CaVEMan WRAPPER_EXIT 25 on native docker

[katlande]

Hello,

I am trying to run ascatNGS in a native docker environment with the following input:

sudo docker run -it --rm
--user 7793:7796
--env HOME=/var/spool/results
-v /gpfs/analyses/kat/WGS_Tools/acatNgs/ref:/var/spool/ref
-v /gpfs/analyses/kat/Schmidt_Karlseder/bam/acatNGS_Chroms:/var/spool/data
-v /gpfs/analyses/kat/Schmidt_Karlseder/acatNGS:/var/spool/results
quay.io/wtsicgp/dockstore-cgpwgs:2.1.0
ds-cgpwgs.pl
-sp "hsapiens"
-as hg38
-r /var/spool/ref
-a /var/spool/ref
-si /var/spool/ref
-cs /var/spool/ref
-qc /var/spool/ref
-c 30
-pl 3.65 -pu 1.0
-e 'MT,GL%,hs37d5,NC_007605'
-t /var/spool/data/PC7L_acatNGS.bam
-tidx /var/spool/data/PC7L_acatNGS.bam.bai
-n /var/spool/data/IMR90E6E7_acatNGS.bam
-nidx /var/spool/data/IMR90E6E7_acatNGS.bam.bai
-o /var/spool/results/results

I have been playing around with the core number and other memory parameters for a while, but I always get an output that looks like this:

Start workflow: Wed Sep 21 17:10:25 UTC 2022

Loading user options from: /var/spool/results/results/run.params
BAM_MT : /var/spool/data/PC7L_acatNGS.bam
BAM_WT : /var/spool/data/IMR90E6E7_acatNGS.bam
NAME_MT : PC7L_CSFP220017735-1a_HK52VDSX3_L3
NAME_WT : IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2
Setting up Parallel block 1
[Parallel block 1] CaVEMan setup added...
[Parallel block 1] Genotype Check added...
[Parallel block 1] VerifyBam Normal added...
Starting Parallel block 1: Wed Sep 21 17:10:25 UTC 2022
Starting geno

• set +x
  Starting CaVEMan_setup
• bash -c '/usr/bin/time -v compareBamGenotypes.pl -o /var/spool/results/results/WGS_PC7L_CSFP220017735-1a_HK52VDSX3_L3_vs_IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2/genotyped -nb /var/spool/results/results/tmp/IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2.bam -j /var/spool/results/results/WGS_PC7L_CSFP220017735-1a_HK52VDSX3_L3_vs_IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2/genotyped/result.json -tb /var/spool/results/results/tmp/PC7L_CSFP220017735-1a_HK52VDSX3_L3.bam -s /var/spool/ref/general.tsv -g /var/spool/ref/gender.tsv >& /var/spool/results/results/timings/WGS_PC7L_CSFP220017735-1a_HK52VDSX3_L3_vs_IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2.time.geno ; echo '''WRAPPER_EXIT: '''$?'
• set +x
  Starting verify_WT
• bash -c '/usr/bin/time -v caveman.pl -r /var/spool/ref/genome.fa.fai -ig /var/spool/ref/caveman/HiDepth.tsv -b /var/spool/ref/caveman/flagging -ab /var/spool/ref/vagrent -u /var/spool/ref/caveman -s '''hsapiens''' -sa hg38 -t 30 -st WGS -tc /var/spool/results/results/tmp/tum.cn.bed -nc /var/spool/results/results/tmp/norm.cn.bed -td 5 -nd 2 -tb /var/spool/results/results/tmp/PC7L_CSFP220017735-1a_HK52VDSX3_L3.bam -nb /var/spool/results/results/tmp/IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2.bam -c /var/spool/results/results/flag.vcf.config.WGS.ini -f /var/spool/ref/caveman/flagging/flag.to.vcf.convert.ini -e 350000 -o /var/spool/results/results/WGS_PC7L_CSFP220017735-1a_HK52VDSX3_L3_vs_IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2/caveman -x MT,GL%,hs37d5,NC_007605 -p setup >& /var/spool/results/results/timings/WGS_PC7L_CSFP220017735-1a_HK52VDSX3_L3_vs_IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2.time.CaVEMan_setup ; echo '''WRAPPER_EXIT: '''$?'
• set +x
• bash -c '/usr/bin/time -v verifyBamHomChk.pl -d 25 -o /var/spool/results/results/WGS_IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2/contamination -b /var/spool/results/results/tmp/IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2.bam -t 30 -j /var/spool/results/results/WGS_IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2/contamination/result.json -s /var/spool/ref/verifyBamID_snps.vcf.gz >& /var/spool/results/results/timings/WGS_PC7L_CSFP220017735-1a_HK52VDSX3_L3_vs_IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2.time.verify_WT ; echo '''WRAPPER_EXIT: '''$?'

Setting up Parallel block 2
[Parallel block 2] CaVEMan split added...
Starting Parallel block 2: Wed Sep 21 17:13:35 UTC 2022
Starting CaVEMan_split

• set +x
• bash -c '/usr/bin/time -v caveman.pl -r /var/spool/ref/genome.fa.fai -ig /var/spool/ref/caveman/HiDepth.tsv -b /var/spool/ref/caveman/flagging -ab /var/spool/ref/vagrent -u /var/spool/ref/caveman -s '''hsapiens''' -sa hg38 -t 30 -st WGS -tc /var/spool/results/results/tmp/tum.cn.bed -nc /var/spool/results/results/tmp/norm.cn.bed -td 5 -nd 2 -tb /var/spool/results/results/tmp/PC7L_CSFP220017735-1a_HK52VDSX3_L3.bam -nb /var/spool/results/results/tmp/IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2.bam -c /var/spool/results/results/flag.vcf.config.WGS.ini -f /var/spool/ref/caveman/flagging/flag.to.vcf.convert.ini -e 350000 -o /var/spool/results/results/WGS_PC7L_CSFP220017735-1a_HK52VDSX3_L3_vs_IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2/caveman -x MT,GL%,hs37d5,NC_007605 -p split >& /var/spool/results/results/timings/WGS_PC7L_CSFP220017735-1a_HK52VDSX3_L3_vs_IMR90E6E7_CSFP220017731-1a_HK52VDSX3_L2.time.CaVEMan_split ; echo '''WRAPPER_EXIT: '''$?'
  ERRORS OCCURRED:
  /var/spool/results/results/CaVEMan_split.wrapper.log

---

CaVEMan_split.wrapper.log contents:
WRAPPER_EXIT: 25

Any advice on how to remedy this error?

Thanks!

[ruolin]

I just encountered the same issue. Did you find a solution?

[katlande]

I just encountered the same issue. Did you find a solution?

Hey yes eventually we got this pipeline working! This specific error was fixed by adding:
-w /var/spool/results \
at the beginning of the command, which forces caveman to start the run in the working directory. So the beginning of my command looked like this:

sudo docker run -it --rm \
 --user 7793:7796 \
 --env HOME=/var/spool/results \
 -w /var/spool/results \
 -v /gpfs/analyses/kat/WGS_Tools/acatNgs/ref:/var/spool/ref \
 -v /gpfs/analyses/kat/Schmidt_Karlseder/bam/acatNGS_Chroms:/var/spool/data \
 -v /gpfs/analyses/kat/Schmidt_Karlseder/acatNGS:/var/spool/results \
 quay.io/wtsicgp/dockstore-cgpwgs:2.1.0 

I hope this helps!