Error 134 while aligning using hisat2
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Entering edit mode
10 months ago
Ngrin • 0

Hello, I am using the below command to align the reads and get bam file:

hisat2 -x /hisat/grch38/genome -1 /fastq/output_forward_paired.fq.gz -2 /fastq/output_reverse_paired.fq.gz | samtools sort -o /bams/outout.bam

This was running perfectly ok for the last try, however, for the new try I got an error as follows:

Error while flushing and closing output
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): hisat2-align exited with value 134

gzip: stdout: Broken pipe

gzip: stdout: Broken pipe
Segmentation fault (core dumped)

I have 2 Tb free space on the server.

What is causing this problem?

hisat2 alignment sam bam • 596 views
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Entering edit mode

Other instances of the same error were indeed related to disk space. Can you post the output of the command: df -h /bams/? Another possibility is that hisat2 writes temp files in a tmp directory. Maybe is that folder that has no space?

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