Entering edit mode
9 weeks 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?
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?