centrifuge database problem

[abdeljalil-senhaji]

(CRISPR)abdeljalil@uv2000:/Users/nfs/abdeljalil/Qsur-69-stains/all-reads> nullarbor.pl --check
[14:45:37] Hello abdeljalil [14:45:37] This is nullarbor.pl 2.0.20191013
[14:45:37] Send complaints to Torsten Seemann
[14:45:37] Found Perl module: Bio::SeqIO
[14:45:37] Found Perl module: Cwd
[14:45:37] Found Perl module: Sys::Hostname
[14:45:37] Found Perl module: Time::Piece
[14:45:37] Found Perl module: List::Util
[14:45:37] Found Perl module: YAML::Tiny
[14:45:38] Found Perl module: Moo
[14:45:38] Found Perl module: Path::Tiny
[14:45:38] Found Perl module: File::Copy
[14:45:38] Found Perl module: File::Which
[14:45:38] Found Perl module: File::Basename
[14:45:38] Found Perl module: File::Spec
[14:45:38] Found Perl module: File::Path
[14:45:38] Found Perl module: Data::Dumper
[14:45:38] Found Perl module: Term::ANSIColor
[14:45:38] Found Perl module: SVG
[14:45:38] Found Perl module: Text::CSV
[14:45:38] Found Perl module: List::MoreUtils
[14:45:38] Found Perl module: IO::File
[14:45:38] Found 'head' => /usr/bin/head
[14:45:38] Found 'cat' => /usr/bin/cat
[14:45:38] Found 'install' => /usr/bin/install
[14:45:38] Found 'env' => /usr/bin/env
[14:45:38] Found 'nl' => /usr/bin/nl
[14:45:38] Found 'grep' => /usr/bin/grep
[14:45:38] Found 'touch' => /usr/bin/touch
[14:45:38] Found 'tr' => /usr/bin/tr
[14:45:38] Found 'seqtk' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/seqtk
[14:45:38] Found 'trimmomatic' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/trimmomatic
[14:45:38] Found 'prokka' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/prokka
[14:45:38] Found 'roary' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/roary
[14:45:38] Found 'mlst' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/mlst
[14:45:38] Found 'abricate' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/abricate
[14:45:38] Found 'any2fasta' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/any2fasta
[14:45:38] Found 'skesa' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/skesa
[14:45:38] Found 'megahit' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/megahit
[14:45:38] Found 'spades.py' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/spades.py
[14:45:38] Found 'shovill' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/shovill
[14:45:38] Found 'snippy' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/snippy
[14:45:38] Found 'snp-dists' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/snp-dists
[14:45:38] Found 'nw_order' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/nw_order
[14:45:38] Found 'nw_display' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/nw_display
[14:45:38] Found 'iqtree' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/iqtree
[14:45:38] Found 'FastTree' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/FastTree
[14:45:38] Found 'quicktree' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/quicktree
[14:45:38] Found 'kraken' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/kraken
[14:45:38] Found 'kraken-report' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/kraken-report
[14:45:38] Found 'kraken2' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/kraken2
[14:45:38] Found 'centrifuge' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/centrifuge
[14:45:38] Found 'centrifuge-kreport' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/centrifuge-kreport
[14:45:38] Found 'fq' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/fq
[14:45:38] Found 'fa' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/fa
[14:45:38] Found 'roary2svg.pl' => /Users/nfs/abdeljalil/anaconda3/envs/CRISPR/bin/roary2svg.pl
[14:45:38] Parsed shovill 1.0 from 'shovill 1.0.9'
[14:45:38] Parsed megahit 1.2 from 'MEGAHIT v1.2.9'
[14:45:38] Parsed skesa 2.3 from 'SKESA v.2.3.0'
[14:45:38] Parsed snippy 4.4 from 'snippy 4.4.3'
[14:45:38] Parsed prokka 1.14 from 'prokka 1.14.6'
[14:45:39] Parsed quicktree 2.5 from 'quicktree 2.5'
[14:45:39] Parsed iqtree 2.0 from 'IQ-TREE multicore version 2.0.3 for Linux 64-bit built Apr 26 2020'
[14:45:40] Parsed roary 3.13 from '3.13.0'
[14:45:40] Parsed mlst 2.19 from 'mlst 2.19.0'
[14:45:40] Parsed abricate 1.0 from 'abricate 1.0.1'
[14:45:40] Parsed snp-dists 0.7 from 'snp-dists 0.7.0'
[14:45:40] Parsed trimmomatic 0.39 from '0.39'
[14:45:40] Parsed spades.py 3.13 from 'SPAdes v3.13.1'
[14:45:40] Parsed kraken 1.1 from 'Kraken version 1.1.1'
[14:45:40] Parsed mash 2.2 from '2.2.2'
[14:45:40] Parsed centrifuge 1.0 from 'Centrifuge version 1.0.4 by the Centrifuge developer team ([email protected])'
[14:45:40] Found kraken env-var KRAKEN_DEFAULT_DB=/Users/nfs/abdeljalil/db-kraken/minikraken_20141208/
[14:45:40] Found file required by kraken: /Users/nfs/abdeljalil/db-kraken/minikraken_20141208//database.idx
[14:45:40] Found file required by kraken: /Users/nfs/abdeljalil/db-kraken/minikraken_20141208//database.kdb
[14:45:40] Found centrifuge env-var CENTRIFUGE_DEFAULT_DB=/Users/nfs/abdeljalil/db-cenrifuge/
[14:45:40] ERROR: Can not find file /Users/nfs/abdeljalil/db-cenrifuge/.1.cf required by centrifuge.
(CRISPR) abdeljalil@uv2000:/Users/nfs/abdeljalil/Qsur-69-stains/all-reads>

[biobrad]

looks like you may have made a typo when specifying the location of your centrifuge file.
[14:45:40] ERROR: Can not find file /Users/nfs/abdeljalil/db-cenrifuge/.1.cf required by centrifuge