Stuck on last step of nullarbor v2 install (Kraken)

[danknight]

Hi Torsten,

I'm going through the process of installing all the required tools and dependencies for v2. I've downloaded the minikraken 4GB file and added to $HOME/.bashrc. Despite this Nullarbor seems unable to locate kraken database.idx Below is the output from nullarbor.pl --check

Any ideas? Cheers Dan

TCD50% ./nullarbor/bin/nullarbor.pl --check [15:44:34] Hello dk [15:44:34] This is nullarbor.pl 2.0.20181010 [15:44:34] Send complaints to Torsten Seemann [15:44:34] Found Perl module: Bio::SeqIO [15:44:34] Found Perl module: Cwd [15:44:34] Found Perl module: Sys::Hostname [15:44:34] Found Perl module: Time::Piece [15:44:34] Found Perl module: List::Util [15:44:34] Found Perl module: YAML::Tiny [15:44:34] Found Perl module: Moo [15:44:34] Found Perl module: Path::Tiny [15:44:34] Found Perl module: File::Copy [15:44:34] Found Perl module: File::Spec [15:44:34] Found Perl module: File::Path [15:44:34] Found Perl module: Data::Dumper [15:44:35] Found Perl module: Term::ANSIColor [15:44:35] Found Perl module: SVG [15:44:35] Found Perl module: Text::CSV [15:44:35] Found Perl module: List::MoreUtils [15:44:35] Found Perl module: IO::File [15:44:35] Found 'head' => /usr/bin/head [15:44:35] Found 'cat' => /bin/cat [15:44:35] Found 'install' => /usr/bin/install [15:44:35] Found 'env' => /usr/bin/env [15:44:35] Found 'nl' => /usr/bin/nl [15:44:35] Found 'grep' => /bin/grep [15:44:35] Found 'touch' => /usr/bin/touch [15:44:35] Found 'seqtk' => /home/linuxbrew/.linuxbrew/bin/seqtk [15:44:35] Found 'trimmomatic' => /home/linuxbrew/.linuxbrew/bin/trimmomatic [15:44:35] Found 'prokka' => /home/linuxbrew/.linuxbrew/bin/prokka [15:44:35] Found 'roary' => /home/dk/perl5/bin/roary [15:44:35] Found 'mlst' => /home/dk/.linuxbrew/bin/mlst [15:44:35] Found 'abricate' => /home/dk/abricate/bin//abricate [15:44:35] Found 'seqret' => /home/linuxbrew/.linuxbrew/bin/seqret [15:44:35] Found 'skesa' => /home/linuxbrew/.linuxbrew/bin/skesa [15:44:35] Found 'megahit' => /home/linuxbrew/.linuxbrew/bin/megahit [15:44:35] Found 'spades.py' => /home/linuxbrew/.linuxbrew/bin/spades.py [15:44:35] Found 'shovill' => /home/linuxbrew/.linuxbrew/bin/shovill [15:44:35] Found 'snippy' => /home/linuxbrew/.linuxbrew/bin/snippy [15:44:35] Found 'snp-dists' => /home/linuxbrew/.linuxbrew/bin/snp-dists [15:44:35] Found 'nw_order' => /home/linuxbrew/.linuxbrew/bin/nw_order [15:44:35] Found 'nw_display' => /home/linuxbrew/.linuxbrew/bin/nw_display [15:44:35] Found 'iqtree' => /home/linuxbrew/.linuxbrew/bin/iqtree [15:44:35] Found 'FastTree' => /home/dk/.linuxbrew/bin/FastTree [15:44:35] Found 'quicktree' => /home/linuxbrew/.linuxbrew/bin/quicktree [15:44:35] Found 'kraken' => /home/linuxbrew/.linuxbrew/bin/kraken [15:44:35] Found 'kraken-report' => /home/linuxbrew/.linuxbrew/bin/kraken-report [15:44:35] Found 'kraken2' => /home/linuxbrew/.linuxbrew/bin/kraken2 [15:44:35] Found 'centrifuge' => /home/linuxbrew/.linuxbrew/bin/centrifuge [15:44:35] Found 'centrifuge-kreport' => /home/linuxbrew/.linuxbrew/bin/centrifuge-kreport [15:44:35] Found 'fq' => ./nullarbor/bin//fq [15:44:35] Found 'fa' => ./nullarbor/bin//fa [15:44:35] Found 'roary2svg.pl' => ./nullarbor/bin//roary2svg.pl [15:44:35] Parsed version '1.0' from 'shovill 1.0.4' [15:44:35] Parsed version '1.1' from 'MEGAHIT v1.1.3' [15:44:35] Parsed version '2.3' from 'SKESA v.2.3.0' [15:44:35] Parsed version '4.3' from 'snippy 4.3.8' [15:44:36] Parsed version '1.13' from 'prokka 1.13' [15:44:36] Parsed version '2.5' from 'quicktree 2.5' [15:44:36] Parsed version '1.6' from 'IQ-TREE multicore version 1.6.10 for Linux 64-bit built May 9 2019' [15:44:39] Parsed version '3.12' from '3.12.0' [15:44:39] Parsed version '2.6' from 'mlst 2.6' [15:44:39] Parsed version '0.8' from 'abricate 0.8.13' [15:44:39] Parsed version '0.6' from 'snp-dists 0.6.3' [15:44:39] Parsed version '0.38' from '0.38' [15:44:40] Parsed version '3.13' from 'SPAdes v3.13.0' [15:44:40] Parsed version '1.0' from 'Kraken version 1.0' [15:44:40] Parsed version '2.1' from '2.1' [15:44:40] Parsed version '1.0' from 'Centrifuge version 1.0.3-beta by the Centrifuge developer team (centrifuge.metagenomics@gmail.com)' [15:44:40] Found kraken env-var KRAKEN_DEFAULT_DB=/home/dk/minikraken_20171019_4GB [15:44:40] ERROR: Can not find file /home/dk/minikraken_20171019_4GB/database.idx required by kraken.

[ghost]

Hi danknight

You need to set your bash_profile.

KRAKEN and CENTRIFUGE database

cd $HOME echo "export KRAKEN_DEFAULT_DB=$HOME/minikraken_20141208" >> ~/.bash_profile echo "export CENTRIFUGE_DEFAULT_DB=$HOME/centrifuge-db/p_compressed+h+v >> ~/.bash_profile source ~/.bash_profile

In your case $HOME = /home/dk/

After that, run nullarbor.py --check again

It worked in my case.!

[danknight]

Thanks Torsten, that worked a treat and all dependencies are now installed. How do I get my medal? :)

So now I'm experiencing a confusing issue relating to accessing the tools and PATH within the makefile.

For example, if I run make -n I can see that the file is trying for to call the nullarbor fq command, only it cant locate it. However, if I try this same exact command manually (pasting into the terminal) it works fine with no issues at all. The same happens for programs like snippy and roary.

The exact error i get is: bin/bash: fq: command not found

Hope this makes sense, sorry in advance if its something terribly obvious

Cheers Dan

[tseemann]

Thank you to @mars3680 for helping with the Kraken problem.

@danknight fq and fa come with Nullarbor in the bin/ folder: https://github.com/tseemann/nullarbor/tree/master/bin

That folder needs to be in your PATH.

[danknight]

Thanks Torsten,

nullarbor.py --check says all is fine and I can invoke fa and fq no problem. It’s just within the makefile that the commands aren’t recognised. It’s like the make file isn’t recognising the PATH environment.

Cheers Dan

From: Torsten Seemann notifications@github.com Sent: Monday, 10 June 2019 8:46 AM To: tseemann/nullarbor nullarbor@noreply.github.com Cc: danknight daniel.knight@uwa.edu.au; Mention mention@noreply.github.com Subject: Re: [tseemann/nullarbor] Stuck on last step of nullarbor v2 install (Kraken) (#221)

Thank you to @mars3680https://github.com/mars3680 for helping with the Kraken problem.

@danknighthttps://github.com/danknight fq and fa come with Nullarbor in the bin/ folder: https://github.com/tseemann/nullarbor/tree/master/bin

That folder needs to be in your PATH.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/tseemann/nullarbor/issues/221?email_source=notifications&email_token=ADFCWMOQFAQJY7RG7L4FAYTPZWP6HA5CNFSM4HTR77OKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXIVUSY#issuecomment-500259403, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ADFCWMNBCXEMYJAUMP2CVB3PZWP6HANCNFSM4HTR77OA.

[tseemann]

That is unexpected. What does which -a make say?