HISAT2 errors meaning

Do you know the meaning of the following error messages from HISAT2 after mapping?

Error, fewer reads in file specified with -2 than in file specified with -1
terminate called after throwing an instance of ‘int’
(ERR): hisat2-align died with signal 6 (ABRT)
[bam_sort_core] merging from 6 files and 1 in-memory blocks…

Especially the “(ERR)” one, I’m afraid my alignment might have not been completed at all.

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Hi Mario

This is paired end data, isn’t-t? And you have provided two fastq files…, well, the alignment process stop (i.e.: died) because of the different number of reads in the two fastq files. Maybe one file is corrupt (e.g.: incomplete download) or something went wrong during the pre-processing?
Check the integrity of the files with FASTQC

Regards, Hans-Rudolf


Thanks! I checked the files and they were indeed corrupt.
Now I have a normal alignment.