Question: RNA STAR and HISAT2 job errors (memory failures)
gravatar for theodorcrispin
12 weeks ago by
theodorcrispin0 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 • 153 views
ADD COMMENTlink modified 12 weeks ago by Jennifer Hillman Jackson25k • written 12 weeks ago by theodorcrispin0
gravatar for Jennifer Hillman Jackson
12 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


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 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.

Galaxy choices:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 12 weeks ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 123 users visited in the last hour