EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length

[maximus3219]

Hi Alex,

I got the same error "FATAL ERROR in reads input: quality string length is not equal to sequence length" in a case recently. Previously, I have processed the fastq files with the same script and pipeline with no problems. Just that this single case got the fatal error message.

I tried to remove the reads with error, then it will output the same "FATAL ERROR in reads input: quality string length is not equal to sequence length" for another sequence.

When I review manually other fastq files that can successfully be aligned, it seems that the some of the quality string length is REALLY not equal to sequence length. But somehow they can be processed. Seems the problem occurs in some specific settings.

Thank you.

Best Regards,
Maximus Yeung

[alexdobin]

Hi Maximus,

gzip complains about the .gz files, it seems it's corrupted.