sambamba-sort: couldn't parse --memory-limit option

guigolab / grape-nf

An automated RNA-seq pipeline using Nextflow

GNU General Public License v3.0

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sambamba-sort: couldn't parse --memory-limit option #60

Open jpang-van opened 3 years ago

jpang-van commented 3 years ago

if I submit grape-nf to the cluster with following params speficed for mapping process in nextflow.config

withName: mapping { cpus = 8 memory = 75.GB time = 6.h }

I got the could n't parse --memory-limit option error, I specify memory in the wrong format or other issue?, but it is ok for index and other process, any comments?

jpang-van commented 3 years ago

Hi @emi80

any comments for the issue I mentioned above, thanks. If you need .nextflow.log, I can upload it. thanks

emi80 commented 3 years ago

Hi @jpang-van,

apologies for the late reply. I will look into the issue. Would it be possible for you to upload a copy of the .command.sh file of the failing process?

mainguyenanhvu commented 2 years ago

I used the command:

sambamba sort -m $MEM -t $NCORE -o $bam_noalt.tmp.bam /dev/stdin