Hello,
I have been running PCGR (v1.4.1, GRCh37) on some clinical samples. These were just tests, so I didn't use proper pipelining workflows. I just used xargs to run samples in parallel :
# Sample names are stored in names.txt (About 16 samples)
cat names.txt | \
xargs -i -P 4 pcgr --assay WES --tumor_only --exclude_dbsnp_nonsomatic --estimate_tmb \
--input_vcf {}/{}-.vcf.gz --pcgr_dir pcgr/ --genome_assembly grch37 \
--sample_id {} --tumor_site 25 --output_dir RESULTS/The following command does run correctly and does generate reports for all samples.
However, upon closer inspection, some outputs (including reports) for different samples are exactly identical, like they were mixed up. I double checked the input VCF files, which were of course very different.
Running xargs without the -P 4 option (ie running all samples sequentially) fixes the problem. In other words, it seems like this may be linked to PCGR running multiple instances in parallel.
Is it a known issue ?
Thanks.
Hello,
I have been running PCGR (v1.4.1, GRCh37) on some clinical samples. These were just tests, so I didn't use proper pipelining workflows. I just used
xargsto run samples in parallel :The following command does run correctly and does generate reports for all samples.
However, upon closer inspection, some outputs (including reports) for different samples are exactly identical, like they were mixed up. I double checked the input VCF files, which were of course very different.
Running
xargswithout the-P 4option (ie running all samples sequentially) fixes the problem. In other words, it seems like this may be linked to PCGR running multiple instances in parallel.Is it a known issue ?
Thanks.