Error When Calculating Polygenic Risk Scores

[siyagoel]

Hi! I am running this line of code:

nextflow run pgscatalog/pgsc_calc -profile docker --input samplesheet.csv --target_build GRCh37 --pgs_id PGS001229

When this happens, the following errors pop up:
......................
NOTE: Process PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS001229, pgp_id:, trait_efo:]) terminated with an error exit status (137) -- Execution is retried (1)
ERROR ~ Error executing process > 'PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (stephen_vcf_subset chromosome ALL)'

Caused by:
Process PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF (stephen_vcf_subset chromosome ALL) terminated with an error exit status (6)

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ ERROR: No scores calculated!

-- Check '.nextflow.log' file for details
....................
I was wondering if anyone know how to solve this issue? Thanks.

[nebfield]

Unfortunately there's not enough information to understand what went wrong.

Did the PLINK2_VCF process print out any additional information? Could you try deleting the cache and re-running the workflow to see if there was a temporary problem?

$ rm -r work
$ nextflow run pgscatalog/pgsc_calc -profile docker --input samplesheet.csv --target_build GRCh37 --pgs_id PGS001229

[siyagoellnew]

Hi! Thanks so much. I was wondering if I could meet with one of the maintainers/people who are experienced with this tool. I am trying to integrate this into AWS and am running into some issues. Thanks a lot.

[smlmbrt]

Are the issues the same as #108 and #155?

[siyagoellnew]

It is the same as 132. I edited both lines 41 and 53. However, I am still getting this error:

ERROR ~ Error executing process > 'PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS001229, pgp_id:, trait_efo:])'

Caused by:
Process PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS001229, pgp_id:, trait_efo:]) terminated with an error exit status (137)

Was wondering if I could meet with someone to help fix this. Thanks.

[bensaini717]

I am facing the same issues and would also find a working session helpful. Please share more info about this possible meeting.

Reading through the links that @smlmbrt has included in the post, I believe the problem primarily comes from the lack of a standard file format and the minimum required values. For example, how to identify an imputed VCF from a generic one. I wonder if someone has a created pipeline that takes a FASTq file and spits out a pgs_calc-compatible VCF file.

[smlmbrt]

@bensaini717 an imputed VCF will often have a dosage genotype field (DS, https://pgsc-calc.readthedocs.io/en/latest/how-to/samplesheet.html#setting-genotype-field) and be generated from an imputation server (e.g. Michigan, TopMed, Sanger). This is more common for larger numbers of samples that have been genotyped using arrays and not sequencing.