mv error about crisprcasfinder HOT 6 CLOSED

Hi @erelior.
Yes actually! The issue in my case was that some contigs in the one fasta file had the same name, more specifically the part of their name after the | was the same.

To solve this, I used this simple awk one-liner to change all my contig names to numbers 1 - n and then re-ran CRISPRCasFinder. (I’m sure something more sophisticated could be used to keep the base name of the contigs.)

awk '/^>/{print ">" ++i; next}{print}' < genome.fasta_edited.fasta > genome_renamed.fasta

Hope this works for you too.

from crisprcasfinder.

I have the similar bug

Sequence number 34..Traceback (most recent call last):
  File "/home/ciillab/huangle/CRISPRCasFinder/bin/macsyfinder", line 329, in <module>
    idx.build(force = config.build_indexes)
  File "/home/ciillab/huangle/CRISPRCasFinder/macsyfinder-1.0.5/macsypy/database.py", line 118, in build
    raise RuntimeError(msg)
RuntimeError: an error occurred during databases indexation see formatdb.log

from crisprcasfinder.

Thank you for your messages. The mv error could be due to permission issues. However, the RuntimeError has been fixed in recently updated version 4.2.19 of CRISPRCasFinder. Other issues will be tentatively fixed.

from crisprcasfinder.

@rfroumine were you able to solve the mv issue? I have the exact same error

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coo. Thanks a lot!

from crisprcasfinder.

@rfroumine worked for me. Thanks!!

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