Open peflanag opened 2 years ago
Hi,
I'm trying to install Nullarbor in a new environment but when I do --check it says it cannot find database.idx
Can anyone help?
Cheers,
P
(Nullarbor) [peflanag@login3 ~]$ mkdir /ichec/work/ndlif083c/local/pkgs/centrifuge-db (Nullarbor) [peflanag@login3 ~]$ tar -C /ichec/work/ndlif083c/local/pkgs/centrifuge-db -zxvf /ichec/work/ndlif083c/local/pkgs/p_compressed+h+v.tar.gz p_compressed+h+v.1.cf p_compressed+h+v.2.cf p_compressed+h+v.3.cf (Nullarbor) [peflanag@login3 ~]$ export CENTRIFUGE_DEFAULT_DB=/ichec/work/ndlif083c/local/pkgs/centrifuge-db/p_compressed+h+v (Nullarbor) [peflanag@login3 ~]$ nullarbor.pl --check [08:42:35] Hello peflanag [08:42:35] This is nullarbor.pl 2.0.20191013 [08:42:35] Send complaints to Torsten Seemann [08:42:35] Found Perl module: Bio::SeqIO [08:42:35] Found Perl module: Cwd [08:42:35] Found Perl module: Sys::Hostname [08:42:35] Found Perl module: Time::Piece [08:42:35] Found Perl module: List::Util [08:42:35] Found Perl module: YAML::Tiny [08:42:35] Found Perl module: Moo [08:42:35] Found Perl module: Path::Tiny [08:42:35] Found Perl module: File::Copy [08:42:35] Found Perl module: File::Which [08:42:35] Found Perl module: File::Basename [08:42:35] Found Perl module: File::Spec [08:42:35] Found Perl module: File::Path [08:42:35] Found Perl module: Data::Dumper [08:42:35] Found Perl module: Term::ANSIColor [08:42:35] Found Perl module: SVG [08:42:35] Found Perl module: Text::CSV [08:42:35] Found Perl module: List::MoreUtils [08:42:35] Found Perl module: IO::File [08:42:35] Found 'head' => /usr/bin/head [08:42:35] Found 'cat' => /usr/bin/cat [08:42:35] Found 'install' => /usr/bin/install [08:42:35] Found 'env' => /usr/bin/env [08:42:35] Found 'nl' => /usr/bin/nl [08:42:35] Found 'grep' => /usr/bin/grep [08:42:35] Found 'touch' => /usr/bin/touch [08:42:35] Found 'tr' => /usr/bin/tr [08:42:35] Found 'seqtk' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/seqtk [08:42:35] Found 'trimmomatic' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/trimmomatic [08:42:35] Found 'prokka' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/prokka [08:42:35] Found 'roary' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/roary [08:42:35] Found 'mlst' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/mlst [08:42:35] Found 'abricate' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/abricate [08:42:35] Found 'any2fasta' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/any2fasta [08:42:35] Found 'skesa' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/skesa [08:42:35] Found 'megahit' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/megahit [08:42:35] Found 'spades.py' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/spades.py [08:42:35] Found 'shovill' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/shovill [08:42:35] Found 'snippy' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/snippy [08:42:35] Found 'snp-dists' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/snp-dists [08:42:35] Found 'nw_order' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/nw_order [08:42:35] Found 'nw_display' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/nw_display [08:42:35] Found 'iqtree' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/iqtree [08:42:35] Found 'FastTree' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/FastTree [08:42:35] Found 'quicktree' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/quicktree [08:42:35] Found 'kraken' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/kraken [08:42:35] Found 'kraken-report' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/kraken-report [08:42:35] Found 'kraken2' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/kraken2 [08:42:35] Found 'centrifuge' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/centrifuge [08:42:35] Found 'centrifuge-kreport' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/centrifuge-kreport [08:42:35] Found 'fq' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/fq [08:42:35] Found 'fa' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/fa [08:42:35] Found 'roary2svg.pl' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/roary2svg.pl [08:42:36] Parsed shovill 1.1 from 'shovill 1.1.0' [08:42:36] Parsed megahit 1.2 from 'MEGAHIT v1.2.9' [08:42:36] Parsed skesa 2.4 from 'SKESA 2.4.0' [08:42:37] Parsed snippy 4.6 from 'snippy 4.6.0' [08:42:37] Parsed prokka 1.14 from 'prokka 1.14.6' [08:42:37] Parsed quicktree 2.5 from 'quicktree 2.5' [08:42:37] Parsed iqtree 2.1 from 'IQ-TREE multicore version 2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021' [08:42:39] Parsed roary 3.13 from '3.13.0' [08:42:39] Parsed mlst 2.19 from 'mlst 2.19.0' [08:42:39] Parsed abricate 1.0 from 'abricate 1.0.1' [08:42:39] Parsed snp-dists 0.8 from 'snp-dists 0.8.2' [08:42:39] Parsed trimmomatic 0.39 from '0.39' [08:42:39] Parsed spades.py 3.14 from 'SPAdes genome assembler v3.14.1' [08:42:40] Parsed kraken 1.1 from 'Kraken version 1.1.1' [08:42:40] Parsed mash 2.3 from '2.3' [08:42:40] Parsed centrifuge 1.0 from 'Centrifuge version 1.0.4 by the Centrifuge developer team (centrifuge.metagenomics@gmail.com)' [08:42:40] Found kraken env-var KRAKEN_DEFAULT_DB=/ichec/work/ndlif083c/local/pkgs/centrifuge-db/p_compressed+h+v. [08:42:40] ERROR: Can not find file /ichec/work/ndlif083c/local/pkgs/centrifuge-db/p_compressed+h+v./database.idx required by kraken. (Nullarbor) [peflanag@login3 ~]$
Hi,
I'm trying to install Nullarbor in a new environment but when I do --check it says it cannot find database.idx
Can anyone help?
Cheers,
P
(Nullarbor) [peflanag@login3 ~]$ mkdir /ichec/work/ndlif083c/local/pkgs/centrifuge-db (Nullarbor) [peflanag@login3 ~]$ tar -C /ichec/work/ndlif083c/local/pkgs/centrifuge-db -zxvf /ichec/work/ndlif083c/local/pkgs/p_compressed+h+v.tar.gz p_compressed+h+v.1.cf p_compressed+h+v.2.cf p_compressed+h+v.3.cf (Nullarbor) [peflanag@login3 ~]$ export CENTRIFUGE_DEFAULT_DB=/ichec/work/ndlif083c/local/pkgs/centrifuge-db/p_compressed+h+v (Nullarbor) [peflanag@login3 ~]$ nullarbor.pl --check [08:42:35] Hello peflanag [08:42:35] This is nullarbor.pl 2.0.20191013 [08:42:35] Send complaints to Torsten Seemann [08:42:35] Found Perl module: Bio::SeqIO [08:42:35] Found Perl module: Cwd [08:42:35] Found Perl module: Sys::Hostname [08:42:35] Found Perl module: Time::Piece [08:42:35] Found Perl module: List::Util [08:42:35] Found Perl module: YAML::Tiny [08:42:35] Found Perl module: Moo [08:42:35] Found Perl module: Path::Tiny [08:42:35] Found Perl module: File::Copy [08:42:35] Found Perl module: File::Which [08:42:35] Found Perl module: File::Basename [08:42:35] Found Perl module: File::Spec [08:42:35] Found Perl module: File::Path [08:42:35] Found Perl module: Data::Dumper [08:42:35] Found Perl module: Term::ANSIColor [08:42:35] Found Perl module: SVG [08:42:35] Found Perl module: Text::CSV [08:42:35] Found Perl module: List::MoreUtils [08:42:35] Found Perl module: IO::File [08:42:35] Found 'head' => /usr/bin/head [08:42:35] Found 'cat' => /usr/bin/cat [08:42:35] Found 'install' => /usr/bin/install [08:42:35] Found 'env' => /usr/bin/env [08:42:35] Found 'nl' => /usr/bin/nl [08:42:35] Found 'grep' => /usr/bin/grep [08:42:35] Found 'touch' => /usr/bin/touch [08:42:35] Found 'tr' => /usr/bin/tr [08:42:35] Found 'seqtk' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/seqtk [08:42:35] Found 'trimmomatic' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/trimmomatic [08:42:35] Found 'prokka' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/prokka [08:42:35] Found 'roary' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/roary [08:42:35] Found 'mlst' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/mlst [08:42:35] Found 'abricate' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/abricate [08:42:35] Found 'any2fasta' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/any2fasta [08:42:35] Found 'skesa' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/skesa [08:42:35] Found 'megahit' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/megahit [08:42:35] Found 'spades.py' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/spades.py [08:42:35] Found 'shovill' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/shovill [08:42:35] Found 'snippy' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/snippy [08:42:35] Found 'snp-dists' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/snp-dists [08:42:35] Found 'nw_order' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/nw_order [08:42:35] Found 'nw_display' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/nw_display [08:42:35] Found 'iqtree' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/iqtree [08:42:35] Found 'FastTree' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/FastTree [08:42:35] Found 'quicktree' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/quicktree [08:42:35] Found 'kraken' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/kraken [08:42:35] Found 'kraken-report' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/kraken-report [08:42:35] Found 'kraken2' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/kraken2 [08:42:35] Found 'centrifuge' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/centrifuge [08:42:35] Found 'centrifuge-kreport' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/centrifuge-kreport [08:42:35] Found 'fq' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/fq [08:42:35] Found 'fa' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/fa [08:42:35] Found 'roary2svg.pl' => /ichec/work/ndlif083c/local/env/Nullarbor/bin/roary2svg.pl [08:42:36] Parsed shovill 1.1 from 'shovill 1.1.0' [08:42:36] Parsed megahit 1.2 from 'MEGAHIT v1.2.9' [08:42:36] Parsed skesa 2.4 from 'SKESA 2.4.0' [08:42:37] Parsed snippy 4.6 from 'snippy 4.6.0' [08:42:37] Parsed prokka 1.14 from 'prokka 1.14.6' [08:42:37] Parsed quicktree 2.5 from 'quicktree 2.5' [08:42:37] Parsed iqtree 2.1 from 'IQ-TREE multicore version 2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021' [08:42:39] Parsed roary 3.13 from '3.13.0' [08:42:39] Parsed mlst 2.19 from 'mlst 2.19.0' [08:42:39] Parsed abricate 1.0 from 'abricate 1.0.1' [08:42:39] Parsed snp-dists 0.8 from 'snp-dists 0.8.2' [08:42:39] Parsed trimmomatic 0.39 from '0.39' [08:42:39] Parsed spades.py 3.14 from 'SPAdes genome assembler v3.14.1' [08:42:40] Parsed kraken 1.1 from 'Kraken version 1.1.1' [08:42:40] Parsed mash 2.3 from '2.3' [08:42:40] Parsed centrifuge 1.0 from 'Centrifuge version 1.0.4 by the Centrifuge developer team (centrifuge.metagenomics@gmail.com)' [08:42:40] Found kraken env-var KRAKEN_DEFAULT_DB=/ichec/work/ndlif083c/local/pkgs/centrifuge-db/p_compressed+h+v. [08:42:40] ERROR: Can not find file /ichec/work/ndlif083c/local/pkgs/centrifuge-db/p_compressed+h+v./database.idx required by kraken. (Nullarbor) [peflanag@login3 ~]$