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

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)

bowtie2 mapping sam signleread
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updated by Istvan Albert Istvan Albert • written by jaqx008 jaqx008

1 answer

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

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written by Istvan Albert Istvan Albert

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

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written by jaqx008 jaqx008

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

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written by Istvan Albert Istvan Albert

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