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CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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merging fails during somatic variant calling (in parallel mode) #108

Closed rdmorin closed 3 years ago

rdmorin commented 3 years ago

We have been encountering a fatal error on some genome pairs when we run lofreq somatic with multiple threads. The error message is not particularly informative but I was able to track this problem down to an error during the merging of individual vcfs to the combined vcf. This step was erroring out with a complaint about multi-allelic variants. I found that switching the merge step to use bcftools concat has resolved the issue. If you are interested in a patch I can start a pull request from our forked version of this repo. 

CRITICAL [2020-12-03 20:50:00,103]: The following command failed with code 1: lofreq call-parallel --pp-threads 24 -d 101000 -f /projects/rmorin/projects/gambl-repos/gambl-mutect2-lhilton/ref/lcr-modules-references/genomes/hg38/genome_fasta/genome.fa --verbose --no-default-filter -b 1 -a 0.010000 -C 7 -s -S results/gambl/lofreq-1.0/01-lofreq/genome--hg38/BLGSP-71-26-00400-01A-01E--BLGSP-71-06-00286-99A-01D--unmatched/normal_stringent.snvs.vcf.gz,results/gambl/lofreq-1.0/01-lofreq/genome--hg38/BLGSP-71-26-00400-01A-01E--BLGSP-71-06-00286-99A-01D--unmatched/normal_stringent.indels.vcf.gz results/gambl/lofreq-1.0/00-inputs/bam/genome--hg38/BLGSP-71-26-00400-01A-01E.bam -o results/gambl/lofreq-1.0/01-lofreq/genome--hg38/BLGSP-71-26-00400-01A-01E--BLGSP-71-06-00286-99A-01D--unmatched/tumor_relaxed.vcf.gz
CRITICAL [2020-12-03 20:50:00,104]: Received the following on stderr:
CRITICAL [2020-12-03 20:50:00,104]: Somatic SNV caller failed. Exiting
andreas-wilm commented 3 years ago

Oh yes please! Thanks so much!

andreas-wilm commented 3 years ago

Just saw the PR #109 . Sorry catching up slowly with LoFreq stuff...