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. nf-core provides a set of example .config files, including examples for both institutional compute clusters (e.g. Cambridge, Sanger) and cloud compute providers (e.g. Google, AWS Tower and Batch). See How do I run pgsc_calc on larger datasets and more powerful computers? for more information.

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

VCF file(s) containing variants on non-standard chromsomes or patches (e.g. chr1_gl000191_random) will also currently fail our pipeline as it only takes human chromosomes as input (1-22, X, Y, XY). One way to remove these variants is to download and run plink2 and convert your data to plink files that can be used with the calculator using the following command:

plink2 --vcf [yourfile] --allow-extra-chr --chr 1-22, X, Y, XY -make-pgen --out [yourfile]_axy

however other methods to filter these variants from VCFs also exist.