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snugel / cas-offinder

An ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.
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Failing to parse input file #44

Closed seanExcisionBio closed 2 years ago

seanExcisionBio commented 3 years ago

cas-offinder fails to parse the input file even when using the example.

I receive the following error message: Critical error! The length of target sequences should match with the length of pattern sequence.

Any ideas as to what is causing this or any possible solutions for remedying it?

pjb7687 commented 3 years ago

Hi, I cannot reproduce this, would be nice if you can upload the input file.

seanExcisionBio commented 3 years ago

Hi @pjb7687, I used the input file provided in the documentation:

/var/chromosomes/human_hg38 NNNNNNNNNNNNNNNNNNNNNRG 2 1 GGCCGACCTGTCGCTGACGCNNN 3 Seq1 CGCCAGCGTCAGCGACAGGTNNN 3 Seq2

For some reason, the script is erroring on a size check for the sequences when the sequences are of the proper identical size.

pjb7687 commented 3 years ago

Ohhh I see. Actually, this is a 'newer' input file format for Cas-OFFinder > 3.0, and it is currently incompatible with 2.x. I am still testing 3.x and it won't be released soon. Would you try the input file format mentioned here instead: https://github.com/snugel/cas-offinder/tree/release

And of course, you're always welcome if you want to try out 3.x: https://github.com/snugel/cas-offinder/releases/tag/3.0.0b3