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Question: RNA STAR error
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gravatar for theodorcrispin
6 months ago by
theodorcrispin • 0
theodorcrispin • 0 wrote:

Hi, I was just trying out RNA STAR for the first time using deafult settings and a reference genome and annotation from NCBI of wheat. It gives me an error after a few minutes of running saying:

slurmstepd: error: Job 3008889 exceeded memory limit (151071308 > 150994944), being killed

slurmstepd: error: Exceeded job memory limit

slurmstepd: error: * JOB 3008889 ON l007 CANCELLED AT 2018-05-17T08:33:34 *

slurmstepd: error: Exceeded step memory limit at some point.

What am I doing wrong?

Best Theodor Crispin
star memory-error hisat2 rna star • 339 views
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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by theodorcrispin • 0
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gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

RNA STAR uses much more memory than the other mapping tools. It looks like your job exceeded the memory allocated to the tool (the maximum). Please considering using HISAT2 instead.

That said, input problems can contribute to job failures. Please see this FAQ for troubleshooting help: https://galaxyproject.org/support/

HISAT2 usage is covered in the Galaxy RNA-seq tutorials: https://galaxyproject.org/learn/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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