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troubleshooting.rst

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Troubleshooting

I get an error about variant matching

  • Are your target genomes and the scoring file in compatible builds?
  • --min_overlap defaults to 0.75 (75% of variants in scoring file must be present in target genomes). Try changing this parameter!

The workflow isn't using many resources (e.g. RAM / CPU)

Did you forget to set --max_cpu or --max_memory?

You can also edit nextflow.config to configure cpu and memory permanently.

When I run the workflow I get an error about software not being installed

pgsc_calc bundles dependencies using containers or conda. Did you remember to specify -profile? e.g. nextflow run pgscatalog/pgsc_calc -profile docker,test

Multiple profiles can be combined with a comma. The test profile is used only for checking the pipeline is installed and working correctly.

I'm having problems with VCF input

If you use a "chr" prefix in the chromosome column of your VCF, please remove it. Here's a simple method to do this (thanks to Rvtests):

(zgrep ^"#" $your_old_vcf; zgrep -v ^"#" $your_old_vcf | sed 's:^chr::ig' | sort -k1,1n -k2,2n) | bgzip -c > $your_vcf_file.gz