Apply Plink2 Score - Error Invalid chromosome code

Question

[h171linux]

I am trying to run a calculator tool for polygenic scores called pgsc_calc (The Polygenic Score Catalog Calculator pipeline) that runs with nextflow and docker in linux, with my own VCF file. Its failing step 8:

process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE

ERROR ~ Error executing process > 'PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE (NG13RY1WV.vcf.gz chromosome ALL effect type additive)'
Caused by:
  Process `PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE (NG13RY1WV.vcf.gz chromosome ALL effect type additive)` terminated with an error exit status (6)

Command executed:

  plink2 \
      --threads 2 \
      --memory 7372 \
      --seed 31 \
       \
      --score NG13RY1WV.vcf.gz_ALL_additive_0.scorefile.gz zs header-read cols=+scoresums,+denom,-fid no-mean-imputation   \
      --pfile vzs vcf_NG13RY1WV.vcf.gz_ALL \
      --out NG13RY1WV.vcf.gz_ALL_additive_0

  cat <<-END_VERSIONS > versions.yml
  PLINK2_SCORE:
      plink2: $(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*$//' )
  END_VERSIONS

Command exit status: 6

Command output:

  PLINK v2.00a3.3LM 64-bit Intel (3 Jun 2022)    www.cog-genomics.org/plink/2.0/
  (C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
  Logging to NG13RY1WV.vcf.gz_ALL_additive_0.log.
  Options in effect:
    --memory 7372
    --out NG13RY1WV.vcf.gz_ALL_additive_0
    --pfile vzs vcf_NG13RY1WV.vcf.gz_ALL
    --score NG13RY1WV.vcf.gz_ALL_additive_0.scorefile.gz zs header-read cols=+scoresums,+denom,-fid no-mean-imputation
    --seed 31
    --threads 2

  Start time: Sun Aug  6 19:41:37 2023
  7818 MiB RAM detected; reserving 7372 MiB for main workspace.
  Using up to 2 compute threads.
  1 sample (0 females, 0 males, 1 ambiguous; 1 founder) loaded from
  vcf_NG13RY1WV.vcf.gz_ALL.psam.

  End time: Sun Aug  6 19:41:39 2023

Command error:

  Error: Invalid chromosome code 'chr1_KI270706v1_random' on line 4713526 of
  .pvar file.
  (Use --allow-extra-chr to force it to be accepted.)
  PLINK v2.00a3.3LM 64-bit Intel (3 Jun 2022)    www.cog-genomics.org/plink/2.0/
  (C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
  Logging to NG13RY1WV.vcf.gz_ALL_additive_0.log.
  Options in effect:
    --memory 7372
    --out NG13RY1WV.vcf.gz_ALL_additive_0
    --pfile vzs vcf_NG13RY1WV.vcf.gz_ALL
    --score NG13RY1WV.vcf.gz_ALL_additive_0.scorefile.gz zs header-read cols=+scoresums,+denom,-fid no-mean-imputation
    --seed 31
    --threads 2

  Start time: Sun Aug  6 19:41:37 2023
  7818 MiB RAM detected; reserving 7372 MiB for main workspace.
  Using up to 2 compute threads.
  1 sample (0 females, 0 males, 1 ambiguous; 1 founder) loaded from
  vcf_NG13RY1WV.vcf.gz_ALL.psam.

  End time: Sun Aug  6 19:41:39 2023

Added --allow-extra-chr to some lines suggested in the modules.config file and still did not complete the step.

Any suggestion on how to fix this problem or on what the reason for this error might be is appreciated. Thank you.

[Ram]

Thank you for the detailed log of what you've done etc., it's extremely useful. I've added some code formatting; with that, your post is perfect.

[Ruijiang HAN]

Hi, I also encountered the same problem when using pgsc. Did you solve it?