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PGScatalog / pgsc_calc

The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation
https://pgsc-calc.readthedocs.io/en/latest/
Apache License 2.0
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Error when running on WGS #374

Open alohasiqi opened 1 week ago

alohasiqi commented 1 week ago

Description of the bug

Hi!

I have been trying to run the workflow on my WGS samples using singularity on HPC but it keeps throwing out errors.

Can you help direct me with the right to run the workflow on WGS? I would greatly appreciate your help.

  1. I have tested on my vcf file, but it gives some error

ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (sle chromosome)' Error: Missing --chr argument.

the code is nextflow run pgscatalog/pgsc_calc \ -profile singularity \ -latest \ --input code/samplesheet.csv --target_build GRCh38 \ --pgs_id PGS000328 \ --parallel -c code/my_custom.config

the sampleshee.csv is sampleset,path_prefix,chrom,format sle,mypath/sle, ,vcf

  1. when converting the vcf to bfiles, it gives another error ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE (sle)'

the sampleshee.csv is sampleset,path_prefix,chrom,format sle,mypath/sle,22,bfile

Command used and terminal output

No response

Relevant files

No response

System information

No response

nebfield commented 1 week ago

Your first samplesheet contains a space in the chromosome field:

sle,mypath/sle, ,vcf

So the workflow is trying to extract variants from chromosome " " (which doesn't exist). Delete the space and it should be OK.

However, WGS data are not yet well supported by the calculator, which is probably why you get an error on the MATCH_COMBINE step. If you'd like to use the calculator with WGS data it's best to preprocess your VCF to include non-variant sites (the docs have a link describing how to do this).