hisat2-map error: "gzip: stdout: Broken pipe, (ERR): hisat2-align died with signal 9 (KILL)"

Question

[poecile.pal]

Good evening,

My mapping process (hisat2) stopped with message in stdout:

gzip: stdout: Broken pipe
(ERR): hisat2-align died with signal 9 (KILL) 

At the same time, the large sam file is partially generated (after few days of running). However, probably not to the end, since I don't see the mapping percentage message in stdout, but only see this error message.

Could you help find out the reason, please?

A. I used the same script that I used before when working with other files. It was working correctly.

hisat2 -x /ref_genome2/indexed -1 /data/ERR1_1.no_adapters_fin.fastq.gz,/data/ERR2_1.no_adapters_fin.fastq.gz,/data/ERR3_1.no_adapters_fin.fastq.gz,/data/ERR4_1.no_adapters_fin.fastq.gz -2 /data/ERR1_2.no_adapters_fin.fastq.gz,/data/ERR2_2.no_adapters_fin.fastq.gz,/data/ERR3_2.no_adapters_fin.fastq.gz,/data/ERR4_2.no_adapters_fin.fastq.gz -S hisat2map.sam 2> hisat2map_stderr.txt 1> hisat2map_stdout.txt

B. The files are also normal in my opinion, fastqc and trimomatic worked successfully with them.

Thank you in advance!

Best regards, Poecile

[lieven.sterck]

My first guess would be that your running out of memory. As such the (built-in) gzip will stop working (== needed to unzip your fastq.gz files on the fly) and it will complain about broken pipes as the data stream from gzip to hisat has stopped causing the whole pipeline to stop.

See if you can track the mem-usage of this cmdline and if it exhausts the available mem in your machine.

[poecile.pal]

Thank you very much for your help!