Getting error 'Killed' upon running in docker container

[shashkat]

Hi there,

I have got a tumour.bam file and want to use fragcounter on it. I am using the docker container consisting of jabba, fragcounter and gGnome, available here - https://hub.docker.com/r/graskind1/jabba. However, upon running the following command, i get an abrupt error: Killed.

command I run (I am in the directory of the bam file):
frag -b sorted_tumour.bam -d ../jabba_files/ -w 200

Error I receive:

Calling samtools view -f 0x02 -F 0x10 ../gatk_mypc/sorted_tumour.bam -q 1 | cut -f "3,4,9"
Killed

I have no clue on how to solve it, as there is no indication on what the issue is. If someone could help, i will be extremely grateful.

Thanks!