Question: setting CPU and max memory for running trinity
0
gravatar for rahmati.razieh83
23 months ago by
rahmati.razieh8330 wrote:

enter image description hereHi everyone

I run Trinity with this command

cd $HOME module load bowtie2 SAMTools-1.4.1 Trinity-2.4.0 Trinity --seqType fq --left all.left.trimmed2.fq --right all.right.trimmed2.fq --CPU 40 --max_memory 40G --bflyCPU 30 --monitoring --bflyCalculateCPU > $HOME/trinity.log 2>&1

but after passing 25 hours it was crashed and I got an error in Log file.

rna-seq • 895 views
ADD COMMENTlink modified 23 months ago • written 23 months ago by rahmati.razieh8330

according to my running command and the error I received, what is the problem? Does it need to I change the settings in command?

ADD REPLYlink written 23 months ago by rahmati.razieh8330

This is the error I have received enter image description here

ADD REPLYlink written 23 months ago by rahmati.razieh8330

Please edit the original post to add new information. You should not use Submit Answer for this purpose to keep threads logically organized.

ADD REPLYlink written 23 months ago by genomax73k
0
gravatar for genomax
23 months ago by
genomax73k
United States
genomax73k wrote:

Trinity requires 1G of RAM per 1M Illumina PE reads. How much data do you have? Unless you post the exact error we have no way of knowing what is going on.

ADD COMMENTlink written 23 months ago by genomax73k

I edited my post and attached the error file.

ADD REPLYlink written 23 months ago by rahmati.razieh8330
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