Comments (6)
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. (Iām 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.
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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
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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.
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@rfroumine were you able to solve the mv issue? I have the exact same error
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coo. Thanks a lot!
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@rfroumine worked for me. Thanks!!
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Related Issues (20)
- CRISPRCasFinder.pl: command not found HOT 5
- Using new version of MacSyFinder on CRISPRCasFinder.pl HOT 7
- Too many intermediate files HOT 2
- CRISPERCasFinder does not handle vmatch results with multi line sequence correctly HOT 2
- Recent Singularity container is not recognized by Singularity versions <2.6.1 HOT 1
- Installation of Date::Calc failed HOT 3
- Dependency issues using Singularity image HOT 1
- Flank sequence near contig edge has negative coordinate HOT 1
- MSG: No file or directory called HOT 1
- Error in `muscle': double free or corruption (out): 0x00007ffceb581bf0 HOT 12
- How to use CRISPRCasFinder through singularity container HOT 4
- error in using crisprcasfinder with subprocess, snakemake and Rscript HOT 10
- The result of CRISPR-Cas_summary.tsv don't have Cas Types/Subtypes HOT 1
- No CRISPR/CAS detection on fasta files with more than 100 contigs HOT 1
- CRISPRCasFinder.pl did not report any errors but produced three unknown core files HOT 2
- [FEATURE REQUEST] macsyfinder models custom dir
- Could not open output GFF in result/result2/ because No such file or directory
- json output sometimes "forgets" closing ] in "Cas": [] line
- a particular set of parameters for CCF fails to produce results for all genomes we tried HOT 3
- Error when result folder is not in source folder
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