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.