RAP Swiss Army Knife - PLINK failed to open bed file

Matthieu Pluntz

Hello,

I am trying to get a list of eid of individuals having a mutation in a specific gene to analyze their phenotypes. To do that, I first want to get the exome sequences on that gene using PLINK.

I have moved (by click and drag) the bim, bed, fam files of interest from the Bulk data to the subfolder where I want to run the analysis. Then I run the Swiss Army Knife with:

inputs:

ukb23158_c19_b0_v1.bed

ukb23158_c19_b0_v1.bim

ukb23158_c19_b0_v1.fam

command line:

plink --bfile ukb_23158_c19_b0_v1 --chr 19 --from-bp 15177812 --to-bp 15197537 --make-bed --out ukb_23158_notch3

I get the error message: “Failed to open ukb_23158_c19_b0_v1.bed.” It also fails with plink2 instead of plink, or when picking the inputs directly from the Bulk (before having moving them), or when picking the inputs from the Bulk and ticking the “ Whether to use "dx-mount-all-inputs" ” option.

This is not a problem of not being able to access the data at all with Swiss Army Knife, because Swiss Army Knife was able to run a simple R script which reads the .fam and writes a copy.

Please help.

---

Edit: I have tried the package dx on my computer command prompt.

“dx run swiss-army-knife” fails the same way.

In case plink could be used outside the swiss-army-knife, I tried “dx describe app-plink”. I get:

dxpy.exceptions.PermissionDenied: User is not a listed authorized user for plink, code 401.

Does this mean that I am actually not allowed to use plink? Why not? I am part of a tier 3 application.

Comments

1 comment

Date Votes
  • Comment author
    Phil John Greer

    You need to provide the location of the bed bim and fam file as inputs to the dx run swiss-army-knife command.

    The command you want would look like this:

        dx run swiss-army-knife -iin="/Bulk/Exome sequences/Population level exome OQFE variants, PLINK format - final release/ukb23158_c19_b0_v1.bed" \
        -iin="/Bulk/Exome sequences/Population level exome OQFE variants, PLINK format - final release/ukb23158_c19_b0_v1.bim" \
        -iin="/Bulk/Exome sequences/Population level exome OQFE variants, PLINK format - final release/ukb23158_c19_b0_v1.fam"\
        -icmd="plink --bfile ukb_23158_c19_b0_v1 --no-pheno --chr 19 --from-bp 15177812 --to-bp 15197537 --make-bed --out ukb_23158_notch3" \
        --tag="exctract-notch3" --instance-type "mem1_ssd1_v2_x8"\
        --destination="${project}:dataoutput" --brief --yes
     

    1

Please sign in to leave a comment.