Question: Plink 1.9 "File read failure" error when merging with --bmerge
2
gravatar for svendula
6 months ago by
svendula20
svendula20 wrote:

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.
error plink gwas • 433 views
ADD COMMENTlink modified 24 days ago by Juan Manuel Berros80 • written 6 months ago by svendula20

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.
code_formatting

ADD REPLYlink written 6 months ago by RamRS23k

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

ADD REPLYlink written 24 days ago by Juan Manuel Berros80
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