Question: Cutadapt Assertionerror
0
gravatar for zhidong.yuan
6.7 years ago by
zhidong.yuan20
United States
zhidong.yuan20 wrote:

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

• 1.2k views
ADD COMMENTlink modified 6.7 years ago by Ryan Dale4.8k • written 6.7 years ago by zhidong.yuan20

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

ADD REPLYlink written 6.7 years ago by Jeremy Leipzig18k
1
gravatar for Ryan Dale
6.7 years ago by
Ryan Dale4.8k
Bethesda, MD
Ryan Dale4.8k wrote:

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.

ADD COMMENTlink written 6.7 years ago by Ryan Dale4.8k

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

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by zhidong.yuan20
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