HISAT2 crash/failure

Hi all,

I have been using HISAT2 for RNAseq reads alignment for quite a while.
Last few days, the tool keeps failing with different error messages, even on inputs that I have used successfully before.
Here a couple of examples of the error messages that I get:

This job failed for reasons that could not be determined

(ERR): hisat2-align died with signal 9 (KILL)
[W::sam_read1_sam] Parse error at line 34126880
samtools sort: truncated file. Aborting
[main_samview] fail to read the header from “-”

This job was terminated because it used more memory than it was allocated

Can anyone help?



The clusters that run this tool have been very busy but these errors look like they are resulting from a job that is too large to execute. I understand that these reads mapped before, but if any of these other items changed, it could impact how “large” a job is:

  1. parameters
  2. reference genome
  3. reference annotation
  4. tool version (always use the most current)

Things to troubleshoot:

  1. Try another rerun to eliminate server side transient issues
  2. Inspect the reads – do these still pass QA tools?
  3. Inspect the target genome if using a custom genome input – is the fasta format correct?
  4. The format/content of any included reference annotation should also be checked, but usually doesn’t lead to an error: the reference annotation would in practical use be ignored instead. So, scientific not technical problems.

I added some tags that link to prior Q&A about those items. In short, this root problem could be input issues OR the job is actually too large to process. The middle message suggests that the target reference genome (fasta) contains a lot of sequences – remember that this tool is expecting a somewhat intact assembly: up to ~ 1000 target sequences but no more.

Hi Jennifer,
thank you for your kind reply.
Reference is human hg38 and annotation file is the same I’ve always used.
QC is fine.
The only thing that’s changed is the amount of available memory quota on my account.

So I will try and delete some old BAM, FastQ and all large files… let’s see if this helps.
Thank you


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