Error 134 while aligning using hisat2
0
0
Entering edit mode
22 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 • 1.1k views
ADD COMMENT
0
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?

ADD REPLY

Login before adding your answer.

Traffic: 2535 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6