gravatar for bertb

4 hours ago by

Hello,

I am trying to complete a gene level count of my RNAseq data, and am running into a problem processing my BAM files with htseq.

When I enter the command:

htseq-count --format bam --order pos --mode intersection-strict  --stranded no --minaqual 1 --type exon --idattr gene_id $RNA_ALIGN_DIR/UWN.bam $RNA_REF_GTF > UWN_gene.tsv

everything appears to be processing well, but after ~9M reads, the output stops and I get the output "Killed"

...

8100000 SAM alignment record pairs processed.
8200000 SAM alignment record pairs processed.
8300000 SAM alignment record pairs processed.
8400000 SAM alignment record pairs processed.
8500000 SAM alignment record pairs processed.
8600000 SAM alignment record pairs processed.
8700000 SAM alignment record pairs processed.
8800000 SAM alignment record pairs processed.
8900000 SAM alignment record pairs processed.
9000000 SAM alignment record pairs processed.
9100000 SAM alignment record pairs processed.
Killed

I have tried this before, and at the time had a "memory failure", so I upgraded my system. I'm on a VM Ubuntu, now with 24G RAM and 2TB disk space, which I thought would be sufficient.

Any help would be appreciated!

Thanks,

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4 hours ago
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bertb10



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