Plink 1.9 "File read failure" error when merging with --bmerge

Question

[svendula]

When trying to merge two bfiles, I keep getting the "File read failure" error just after the merging starts, even though the files were obviously read and recognised. Any suggestions what I might be doing wrong? See below.

PLINK v1.90b6.6 64-bit (10 Oct 2018)           www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to file1_file2_merged.log.
Options in effect:

  --allow-no-sex
  --bfile file1
  --bmerge file2
  --keep-allele-order
  --make-bed
  --out file1_file2_merged

128823 MB RAM detected; reserving 64411 MB for main workspace.
399 people loaded from file1.fam.
1239 people to be merged from file2.fam.
Of these, 1239 are new, while 0 are present in the base dataset.
580127 markers loaded from file1.bim.
562582 markers to be merged from file2.bim.
Of these, 155 are new, while 562427 are present in the base dataset.
Performing single-pass merge (1638 people, 580282 variants).

Pass 1: fileset #1 complete.
Error: File read failure.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[Juan Manuel Berros]

Any news on this, @svendula? I'm facing the same issue.

[okiedokie1208]

same problem here

[chrchang523]

Can you post a set of files I can use to replicate what you’re seeing?

[okiedokie1208]

I'm trying to merge chr10-12 to chr1. and Here is my log file looks like:

    PLINK v1.90b3.42 64-bit (20 Sep 2016)
Options in effect:
  --bed ukb_cal_chr1_v2.bed
  --bim ukb_snp_chr1_v2.bim
  --fam ukb41999_cal_chr1_v2_s488264.fam
  --make-bed
  --merge-list list_beds.txt
  --out ukb_cal_allChrs_sample

Hostname: nodea1401
Working directory: /gpfs/group/home/yucheng/genotype_beds
Start time: Fri Jun 18 22:20:39 2021

Random number seed: 1624080039
96602 MB RAM detected; reserving 48301 MB for main workspace.
Performing single-pass merge (488377 people, 179921 variants).

Error: File read failure.

and my list_beds.txt looks like:

ukb_cal_chr10_v2.bed ukb_snp_chr10_v2.bim ukb41999_cal_chr10_v2_s488264.fam
ukb_cal_chr11_v2.bed ukb_snp_chr11_v2.bim ukb41999_cal_chr11_v2_s488264.fam
ukb_cal_chr12_v2.bed ukb_snp_chr12_v2.bim ukb41999_cal_chr12_v2_s488264.fam

[chrchang523]

You should be able to use plink 2.0 --pmerge-list for this. If it fails, it should provide a more useful error message.

[okiedokie1208]

Yeah now I'm able to run it with plink 2.0! Thank you so much!!