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,
trimomatic worked successfully with them.
Thank you in advance!
Best regards, Poecile