File write failure: Input/output error.

[jjan...@gmail.com]

Making pgen succeeded for chromosome 21, but failed for chr22 in the middle of the process (10G chr22.pgen already written from 15G  chr22-temporary.pgen ). Here is the log info:

 PLINK v2.00a6LM AVX2 Intel (24 Oct 2023)
Options in effect:
  --double-id
  --keep list.all.txt
  --make-pgen
  --out /Project1/CRC_chr22
  --vcf /Project1/chr22_filtered.dose.vcf.gz dosage=DS

Hostname: cn1614.hw.accre.vu
Working directory: /home/Shinj18/
Start time: Sun Jul 20 09:35:48 2025

Random number seed: 1753022148
1031088 MiB RAM detected, ~950781 available; reserving 515544 MiB for main
workspace.
Using up to 20 threads (change this with --threads).
--vcf: 329862 variants scanned.
--vcf: /Project1/CRC_chr22-temporary.pgen +
/Project1/CRC_chr22-temporary.pvar.zst +
/Project1/CRC_chr22-temporary.psam written.
64693 samples (0 females, 0 males, 64693 ambiguous; 64693 founders) loaded from
/Project1/CRC_chr22-temporary.psam.
329862 variants loaded from
/Project1/CRC_chr22-temporary.pvar.zst.
Note: No phenotype data present.
--keep: 64693 samples remaining.
64693 samples (0 females, 0 males, 64693 ambiguous; 64693 founders) remaining
after main filters.
Writing /Project1/CRC_chr22.psam ... done.
Writing /Project1/CRC_chr22.pvar ... done.
Writing /Project1/CRC_chr22.pgen ...
Error: File write failure: Input/output error.

Any comments or suggestions?

Thanks,

[Chris Chang]

0. You should update your plink2 build.

1. Are you sure you have enough disk space/quota?

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