Why does bowtie2 Terminate with: Saw ASCII character 10 but expected 33-based Phred qual....?

Question

[jaqx008]

Hello all, I am trying to map some seq data and bowtie2 produced the following error for some of my fastq files, while it mapped ok and gave statistics of mapping for others. It however gave a sam output that is some GB large. did this mapping work ok? can I go on to use the sam generated (but I need the mapping information)? what should I do?

bowtie2 -p 8 -x A.index -U file.fastq  -S file.sam

Saw ASCII character 10 but expected 33-based Phred qual. libc++abi.dylib: terminating with uncaught exception of type int (ERR): bowtie2-align died with signal 6 (ABRT)

Answer 1

[Istvan Albert]

Most likely your FASTQ file is corrupted and contains an invalid quality code.

[jaqx008]

I see, could it be that the download didn't complete?

[Istvan Albert]

perhaps, that is a common source of problems of this kind, look at the last lines with tail