Hi,

I am trying two merge 1000Genomes with another already merged data set using PLINK 1.9. I am flipping and excluding variants as described in the PLINK 1.9 Data Management page.

plink --bfile source2 --flip merged.missnp --make-bed --out source2_trial
plink --bfile source1 --bmerge source2_trial --make-bed --out merged_trial

Then, excluding merged-trial.missnp from both the files and eventually merging. However, I am getting a unique error with the 1000Genomes data set.

I am attaching the log here for better understanding of the error.

./plink --bfile 1000Genomes --exclude trial2-merge.missnp --make-bed --out source1_tmp
PLINK v1.90b3w 64-bit (3 Sep 2015)         https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to source1_tmp.log.
Options in effect:
  --bfile 1000Genomes
  --exclude trial2-merge.missnp
  --make-bed
  --out source1_tmp

257857 MB RAM detected; reserving 128928 MB for main workspace.
39517397 variants loaded from .bim file.
2504 people (1233 males, 1271 females) loaded from .fam.
2504 phenotype values loaded from .fam.
--exclude: 39514129 variants remaining.
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 2504 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.9997.
39514129 variants and 2504 people pass filters and QC.
Among remaining phenotypes, 0 are cases and 2504 are controls.
--make-bed to source1_tmp.bed + source1_tmp.bim + source1_tmp.fam ... 79%
Error: File write failure.
Error: Failed to finish writing to log.

I have no clue why its failing at 79%. This procedure has worked for other data sets, but not this particular data set. It would be great if someone can give me some insight on this.

Thanks,
Aritra