Centrifuge Issue on Install

[peflanag]

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 ([email protected])'
[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 ~]$