Question: setting CPU and max memory for running trinity
0
gravatar for rahmati.razieh83
2.8 years 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 • 1.2k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years 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 2.8 years ago by rahmati.razieh8330

This is the error I have received enter image description here

ADD REPLYlink written 2.8 years 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 2.8 years ago by genomax89k
0
gravatar for genomax
2.8 years ago by
genomax89k
United States
genomax89k 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 2.8 years ago by genomax89k

I edited my post and attached the error file.

ADD REPLYlink written 2.8 years ago by rahmati.razieh8330
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