RenzoTale88
commented
1 month ago @graemefox can you please try the new version of the workflow without the -resume option and report back if you still encounter the same issue?
Closed graemefox closed 1 month ago
RenzoTale88
commented
1 month ago @graemefox can you please try the new version of the workflow without the -resume option and report back if you still encounter the same issue?
graemefox
commented
1 month ago Hi @RenzoTale88. Re-ran without -resume and I have the same error:
nextflow run epi2me-labs/wf-human-variation -r master --bam NUH0001_1_P1_sup_5mCG_5hmCG.hg38.bam --ref /data/refs/hg38_simple.fa --sample_name 'NUH0001_hv_2.2.0' -profile standard --mod --snp --cnv --sv --out_dir NUH0001_2.2.0_outputproduced:
WARN: Found zero basecall_model in the input alignment header, falling back to the model provided with --basecaller_cfg: dna_r10.4.1_e8.2_400bps_sup@v4.1.0
WARN: Automatically selecting TR BED: hg38.trf.bed
ERROR ~ Error executing process > 'sv:variantCall:sniffles2 (1)'
Caused by:
Process `sv:variantCall:sniffles2 (1)` terminated with an error exit status (1)
Command executed:
sniffles --threads 4 --sample-id NUH0001_hv_2.2.0 --output-rnames --minsvlen 30 --cluster-merge-pos 150 --input reads.bam --reference hg38_simple.fa --input-exclude-flags 2308 --tandem-repeats ${WFSV_TRBED_PATH}/hg38.trf.bed --vcf NUH0001_hv_2.2.0.sniffles.vcf
sed '/.:0:0:0:NULL/d' NUH0001_hv_2.2.0.sniffles.vcf > tmp.vcf
mv tmp.vcf NUH0001_hv_2.2.0.sniffles.vcf
Command exit status:
1
Command output:
Running Sniffles2, build 2.0.7-epi2me
Run Mode: call_sample
Start on: 2024/05/23 18:32:47
Working dir: /data/graeme/work/f2/34d44dc44e30f69320f6911bb01002
Used command: /home/epi2melabs/conda/bin/sniffles --threads 4 --sample-id NUH0001_hv_2.2.0 --output-rnames --minsvlen 30 --cluster-merge-pos 150 --input reads.bam --reference hg38_simple.fa --input-exclude-flags 2308 --tandem-repeats /data/wf_human_sv_trbed/hg38.trf.bed --vcf NUH0001_hv_2.2.0.sniffles.vcf
==============================
Opening for reading: reads.bam
Command error:
Running Sniffles2, build 2.0.7-epi2me
Run Mode: call_sample
Start on: 2024/05/23 18:32:47
Working dir: /data/graeme/work/f2/34d44dc44e30f69320f6911bb01002
Used command: /home/epi2melabs/conda/bin/sniffles --threads 4 --sample-id NUH0001_hv_2.2.0 --output-rnames --minsvlen 30 --cluster-merge-pos 150 --input reads.bam --reference hg38_simple.fa --input-exclude-flags 2308 --tandem-repeats /data/wf_human_sv_trbed/hg38.trf.bed --vcf NUH0001_hv_2.2.0.sniffles.vcf
==============================
Opening for reading: reads.bam
Traceback (most recent call last):
File "/home/epi2melabs/conda/bin/sniffles", line 616, in <module>
Sniffles2_Main(config.from_cmdline(),processes)
File "/home/epi2melabs/conda/bin/sniffles", line 130, in Sniffles2_Main
contig_tandem_repeats=util.load_tandem_repeats(config.tandem_repeats,config.tandem_repeat_region_pad)
File "/home/epi2melabs/conda/lib/python3.8/site-packages/sniffles/util.py", line 104, in load_tandem_repeats
with open(filename,"r") as handle:
FileNotFoundError: [Errno 2] No such file or directory: '/data/wf_human_sv_trbed/hg38.trf.bed'
Work dir:
/data/graeme/work/f2/34d44dc44e30f69320f6911bb01002
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for detailsMany thanks for looking into this for me.
RenzoTale88
commented
1 month ago Hi @graemefox thanks for confirming this. Could you confirm the docker command in the .command.run script within the work directory please?
grep docker /data/graeme/work/39/bbde85ed7ade2519dd0c81276b2aa0/.command.runThat gives
docker rm $NXF_BOXID &>/dev/null || true
docker kill $NXF_BOXID
docker run -i --cpu-shares 4096 --memory 6144m -e "NXF_DEBUG=${NXF_DEBUG:=0}" -v /data:/data -v /home/mbzgf/.nextflow/assets/epi2me-labs/wf-human-variation:/home/mbzgf/.nextflow/assets/epi2me-labs/wf-human-variation -w "$PWD" --user $(id -u):$(id -g) --group-add 100 --name $NXF_BOXID ontresearch/wf-human-variation-sv:sha8f02fbfaea233fe4763f7c7142696efcadab2f4d /bin/bash -c "eval $(nxf_container_env); /bin/bash /data/graeme/work/39/bbde85ed7ade2519dd0c81276b2aa0/.command.run nxf_trace"
SamStudio8
commented
1 month ago @graemefox Apologies - this is our fault as 2.2.0 ships some data inside the container in /data/ which is being shadowed by your inputs from /data/. We are prepping a patch release of the workflow for this week so I'll update the container and slip in a fix for this week.
graemefox
commented
1 month ago No worries @SamStudio8 thanks for figuring this one out!
SamStudio8
commented
1 month ago @graemefox This should be fixed in the hot-off-the-press v2.2.2 release - please let us know how you get on!
graemefox
commented
1 month ago Awsome. Just ran it again with 2.2.2 and it runs with no issues. Thanks again!
Operating System
Other Linux (please specify below)
Other Linux
Ubuntu 20.04
Workflow Version
v2.2.0
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
Hello! I'm running into issues running wf-human-variation since the release of v2.2.0; specifically the --sv module is causing an error.
My command above gives the log output below. I can run the pipeline successfully if I leave out the --sv flag, and also if I use --sv with revision v2.1.0. The demo data also runs without any issues, --sv included.
Many thanks
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response