Cause I want to know the crispr/cas in genomes(refseq of bac and arc in NCBI), so I run this command,
perl CRISPRCasFinder.pl -in ~/database_db/refseq/archaea_library.fna -so sel392v2.so -cas -keep -out ~/software/crisprcasfinder/test
but I got this error,
################################################################
# --> Welcome to CRISPRCasFinder.pl (version 4.3.2)
################################################################
vmatch is...............OK
mkvtree is...............OK
vsubseqselect is...............OK
fuzznuc (from emboss) is...............OK
needle (from emboss) is...............OK
---> Results will be stored in /beegfs/home/syl/software/crisprcasfinder/test
( Input file: NC_002607.fna, Sequence ID: NC_002607, Sequence name = Halobacterium salinarum NRC-1, complete sequence )
Sequence number 1..
muscle 5.1.linux64 [] 132Gb RAM, 72 cores
Built Feb 24 2022 03:16:15
(C) Copyright 2004-2021 Robert C. Edgar.
https://drive5.com
Input: 5 seqs, avg length 35, max 70
00:00 18Mb CPU has 72 cores, defaulting to 20 threads
WARNING: Max OMP threads 2
00:00 93Mb 100.0% Calc posteriors
00:00 93Mb 100.0% Consistency (1/2)
00:00 93Mb 100.0% Consistency (2/2)
00:00 93Mb 100.0% UPGMA5
00:00 93Mb 100.0% Refining
muscle 5.1.linux64 [] 132Gb RAM, 72 cores
Built Feb 24 2022 03:16:15
(C) Copyright 2004-2021 Robert C. Edgar.
https://drive5.com
Input: 2 seqs, avg length 31, max 40
00:00 18Mb CPU has 72 cores, defaulting to 20 threads
WARNING: Max OMP threads 2
00:00 26Mb 100.0% Calc posteriors
00:00 26Mb 100.0% UPGMA5
muscle 5.1.linux64 [] 132Gb RAM, 72 cores
Built Feb 24 2022 03:16:15
(C) Copyright 2004-2021 Robert C. Edgar.
https://drive5.com
Input: 2 seqs, avg length 41, max 41
00:00 18Mb CPU has 72 cores, defaulting to 20 threads
WARNING: Max OMP threads 2
00:00 26Mb 100.0% Calc posteriors
00:00 26Mb 100.0% UPGMA5
------------- EXCEPTION -------------
MSG: No file or directory called 'NC_002607.fna'
STACK Bio::DB::IndexedBase::new /beegfs/home/syl/anaconda3/envs/crisprcasfinder/lib/perl5/site_perl/Bio/DB/IndexedBase.pm:368
STACK main::reportToGff CRISPRCasFinder.pl:2545
STACK main::makeGff CRISPRCasFinder.pl:2427
STACK toplevel CRISPRCasFinder.pl:653
-------------------------------------
the seq names in archaea_library.fna are like this,
Hi @TKsh6 ,
Thank you for your message. I have never seen this mistake before. Please try to simplify sequence IDs and avoid the dot in these IDs.
Hope this will solve the problem.
Best,
David
Cause I want to know the crispr/cas in genomes(refseq of bac and arc in NCBI), so I run this command,
perl CRISPRCasFinder.pl -in ~/database_db/refseq/archaea_library.fna -so sel392v2.so -cas -keep -out ~/software/crisprcasfinder/test
but I got this error,the seq names in archaea_library.fna are like this,
I don't know how to solve this, can you help me?
yours tk,