Installing Nullarbor in python environment

Hi,

Please, I would like advice on how to install Nullarbor in my python environment?

Grateful for your kind assistance.
Ebenn

I’m really sorry, but I don’t understand the question!

Please could you break down and spell out to me what you’re trying to achieve?

Ermm…Sorry for not coming out clearly enough…I guess I should start with how to install Nullarbor on my VM.

I am unable to run nullarbor on my VM. I got the following error,

read_dir ‘/home/linuxbrew/.linuxbrew/bin/…/plugins’ - opendir: No such file or directory at /home/linuxbrew/.linuxbrew/Cellar/nullarbor/HEAD-1495981/bin/…/perl5/Nullarbor/Plugins.pm line 20.

So I tried to install Nullarbor with the command, brew install Nullarbor. That returned the following error:

Warning: Calling ‘depends_on … => :perl’ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:12:in `class:Nullarbor’
Please report this to the tseemann/bioinformatics-linux tap!

Warning: Calling ‘depends_on … => :perl’ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:13:in `class:Nullarbor’
Please report this to the tseemann/bioinformatics-linux tap!

Warning: Calling ‘depends_on … => :perl’ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:14:in `class:Nullarbor’
Please report this to the tseemann/bioinformatics-linux tap!

Warning: Calling ‘depends_on … => :perl’ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:15:in `class:Nullarbor’
Please report this to the tseemann/bioinformatics-linux tap!

Warning: Calling ‘depends_on … => :perl’ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:16:in `class:Nullarbor’
Please report this to the tseemann/bioinformatics-linux tap!

Warning: Calling ‘depends_on … => :perl’ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:17:in `class:Nullarbor’
Please report this to the tseemann/bioinformatics-linux tap!

Warning: Calling ‘depends_on … => :perl’ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:18:in `class:Nullarbor’
Please report this to the tseemann/bioinformatics-linux tap!

Warning: Calling ‘depends_on … => :perl’ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:19:in `class:Nullarbor’
Please report this to the tseemann/bioinformatics-linux tap!

==> Installing nullarbor from tseemann/bioinformatics-linux
Error: Formulae found in multiple taps:
* brewsci/bio/abricate
* tseemann/bioinformatics-linux/abricate

Please use the fully-qualified name e.g. brewsci/bio/abricate to refer the formula.

I see - “Python Environment” confused me!

Fix for the Nullarbor problem is given here:

Nullarbor is already installed, so there is no need to run brew install nullarbor, just implement the fix above.


The brew installation “Warnings” are just informational and shouldn’t cause any issue. They are concerned with the packaging of software in https://github.com/tseemann/homebrew-bioinformatics-linux, which we have no control over.

The brew “Error” is thrown because the abricate package is listed in two brew repositories. This might be solved by pulling the latest brew packaging updates:

brew update

or by installing from a specific tap:

brew install brewsci/bio/abricate

But as above, you shouldn’t need to fix this problem, as nullarbor is already installed.

Pardon my ignorance–and sorry again for the confusion!

I thought of installing Nullarbor in my python environment because from experience trying to run snippy on its own, it failed to call any variants. I got an error, and the snps.log file read:

samtools faidx reference/ref.fa

bwa index reference/ref.fa

[bwa_index] Pack FASTA… 0.15 sec
[bwa_index] Construct BWT for the packed sequence…
[bwa_index] 4.40 seconds elapse.
[bwa_index] Update BWT… 0.07 sec
[bwa_index] Pack forward-only FASTA… 0.08 sec
[bwa_index] Construct SA from BWT and Occ… 1.17 sec
[main] Version: 0.7.16a-r1181
[main] CMD: bwa index reference/ref.fa
[main] Real time: 6.135 sec; CPU: 5.872 sec

mkdir reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa

mkdir reference/ref && bgzip -c reference/ref.gff > reference/ref/genes.gff.gz

(bwa mem -v 2 -M -R ‘@RG ID:snps SM:snps’ -t 8 reference/ref.fa /home/ubuntu/efn/concat_reads/trimmed_reads/580-5_cat_forward.fastq.gz /home/ubuntu/efn/concat_reads/trimmed_reads/580-5_cat_reverse.fastq.gz | samtools view -@ 8 -F 3844 -q 60 -S -b -u -T reference/ref.fa - | samtools sort -O bam -o snps.bam -@ 8 -)

[E::bwa_set_rg] the read group line contained literal characters – replace with escaped tabs: \t

samtools index snps.bam

samtools depth -q 20 snps.bam | bgzip > snps.depth.gz

tabix -s 1 -b 2 -e 2 snps.depth.gz

fasta_generate_regions.py reference/ref.fa.fai 165277 > reference/ref.txt

File “/home/linuxbrew/.linuxbrew/bin/fasta_generate_regions.py”, line 7
print "usage: ", sys.argv[0], " "
^
SyntaxError: Missing parentheses in call to ‘print’. Did you mean print(int "usage: ", sys.argv[0], " ")?

However, when I installed and run snippy in my python environment it worked fine. I inferred from this that snippy in climb might be broken or something, and will affect/was affecting Nullarbor. I will update brew and install brewsci/bio/abricate as you have suggested and run nullarbor again.

Thx

Hi again,
I run the fix as described here

//You can patch this yourself by changing the following file: /home/linuxbrew/.linuxbrew/Cellar/nullarbor/HEAD-1495981/perl5/Nullarbor/Plugins.pm Line 10 from: my $RUNNER_DIR = “$FindBin::Bin/…/plugins”; to my $RUNNER_DIR = “$FindBin::RealBin/…/plugins”;//

Then tried to update brew. It was already up to date.

I tried to run Nullarbor, but got the following error:

ubuntu@ebenn:~/efn/concat_reads$ nullarbor.pl --name efn_nullarborrun1 --mlst ecoli --ref /home/ubuntu/efn/reference_new_EcoliUMN206.fasta --input nullarbor_input_files.tab --outdir efn_nullarbor_run03Apr2018
[13:36:24] Hello ubuntu
[13:36:24] This is nullarbor.pl 1.30-dev
[13:36:24] Send complaints to Torsten Seemann torsten.seemann@gmail.com
[13:36:24] Using reference genome: /home/ubuntu/efn/reference_new_EcoliUMN206.fasta
[13:36:24] Loaded 4 isolates: sample1 sample2 sample3~13-6929599-1_S30_L999_R1_001.fastq.gz sample4
[13:36:24] Found ‘mlst’ => /home/linuxbrew/.linuxbrew/bin/mlst
[13:36:25] Found 127 MLST schemes
[13:36:25] Using scheme: ecoli
[13:36:25] Making output folder: /home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018
[13:36:25] Found ‘convert’ => /home/linuxbrew/.linuxbrew/bin/convert
[13:36:25] Found ‘head’ => /usr/bin/head
[13:36:25] Found ‘cat’ => /bin/cat
[13:36:25] Found ‘install’ => /usr/bin/install
[13:36:25] Found ‘env’ => /usr/bin/env
[13:36:25] Found ‘nl’ => /usr/bin/nl
[13:36:25] Found ‘trimmomatic’ => /home/linuxbrew/.linuxbrew/bin/trimmomatic
[13:36:25] Found ‘prokka’ => /home/linuxbrew/.linuxbrew/bin/prokka
[13:36:25] Found ‘roary’ => /usr/local/bin/roary
[13:36:25] Found ‘kraken’ => /home/linuxbrew/.linuxbrew/bin/kraken
[13:36:25] Found ‘snippy’ => /home/linuxbrew/.linuxbrew/bin/snippy
[13:36:25] Found ‘mlst’ => /home/linuxbrew/.linuxbrew/bin/mlst
[13:36:25] Found ‘abricate’ => /home/linuxbrew/.linuxbrew/bin/abricate
[13:36:25] Found ‘megahit’ => /home/linuxbrew/.linuxbrew/bin/megahit
[13:36:25] Found ‘spades.py’ => /home/linuxbrew/.linuxbrew/bin/spades.py
[13:36:25] Could not find ‘shovill’. Please install it and ensure it is in the PATH.

I have tried to install Shovill with brew install, and pip install, however I didn’t have any joy with either.
Any help please?

Thx
Ebenn

What is the output from

brew install shovill

?

It’s quite a long one! It says something about post-installation issues. Here it is:

ubuntu@ebenn:/home/linuxbrew/.linuxbrew/bin$ brew install shovill
==> Installing shovill from brewsci/bio
==> Installing dependencies for brewsci/bio/shovill: bwa, kmc, lighter, pigz, openssl, curl, htslib, ncurses, samtools, gmp, mpfr, libmpc, isl@0.18, gcc, gdbm, sqlite, python@2, spades
==> Installing brewsci/bio/shovill dependency: bwa
==> Downloading https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.
==> Downloading from https://github-production-release-asset-2e65be.s3.amazonaws
######################################################################## 100.0%
==> make
:beer: /home/linuxbrew/.linuxbrew/Cellar/bwa/0.7.17: 8 files, 1.5MB, built in 11 seconds
==> Installing brewsci/bio/shovill dependency: kmc
==> Downloading https://linuxbrew.bintray.com/bottles-bio/kmc-3.0.1_1.x86_64_lin
==> Downloading from https://akamai.bintray.com/af/afd0759beef802e266f150b2f5054
######################################################################## 100.0%
==> Pouring kmc-3.0.1_1.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/kmc/3.0.1_1: 8 files, 14.4MB
==> Installing brewsci/bio/shovill dependency: lighter
==> Downloading https://linuxbrew.bintray.com/bottles-bio/lighter-1.1.1_2.x86_64
######################################################################## 100.0%
==> Pouring lighter-1.1.1_2.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/lighter/1.1.1_2: 5 files, 140.5KB
==> Installing brewsci/bio/shovill dependency: pigz
==> Downloading https://linuxbrew.bintray.com/bottles/pigz-2.4.x86_64_linux.bott
######################################################################## 100.0%
==> Pouring pigz-2.4.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/pigz/2.4: 7 files, 178.6KB
==> Installing brewsci/bio/shovill dependency: openssl
==> Downloading https://linuxbrew.bintray.com/bottles/openssl-1.0.2o_1.x86_64_li
==> Downloading from https://akamai.bintray.com/d6/d6d2abf594a1639e3bdd235a3e325
######################################################################## 100.0%
==> Pouring openssl-1.0.2o_1.x86_64_linux.bottle.tar.gz
==> Downloading https://curl.haxx.se/ca/cacert-2017-01-18.pem

curl: (77) error setting certificate verify locations:
CAfile: /home/linuxbrew/.linuxbrew/etc/openssl/cert.pem
CApath: /home/linuxbrew/.linuxbrew/etc/openssl/certs
Trying a mirror…
==> Downloading http://cdn.rawgit.com/sjackman/e4066d2cb6b45fbb6d213e676cb109d0/
==> Downloading from https://cdn.rawgit.com/sjackman/e4066d2cb6b45fbb6d213e676cb

curl: (77) error setting certificate verify locations:
CAfile: /home/linuxbrew/.linuxbrew/etc/openssl/cert.pem
CApath: /home/linuxbrew/.linuxbrew/etc/openssl/certs
Warning: The post-install step did not complete successfully
You can try again using brew postinstall openssl
==> Caveats
A CA file has been bootstrapped using certificates from the SystemRoots
keychain. To add additional certificates (e.g. the certificates added in
the System keychain), place .pem files in
/home/linuxbrew/.linuxbrew/etc/openssl/certs

and run
/home/linuxbrew/.linuxbrew/opt/openssl/bin/c_rehash
==> Summary
:beer: /home/linuxbrew/.linuxbrew/Cellar/openssl/1.0.2o_1: 1,798 files, 14.8MB
==> Installing brewsci/bio/shovill dependency: curl
==> Downloading https://linuxbrew.bintray.com/bottles/curl-7.59.0.x86_64_linux.b
==> Downloading from https://akamai.bintray.com/15/15cf76eb58b7ce1e3062c88e2c578
######################################################################## 100.0%
==> Pouring curl-7.59.0.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/curl/7.59.0: 422 files, 3.5MB
==> Installing brewsci/bio/shovill dependency: htslib
==> Downloading https://linuxbrew.bintray.com/bottles/htslib-1.7.x86_64_linux.bo
==> Downloading from https://akamai.bintray.com/12/12a46ae703dbf7113d8384f66abc6
######################################################################## 100.0%
==> Pouring htslib-1.7.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/htslib/1.7: 140 files, 20.5MB
==> Installing brewsci/bio/shovill dependency: ncurses
==> Downloading https://linuxbrew.bintray.com/bottles/ncurses-6.1.x86_64_linux.b
==> Downloading from https://akamai.bintray.com/5e/5eb929e69e3a2b71c2161551825fd
######################################################################## 100.0%
==> Pouring ncurses-6.1.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/ncurses/6.1: 3,856 files, 15.4MB
==> Installing brewsci/bio/shovill dependency: samtools
==> Downloading https://linuxbrew.bintray.com/bottles/samtools-1.7.x86_64_linux.
==> Downloading from https://akamai.bintray.com/eb/eb1340430ede2a625b2410d1c4683
######################################################################## 100.0%
==> Pouring samtools-1.7.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/samtools/1.7: 29 files, 2.8MB
==> Installing brewsci/bio/shovill dependency: gmp
==> Downloading https://linuxbrew.bintray.com/bottles/gmp-6.1.2_2.x86_64_linux.b
==> Downloading from https://akamai.bintray.com/bb/bbe7a837bc882cfb9a79c7e0f1113
######################################################################## 100.0%
==> Pouring gmp-6.1.2_2.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/gmp/6.1.2_2: 20 files, 3.8MB
==> Installing brewsci/bio/shovill dependency: mpfr
==> Downloading https://linuxbrew.bintray.com/bottles/mpfr-4.0.1.x86_64_linux.bo
==> Downloading from https://akamai.bintray.com/a4/a4ebaaa0612b82dd0848389116169
######################################################################## 100.0%
==> Pouring mpfr-4.0.1.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/mpfr/4.0.1: 29 files, 10.4MB
==> Installing brewsci/bio/shovill dependency: libmpc
==> Downloading https://linuxbrew.bintray.com/bottles/libmpc-1.1.0.x86_64_linux.
==> Downloading from https://akamai.bintray.com/b3/b31648a86228a042aaa8e7d58faba
######################################################################## 100.0%
==> Pouring libmpc-1.1.0.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/libmpc/1.1.0: 13 files, 1.5MB
==> Installing brewsci/bio/shovill dependency: isl@0.18
==> Downloading https://linuxbrew.bintray.com/bottles/isl@0.18-0.18.x86_64_linux
==> Downloading from https://akamai.bintray.com/3e/3ef95686496676a3c73c57db6eee3
######################################################################## 100.0%
==> Pouring isl@0.18-0.18.x86_64_linux.bottle.tar.gz
==> Caveats
This formula is keg-only, which means it was not symlinked into /home/linuxbrew/.linuxbrew,
because this is an alternate version of another formula.

For compilers to find this software you may need to set:
LDFLAGS: -L/home/linuxbrew/.linuxbrew/opt/isl@0.18/lib
CPPFLAGS: -I/home/linuxbrew/.linuxbrew/opt/isl@0.18/include
For pkg-config to find this software you may need to set:
PKG_CONFIG_PATH: /home/linuxbrew/.linuxbrew/opt/isl@0.18/lib/pkgconfig

==> Summary
:beer: /home/linuxbrew/.linuxbrew/Cellar/isl@0.18/0.18: 81 files, 6.4MB
==> Installing brewsci/bio/shovill dependency: gcc
==> Downloading https://linuxbrew.bintray.com/bottles/gcc-5.5.0_3.x86_64_linux.b
==> Downloading from https://akamai.bintray.com/d7/d7b3eac337a9624a123de24f55c3a
######################################################################## 100.0%
==> Pouring gcc-5.5.0_3.x86_64_linux.bottle.tar.gz
==> Creating the GCC specs file: /home/linuxbrew/.linuxbrew/Cellar/gcc/5.5.0_3/l
:beer: /home/linuxbrew/.linuxbrew/Cellar/gcc/5.5.0_3: 1,355 files, 164.7MB
==> Installing brewsci/bio/shovill dependency: gdbm
==> Downloading https://linuxbrew.bintray.com/bottles/gdbm-1.14.1_1.x86_64_linux
==> Downloading from https://akamai.bintray.com/2e/2e45e9dd356df975c805ca596efe5
######################################################################## 100.0%
==> Pouring gdbm-1.14.1_1.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/gdbm/1.14.1_1: 37 files, 2.1MB
==> Installing brewsci/bio/shovill dependency: sqlite
==> Downloading https://linuxbrew.bintray.com/bottles/sqlite-3.22.0.x86_64_linux
==> Downloading from https://akamai.bintray.com/e3/e3536fd6150f5c8721b406cb85d79
######################################################################## 100.0%
==> Pouring sqlite-3.22.0.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/sqlite/3.22.0: 12 files, 19.7MB
==> Installing brewsci/bio/shovill dependency: python@2
==> Downloading https://linuxbrew.bintray.com/bottles/python@2-2.7.14_4.x86_64_l
==> Downloading from https://akamai.bintray.com/9d/9d14d6ba5e52914a8ea0422688e30
######################################################################## 100.0%
==> Pouring python@2-2.7.14_4.x86_64_linux.bottle.1.tar.gz
Error: The brew link step did not complete successfully
The formula built, but is not symlinked into /home/linuxbrew/.linuxbrew
Could not symlink bin/python2
Target /home/linuxbrew/.linuxbrew/bin/python2
is a symlink belonging to python. You can unlink it:
brew unlink python

To force the link and overwrite all conflicting files:
brew link --overwrite python@2

To list all files that would be deleted:
brew link --overwrite --dry-run python@2

Possible conflicting files are:
/home/linuxbrew/.linuxbrew/bin/python2 -> /home/linuxbrew/.linuxbrew/Cellar/python/2.7.14/bin/python2
/home/linuxbrew/.linuxbrew/bin/python2-config -> /home/linuxbrew/.linuxbrew/Cellar/python/2.7.14/bin/python2-config
/home/linuxbrew/.linuxbrew/bin/python2.7 ->

The list of possible conflicting files is quite long so I have shared only the first few lines. Here is the end of the output:

home/linuxbrew/.linuxbrew/lib/python2.7/xmllib.py -> /home/linuxbrew/.linuxbrew/Cellar/python/2.7.14/lib/python2.7/xmllib.py
/home/linuxbrew/.linuxbrew/lib/python2.7/xmlrpclib.py -> /home/linuxbrew/.linuxbrew/Cellar/python/2.7.14/lib/python2.7/xmlrpclib.py
/home/linuxbrew/.linuxbrew/lib/python2.7/zipfile.py -> /home/linuxbrew/.linuxbrew/Cellar/python/2.7.14/lib/python2.7/zipfile.py
==> /home/linuxbrew/.linuxbrew/Cellar/python@2/2.7.14_4/bin/python -s setup.py -
==> /home/linuxbrew/.linuxbrew/Cellar/python@2/2.7.14_4/bin/python -s setup.py -
==> /home/linuxbrew/.linuxbrew/Cellar/python@2/2.7.14_4/bin/python -s setup.py -
==> Caveats
Pip and setuptools have been installed. To update them
pip install --upgrade pip setuptools

You can install Python packages with
pip install

They will install into the site-package directory
/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages

See: https://docs.brew.sh/Homebrew-and-Python
==> Summary
:beer: /home/linuxbrew/.linuxbrew/Cellar/python@2/2.7.14_4: 3,006 files, 72.6MB
==> Installing brewsci/bio/shovill dependency: spades
==> Downloading https://linuxbrew.bintray.com/bottles/spades-3.11.1_2.x86_64_lin
==> Downloading from https://akamai.bintray.com/1b/1bea6164c9a61d187b7965275f80a
######################################################################## 100.0%
==> Pouring spades-3.11.1_2.x86_64_linux.bottle.tar.gz
:beer: /home/linuxbrew/.linuxbrew/Cellar/spades/3.11.1_2: 144 files, 21.8MB
==> Installing brewsci/bio/shovill
==> Downloading https://github.com/tseemann/shovill/archive/v0.9.0.tar.gz

curl: (77) error setting certificate verify locations:
CAfile: /home/linuxbrew/.linuxbrew/etc/openssl/cert.pem
CApath: /home/linuxbrew/.linuxbrew/etc/openssl/certs
Error: Failed to download resource “shovill”
Download failed: https://github.com/tseemann/shovill/archive/v0.9.0.tar.gz

Hope this helps?
Thx

cURL is broken. Please could you follow the instructions in the “Why does curl fail?” section here:

Then run:

brew update
brew install shovill

Many thanks Matt. I believe the problem is solved now.

Cheers,
Ebenn

Hi Matt,

Sorry to come back on this!
Nullarbor terminated prematurely with the following error message:

8
make: Entering directory ‘/home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018’
mkdir -p sample1
mkdir -p sample2
mkdir -p sample3
mkdir -p sample4
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929580-1_S95_L999_R1_001.fastq.gz’ ‘sample1/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929580-1_S95_L999_R2_001.fastq.gz’ ‘sample1/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929583-1_S83_L999_R1_001.fastq.gz’ ‘sample2/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929583-1_S83_L999_R2_001.fastq.gz’ ‘sample2/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-1_S80_L999_R1_001.fastq.gz’ ‘sample3/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-1_S80_L999_R2_001.fastq.gz’ ‘sample3/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929580-10_S68_L999_R1_001.fastq.gz’ ‘sample4/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929580-10_S68_L999_R2_001.fastq.gz’ ‘sample4/R2.fq.gz’
prokka --centre X --compliant --force --fast --gcode 0 --locustag sample1 --prefix sample1 --outdir sample1/prokka --cpus 4 sample1/contigs.fa
Can’t locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /home/ubuntu/efn/miniconda3/envs/efn_env/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /home/ubuntu/efn/miniconda3/envs/efn_env/lib/perl5/site_perl/5.22.0 /home/ubuntu/efn/miniconda3/envs/efn_env/lib/perl5/5.22.0/x86_64-linux-thread-multi /home/ubuntu/efn/miniconda3/envs/efn_env/lib/perl5/5.22.0 .) at /home/linuxbrew/.linuxbrew/bin/prokka line 25.
BEGIN failed–compilation aborted at /home/linuxbrew/.linuxbrew/bin/prokka line 25.
Makefile:134: recipe for target ‘sample1/prokka/sample1.gff’ failed
make: *** [sample1/prokka/sample1.gff] Error 2
make: Leaving directory ‘/home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018’

I attempted to install XML::Simple, with the command, ‘conda install perl-xml-libxml’. The installation was successful, but still no joy with Nullarbor. When I resume with the command ‘nice make -j 1 -C /home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018’ it returns the same error message as before. :sweat:

Grateful for your kind assistance as always.
Ebenn

Use cpanm, it’s installed on GVL:

sudo cpanm XML::Simple

Yes please, the installation is up to date, as I had successfully installed it. Here’s the output when I do sudo cpanp XML::Simple:

(efn_env) ubuntu@ebenn:~/efn/miniconda3$ sudo cpanm XML::Simple
XML::Simple is up to date. (2.25)

However, nullarbor is retuning the same error I’m afraid:

(efn_env) ubuntu@ebenn:~/efn/concat_reads/efn_nullarbor_run03Apr2018$ nice make -j 1 -C /home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018
make: Entering directory ‘/home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018’
mkdir -p sample1
mkdir -p sample2
mkdir -p sample3
mkdir -p sample4
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929580-1_S95_L999_R1_001.fastq.gz’ ‘sample1/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929580-1_S95_L999_R2_001.fastq.gz’ ‘sample1/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929583-1_S83_L999_R1_001.fastq.gz’ ‘sample2/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929583-1_S83_L999_R2_001.fastq.gz’ ‘sample2/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-1_S80_L999_R1_001.fastq.gz’ ‘sample3/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-1_S80_L999_R2_001.fastq.gz’ ‘sample3/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929580-10_S68_L999_R1_001.fastq.gz’ ‘sample4/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929580-10_S68_L999_R2_001.fastq.gz’ ‘sample4/R2.fq.gz’
prokka --centre X --compliant --force --fast --gcode 0 --locustag sample1 --prefix sample1 --outdir sample1/prokka --cpus 4 sample1/contigs.fa
Can’t locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /home/ubuntu/efn/miniconda3/envs/efn_env/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /home/ubuntu/efn/miniconda3/envs/efn_env/lib/perl5/site_perl/5.22.0 /home/ubuntu/efn/miniconda3/envs/efn_env/lib/perl5/5.22.0/x86_64-linux-thread-multi /home/ubuntu/efn/miniconda3/envs/efn_env/lib/perl5/5.22.0 .) at /home/linuxbrew/.linuxbrew/bin/prokka line 25.
BEGIN failed–compilation aborted at /home/linuxbrew/.linuxbrew/bin/prokka line 25.
Makefile:134: recipe for target ‘sample1/prokka/sample1.gff’ failed
make: *** [sample1/prokka/sample1.gff] Error 2
make: Leaving directory ‘/home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018’
(efn_env) ubuntu@ebenn:~/efn/concat_reads/efn_nullarbor_run03Apr2018$

Oh, my mistake, the problem is miniconda hijacking your PERL5LIB.

How did you install miniconda?
Have you got any conda environments attached?
What is the output from:

echo $PERL5LIB

Erm… echo $PERL5LIB returns no output (blank!)

Yes, I’ve got a conda environment attached, and I installed conda following the instructions here ‘https://conda.io/docs/user-guide/install/linux.html’

Please could you try deactivating the conda environment before running the same command again? This would help rule miniconda in/out as the culprit.

Ok please.
I have deactivated the conda environment but still the command does not yield any ouptut.

Thx,
Ebenn

Is the same true for prokka as well?

I beg your pardon, I meant that when I run echo $PERL5LIB again, I did not get any output. I’m not clear with re prokka. What would you like me to check pls?

nullarbor is failing at the prokka stage:

This is likely because you have a conda environment active, which has pretty comprehensively changed your environment (PATH, @INC, etc). Nullarbor is difficult to install, which is why its managed by brew - to ensure that all executables, modules and paths are where they are expected to be.

To test this, you could either try running a complete nullarbor pipeline again, without the conda environment attached, or just check that the prokka stage works, again without the conda environment attached.

So, its up to you, please could you show me the output from either:

prokka

or

nice make -j 1 -C /home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018

without the conda environment active?