Question: bcftools isec tries to create a directory called README.txt inside target directory
0
gravatar for douwevanderleest
10 days ago by
douwevanderleest0 wrote:

I am running bcftools isec on two bcftools compressed vcf files (vcf.gz) with root permission. However, bcftools (1.5-17-g4f134df-dirty) isec tries to create a directory called README.txt inside the target directory.

bcftools isec test1.vcf.gz test2.vcf.gz -p MyDir -Oz -o MyOut.vcf.gz

The notification I recieve is:

MyDir/README.txt: Is a directory

I would like a quick fix, without having to reinstall bcftools.

Thanks in advance!

ADD COMMENTlink modified 10 days ago • written 10 days ago by douwevanderleest0

what is the output of

ls -la MyDir

?

ADD REPLYlink written 10 days ago by Pierre Lindenbaum106k
[username2@cloud vcf]$ ls -la MyDir
total 2
drwxr-xr-x 1 u username1 0 Apr 16 16:24 .
drwxrwxr-- 1 u username1 0 Jan  1  1970 ..
drwxr-xr-x 1 username1 admins 0 Apr 16 16:25 README.txt

[username2@cloud vcf]$ ls -la MyDir/README.txt/
total 1
drwxr-xr-x 1 username1 admins 0 Apr 16 16:25 .
drwxr-xr-x 1 username1 admins 0 Apr 16 16:24 ..
ADD REPLYlink modified 9 days ago • written 9 days ago by douwevanderleest0

can you

rmdir MyDir/README.txt

and try again ?

ADD REPLYlink written 9 days ago by Pierre Lindenbaum106k
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