Question: Prinseq running error
0
gravatar for snanda73
2.7 years ago by
snanda730
snanda730 wrote:

Skipping 'prinseq_1.fq' which didn't exist, or couldn't be read When i do ls i do see the listing, but when doing a fastqc after dump, i get the above error.

fastqc • 615 views
ADD COMMENTlink modified 2.7 years ago by WouterDeCoster42k • written 2.7 years ago by snanda730

Your question needs far more information. The title suggests there is an error with prinseq, but your post itself suggest a problem with fastqc. You also didn't specify which commands were used, while that's important information. You added "software error" as a tag, while I expect this to be more of a usage error. You haven't identified a bug, so far. I removed the tag and added "fastqc" instead, which seems more specific. You also didn't state the version of the software you are using.

When in doubt you can also visually check if the prinseq_1.fq file is a normal fastq file, e.g. using head -n 20 prinseq_1.fq | less -S

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by WouterDeCoster42k

There is a program called prinseq. I think this question is about that program rather than FastQC.

ADD REPLYlink written 2.7 years ago by genomax74k

Yes, I know that program. But the error "Skipping 'prinseq_1.fq' which didn't exist, or couldn't be read" suggests me OP used prinseq for trimming and is now trying the resulting file in fastqc. But that's just an interpretation, we need more information.

ADD REPLYlink written 2.7 years ago by WouterDeCoster42k
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