Comments (2)
Oh I didn't know the version can be specified this way, very good to learn! Sorry to leave out the critical piece of info... our samtools is 1.9. mpileup
is a samtools function that is now moved into bcftools, and I tested samtools 1.9 and bcftools 1.11, both of which need the -L
flag. I passed all related info and files to Katrina.
from idseq-workflows.
Hi @danrlu, thanks for letting us know. IDseq does indeed set a specific samtools version, by installing the version that ships with Ubuntu 20.04 LTS in the Dockerfile for the workflow (https://github.com/chanzuckerberg/idseq-workflows/blob/main/consensus-genome/Dockerfile). The specific version can be found at https://packages.ubuntu.com/focal/samtools - it's version 1.10.
It's not clear to me from reading czbiohub-sf/sc2-illumina-pipeline#80 and czbiohub-sf/sc2-illumina-pipeline#81 which samtools versions have the issue you refer to, and whether we need to add a custom -L
setting when calling samtools mpileup
. Can you clarify? cc @katrinakalantar
from idseq-workflows.
Related Issues (8)
- Error while Running Test Example - Consensus Genome HOT 11
- Unable to Fetch Some Archives HOT 2
- Pipeline continue downloading essential files at every run HOT 2
- Running test locally fail HOT 1
- add test cases for maximum e-value filter on alignment results
- Size of VMs needed for full metagenomics test
- Question - workflow language selection evaluation? HOT 2
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