Bowtie2 Alignment Error

Question

[chaudharyc61]

Hi I'm aligning Paired-end data using bowtie2 aligner and got this 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): bowtie2-align exited with value 134

In bowtie2, by default there's an option if mates are not paired it will search for unpaired mate's alignment to reference genome which isn't working in my case !!!

[WouterDeCoster]

Rather than fixing this alignment step, you should go back and figure out what went wrong to your fastq files. What did you do to these files before the alignment?

Also: please include the full commands you are using when posting questions. See also Brief Reminder On How To Ask A Good Question

[chaudharyc61]

I just filtered my read files based on quality score; because of that the number of reads in both files (Read 1 and Read2) are not same.

This is the full command I'm using: bowtie2 -x Arth_Test -1 R1_filtered_trimmed.fastq -2 R2_filtered_trimmed.fastq --local --very-sensitive-local --un Unpaired_Not_Aligned --al Unpaired_aligned --un-conc Paired_not_concord --al-conc Paired_concord -S Alignment_done.sam

[WouterDeCoster]

I just filtered my read files based on quality score; because of that the number of reads in both files (Read 1 and Read2) are not same.

Yeah that's just not a good idea. Try to keep the number of reads in both files the same. You'll get in trouble. If you are sure you want such stringent filters (problably too stringent?) then I would suggest you drop the mate as well if a read fails your quality score filter.

[ATpoint]

I do not know if bowtie2 has such an option. BWA mem has a smart-pairing option given input is interleaved where it will treat reads with missing mates as singletons, still paired-end files should not have missing reads. Use e.g. repair.sh from BBMap to repair the files (=removing the unpaired reads). Is this your data or downloaded, and how did you obtain it?

[Giovy]

Hi, how did you solve it? I got the same error...

[GenoMax]

You can use repair.sh as suggested by @ATpoint above to ensure that your files are in sync and contain an equal number of reads. A guide to use repair.sh is available.