa
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
@@ -15,7 +15,7 @@
 ##FILTER=<ID=min_indelqual_64,Description="Minimum Indel Quality (Phred) 64">
 ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
 ##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani"
-##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /Users/mvandenb/src/galaxy/database/files/8/c/5/dataset_8c59d777-b160-4e19-a2bd-7da3b8b7d54c.dat NC_045512.2 /Users/mvandenb/src/galaxy/database/files/4/f/7/dataset_4f741f76-a82b-464c-85a3-7d29422a36ab.dat "
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /tmp/tmpqzv4nshl/job_working_directory/000/14/outputs/dataset_92ce6f35-d2e3-477f-a0d4-04ae81f0fc8d.dat NC_045512.2 /tmp/tmpqzv4nshl/files/6/9/c/dataset_69c2cc54-f059-4e54-ab05-c4569d9383ff.dat "
 ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
 ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
 ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
@@ -58,9 +58,9 @@
 NC_045512.2	21134	.	A	G	163.0	PASS	DP=1677;AF=0.008945;SB=3;DP4=218,1441,3,12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q6957R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q159R|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
 NC_045512.2	21526	.	A	T	111.0	PASS	DP=1208;AF=0.011589;SB=23;DP4=783,404,7,14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I7088F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I290F|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
 NC_045512.2	21578	.	G	T	76.0	PASS	DP=1345;AF=0.008178;SB=13;DP4=476,850,2,15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V6F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
-NC_045512.2	22712	.	C	T	125.0	sb_fdr	DP=8681;AF=0.003456;SB=99;DP4=4028,4617,30,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P384S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
-NC_045512.2	22721	.	T	A	98.0	sb_fdr	DP=8884;AF=0.003489;SB=139;DP4=3798,5040,42,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Ata|L387I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
-NC_045512.2	22810	.	A	G	72.0	sb_fdr	DP=6269;AF=0.003828;SB=142;DP4=1565,4675,26,1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G416|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512.2	22712	.	C	T	133.0	sb_fdr	DP=8727;AF=0.003552;SB=101;DP4=4072,4618,31,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P384S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512.2	22721	.	T	A	102.0	sb_fdr	DP=8935;AF=0.003581;SB=141;DP4=3847,5041,43,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Ata|L387I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512.2	22810	.	A	G	80.0	sb_fdr	DP=6382;AF=0.004074;SB=148;DP4=1595,4757,27,1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G416|1273|S|protein_coding|CODING|GU280_gp02|1|G)
 NC_045512.2	23262	.	G	A	131.0	sb_fdr	DP=7418;AF=0.003101;SB=126;DP4=5307,2085,0,23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R567K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
 NC_045512.2	23269	.	T	C	2250.0	PASS	DP=7958;AF=0.020985;SB=3;DP4=5454,2326,126,46;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I569|1273|S|protein_coding|CODING|GU280_gp02|1|C)
 NC_045512.2	23280	.	C	A	108.0	sb_fdr	DP=8464;AF=0.003781;SB=63;DP4=5576,2848,37,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T573N|1273|S|protein_coding|CODING|GU280_gp02|1|A)

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: NC_045512.2 FASTA sequence of SARS-CoV-2:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpqzv4nshl/files/1/2/e/dataset_12ec7544-9958-4e29-81fe-81ccb3468189.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  ln -s '/tmp/tmpqzv4nshl/files/f/2/d/dataset_f2d57bba-4e1a-4a79-9905-664c892d26ec.dat' reads.bam && ln -s -f '/tmp/tmpqzv4nshl/files/_metadata_files/0/c/b/metadata_0cb91961-b241-4ba8-b893-87f8f3fc7a77.dat' reads.bam.bai &&   lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose  --ref 'reference.fa' --out variants.vcf --call-indels   --min-cov 5 --max-depth 1000000  --min-bq 30 --min-alt-bq 30    --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0  --sig 0.0005 --bonf dynamic --no-default-filter  reads.bam 2>&1  || (tool_exit_code=$? && cat "$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit $tool_exit_code)  && echo set_custom

Exit Code:

```
0
```

Standard Output:

INFO [2024-09-23 15:14:37,986]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter reads.bam

INFO [2024-09-23 15:14:37,990]: Adding 3 commands to mp-pool
Number of substitution tests performed: 8244
Number of indel tests performed: 1172
INFO [2024-09-23 15:15:00,527]: Executing lofreq filter -i /tmp/tmpqzv4nshl/tmp/lofreq2_call_paralleljay8oa8u/concat.vcf.gz -o variants.vcf --no-defaults --snvqual-thresh 72 --indelqual-thresh 64

set_custom

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4134920679be11ef88f891b48f7ce313"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "20", "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/tmpqzv4nshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

lofreq filter -i /tmp/tmpqzv4nshl/files/c/8/d/dataset_c8d64687-6395-4757-9cd8-2a0e878427da.dat --no-defaults --verbose --print-all  -v 0 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001   -o filtered.vcf

Exit Code:

```
0
```

Standard Error:

Skipping default settings
At least one type of multiple testing correction requested. Doing first pass of vcf
MTC application completed
Successful exit.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4134920679be11ef88f891b48f7ce313"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpqzv4nshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 13: SnpEff eff covid19 version:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m eff -i vcf -o vcf -upDownStreamLen 0 -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr                  -stats '/tmp/tmpqzv4nshl/job_working_directory/000/14/outputs/dataset_92ce6f35-d2e3-477f-a0d4-04ae81f0fc8d.dat' -noLog  NC_045512.2  '/tmp/tmpqzv4nshl/files/6/9/c/dataset_69c2cc54-f059-4e54-ab05-c4569d9383ff.dat' > '/tmp/tmpqzv4nshl/job_working_directory/000/14/outputs/dataset_c24a33bc-2e2a-468e-933d-192eac5208a0.dat'  && mkdir '/tmp/tmpqzv4nshl/job_working_directory/000/14/outputs/dataset_92ce6f35-d2e3-477f-a0d4-04ae81f0fc8d_files' && mv '/tmp/tmpqzv4nshl/job_working_directory/000/14/outputs/dataset_92ce6f35-d2e3-477f-a0d4-04ae81f0fc8d.dat.genes.txt' '/tmp/tmpqzv4nshl/job_working_directory/000/14/outputs/dataset_92ce6f35-d2e3-477f-a0d4-04ae81f0fc8d_files/dataset_92ce6f35-d2e3-477f-a0d4-04ae81f0fc8d.dat.genes.txt'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"4134920679be11ef88f891b48f7ce313"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpqzv4nshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-upstream", "-no-utr"]`
generate_stats	`true`
genome_version	`"NC_045512.2"`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
transcripts	`None`
udLength	`"0"`

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmpqzv4nshl/files/c/b/8/dataset_cb827cab-5af0-43ca-9371-0f642da35e0e.dat' 'SRR11578257.fastq.gz' && ln -sf '/tmp/tmpqzv4nshl/files/6/f/b/dataset_6fb075c6-4c20-4f70-9bed-5dda678be693.dat' 'SRR11578257_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for SRR11578257.fastq.gz'   -i 'SRR11578257.fastq.gz' -o first.fastq.gz  -I 'SRR11578257_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmpqzv4nshl/job_working_directory/000/4/outputs/dataset_749ab53a-c84f-474a-a03e-bdbb615ada5f.dat' && mv second.fastq.gz '/tmp/tmpqzv4nshl/job_working_directory/000/4/outputs/dataset_52e3c90a-f5fa-4246-af7a-12323bfca7f0.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 201367
total bases: 29302687
Q20 bases: 28139796(96.0315%)
Q30 bases: 27281893(93.1037%)

Read2 before filtering:
total reads: 201367
total bases: 29398146
Q20 bases: 27778430(94.4904%)
Q30 bases: 26748339(90.9865%)

Read1 after filtering:
total reads: 197961
total bases: 28794778
Q20 bases: 27771017(96.4446%)
Q30 bases: 26956923(93.6174%)

Read2 after filtering:
total reads: 197961
total bases: 28807154
Q20 bases: 27394032(95.0945%)
Q30 bases: 26419337(91.711%)

Filtering result:
reads passed filter: 395922
reads failed due to low quality: 5636
reads failed due to too many N: 1176
reads failed due to too short: 0
reads with adapter trimmed: 16490
bases trimmed due to adapters: 89039

Duplication rate: 20.2521%

Insert size peak (evaluated by paired-end reads): 230

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

fastp --thread 1 --report_title fastp report for SRR11578257.fastq.gz -i SRR11578257.fastq.gz -o first.fastq.gz -I SRR11578257_R2.fastq.gz -O second.fastq.gz 
fastp v0.23.4, time used: 4 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4134920679be11ef88f891b48f7ce313"`
chromInfo	`"/tmp/tmpqzv4nshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 4: 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/tmpqzv4nshl/files/1/2/e/dataset_12ec7544-9958-4e29-81fe-81ccb3468189.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1                 'localref.fa' '/tmp/tmpqzv4nshl/files/7/4/9/dataset_749ab53a-c84f-474a-a03e-bdbb615ada5f.dat' '/tmp/tmpqzv4nshl/files/5/2/e/dataset_52e3c90a-f5fa-4246-af7a-12323bfca7f0.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpqzv4nshl/job_working_directory/000/5/outputs/dataset_351a7b7e-7850-4c8e-bf04-3ee8b32298a3.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 0.012 sec; CPU: 0.008 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: (188, 240, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503)
[M::mem_pestat] mean and std.dev: (236.48, 72.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 608)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (188, 239, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503)
[M::mem_pestat] mean and std.dev: (235.85, 72.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 608)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (187, 239, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 505)
[M::mem_pestat] mean and std.dev: (235.52, 72.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 611)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (188, 240, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503)
[M::mem_pestat] mean and std.dev: (236.18, 72.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 608)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (186, 239, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 504)
[M::mem_pestat] mean and std.dev: (235.20, 72.50)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 610)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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, 238, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 506)
[M::mem_pestat] mean and std.dev: (234.36, 72.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 613)
[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 localref.fa /tmp/tmpqzv4nshl/files/7/4/9/dataset_749ab53a-c84f-474a-a03e-bdbb615ada5f.dat /tmp/tmpqzv4nshl/files/5/2/e/dataset_52e3c90a-f5fa-4246-af7a-12323bfca7f0.dat
[main] Real time: 10.084 sec; CPU: 9.821 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4134920679be11ef88f891b48f7ce313"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpqzv4nshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 1, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 5: 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/tmpqzv4nshl/files/3/5/1/dataset_351a7b7e-7850-4c8e-bf04-3ee8b32298a3.dat' infile && ln -s '/tmp/tmpqzv4nshl/files/_metadata_files/d/a/6/metadata_da6856b1-2802-43e0-86dc-56add52075a9.dat' infile.bai &&               samtools view -@ $addthreads -b  -q 20 -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__	`"4134920679be11ef88f891b48f7ce313"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpqzv4nshl/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": "20", "tag": null}, "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 6: 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/tmpqzv4nshl/files/2/5/4/dataset_25412e6d-17cf-4801-a04c-8805088e28fc.dat' 'SRR11578257' &&  picard MarkDuplicates  --INPUT 'SRR11578257' --OUTPUT '/tmp/tmpqzv4nshl/job_working_directory/000/7/outputs/dataset_0ad6130a-781b-48e8-b0cc-15c8be85dce5.dat'  --METRICS_FILE '/tmp/tmpqzv4nshl/job_working_directory/000/7/outputs/dataset_dcecc8f8-9f52-4b34-aa38-5a0fd922958c.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/tmpqzv4nshl/tmp
Sep 23, 2024 3:14:01 PM 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__	`"4134920679be11ef88f891b48f7ce313"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpqzv4nshl/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 7: 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/tmpqzv4nshl/files/2/5/4/dataset_25412e6d-17cf-4801-a04c-8805088e28fc.dat' infile && ln -s '/tmp/tmpqzv4nshl/files/_metadata_files/1/6/b/metadata_16b9109a-360b-45fa-b2bd-25a70c156c94.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmpqzv4nshl/job_working_directory/000/8/outputs/dataset_a79464ac-631a-4ed8-96b6-d99b4bee7f59.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4134920679be11ef88f891b48f7ce313"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpqzv4nshl/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 8: 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/tmpqzv4nshl/files/1/2/e/dataset_12ec7544-9958-4e29-81fe-81ccb3468189.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/tmpqzv4nshl/files/0/a/d/dataset_0ad6130a-781b-48e8-b0cc-15c8be85dce5.dat' &&  samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmpqzv4nshl/job_working_directory/000/9/outputs/dataset_12a1db88-d781-4932-834e-528823e05a25.dat' tmp.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4134920679be11ef88f891b48f7ce313"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpqzv4nshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}`

Step 9: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmpqzv4nshl/files/f/7/0/dataset_f70c6268-d86e-48f6-a8d6-a25fc80313fe.dat' 'multiqc_WDir/fastp_0/SRR11578257fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/SRR11578257fastp.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/tmpqzv4nshl/files/a/7/9/dataset_a79464ac-631a-4ed8-96b6-d99b4bee7f59.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'SRR11578257'" && ln -s '/tmp/tmpqzv4nshl/files/a/7/9/dataset_a79464ac-631a-4ed8-96b6-d99b4bee7f59.dat' 'multiqc_WDir/samtools_1/stats_0/SRR11578257'  &&    mkdir multiqc_WDir/picard_2 &&      mkdir 'multiqc_WDir/picard_2/markdups_0' &&    grep -q 'MarkDuplicates' /tmp/tmpqzv4nshl/files/d/c/e/dataset_dcecc8f8-9f52-4b34-aa38-5a0fd922958c.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'SRR11578257'" && ln -s '/tmp/tmpqzv4nshl/files/d/c/e/dataset_dcecc8f8-9f52-4b34-aa38-5a0fd922958c.dat' 'multiqc_WDir/picard_2/markdups_0/SRR11578257'  &&     multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:


/// MultiQC 🔍 v1.24.1

     version_check | MultiQC Version v1.25 now available!
       file_search | Search path: /tmp/tmpqzv4nshl/job_working_directory/000/10/working/multiqc_WDir

            picard | Found 1 MarkDuplicates reports
          samtools | Found 1 stats reports
             fastp | Found 1 reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 1188
-rw-r--r-- 1 1001 127   7517 Sep 23 15:14 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 127   2973 Sep 23 15:14 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127   2991 Sep 23 15:14 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127   2973 Sep 23 15:14 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127   3035 Sep 23 15:14 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127   2317 Sep 23 15:14 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127   2511 Sep 23 15:14 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127   2259 Sep 23 15:14 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127   2452 Sep 23 15:14 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127   2644 Sep 23 15:14 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127   2651 Sep 23 15:14 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127   2657 Sep 23 15:14 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127   2655 Sep 23 15:14 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127     73 Sep 23 15:14 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 127    183 Sep 23 15:14 multiqc_citations.txt
-rw-r--r-- 1 1001 127 984537 Sep 23 15:14 multiqc_data.json
-rw-r--r-- 1 1001 127 128972 Sep 23 15:14 multiqc_fastp.txt
-rw-r--r-- 1 1001 127   1108 Sep 23 15:14 multiqc_general_stats.txt
-rw-r--r-- 1 1001 127    305 Sep 23 15:14 multiqc_picard_dups.txt
-rw-r--r-- 1 1001 127   1305 Sep 23 15:14 multiqc_samtools_stats.txt
-rw-r--r-- 1 1001 127     51 Sep 23 15:14 multiqc_software_versions.txt
-rw-r--r-- 1 1001 127    424 Sep 23 15:14 multiqc_sources.txt
-rw-r--r-- 1 1001 127     73 Sep 23 15:14 picard_deduplication.txt
-rw-r--r-- 1 1001 127      0 Sep 23 15:14 picard_histogram.txt
-rw-r--r-- 1 1001 127      0 Sep 23 15:14 picard_histogram_1.txt
-rw-r--r-- 1 1001 127      0 Sep 23 15:14 picard_histogram_2.txt
-rw-r--r-- 1 1001 127    344 Sep 23 15:14 samtools-stats-dp.txt
-rw-r--r-- 1 1001 127     45 Sep 23 15:14 samtools_alignment_plot.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4134920679be11ef88f891b48f7ce313"`
chromInfo	`"/tmp/tmpqzv4nshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpqzv4nshl/files/1/2/e/dataset_12ec7544-9958-4e29-81fe-81ccb3468189.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq indelqual --dindel --ref reference.fa -o output.bam /tmp/tmpqzv4nshl/files/1/2/a/dataset_12a1db88-d781-4932-834e-528823e05a25.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4134920679be11ef88f891b48f7ce313"`
chromInfo	`"/tmp/tmpqzv4nshl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Other invocation details
- history_id
  - 7d36643008293abf
- history_state
  - ok
- invocation_id
  - 7d36643008293abf
- invocation_state
  - scheduled
- workflow_id
  - 7d36643008293abf

Sep 23 '24 15:09 github-actions[bot]

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

Sep 24 '24 14:09 gxydevbot

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

❌ pe-wgs-variation.ga_0

Problems:

Output with path /tmp/tmp0p080_8x/Final (SnpEff-)annotated variants__3e9ee67e-39b1-4ca5-9c93-499a9280945e different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/test-data/final_snpeff_annotated_variants.vcf v. /tmp/tmpb7v24nudfinal_snpeff_annotated_variants.vcf )
--- local_file
+++ history_data
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.0
-##fileDate=20210221
-##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /tmp/lofreq2_call_parallelxh3mih1k/0.vcf.gz reads.bam 
+##fileDate=20240924
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /tmp/tmpfk43z5m9/tmp/lofreq2_call_parallelt18n3hcy/0.vcf.gz reads.bam 
 ##reference=reference.fa
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
@@ -15,7 +15,7 @@
 ##FILTER=<ID=min_indelqual_64,Description="Minimum Indel Quality (Phred) 64">
 ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
 ##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani"
-##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /Users/mvandenb/src/galaxy/database/files/8/c/5/dataset_8c59d777-b160-4e19-a2bd-7da3b8b7d54c.dat NC_045512.2 /Users/mvandenb/src/galaxy/database/files/4/f/7/dataset_4f741f76-a82b-464c-85a3-7d29422a36ab.dat "
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /tmp/tmpfk43z5m9/job_working_directory/000/14/outputs/dataset_366e2a75-d5c6-4957-acca-307547345c6e.dat NC_045512.2 /tmp/tmpfk43z5m9/files/a/9/d/dataset_a9d6455f-be54-4c6a-b4a0-e1b19170abe2.dat "
 ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
 ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
 ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
@@ -58,9 +58,9 @@
 NC_045512.2	21134	.	A	G	163.0	PASS	DP=1677;AF=0.008945;SB=3;DP4=218,1441,3,12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q6957R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q159R|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
 NC_045512.2	21526	.	A	T	111.0	PASS	DP=1208;AF=0.011589;SB=23;DP4=783,404,7,14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I7088F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I290F|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
 NC_045512.2	21578	.	G	T	76.0	PASS	DP=1345;AF=0.008178;SB=13;DP4=476,850,2,15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V6F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
-NC_045512.2	22712	.	C	T	125.0	sb_fdr	DP=8681;AF=0.003456;SB=99;DP4=4028,4617,30,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P384S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
-NC_045512.2	22721	.	T	A	98.0	sb_fdr	DP=8884;AF=0.003489;SB=139;DP4=3798,5040,42,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Ata|L387I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
-NC_045512.2	22810	.	A	G	72.0	sb_fdr	DP=6269;AF=0.003828;SB=142;DP4=1565,4675,26,1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G416|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512.2	22712	.	C	T	133.0	sb_fdr	DP=8727;AF=0.003552;SB=101;DP4=4072,4618,31,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P384S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512.2	22721	.	T	A	102.0	sb_fdr	DP=8935;AF=0.003581;SB=141;DP4=3847,5041,43,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Ata|L387I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512.2	22810	.	A	G	80.0	sb_fdr	DP=6382;AF=0.004074;SB=148;DP4=1595,4757,27,1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G416|1273|S|protein_coding|CODING|GU280_gp02|1|G)
 NC_045512.2	23262	.	G	A	131.0	sb_fdr	DP=7418;AF=0.003101;SB=126;DP4=5307,2085,0,23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R567K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
 NC_045512.2	23269	.	T	C	2250.0	PASS	DP=7958;AF=0.020985;SB=3;DP4=5454,2326,126,46;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I569|1273|S|protein_coding|CODING|GU280_gp02|1|C)
 NC_045512.2	23280	.	C	A	108.0	sb_fdr	DP=8464;AF=0.003781;SB=63;DP4=5576,2848,37,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T573N|1273|S|protein_coding|CODING|GU280_gp02|1|A)

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: NC_045512.2 FASTA sequence of SARS-CoV-2:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpfk43z5m9/files/a/4/9/dataset_a4960813-eb19-486c-9f21-6a18d75cf566.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  ln -s '/tmp/tmpfk43z5m9/files/e/1/2/dataset_e124e874-1347-4a02-a3a0-30c518e11701.dat' reads.bam && ln -s -f '/tmp/tmpfk43z5m9/files/_metadata_files/3/b/a/metadata_3ba87846-58d9-4eb7-92f7-b427b66772e9.dat' reads.bam.bai &&   lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose  --ref 'reference.fa' --out variants.vcf --call-indels   --min-cov 5 --max-depth 1000000  --min-bq 30 --min-alt-bq 30    --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0  --sig 0.0005 --bonf dynamic --no-default-filter  reads.bam 2>&1  || (tool_exit_code=$? && cat "$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit $tool_exit_code)  && echo set_custom

Exit Code:

```
0
```

Standard Output:

INFO [2024-09-24 14:32:33,460]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter reads.bam

INFO [2024-09-24 14:32:33,466]: Adding 3 commands to mp-pool
Number of substitution tests performed: 8244
Number of indel tests performed: 1172
INFO [2024-09-24 14:32:55,939]: Executing lofreq filter -i /tmp/tmpfk43z5m9/tmp/lofreq2_call_parallelt18n3hcy/concat.vcf.gz -o variants.vcf --no-defaults --snvqual-thresh 72 --indelqual-thresh 64

set_custom

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8f67b9267a8111efb78acb984a700661"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "20", "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/tmpfk43z5m9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

lofreq filter -i /tmp/tmpfk43z5m9/files/4/e/8/dataset_4e882542-73e7-4be3-a2a7-78c633558475.dat --no-defaults --verbose --print-all  -v 0 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001   -o filtered.vcf

Exit Code:

```
0
```

Standard Error:

Skipping default settings
At least one type of multiple testing correction requested. Doing first pass of vcf
MTC application completed
Successful exit.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8f67b9267a8111efb78acb984a700661"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpfk43z5m9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 13: SnpEff eff covid19 version:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m eff -i vcf -o vcf -upDownStreamLen 0 -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr                  -stats '/tmp/tmpfk43z5m9/job_working_directory/000/14/outputs/dataset_366e2a75-d5c6-4957-acca-307547345c6e.dat' -noLog  NC_045512.2  '/tmp/tmpfk43z5m9/files/a/9/d/dataset_a9d6455f-be54-4c6a-b4a0-e1b19170abe2.dat' > '/tmp/tmpfk43z5m9/job_working_directory/000/14/outputs/dataset_3e9ee67e-39b1-4ca5-9c93-499a9280945e.dat'  && mkdir '/tmp/tmpfk43z5m9/job_working_directory/000/14/outputs/dataset_366e2a75-d5c6-4957-acca-307547345c6e_files' && mv '/tmp/tmpfk43z5m9/job_working_directory/000/14/outputs/dataset_366e2a75-d5c6-4957-acca-307547345c6e.dat.genes.txt' '/tmp/tmpfk43z5m9/job_working_directory/000/14/outputs/dataset_366e2a75-d5c6-4957-acca-307547345c6e_files/dataset_366e2a75-d5c6-4957-acca-307547345c6e.dat.genes.txt'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"8f67b9267a8111efb78acb984a700661"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpfk43z5m9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-upstream", "-no-utr"]`
generate_stats	`true`
genome_version	`"NC_045512.2"`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
transcripts	`None`
udLength	`"0"`

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmpfk43z5m9/files/a/9/c/dataset_a9c255a8-083b-41f5-ae63-d7f499da39aa.dat' 'SRR11578257.fastq.gz' && ln -sf '/tmp/tmpfk43z5m9/files/a/3/f/dataset_a3f38bcb-c785-4d34-b798-c457c565c629.dat' 'SRR11578257_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for SRR11578257.fastq.gz'   -i 'SRR11578257.fastq.gz' -o first.fastq.gz  -I 'SRR11578257_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmpfk43z5m9/job_working_directory/000/4/outputs/dataset_6b118a5a-8019-4594-9f18-9ac7dc2a3b86.dat' && mv second.fastq.gz '/tmp/tmpfk43z5m9/job_working_directory/000/4/outputs/dataset_5d9d27fc-99d9-48e8-b62e-b0aa5395a257.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 201367
total bases: 29302687
Q20 bases: 28139796(96.0315%)
Q30 bases: 27281893(93.1037%)

Read2 before filtering:
total reads: 201367
total bases: 29398146
Q20 bases: 27778430(94.4904%)
Q30 bases: 26748339(90.9865%)

Read1 after filtering:
total reads: 197961
total bases: 28794778
Q20 bases: 27771017(96.4446%)
Q30 bases: 26956923(93.6174%)

Read2 after filtering:
total reads: 197961
total bases: 28807154
Q20 bases: 27394032(95.0945%)
Q30 bases: 26419337(91.711%)

Filtering result:
reads passed filter: 395922
reads failed due to low quality: 5636
reads failed due to too many N: 1176
reads failed due to too short: 0
reads with adapter trimmed: 16490
bases trimmed due to adapters: 89039

Duplication rate: 20.2521%

Insert size peak (evaluated by paired-end reads): 230

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

fastp --thread 1 --report_title fastp report for SRR11578257.fastq.gz -i SRR11578257.fastq.gz -o first.fastq.gz -I SRR11578257_R2.fastq.gz -O second.fastq.gz 
fastp v0.23.4, time used: 4 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8f67b9267a8111efb78acb984a700661"`
chromInfo	`"/tmp/tmpfk43z5m9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 4: 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/tmpfk43z5m9/files/a/4/9/dataset_a4960813-eb19-486c-9f21-6a18d75cf566.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1                 'localref.fa' '/tmp/tmpfk43z5m9/files/6/b/1/dataset_6b118a5a-8019-4594-9f18-9ac7dc2a3b86.dat' '/tmp/tmpfk43z5m9/files/5/d/9/dataset_5d9d27fc-99d9-48e8-b62e-b0aa5395a257.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpfk43z5m9/job_working_directory/000/5/outputs/dataset_b3cd40bb-6d4d-46f4-9d10-e2ca681d1adb.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 0.011 sec; CPU: 0.008 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: (188, 240, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503)
[M::mem_pestat] mean and std.dev: (236.48, 72.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 608)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (188, 239, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503)
[M::mem_pestat] mean and std.dev: (235.85, 72.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 608)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (187, 239, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 505)
[M::mem_pestat] mean and std.dev: (235.52, 72.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 611)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (188, 240, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503)
[M::mem_pestat] mean and std.dev: (236.18, 72.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 608)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (186, 239, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 504)
[M::mem_pestat] mean and std.dev: (235.20, 72.50)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 610)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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, 238, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 506)
[M::mem_pestat] mean and std.dev: (234.36, 72.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 613)
[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 localref.fa /tmp/tmpfk43z5m9/files/6/b/1/dataset_6b118a5a-8019-4594-9f18-9ac7dc2a3b86.dat /tmp/tmpfk43z5m9/files/5/d/9/dataset_5d9d27fc-99d9-48e8-b62e-b0aa5395a257.dat
[main] Real time: 10.113 sec; CPU: 9.891 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8f67b9267a8111efb78acb984a700661"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmpfk43z5m9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 1, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 5: 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/tmpfk43z5m9/files/b/3/c/dataset_b3cd40bb-6d4d-46f4-9d10-e2ca681d1adb.dat' infile && ln -s '/tmp/tmpfk43z5m9/files/_metadata_files/b/8/8/metadata_b88e13db-a700-4c93-95f9-ef89648f2bc6.dat' infile.bai &&               samtools view -@ $addthreads -b  -q 20 -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__	`"8f67b9267a8111efb78acb984a700661"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpfk43z5m9/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": "20", "tag": null}, "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 6: 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/tmpfk43z5m9/files/8/6/6/dataset_8661f774-d405-484c-9341-67a05e7ed0d6.dat' 'SRR11578257' &&  picard MarkDuplicates  --INPUT 'SRR11578257' --OUTPUT '/tmp/tmpfk43z5m9/job_working_directory/000/7/outputs/dataset_5b08fec6-355b-42a9-8b2f-93dd2370e44b.dat'  --METRICS_FILE '/tmp/tmpfk43z5m9/job_working_directory/000/7/outputs/dataset_6a4fd769-bf92-4d4c-9228-c17b03f62718.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/tmpfk43z5m9/tmp
Sep 24, 2024 2:31:57 PM 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__	`"8f67b9267a8111efb78acb984a700661"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpfk43z5m9/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 7: 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/tmpfk43z5m9/files/8/6/6/dataset_8661f774-d405-484c-9341-67a05e7ed0d6.dat' infile && ln -s '/tmp/tmpfk43z5m9/files/_metadata_files/c/1/6/metadata_c16b6d3c-433b-4b15-bce4-b9edbada96ab.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmpfk43z5m9/job_working_directory/000/8/outputs/dataset_fc59c185-b7f5-441a-a39a-492d9a0aba44.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8f67b9267a8111efb78acb984a700661"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpfk43z5m9/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 8: 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/tmpfk43z5m9/files/a/4/9/dataset_a4960813-eb19-486c-9f21-6a18d75cf566.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/tmpfk43z5m9/files/5/b/0/dataset_5b08fec6-355b-42a9-8b2f-93dd2370e44b.dat' &&  samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmpfk43z5m9/job_working_directory/000/9/outputs/dataset_3f3c9f7e-3422-4197-8dff-5aad18292243.dat' tmp.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8f67b9267a8111efb78acb984a700661"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpfk43z5m9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}`

Step 9: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmpfk43z5m9/files/e/4/6/dataset_e4672232-386e-473d-91d1-5d399175a981.dat' 'multiqc_WDir/fastp_0/SRR11578257fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/SRR11578257fastp.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/tmpfk43z5m9/files/f/c/5/dataset_fc59c185-b7f5-441a-a39a-492d9a0aba44.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'SRR11578257'" && ln -s '/tmp/tmpfk43z5m9/files/f/c/5/dataset_fc59c185-b7f5-441a-a39a-492d9a0aba44.dat' 'multiqc_WDir/samtools_1/stats_0/SRR11578257'  &&    mkdir multiqc_WDir/picard_2 &&      mkdir 'multiqc_WDir/picard_2/markdups_0' &&    grep -q 'MarkDuplicates' /tmp/tmpfk43z5m9/files/6/a/4/dataset_6a4fd769-bf92-4d4c-9228-c17b03f62718.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'SRR11578257'" && ln -s '/tmp/tmpfk43z5m9/files/6/a/4/dataset_6a4fd769-bf92-4d4c-9228-c17b03f62718.dat' 'multiqc_WDir/picard_2/markdups_0/SRR11578257'  &&     multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:


/// MultiQC 🔍 v1.24.1

     version_check | MultiQC Version v1.25 now available!
       file_search | Search path: /tmp/tmpfk43z5m9/job_working_directory/000/10/working/multiqc_WDir

            picard | Found 1 MarkDuplicates reports
          samtools | Found 1 stats reports
             fastp | Found 1 reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 1188
-rw-r--r-- 1 1001 127   7517 Sep 24 14:32 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 127   2973 Sep 24 14:32 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127   2991 Sep 24 14:32 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127   2973 Sep 24 14:32 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127   3035 Sep 24 14:32 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127   2317 Sep 24 14:32 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127   2511 Sep 24 14:32 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127   2259 Sep 24 14:32 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127   2452 Sep 24 14:32 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127   2644 Sep 24 14:32 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127   2651 Sep 24 14:32 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127   2657 Sep 24 14:32 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127   2655 Sep 24 14:32 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127     73 Sep 24 14:32 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 127    183 Sep 24 14:32 multiqc_citations.txt
-rw-r--r-- 1 1001 127 984537 Sep 24 14:32 multiqc_data.json
-rw-r--r-- 1 1001 127 128972 Sep 24 14:32 multiqc_fastp.txt
-rw-r--r-- 1 1001 127   1108 Sep 24 14:32 multiqc_general_stats.txt
-rw-r--r-- 1 1001 127    305 Sep 24 14:32 multiqc_picard_dups.txt
-rw-r--r-- 1 1001 127   1305 Sep 24 14:32 multiqc_samtools_stats.txt
-rw-r--r-- 1 1001 127     51 Sep 24 14:32 multiqc_software_versions.txt
-rw-r--r-- 1 1001 127    424 Sep 24 14:32 multiqc_sources.txt
-rw-r--r-- 1 1001 127     73 Sep 24 14:32 picard_deduplication.txt
-rw-r--r-- 1 1001 127      0 Sep 24 14:32 picard_histogram.txt
-rw-r--r-- 1 1001 127      0 Sep 24 14:32 picard_histogram_1.txt
-rw-r--r-- 1 1001 127      0 Sep 24 14:32 picard_histogram_2.txt
-rw-r--r-- 1 1001 127    344 Sep 24 14:32 samtools-stats-dp.txt
-rw-r--r-- 1 1001 127     45 Sep 24 14:32 samtools_alignment_plot.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8f67b9267a8111efb78acb984a700661"`
chromInfo	`"/tmp/tmpfk43z5m9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpfk43z5m9/files/a/4/9/dataset_a4960813-eb19-486c-9f21-6a18d75cf566.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq indelqual --dindel --ref reference.fa -o output.bam /tmp/tmpfk43z5m9/files/3/f/3/dataset_3f3c9f7e-3422-4197-8dff-5aad18292243.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8f67b9267a8111efb78acb984a700661"`
chromInfo	`"/tmp/tmpfk43z5m9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Other invocation details
- history_id
  - 923961480c7126eb
- history_state
  - ok
- invocation_id
  - 923961480c7126eb
- invocation_state
  - scheduled
- workflow_id
  - 923961480c7126eb

Sep 24 '24 14:09 github-actions[bot]

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

Oct 07 '24 05:10 gxydevbot

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

❌ pe-wgs-variation.ga_0

Problems:

Output with path /tmp/tmp2etw26pl/Final (SnpEff-)annotated variants__9a20df9b-9bcc-4200-8f70-42155e8494f9 different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/test-data/final_snpeff_annotated_variants.vcf v. /tmp/tmpqa6q9iiofinal_snpeff_annotated_variants.vcf )
--- local_file
+++ history_data
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.0
-##fileDate=20210221
-##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /tmp/lofreq2_call_parallelxh3mih1k/0.vcf.gz reads.bam 
+##fileDate=20241007
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /tmp/tmp4yeaqpe1/tmp/lofreq2_call_paralleld6l27u9l/0.vcf.gz reads.bam 
 ##reference=reference.fa
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
@@ -15,7 +15,7 @@
 ##FILTER=<ID=min_indelqual_64,Description="Minimum Indel Quality (Phred) 64">
 ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
 ##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani"
-##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /Users/mvandenb/src/galaxy/database/files/8/c/5/dataset_8c59d777-b160-4e19-a2bd-7da3b8b7d54c.dat NC_045512.2 /Users/mvandenb/src/galaxy/database/files/4/f/7/dataset_4f741f76-a82b-464c-85a3-7d29422a36ab.dat "
+##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /tmp/tmp4yeaqpe1/job_working_directory/000/14/outputs/dataset_5863c51d-36f4-42f6-a03b-7a63b1355386.dat NC_045512.2 /tmp/tmp4yeaqpe1/files/6/6/c/dataset_66c02390-b073-48fb-b6bc-fb509ccd0dd1.dat "
 ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
 ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
 ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
@@ -58,9 +58,9 @@
 NC_045512.2	21134	.	A	G	163.0	PASS	DP=1677;AF=0.008945;SB=3;DP4=218,1441,3,12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q6957R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q159R|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
 NC_045512.2	21526	.	A	T	111.0	PASS	DP=1208;AF=0.011589;SB=23;DP4=783,404,7,14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I7088F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I290F|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
 NC_045512.2	21578	.	G	T	76.0	PASS	DP=1345;AF=0.008178;SB=13;DP4=476,850,2,15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V6F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
-NC_045512.2	22712	.	C	T	125.0	sb_fdr	DP=8681;AF=0.003456;SB=99;DP4=4028,4617,30,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P384S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
-NC_045512.2	22721	.	T	A	98.0	sb_fdr	DP=8884;AF=0.003489;SB=139;DP4=3798,5040,42,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Ata|L387I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
-NC_045512.2	22810	.	A	G	72.0	sb_fdr	DP=6269;AF=0.003828;SB=142;DP4=1565,4675,26,1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G416|1273|S|protein_coding|CODING|GU280_gp02|1|G)
+NC_045512.2	22712	.	C	T	133.0	sb_fdr	DP=8727;AF=0.003552;SB=101;DP4=4072,4618,31,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P384S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
+NC_045512.2	22721	.	T	A	102.0	sb_fdr	DP=8935;AF=0.003581;SB=141;DP4=3847,5041,43,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Ata|L387I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
+NC_045512.2	22810	.	A	G	80.0	sb_fdr	DP=6382;AF=0.004074;SB=148;DP4=1595,4757,27,1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G416|1273|S|protein_coding|CODING|GU280_gp02|1|G)
 NC_045512.2	23262	.	G	A	131.0	sb_fdr	DP=7418;AF=0.003101;SB=126;DP4=5307,2085,0,23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R567K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
 NC_045512.2	23269	.	T	C	2250.0	PASS	DP=7958;AF=0.020985;SB=3;DP4=5454,2326,126,46;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I569|1273|S|protein_coding|CODING|GU280_gp02|1|C)
 NC_045512.2	23280	.	C	A	108.0	sb_fdr	DP=8464;AF=0.003781;SB=63;DP4=5576,2848,37,0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T573N|1273|S|protein_coding|CODING|GU280_gp02|1|A)

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: NC_045512.2 FASTA sequence of SARS-CoV-2:
- step_state: scheduled

Step 11: 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/tmp4yeaqpe1/files/9/d/c/dataset_9dcf06ed-958a-4f8a-bf69-430d1fd77ee3.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  ln -s '/tmp/tmp4yeaqpe1/files/c/6/c/dataset_c6c63cf8-0ea1-4c69-8588-8f74f75ca03e.dat' reads.bam && ln -s -f '/tmp/tmp4yeaqpe1/files/_metadata_files/5/0/4/metadata_50428f17-54cd-4bd7-a59a-2acbffba453d.dat' reads.bam.bai &&   lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose  --ref 'reference.fa' --out variants.vcf --call-indels   --min-cov 5 --max-depth 1000000  --min-bq 30 --min-alt-bq 30    --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0  --sig 0.0005 --bonf dynamic --no-default-filter  reads.bam 2>&1  || (tool_exit_code=$? && cat "$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit $tool_exit_code)  && echo set_custom

Exit Code:

```
0
```

Standard Output:

INFO [2024-10-07 05:30:22,392]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter reads.bam

INFO [2024-10-07 05:30:22,397]: Adding 3 commands to mp-pool
Number of substitution tests performed: 8244
Number of indel tests performed: 1172
INFO [2024-10-07 05:30:44,390]: Executing lofreq filter -i /tmp/tmp4yeaqpe1/tmp/lofreq2_call_paralleld6l27u9l/concat.vcf.gz -o variants.vcf --no-defaults --snvqual-thresh 72 --indelqual-thresh 64

set_custom

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6fbdb68846c11ef82863bb8a8e94682"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "20", "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/tmp4yeaqpe1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

lofreq filter -i /tmp/tmp4yeaqpe1/files/1/6/6/dataset_166bc6ea-bbb6-4fae-bb13-f99fe6657599.dat --no-defaults --verbose --print-all  -v 0 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001   -o filtered.vcf

Exit Code:

```
0
```

Standard Error:

Skipping default settings
At least one type of multiple testing correction requested. Doing first pass of vcf
MTC application completed
Successful exit.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6fbdb68846c11ef82863bb8a8e94682"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmp4yeaqpe1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 13: SnpEff eff covid19 version:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m eff -i vcf -o vcf -upDownStreamLen 0 -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr                  -stats '/tmp/tmp4yeaqpe1/job_working_directory/000/14/outputs/dataset_5863c51d-36f4-42f6-a03b-7a63b1355386.dat' -noLog  NC_045512.2  '/tmp/tmp4yeaqpe1/files/6/6/c/dataset_66c02390-b073-48fb-b6bc-fb509ccd0dd1.dat' > '/tmp/tmp4yeaqpe1/job_working_directory/000/14/outputs/dataset_9a20df9b-9bcc-4200-8f70-42155e8494f9.dat'  && mkdir '/tmp/tmp4yeaqpe1/job_working_directory/000/14/outputs/dataset_5863c51d-36f4-42f6-a03b-7a63b1355386_files' && mv '/tmp/tmp4yeaqpe1/job_working_directory/000/14/outputs/dataset_5863c51d-36f4-42f6-a03b-7a63b1355386.dat.genes.txt' '/tmp/tmp4yeaqpe1/job_working_directory/000/14/outputs/dataset_5863c51d-36f4-42f6-a03b-7a63b1355386_files/dataset_5863c51d-36f4-42f6-a03b-7a63b1355386.dat.genes.txt'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"f6fbdb68846c11ef82863bb8a8e94682"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmp4yeaqpe1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-upstream", "-no-utr"]`
generate_stats	`true`
genome_version	`"NC_045512.2"`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
transcripts	`None`
udLength	`"0"`

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -sf '/tmp/tmp4yeaqpe1/files/1/2/3/dataset_1239507e-5002-4bce-b355-11d8c96b7baa.dat' 'SRR11578257.fastq.gz' && ln -sf '/tmp/tmp4yeaqpe1/files/8/7/c/dataset_87c29e3f-b6a9-4e3b-9d05-50c841a2445e.dat' 'SRR11578257_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for SRR11578257.fastq.gz'   -i 'SRR11578257.fastq.gz' -o first.fastq.gz  -I 'SRR11578257_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmp4yeaqpe1/job_working_directory/000/4/outputs/dataset_1095d92b-04e4-4c99-bf83-2cbc750b777e.dat' && mv second.fastq.gz '/tmp/tmp4yeaqpe1/job_working_directory/000/4/outputs/dataset_61587df4-626a-4640-82da-e2138be71cfd.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 201367
total bases: 29302687
Q20 bases: 28139796(96.0315%)
Q30 bases: 27281893(93.1037%)

Read2 before filtering:
total reads: 201367
total bases: 29398146
Q20 bases: 27778430(94.4904%)
Q30 bases: 26748339(90.9865%)

Read1 after filtering:
total reads: 197961
total bases: 28794778
Q20 bases: 27771017(96.4446%)
Q30 bases: 26956923(93.6174%)

Read2 after filtering:
total reads: 197961
total bases: 28807154
Q20 bases: 27394032(95.0945%)
Q30 bases: 26419337(91.711%)

Filtering result:
reads passed filter: 395922
reads failed due to low quality: 5636
reads failed due to too many N: 1176
reads failed due to too short: 0
reads with adapter trimmed: 16490
bases trimmed due to adapters: 89039

Duplication rate: 20.2521%

Insert size peak (evaluated by paired-end reads): 230

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

fastp --thread 1 --report_title fastp report for SRR11578257.fastq.gz -i SRR11578257.fastq.gz -o first.fastq.gz -I SRR11578257_R2.fastq.gz -O second.fastq.gz 
fastp v0.23.4, time used: 4 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6fbdb68846c11ef82863bb8a8e94682"`
chromInfo	`"/tmp/tmp4yeaqpe1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 4: 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/tmp4yeaqpe1/files/9/d/c/dataset_9dcf06ed-958a-4f8a-bf69-430d1fd77ee3.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1                 'localref.fa' '/tmp/tmp4yeaqpe1/files/1/0/9/dataset_1095d92b-04e4-4c99-bf83-2cbc750b777e.dat' '/tmp/tmp4yeaqpe1/files/6/1/5/dataset_61587df4-626a-4640-82da-e2138be71cfd.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmp4yeaqpe1/job_working_directory/000/5/outputs/dataset_93242ace-3fd4-4c87-adca-846d98107e2a.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa index localref.fa
[main] Real time: 0.013 sec; CPU: 0.008 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: (188, 240, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503)
[M::mem_pestat] mean and std.dev: (236.48, 72.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 608)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (188, 239, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503)
[M::mem_pestat] mean and std.dev: (235.85, 72.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 608)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (187, 239, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 505)
[M::mem_pestat] mean and std.dev: (235.52, 72.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 611)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (188, 240, 293)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503)
[M::mem_pestat] mean and std.dev: (236.18, 72.42)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 608)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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: (186, 239, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 504)
[M::mem_pestat] mean and std.dev: (235.20, 72.50)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 610)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[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, 238, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 506)
[M::mem_pestat] mean and std.dev: (234.36, 72.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 613)
[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 localref.fa /tmp/tmp4yeaqpe1/files/1/0/9/dataset_1095d92b-04e4-4c99-bf83-2cbc750b777e.dat /tmp/tmp4yeaqpe1/files/6/1/5/dataset_61587df4-626a-4640-82da-e2138be71cfd.dat
[main] Real time: 10.101 sec; CPU: 9.829 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6fbdb68846c11ef82863bb8a8e94682"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "illumina"}`
chromInfo	`"/tmp/tmp4yeaqpe1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 1, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 5: 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/tmp4yeaqpe1/files/9/3/2/dataset_93242ace-3fd4-4c87-adca-846d98107e2a.dat' infile && ln -s '/tmp/tmp4yeaqpe1/files/_metadata_files/f/3/2/metadata_f32b521f-d50e-41e3-ad6b-0c9ddaf8e2b8.dat' infile.bai &&               samtools view -@ $addthreads -b  -q 20 -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__	`"f6fbdb68846c11ef82863bb8a8e94682"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp4yeaqpe1/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": "20", "tag": null}, "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 6: 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/tmp4yeaqpe1/files/9/8/a/dataset_98a45b89-bfd5-4060-b252-7b7d2a1f2f42.dat' 'SRR11578257' &&  picard MarkDuplicates  --INPUT 'SRR11578257' --OUTPUT '/tmp/tmp4yeaqpe1/job_working_directory/000/7/outputs/dataset_d97459c4-2dd2-4dfb-a3b3-41a8ec6cffdd.dat'  --METRICS_FILE '/tmp/tmp4yeaqpe1/job_working_directory/000/7/outputs/dataset_378c0c33-cf7c-404e-8f6a-c8b4feb23fb3.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/tmp4yeaqpe1/tmp
Oct 07, 2024 5:29:46 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__	`"f6fbdb68846c11ef82863bb8a8e94682"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmp4yeaqpe1/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 7: 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/tmp4yeaqpe1/files/9/8/a/dataset_98a45b89-bfd5-4060-b252-7b7d2a1f2f42.dat' infile && ln -s '/tmp/tmp4yeaqpe1/files/_metadata_files/6/e/a/metadata_6ea85197-ff80-44f1-8102-be3819f72bea.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmp4yeaqpe1/job_working_directory/000/8/outputs/dataset_6e3f6253-f720-47a6-859b-c51194791136.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6fbdb68846c11ef82863bb8a8e94682"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp4yeaqpe1/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 8: 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/tmp4yeaqpe1/files/9/d/c/dataset_9dcf06ed-958a-4f8a-bf69-430d1fd77ee3.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/tmp4yeaqpe1/files/d/9/7/dataset_d97459c4-2dd2-4dfb-a3b3-41a8ec6cffdd.dat' &&  samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmp4yeaqpe1/job_working_directory/000/9/outputs/dataset_ec73d4a4-1a09-4e51-a73f-674c3e74998c.dat' tmp.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6fbdb68846c11ef82863bb8a8e94682"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmp4yeaqpe1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}`

Step 9: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmp4yeaqpe1/files/e/1/3/dataset_e13bcd88-78c2-48fd-81d2-718e24384f7f.dat' 'multiqc_WDir/fastp_0/SRR11578257fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/SRR11578257fastp.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/tmp4yeaqpe1/files/6/e/3/dataset_6e3f6253-f720-47a6-859b-c51194791136.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'SRR11578257'" && ln -s '/tmp/tmp4yeaqpe1/files/6/e/3/dataset_6e3f6253-f720-47a6-859b-c51194791136.dat' 'multiqc_WDir/samtools_1/stats_0/SRR11578257'  &&    mkdir multiqc_WDir/picard_2 &&      mkdir 'multiqc_WDir/picard_2/markdups_0' &&    grep -q 'MarkDuplicates' /tmp/tmp4yeaqpe1/files/3/7/8/dataset_378c0c33-cf7c-404e-8f6a-c8b4feb23fb3.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'SRR11578257'" && ln -s '/tmp/tmp4yeaqpe1/files/3/7/8/dataset_378c0c33-cf7c-404e-8f6a-c8b4feb23fb3.dat' 'multiqc_WDir/picard_2/markdups_0/SRR11578257'  &&     multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:


/// MultiQC 🔍 v1.24.1

     version_check | MultiQC Version v1.25.1 now available!
       file_search | Search path: /tmp/tmp4yeaqpe1/job_working_directory/000/10/working/multiqc_WDir

            picard | Found 1 MarkDuplicates reports
          samtools | Found 1 stats reports
             fastp | Found 1 reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 1188
-rw-r--r-- 1 1001 127   7517 Oct  7 05:30 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 127   2973 Oct  7 05:30 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127   2991 Oct  7 05:30 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127   2973 Oct  7 05:30 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127   3035 Oct  7 05:30 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127   2317 Oct  7 05:30 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127   2511 Oct  7 05:30 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127   2259 Oct  7 05:30 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127   2452 Oct  7 05:30 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127   2644 Oct  7 05:30 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 127   2651 Oct  7 05:30 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 127   2657 Oct  7 05:30 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 127   2655 Oct  7 05:30 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 127     73 Oct  7 05:30 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 127    183 Oct  7 05:30 multiqc_citations.txt
-rw-r--r-- 1 1001 127 984537 Oct  7 05:30 multiqc_data.json
-rw-r--r-- 1 1001 127 128972 Oct  7 05:30 multiqc_fastp.txt
-rw-r--r-- 1 1001 127   1108 Oct  7 05:30 multiqc_general_stats.txt
-rw-r--r-- 1 1001 127    305 Oct  7 05:30 multiqc_picard_dups.txt
-rw-r--r-- 1 1001 127   1305 Oct  7 05:30 multiqc_samtools_stats.txt
-rw-r--r-- 1 1001 127     51 Oct  7 05:30 multiqc_software_versions.txt
-rw-r--r-- 1 1001 127    424 Oct  7 05:30 multiqc_sources.txt
-rw-r--r-- 1 1001 127     73 Oct  7 05:30 picard_deduplication.txt
-rw-r--r-- 1 1001 127      0 Oct  7 05:30 picard_histogram.txt
-rw-r--r-- 1 1001 127      0 Oct  7 05:30 picard_histogram_1.txt
-rw-r--r-- 1 1001 127      0 Oct  7 05:30 picard_histogram_2.txt
-rw-r--r-- 1 1001 127    344 Oct  7 05:30 samtools-stats-dp.txt
-rw-r--r-- 1 1001 127     45 Oct  7 05:30 samtools_alignment_plot.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6fbdb68846c11ef82863bb8a8e94682"`
chromInfo	`"/tmp/tmp4yeaqpe1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp4yeaqpe1/files/9/d/c/dataset_9dcf06ed-958a-4f8a-bf69-430d1fd77ee3.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq indelqual --dindel --ref reference.fa -o output.bam /tmp/tmp4yeaqpe1/files/e/c/7/dataset_ec73d4a4-1a09-4e51-a73f-674c3e74998c.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f6fbdb68846c11ef82863bb8a8e94682"`
chromInfo	`"/tmp/tmp4yeaqpe1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Other invocation details
- history_id
  - 7dd7b6f8a936e6fe
- history_state
  - ok
- invocation_id
  - 7dd7b6f8a936e6fe
- invocation_state
  - scheduled
- workflow_id
  - 7dd7b6f8a936e6fe

Oct 07 '24 05:10 github-actions[bot]