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mskilab-org / fragCounter

GC and mappability corrected fragment coverage for paired end whole genome sequencing
MIT License
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Getting error 'Killed' upon running in docker container #22

Open shashkat opened 1 year ago

shashkat commented 1 year ago

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!