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maximilianh / crisporWebsite

All source code of the crispor.org website
http://crispor.org
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Error using rat rn6 genome on local installation #54

Closed Lukas-1 closed 3 years ago

Lukas-1 commented 3 years ago

I downloaded the rat rn6 genome provided on the CRISPOR website, and tried to use it to find off-target locations for gRNAs using a .bed file as an input. This has previously worked for me very well using the hg38anset and mm10 genomes.

However, with the rn6 genome, I get an error:

python crisporWebsite/crispor.py rn6 Input_for_CRISPOR/input.bed Output_from_CRISPOR/output.tsv -o Output_from_CRISPOR/output_offs.tsv Traceback (most recent call last): File "crisporWebsite/crispor.py", line 8482, in main() File "crisporWebsite/crispor.py", line 8479, in main mainCommandLine() File "crisporWebsite/crispor.py", line 8241, in mainCommandLine seqList = getGenomeSeqs(org, regions) File "crisporWebsite/crispor.py", line 6979, in getGenomeSeqs seq = tbf[chrom][start:end] File "/usr/local/lib/python2.7/dist-packages/twobitreader/init.py", line 432, in getitem return self.getslice(min=slice_orkey.start, max=slice_or_key.stop) File "/usr/local/lib/python2.7/dist-packages/twobitreader/init.py", line 517, in get_slice more_bytes=morebytes) File "/usr/local/lib/python2.7/dist-packages/twobitreader/init.py", line 158, in longs_to_char_array raise ValueError('array_size must be at least 0') ValueError: array_size must be at least 0

I haven't been able to figure out what might cause this error... Any help would be much appreciated!

Lukas-1 commented 3 years ago

Sorry, the error was on my side. I submitted a file that erroneously included a position on chromosome 22, which doesn't exist in the rat genome. This immediately caused the error above. The error isn't very informative, but I guess that's the fault of the twobitreader package...

maximilianh commented 3 years ago

Thanks for solving the problem yourself! Yes, you could post this on the twobitreader github.

On Fri, Nov 20, 2020 at 1:36 PM Lukas-1 notifications@github.com wrote:

Sorry, the error was on my side. I submitted a file that erroneously included a position on chromosome 22, which doesn't exist in the rat genome. This immediately caused the error above. The error isn't very informative, but I guess that's the fault of the twobitreader package...

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