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Question: RNA STAR and HISAT2 job errors (memory failures)
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6 months ago by
theodorcrispin • 0
theodorcrispin • 0 wrote:

Hi I prevously wrote about the RNA STAR program running out of memory for my wheat alignment. At oyur suggestion I tried using HISAT2 instead. However, HISAT2 gives me an exit code 137 after a while. Can someone please help me? Best Theodor Crispin
error memory star rna-seq hisat2 • 298 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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6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The job is failing due to running out of memory during execution. This error can result when a custom target genome/transcriptome is too large to use at https://usegalaxy.org. This can lead to memory or runtime errors.

A less fragmented target could be tested -- try using just the primary chromosomes + plasmid(s) -- or possibly a local/cloud/docker Galaxy given scaled-up compute resources.

But also double check your inputs, as problematic formatting/content (fastq or fasta) can mimic this type of error and is usually fixable. https://galaxyproject.org/support/tool-error/

Galaxy choices:

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