Question: Someone has tried CAP-MIRSEQ pipeline to analyze miRNA NGS data?
0
gravatar for Kato
6.2 years ago by
Kato50
Japan
Kato50 wrote:

I'm trying now to test this new pipeline called CAP-MIRSEQ but I have a few problems. Someone has tried this pipeline?

My problem is about one tool inside this pipeline, cutadapt. During the test with the sample inside the tool this message appear.

 

+ $HOME/tools/captools/bin/cutadapt -b AATCTCGTATGCCGTCTTCTGCTTGC -O 3 -m 17 -f fastq -q 20 $HOME/tools/CAP-miRSEQ/sample_data/SRR326279_R1.fastq -o $HOME/tools/CAP-miRSEQ/sample_output/fastqs//SRR326279.cutadapt.fastq --too-short-output=$HOME/tools/CAP-miRSEQ/sample_output/fastqs//SRR326279.tooshort.fastq Traceback (most recent call last):

File "$HOME/bin/cutadapt", line 600, in sys.exit(main())

File "$HOME/bin/cutadapt", line 548, in main for desc, seq, qualities in reader:

ValueError: too many values to unpack

 

What is the meaning of the error?  Thanks in advance

cutadapt tool ngs mirna tools • 2.3k views
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Kato50
1

I wonder if the error is caused by having the arguments in the wrong order (I'm not sure how cutadapt parses its arguments). What happens if you run the following yourself:

~/tools/captools/bin/cutadapt -b AATCTCGTATGCCGTCTTCTGCTTGC -O 3 -m 17 -f fastq -q 20 -o ~/tools/CAP-miRSEQ/sample_output/fastqs//SRR326279.cutadapt.fastq --too-short-output=$HOME/tools/CAP-miRSEQ/sample_output/fastqs//SRR326279.tooshort.fastq ~/tools/CAP-miRSEQ/sample_data/SRR326279_R1.fastq

Note that I replaced $HOME with ~. I assume that's correct for your system.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Devon Ryan97k
3
gravatar for Kato
6.2 years ago by
Kato50
Japan
Kato50 wrote:

Thanks Devon,

I tried what you said but the same problem appear again. 

EDIT> I found the solution:

It's a problem with the cutadapt version that comes with the pipeline. The solution is download the last cutadapt version and look for 'cutadapt.sh' in scripts CAP-miRSeq folder and them change the pathway to the program. Under '#run cutadapt'  

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Kato50
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