bowtie-align error

Saw ASCII character 0 but expected 33-based Phred qual. terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 13 (PIPE)

what should I do ? thanks!

It's very difficult to debug the issue with the information provided. Here are a few follow ups:

• What version of bowtie2 are you using?
• What command line options did you specify when running bowtie2?
• Is it possible to at least provide the sample input (read) files used?

 Hi, I just encountered the same problem. The version of bowtie2 I use is  2.2.5, and command is "bowtie2 -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 -p 9 --mm -k 200 -x  ref_genome.fa -1 fastq_1.gz -2 fastq_2.gz | samtools view -S -b -o ./xxx.bam -". I think the possible reason is that the index file is too large. My index file is 61G, so is there any way to solve it?Look forward to your reply.

This is not an issue with the index but with the reads being processed. It's possible that your read file has (invisible) control characters. We added code in more recent versions to ignore such characters. Can you try with a more recent version of bowtie2?