plink stalls when using --update-map option

Question

[kipp]

Hi Folks,

Plink seems to be taking forever to update map locations for me. I let plink run ~20 hours before finally killing the task. I feel like something must be wrong. I've successfully used plink on this machine before this command, converting my .ped and .map files to .bed/bim/fam and reducing my SNPs. I've copied the log file below, it just hangs on that last line. I'd appreciate any help you could give, thanks!!

Command:

~/plink-1.07-x86_64/plink --bfile JHS_nofam_reducedsnps --update-map overlap_snps_location.txt --out JHS_nofam.b37 --make-bed --noweb &

The data:

~900,000 SNPs
828 individuals

My computer:

Redhat 6.5
8x Intel(R) Xeon(R) CPU E5420  @ 2.50GHz
63Gb RAM

about 61Gb are in use with Plink running, with pretty minimal swap getting used. Also 100% of 1 CPU.

cat ./JHS_nofam.b37.log
@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ]
Writing this text to log file [ JHS_nofam.b37.log ]
Analysis started: Wed Apr 16 12:38:53 2014

Options in effect:
        --bfile JHS_nofam_reducedsnps
        --update-map overlap_snps_location.txt
        --out JHS_nofam.b37
        --make-bed
        --noweb

** For gPLINK compatibility, do not use '.' in --out **
Reading map (extended format) from [ JHS_nofam_reducedsnps.bim ]
900544 markers to be included from [ JHS_nofam_reducedsnps.bim ]
Reading pedigree information from [ JHS_nofam_reducedsnps.fam ]
828 individuals read from [ JHS_nofam_reducedsnps.fam ]
828 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 828 controls and 0 missing
362 males, 466 females, and 0 of unspecified sex
Reading genotype bitfile from [ JHS_nofam_reducedsnps.bed ]
Detected that binary PED file is v1.00 SNP-major mode
Reading new physical positions from [ overlap_snps_location.txt ]

Answer 1

[kipp]

A little bit of digging and I found this: https://www.cog-genomics.org/plink2/ which does the above command in a few seconds. Not sure what the problem was with plink1.07, but maybe that will help someone too!

[Istvan Albert]

thanks for sharing the solution that you found