No output - docker

[krukanna]

Hi, I'm using docker image, docker command extract works fine and I got outputs in right directory, but docker relate gives such information:

somalier version: 0.2.15
[somalier] starting read of 102 samples
[somalier] time to read files and get per-sample stats for 102 samples: 0.07
[somalier] time to get expected relatedness from pedigree graph: 0.00
couldn't open output file

I cannot find any output. I need to use it in nextflow.
Thanks in advance.

[Brent Pedersen]

this likely means you don't have write permission in the directory where you specified the --output-prefix you'll have to mount that directory, or use a different one.

[krukanna]

I run this with command:

docker run --user $(id -u):$(id -g) -v /home/bioinf/:/data/ brentp/somalier:latest somalier relate --ped data/shared/RodzWES/fam_file.fam /data/Relatedness/docker/extract/*.somalier

Tried also with -o, but the same result.

[Brent Pedersen]

you'll probably need to add --output-prefix /data/rodzwes

[krukanna]

thanks a lot