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.