HISAT2 error for paired sample

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1 

IAm receiving this Error while performing Hisat2 using paired and R1 and R1 of the same sample 

  Fatal error: Exit code 1 ()

Tool generated the following standard error:

            Error, fewer reads in file specified with -1 than in file specified with -2
terminate called after throwing an instance of 'int'
(ERR): hisat2-align died with signal 6 (ABRT) (core dumped)
[bam_sort_core] merging from 11 files and 1 in-memory blocks...

Iam receiving

2

Hi @Dr_Nagarajan,

this typically happens with paired-end input that has undergone inappropriate quality-based filtering before. With paired-end input, each of the reads in file 1 needs to have an exact counterpart (mate) in file2.

Now if a quality control tool filters out a read from file 1, it has to also discard the corresponding read from file 2, or those two files get out of sync.

Cheers,

Wolfgang