Hi,
Please, I would like advice on how to install Nullarbor in my python environment?
Grateful for your kind assistance.
Ebenn
Hi,
Please, I would like advice on how to install Nullarbor in my python environment?
Grateful for your kind assistance.
Ebenn
Iâm really sorry, but I donât understand the question!
Please could you break down and spell out to me what youâre trying to achieve?
ErmmâŚSorry for not coming out clearly enoughâŚI 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 â/home/linuxbrew/.linuxbrew/bin/âŚ/pluginsâ - opendir: No such file or directory at /home/linuxbrew/.linuxbrew/Cellar/nullarbor/HEAD-1495981/bin/âŚ/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 âdepends_on ⌠=> :perlâ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:12:in `class:Nullarborâ
Please report this to the tseemann/bioinformatics-linux tap!
Warning: Calling âdepends_on ⌠=> :perlâ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:13:in `class:Nullarborâ
Please report this to the tseemann/bioinformatics-linux tap!
Warning: Calling âdepends_on ⌠=> :perlâ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:14:in `class:Nullarborâ
Please report this to the tseemann/bioinformatics-linux tap!
Warning: Calling âdepends_on ⌠=> :perlâ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:15:in `class:Nullarborâ
Please report this to the tseemann/bioinformatics-linux tap!
Warning: Calling âdepends_on ⌠=> :perlâ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:16:in `class:Nullarborâ
Please report this to the tseemann/bioinformatics-linux tap!
Warning: Calling âdepends_on ⌠=> :perlâ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:17:in `class:Nullarborâ
Please report this to the tseemann/bioinformatics-linux tap!
Warning: Calling âdepends_on ⌠=> :perlâ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:18:in `class:Nullarborâ
Please report this to the tseemann/bioinformatics-linux tap!
Warning: Calling âdepends_on ⌠=> :perlâ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/nullarbor.rb:19:in `class:Nullarborâ
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 - âPython Environmentâ 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 âWarningsâ are just informational and shouldnât 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 âErrorâ 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 shouldnât need to fix this problem, as nullarbor
is already installed.
Pardon my ignoranceâand 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:
[bwa_index] Pack FASTA⌠0.15 sec
[bwa_index] Construct BWT for the packed sequenceâŚ
[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
[E::bwa_set_rg] the read group line contained literal characters â replace with escaped tabs: \t
File â/home/linuxbrew/.linuxbrew/bin/fasta_generate_regions.pyâ, line 7
print "usage: ", sys.argv[0], " "
^
SyntaxError: Missing parentheses in call to âprintâ. 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 $RUNNER_DIR = â$FindBin::Bin/âŚ/pluginsâ; to my $RUNNER_DIR = â$FindBin::RealBin/âŚ/pluginsâ;//
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 âmlstâ => /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 âconvertâ => /home/linuxbrew/.linuxbrew/bin/convert
[13:36:25] Found âheadâ => /usr/bin/head
[13:36:25] Found âcatâ => /bin/cat
[13:36:25] Found âinstallâ => /usr/bin/install
[13:36:25] Found âenvâ => /usr/bin/env
[13:36:25] Found ânlâ => /usr/bin/nl
[13:36:25] Found âtrimmomaticâ => /home/linuxbrew/.linuxbrew/bin/trimmomatic
[13:36:25] Found âprokkaâ => /home/linuxbrew/.linuxbrew/bin/prokka
[13:36:25] Found âroaryâ => /usr/local/bin/roary
[13:36:25] Found âkrakenâ => /home/linuxbrew/.linuxbrew/bin/kraken
[13:36:25] Found âsnippyâ => /home/linuxbrew/.linuxbrew/bin/snippy
[13:36:25] Found âmlstâ => /home/linuxbrew/.linuxbrew/bin/mlst
[13:36:25] Found âabricateâ => /home/linuxbrew/.linuxbrew/bin/abricate
[13:36:25] Found âmegahitâ => /home/linuxbrew/.linuxbrew/bin/megahit
[13:36:25] Found âspades.pyâ => /home/linuxbrew/.linuxbrew/bin/spades.py
[13:36:25] Could not find âshovillâ. Please install it and ensure it is in the PATH.
I have tried to install Shovill with brew install, and pip install, however I didnât have any joy with either.
Any help please?
Thx
Ebenn
What is the output from
brew install shovill
?
Itâs 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
/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
/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
/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
/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 mirrorâŚ
==> 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
/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
/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
/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
/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
/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
/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
/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
/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
/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
/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
/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
/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
/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
/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 âshovillâ
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 âWhy does curl fail?â 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 â/home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018â
mkdir -p sample1
mkdir -p sample2
mkdir -p sample3
mkdir -p sample4
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929580-1_S95_L999_R1_001.fastq.gzâ âsample1/R1.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929580-1_S95_L999_R2_001.fastq.gzâ âsample1/R2.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929583-1_S83_L999_R1_001.fastq.gzâ âsample2/R1.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929583-1_S83_L999_R2_001.fastq.gzâ âsample2/R2.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929606-1_S80_L999_R1_001.fastq.gzâ âsample3/R1.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929606-1_S80_L999_R2_001.fastq.gzâ âsample3/R2.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929580-10_S68_L999_R1_001.fastq.gzâ âsample4/R1.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929580-10_S68_L999_R2_001.fastq.gzâ âsample4/R2.fq.gzâ
prokka --centre X --compliant --force --fast --gcode 0 --locustag sample1 --prefix sample1 --outdir sample1/prokka --cpus 4 sample1/contigs.fa
Canât 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 failedâcompilation aborted at /home/linuxbrew/.linuxbrew/bin/prokka line 25.
Makefile:134: recipe for target âsample1/prokka/sample1.gffâ failed
make: *** [sample1/prokka/sample1.gff] Error 2
make: Leaving directory â/home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018â
I attempted to install XML::Simple, with the command, âconda install perl-xml-libxmlâ. The installation was successful, but still no joy with Nullarbor. When I resume with the command ânice make -j 1 -C /home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018â it returns the same error message as before.
Grateful for your kind assistance as always.
Ebenn
Yes please, the installation is up to date, as I had successfully installed it. Hereâs 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 Iâm 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 â/home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018â
mkdir -p sample1
mkdir -p sample2
mkdir -p sample3
mkdir -p sample4
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929580-1_S95_L999_R1_001.fastq.gzâ âsample1/R1.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929580-1_S95_L999_R2_001.fastq.gzâ âsample1/R2.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929583-1_S83_L999_R1_001.fastq.gzâ âsample2/R1.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929583-1_S83_L999_R2_001.fastq.gzâ âsample2/R2.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929606-1_S80_L999_R1_001.fastq.gzâ âsample3/R1.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929606-1_S80_L999_R2_001.fastq.gzâ âsample3/R2.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929580-10_S68_L999_R1_001.fastq.gzâ âsample4/R1.fq.gzâ
ln -f -s â/home/ubuntu/efn/concat_reads/13-6929580-10_S68_L999_R2_001.fastq.gzâ âsample4/R2.fq.gzâ
prokka --centre X --compliant --force --fast --gcode 0 --locustag sample1 --prefix sample1 --outdir sample1/prokka --cpus 4 sample1/contigs.fa
Canât 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 failedâcompilation aborted at /home/linuxbrew/.linuxbrew/bin/prokka line 25.
Makefile:134: recipe for target âsample1/prokka/sample1.gffâ failed
make: *** [sample1/prokka/sample1.gff] Error 2
make: Leaving directory â/home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018â
(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, Iâve got a conda environment attached, and I installed conda following the instructions here âhttps://conda.io/docs/user-guide/install/linux.htmlâ
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. Iâm 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?