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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
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centrifuge database problem #275

Open abdeljalil-senhaji opened 4 years ago

abdeljalil-senhaji commented 4 years ago

(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 (centrifuge.metagenomics@gmail.com)' [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 commented 3 years ago

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