Someone has tried CAP-MIRSEQ pipeline to analyze miRNA NGS data?
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
1 answer
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'
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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.fastqNote that I replaced
$HOMEwith~. I assume that's correct for your system.