hello, i was doing the alignment of my rnaseq data to the reference genome (build it using hisat) and i run in this error:
i run the command as fellow:
hisat2 -p 10 --dta -x 2.index/salmo_salar \
∙ --summary-file 3.hisat2_bams/test1_rep1_summary.txt \
∙ -1 2.clean_fq/alevin-RNA-1_R1.fq.gz \
∙ -2 2.clean_fq/alevin-RNA-1_R2.fq.gz \
∙ | samtools sort -@ 10 -o 3.hisat2_bams/alevin-RNA-1.sorted.bam
and I got the fellowing error:
Error, fewer reads in file specified with -2 than in file specified with -1
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): hisat2-align exited with value 134
[bam_sort_core] merging from 30 files and 10 in-memory blocks...
what is the possible issue and how to fix it?
hello, i was doing the alignment of my rnaseq data to the reference genome (build it using hisat) and i run in this error: i run the command as fellow: hisat2 -p 10 --dta -x 2.index/salmo_salar \ ∙ --summary-file 3.hisat2_bams/test1_rep1_summary.txt \ ∙ -1 2.clean_fq/alevin-RNA-1_R1.fq.gz \ ∙ -2 2.clean_fq/alevin-RNA-1_R2.fq.gz \ ∙ | samtools sort -@ 10 -o 3.hisat2_bams/alevin-RNA-1.sorted.bam and I got the fellowing error: Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134 [bam_sort_core] merging from 30 files and 10 in-memory blocks... what is the possible issue and how to fix it?