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ctSkennerton / crass

The CRISPR assembler
http://ctskennerton.github.io/crass
GNU General Public License v3.0
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crass : [ERROR] Could not open FASTQ <groupfile.fa> for reading. #88

Closed josmos closed 7 years ago

josmos commented 7 years ago

Hi,

I am not sure wether this is a bug or I am getting something wrong. I was running crass with standard parameters on fastq files, which worked. However, if I try to assemble CRISPRS with crass-assembler --velvet -g 24159 -s 23,158,189 -x crass.crispr -i . i get the following error:

crass : [ERROR] Could not open FASTQ .Group_24159_CAAACTGAGTACCTTGAGGTTGCCCCCCAGGCA.fa for reading.

Thanks for your support, Josef

ctSkennerton commented 7 years ago

Hi Josef,

could you try putting "./" as the argument to -i. I think this could be a silly bug where the directory and the file aren't getting joined properly and so the file name comes out as ".Group_24159_CAAACTGAGTACCTTGAGGTTGCCCCCCAGGCA.fa" rather than "./Group_24159_CAAACTGAGTACCTTGAGGTTGCCCCCCAGGCA.fa"

josmos commented 7 years ago

It worked!

I didn't think of that, thank you!