My issue is quite strange. I have in total 16 RNA seq data. After trimming, I move on to HISAT2 for alignment.
6 out of 16 sample give me error while other turned green.
" 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) gzip: stdout: Broken pipe [bam_sort_core] merging from 32 files
i dont know why it should merging 32 file, I did these pair individullly.
Hi @ks7515
this is the key message: Error, fewer reads in file specified with -1 than in file specified with -2.
Please check the input files used for the failed jobs. Properly paired reads should have identical number of F and R reads present in the same order. Two common causes: F and R reads are from different samples, or reads were trimmed as single end data resulting in different number of F and R reads.
The ‘merging’ part of the message probably refers to processing temporary files. Many aligners produce small files during mapping, and these files were merged into a single alignment.
Kind regards,
Igor