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

[abulislam]

Hi,

I have paired end ATACseq data.

bowtie2 -p 110 --local --no-mixed --no-discordant --very-sensitive -I 25 -X 5000 -x "$bt2/GRCh38" -1 "$read1" -2 "$read2" -S "${name}.sam" 2> "${name}.bw.map.stat"

Error, fewer reads in file specified with -1 than in file specified with -2
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134

However, after counting the reads were same in both R1 and R2. I downloaded file two times from the source and re-run several times, the problem remains the same.

thanks,

[ch4rr0]

Hello,

Would it be possible to share a link to the file?

[abulislam]

We solved it. There was naming problem in one of the paired reads. Renaming it solved the issue.
Thanks.

[ch4rr0]

Great!

I still think it's a good idea to better our error messages in such circumstances to point out the read that caused the bowtie2 parser to fail. This will help both users and maintainers.

[SlowSD]

We solved it. There was naming problem in one of the paired reads. Renaming it solved the issue. Thanks.

Hello, I am encountering the same issue. Could you explain briefly, how you resolved the issue using rename?

In my case, due to adapter removal I had different number of reads in paired fastq files.

Thanks.

[ch4rr0]

Hello,

If you are aligning pairs, the number of reads in each file needs to be the same. Removing the extra reads should resolve your issue.