Question

setting CPU and max memory for running trinity

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7.0 years ago

rahmati.razieh83 ▴ 30

enter image description here Hi 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 • 3.2k views

ADD COMMENT • link 7.0 years ago by rahmati.razieh83 ▴ 30

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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 REPLY • link 7.0 years ago by rahmati.razieh83 ▴ 30

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This is the error I have received enter image description here

ADD REPLY • link 7.0 years ago by rahmati.razieh83 ▴ 30

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

ADD REPLY • link 7.0 years ago by GenoMax 147k

score 0 · Answer 1 · 2017-11-24

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7.0 years ago

GenoMax 147k

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.