Comments (3)
dcouvin
commented on September 3, 2024
Dear @drob2727 ,
Please note that you should try a command like this (taking into account the paths existing inside the singularity image): singularity exec -B $PWD CrisprCasFinder.simg perl /usr/local/CRISPRCasFinder/CRISPRCasFinder.pl -so /usr/local/CRISPRCasFinder/sel392v2.so -cf /usr/local/CRISPRCasFinder/CasFinder-2.0.3 -drpt /usr/local/CRISPRCasFinder/supplementary_files/repeatDirection.tsv -rpts /usr/local/CRISPRCasFinder/supplementary_files/Repeat_List.csv -cas -def G -out RESULTfolder -in sequence.fasta
Hope this will help!
Best regards and happy 2021!
David
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drob2727
commented on September 3, 2024
Thanks! Do I need to have all the sequences from the metagenomes classified before I run this program or can I just use the contig names to see what comes up?
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From: David Couvin <[email protected]>
Sent: Wednesday, January 6, 2021 3:37:33 PM
To: dcouvin/CRISPRCasFinder <[email protected]>
Cc: David Robinson <[email protected]>; Mention <[email protected]>
Subject: Re: [dcouvin/CRISPRCasFinder] vmatch2 (#30)
[EXTERNAL]
Dear @drob2727<https://github.com/drob2727> ,
Please note that you should try a command like this (taking into account the paths existing inside the singularity image): singularity exec -B $PWD CrisprCasFinder.simg perl /usr/local/CRISPRCasFinder/CRISPRCasFinder.pl -so /usr/local/CRISPRCasFinder/sel392v2.so -cf /usr/local/CRISPRCasFinder/CasFinder-2.0.3 -drpt /usr/local/CRISPRCasFinder/supplementary_files/repeatDirection.tsv -rpts /usr/local/CRISPRCasFinder/supplementary_files/Repeat_List.csv -cas -def G -out RESULTfolder -in sequence.fasta
Hope this will help!
Best regards and happy 2021!
David
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dcouvin
commented on September 3, 2024
You will need to have your sequences in a multi-FASTA file to run the program
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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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