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BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
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Error, fewer reads in file specified with -1 than in file specified with -2 #472

Open abulislam opened 2 months ago

abulislam commented 2 months ago

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 commented 2 months ago

Hello,

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

abulislam commented 2 months ago

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

ch4rr0 commented 2 months ago

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 commented 1 month ago

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.