Error, fewer reads in file specified with -2 than in file specified with -1

Question

[manojkumarbioinfo]

Hai,

I'm using bowtie2 as my aliner to align my sequence. I'm getting an error Fewer reads in the file specified with -2 than in file specified with -1. i used the same file to align with BWA-mem it does not show any error. but botie2 is still running for more than 1week with the same file size.

the command i used to run bowtie2

bowtie2 -p 30 -x Reference/bowti_hg38 -1 Data/SRR622457_1.fastq -2 Data/SRR622457_2.fastq -S Output/Bowtie/Alignment/bowtie.sam

[Mark]

You need to repair the fastq files: Error with Bowtie 2

use BBMap

[ATpoint]

Did you check if there are indeed fewer sequences in one file e.g. using wc -l? Also, one week is overly long even for a WGS sample. Probably the process died somehow and simply did not terminate properly, use top to check if it is really running.

[manojkumarbioinfo]

I used BBmap repair.sh in1=r1.fq.gz in2=r2.fq.gz out1=fixed1.fq.gz out2=fixed2.fq.gz outsingle=singletons.fq.gz to fix this issue