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Possible reasons for returning "Killed" after jellyfish count

Open MikeEHMatson opened this issue 6 years ago • 1 comments

Hello, I am trying to use HAWK to count kmers in Illumina reads. HAWK used a modified version of jellyfish 1.1.6, though the extent to which it is modified is beyond me.

I am trying to run:

$ module load HAWK
$ HAWK=/path/to/HAWK/
$ modifiedJellyfishDir=$HAWK/supplements/jellyfish-Hawk/bin/
$ $modifiedJellyfishDir/jellyfish count -L 1 -U 1000000 -C -o $sample.kmers/tmp -m 31 -t 12 -s 20G <( zcat $sample.fastq.gz)

Though this only returns:

$ Killed

I am giving it 64GB of RAM for ~40x coverage of 150x1 reads over a ~50Mb genome.

Are there any potential reasons to only return "killed" as my error message? It is also likely not possible to use a more recent version of Jellyfish given how it is engrained in the HAWK workflow.

Thanks Mike

MikeEHMatson avatar Feb 13 '19 00:02 MikeEHMatson

I also get killed. Memory consumption rises constantly, I don't know why..

ViriatoII avatar Jun 13 '19 10:06 ViriatoII