Question: plink stalls when using --update-map option
gravatar for kipp
6.0 years ago by
United States
kipp40 wrote:

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!!  


~/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:  |

|        |



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




** 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 ]

snp plink • 2.6k views
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by kipp40
gravatar for kipp
6.0 years ago by
United States
kipp40 wrote:

A little bit of digging and I found this: 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! 

ADD COMMENTlink written 6.0 years ago by kipp40

thanks for sharing the solution that you found

ADD REPLYlink written 6.0 years ago by Istvan Albert ♦♦ 83k
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