#305 bowtie2-align died with signal 6 (ABRT)

[sam qin]

sam@sam-Precision-WorkStation-T7500[index] /sam/bowtie2/bowtie2 -x scaffold -1 /sam/idba_ud/myproject/reads2/total_clean.1.fq -2 /sam/idba_ud/myproject/reads2/total_clean.2.fq -S eg2.sam

Error, fewer reads in file specified with -2 than in file specified with -1
terminate called after throwing an instance of 'int'
bowtie2-align died with signal 6 (ABRT)

I use trimmomatic to trim my PE reads data ,so get 4 output,I cat the output together:
cat output_forward_paired.fq output_forward_unpaired.fq >total_clean.1.fq
cat output_reverse_paired.fq output_reverse_unpaired.fq >total_clean.2.fq

does't bowtie can deal reads with mix files paired and unpaired together,how I can solve the problem?

[Val]

Hi sam,

You need to search the pairs files separate from unpaired ones.

hope this helps,
Val

[sam qin]

Thank you very much ! Now I know how to do ,I use bowtie to align my paired reads and unpaired reads seperately,the cat the output together,then use samtools to sort he output!
it wortks

[sam qin]

Thank you very much ! Now I know how to do ,I use bowtie to align my paired reads and unpaired reads seperately,the cat the output together,then use samtools to sort he output!
it wortks