"index files are missing" error when running test command

[robinengler]

Hi, I'm trying to run the command to test my local install of CRISPRCasFinder.pl.

perl CRISPRCasFinder.pl -in install_test/sequence.fasta -cas -cf CasFinder-2.0.3 -def G -keep -soFile $VMATCH_SEL392

but macsyfinder is telling me that it can't find some of the index files it needs (see error message below).

I read through the documentation to see if there is an option to tell CRISPRCasFinder to build these index files, but didn't see anything. Or maybe I got something wrong in my macsyfinder installation.

Would you have any idea of what I'm not doing correctly? Thanks in advance for any help.

...
...

prodigal installation is.............OK 
macsyfinder installation is...........OK 
-------------------------------------
PRODIGAL v2.6.3 [February, 2016]         
Univ of Tenn / Oak Ridge National Lab
Doug Hyatt, Loren Hauser, et al.     
-------------------------------------
Request:  Single Genome, Phase:  Training
Reading in the sequence(s) to train...526169 bp seq created, 52.76 pct GC
Locating all potential starts and stops...27714 nodes
Looking for GC bias in different frames...frame bias scores: 1.12 0.26 1.63
Building initial set of genes to train from...done!
Creating coding model and scoring nodes...done!
Examining upstream regions and training starts...done!
-------------------------------------
Request:  Single Genome, Phase:  Gene Finding
Finding genes in sequence #1 (526169 bp)...done!
Traceback (most recent call last):
  File "/software/UHTS/Analysis/macsyfinder/1.0.5/bin/macsyfinder", line 329, in <module>
    idx.build(force = config.build_indexes)
  File "/software/UHTS/Analysis/macsyfinder/1.0.5/lib/python2.7/site-packages/macsypy/database.py", line 119, in build
    self._hmmer_indexes = self.find_hmmer_indexes()
  File "/software/UHTS/Analysis/macsyfinder/1.0.5/lib/python2.7/site-packages/macsypy/database.py", line 142, in find_hmmer_indexes
    raise RuntimeError(msg)
RuntimeError: some index files are missing. Delete all index files (*.phr, *.pin, *.psd, *.psi, *.psq, *.pal) and try to rebuild them.
No Cas results
Nb of Cas in this sequence = 0
Secondary folders/files (Prodigal, CasFinder, rawFASTA, CRISPRFinderProperties) have been created

All CRISPRs = 9
All Cas = 0

[14:55:46] Thank you for using CRISPRCasFinder.pl! Thank you for your patience!

[14:55:46] The script lasted: 0 year(s) 0 month(s) 0 day(s) , 0 hour(s) 0 minute(s) 4 second(s)

[dcouvin]

Hi @robinengler , Thank you for your message. Unfortunately, I have not seen this error yet. Please try to re-install MacSyFinder following these instructions : https://macsyfinder.readthedocs.io/en/latest/installation.html I hope this could help. Maybe @bneron could provide further help. Best regards, @dcouvin

[dcouvin]

Hi @robinengler, Otherwise, you can use the new Singularity container available at : https://crisprcas.i2bc.paris-saclay.fr/Home/Download Best

[ftianRF]

It is due to the incompatibility of macsyfinder with BLAST+ 2.10.0. https://githubhot.com/repo/gem-pasteur/macsyfinder/issues/30