Cutadapt Assertionerror

Question

[zhidong.yuan]

Could someone please help me with the problem produced from using cutadapt? Thanks.

$cutadapt -c -e 0.12 -a 330201030313112312 -m 15 --bwa -f fastq SRR029966.fastq

Traceback (most recent call last): File "/usr/bin/cutadapt", line 600, in <module> sys.exit(main()) File "/usr/bin/cutadapt", line 570, in main desc, seq, qualities, trimmed = cutter.cut(desc, seq, qualities) File "/usr/bin/cutadapt", line 386, in cut assert not qualities or len(seq) == len(qualities) AssertionError

[Jeremy Leipzig]

Debugging strategy #1: find the offending sequence. Show it to us.

Answer 1

[Ryan Dale]

From the error message, it looks like for at least one read the sequence length is not the same as the quality string length.

Perhaps your version of the fastq file got truncated somehow? A tail on the fastq file might reveal a truncation problem.

Running cutadapt v1.0 on a fresh copy of SRR029966.fastq from the SRA works fine for me, so you could always just re-download (and/or update your cutadapt version) and try again.

[zhidong.yuan]

Thank you, Daler. I have re-downloaded the cutadapt (v1.0). And it can work now.