Your copy of tbl2asn has expired.
You can renew it with:
brew uninstall --ignore-dependencies tbl2asn
brew uninstall --force tbl2asn
brew install tbl2asn
Then just check that your copy of tbl2asn works by running:
tbl2asn --help
You should get the help and not an expired license warning.
Hi Matt,
Thx for your response. I have carried out the uninstallation and re-installation as above. tbl2asn is working fine now. May I resume Nullarbor? Should I re-run ‘nice make -j 1 -C /home/ubuntu/efn/concat_reads/efn_nullarbor_run03Apr2018’ now pls?
Cheers,
Ebenn
Yup, carry on with nullarbor.
Thx so much again Matt. Nullarbor run has completed successfully!
Cheers,
Ebenn
Hi Matt,
Good afternoon and trust you’ve had a good weekend?
After the successful nullarbor run on four samples, I started a run with 42 samples in a screen last Friday. This morning I am noticing that it has terminated abruptly with the following error message:
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929599-6_S24_L999_R1_001.fastq.gz’ ‘599-6/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929599-6_S24_L999_R2_001.fastq.gz’ ‘599-6/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929599-7_S49_L999_R1_001.fastq.gz’ ‘599-7/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929599-7_S49_L999_R2_001.fastq.gz’ ‘599-7/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929599-8_S3_L999_R1_001.fastq.gz’ ‘599-8/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929599-8_S3_L999_R2_001.fastq.gz’ ‘599-8/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929599-9_S67_L999_R1_001.fastq.gz’ ‘599-9/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929599-9_S67_L999_R2_001.fastq.gz’ ‘599-9/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-1_S80_L999_R1_001.fastq.gz’ ‘606-1/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-1_S80_L999_R2_001.fastq.gz’ ‘606-1/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-2_S48_L999_R1_001.fastq.gz’ ‘606-2/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-2_S48_L999_R2_001.fastq.gz’ ‘606-2/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-3_S2_L999_R1_001.fastq.gz’ ‘606-3/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-3_S2_L999_R2_001.fastq.gz’ ‘606-3/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-4_S61_L999_R1_001.fastq.gz’ ‘606-4/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-4_S61_L999_R2_001.fastq.gz’ ‘606-4/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-5_S66_L999_R1_001.fastq.gz’ ‘606-5/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-5_S66_L999_R2_001.fastq.gz’ ‘606-5/R2.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-6_S23_L999_R1_001.fastq.gz’ ‘606-6/R1.fq.gz’
ln -f -s ‘/home/ubuntu/efn/concat_reads/13-6929606-6_S23_L999_R2_001.fastq.gz’ ‘606-6/R2.fq.gz’
rm -f -r 583-P1/megahit
mkdir -p 583-P1
megahit --min-count 3 --k-list 21,31,41,53,75,97,111,127 -t 4 --memory 0.5 -1 583-P1/R1.fq.gz -2 583-P1/R2.fq.gz --out-dir 583-P1/megahit --min-contig-len 500
31.421Gb memory in total.
Using: 15.711Gb.
MEGAHIT v1.1.2
— [Sun Apr 8 14:32:40 2018] Start assembly. Number of CPU threads 4 —
— [Sun Apr 8 14:32:40 2018] Available memory: 33738153984, used: 16869076992
— [Sun Apr 8 14:32:40 2018] Converting reads to binaries —
b’ [ERROR] [sequence_manager.cpp : 151]: File(s) 583-P1/R1.fq.gz,583-P1/R2.fq.gz: Number of sequences not the same in paired files. Abort.’
Error occurs when running “megahit_asm_core buildlib”; please refer to 583-P1/megahit/log for detail
[Exit code 1]
Makefile:1395: recipe for target ‘583-P1/contigs.fa’ failed
make: *** [583-P1/contigs.fa] Error 1
make: Leaving directory ‘/home/ubuntu/efn/concat_reads/nullarbor_all_samples_run06Apr2018’
ubuntu@ebenn:~/efn/concat_reads$ nullarbor.pl --name efn_nullarbor_all_samples --mlst ecoli --ref /home/ubuntu/efn/reference_new_EcoliUMN206.fasta --input nullarbor_input_files_all_samples_06Apr2018.tab --outdir nullarbor_all_samples_run06Apr2018
Can’t locate YAML/Tiny.pm in @INC (you may need to install the YAML::Tiny 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/nullarbor.pl line 13.
BEGIN failed–compilation aborted at /home/linuxbrew/.linuxbrew/bin/nullarbor.pl line 13.
I wanted to check with you before attempting to install ‘YAML::Tiny module’ as the last nullarbor run completed without any hitches (after fixing the tbl2asn problem).
Standing by to hear from you please.
Grateful as always,
Ebenn
You have two problems here…
megahit is failing because you have a broken pair of fastq files:Check that the paths to these files are correct in nullarbor_input_files_all_samples_06Apr2018.tab and that they are valid and correctly paired fastq files (you may have made a mistake concatenating them).
perl modules aren’t being found:Please deactivate the efn_env conda environment and to remove all traces of conda environment variables.
All of the perl modules needed for nullarbor are installed by default on GVL, so you shouldn’t need to install any perl modules, just make sure that you aren’t attached to any environments that make large-scale changes to your environment.
Dear Matt,
Many thx!
I have not activated conda environment this time, to be honest. What else might be the problem do you think?
Re the problematic reads, is it OK to remove them from the input sample list and continue without it?
Cheers,
Ebenn
To clarify - it is important that the terminal session that you used to run the nullarbor make command isn’t/wasn’t attached to a conda environment, its not important that your current terminal session doesn’t have an active conda environment.
@INC (which is where perl looks for installed modules) on a standard GVL, with no conda envs active contains:
/home/linuxbrew/.linuxbrew/Cellar/perl/5.26.1_1/lib/perl5/site_perl/5.26.1/x86_64-linux-thread-multi
/home/linuxbrew/.linuxbrew/Cellar/perl/5.26.1_1/lib/perl5/site_perl/5.26.1
/home/linuxbrew/.linuxbrew/Cellar/perl/5.26.1_1/lib/perl5/5.26.1/x86_64-linux-thread-multi
/home/linuxbrew/.linuxbrew/Cellar/perl/5.26.1_1/lib/perl5/5.26.1
/home/linuxbrew/.linuxbrew/lib/perl5/site_perl/5.26.1/x86_64-linux-thread-multi
/home/linuxbrew/.linuxbrew/lib/perl5/site_perl/5.26.1
As you can see from the logfile you pasted above, the @INC of the terminal session that you used to run the nullarbor make command contained:
/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
These are all conda paths, so unless you’re using a non-standard conda install, you may have mistakenly had an environment attached when you started the pipeline.
You can check @INC of your current terminal session by running:
perl -V
and looking at the final section of the output. If you do this before running nullarbor or the make part of the pipeline, you can be sure that you won’t run into any problems with perl modules.
It entirely depends on how important it is to you that this sample is included in the analysis. If you can forego the sample, then remove it from the tab-delimited input file. If you would like to include it, then you will need to troubleshoot and verify that the fastq files are OK before you can work on it.
Ok please.
Here is the final section of perl -V output:
DEBPKG:fixes/podman-source-date-epoch-testfix - http://bugs.debian.org/807086 Guard for building with SOURCE_DATE_EPOCH or POD_MAN_DATE set
DEBPKG:debian/devel-ppport-reproducibility - http://bugs.debian.org/801523 Sort the list of XS code files when generating RealPPPort.xs
DEBPKG:fixes/encode-unicode-bom - http://bugs.debian.org/798727 [rt.cpan.org #107043] Address https://rt.cpan.org/Public/Bug/Display.html?id=107043
DEBPKG:debian/encode-unicode-bom-doc - http://bugs.debian.org/798727 Document Debian backport of Encode::Unicode fix
DEBPKG:debian/kfreebsd-softupdates - http://bugs.debian.org/796798 Work around Debian Bug#796798
DEBPKG:fixes/autodie-scope - http://bugs.debian.org/798096 Fix a scoping issue with "no autodie" and the "system" sub
DEBPKG:debian/debugperl-compat-fix - [perl #127212] http://bugs.debian.org/810326 Disable PERL_TRACK_MEMPOOL for debugging builds
DEBPKG:fixes/CVE-2015-8607_file_spec_taint_fix - http://bugs.debian.org/810719 [perl #126862] ensure File::Spec::canonpath() preserves taint
DEBPKG:fixes/mkstemp-umask - http://bugs.debian.org/810924 [perl #127322] [e57270b] Fix umask for mkstemp(3) calls
DEBPKG:fixes/crosscompile-no-targethost - [perl #127234] Fix the Configure escape with usecrosscompile but no targethost
DEBPKG:fixes/podlators-no-encode - [rt.cpan.org #111156] Degrade gracefully if utf8 is requested but Encode is not available
DEBPKG:debian/cross-time-hires - [rt.cpan.org #111391] Add an environment variable to skip running configuration probes
DEBPKG:fixes/encode-unicode-pod - Unicode.pm: Fix POD error
DEBPKG:fixes/memoize-pod - [rt.cpan.org #89441] Fix POD errors in Memoize
DEBPKG:fixes/ok-pod - Added encoding for pod.
DEBPKG:fixes/CVE-2016-2381_duplicate_env - remove duplicate environment variables from environ
DEBPKG:fixes/CVE-2017-12837.patch - [PATCH] regcomp [perl #131582]
DEBPKG:fixes/CVE-2017-12883.patch - [PATCH] PATCH: [perl #131598]
Built under linux
Compiled at Nov 10 2017 14:39:06
@INC:
/etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22
/usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base
I will open a new screen and resume nullarbor from here. I’ll revert with feedback pls.
Thx
Ebenn
Hi,
Nullarbor has terminated at snippy stage with an “Error 2”. Here’s the end of the output message:
denovo.tab 580-6/denovo.tab 580-7/denovo.tab 580-8/denovo.tab 580-9/denovo.tab 583-1/denovo.tab 583-10/denovo.tab 583-11/denovo.tab 583-12/denovo.tab 583-2/denovo.tab 583-3/denovo.tab 583-4/denovo.tab 583-5/denovo.tab 583-6/denovo.tab 583-7/denovo.tab 583-8/denovo.tab 583-9/denovo.tab 599-1/denovo.tab 599-10/denovo.tab 599-11/denovo.tab 599-12/denovo.tab 599-2/denovo.tab 599-3/denovo.tab 599-4/denovo.tab 599-5/denovo.tab 599-6/denovo.tab 599-7/denovo.tab 599-8/denovo.tab 599-9/denovo.tab 606-1/denovo.tab 606-2/denovo.tab 606-3/denovo.tab 606-4/denovo.tab 606-5/denovo.tab 606-6/denovo.tab) > denovo.tab
snippy --cpus 4 --force --outdir 580-1/580-1 --ref /home/ubuntu/efn/reference_new_EcoliUMN206.fasta --R1 580-1/R1.fq.gz --R2 580-1/R2.fq.gz
[02:57:32] This is snippy 3.1
[02:57:32] Written by Torsten Seemann torsten.seemann@gmail.com
[02:57:32] Obtained from https://github.com/tseemann/snippy
[02:57:32] Detected operating system: linux
[02:57:32] Enabling bundled linux tools.
[02:57:32] Found bwa - /home/linuxbrew/.linuxbrew/bin/bwa
[02:57:32] Found samtools - /home/linuxbrew/.linuxbrew/bin/samtools
[02:57:32] Found tabix - /home/linuxbrew/.linuxbrew/bin/tabix
[02:57:32] Found bgzip - /home/linuxbrew/.linuxbrew/bin/bgzip
[02:57:32] Found snpEff - /home/linuxbrew/.linuxbrew/Cellar/snippy/3.1/bin/…/binaries/noarch/snpEff
[02:57:32] Found java - /home/linuxbrew/.linuxbrew/bin/java
[02:57:32] Found gzip - /bin/gzip
[02:57:32] Found parallel - /home/linuxbrew/.linuxbrew/bin/parallel
[02:57:32] Found freebayes - /home/linuxbrew/.linuxbrew/bin/freebayes
[02:57:32] Found freebayes-parallel - /home/linuxbrew/.linuxbrew/bin/freebayes-parallel
[02:57:32] Found fasta_generate_regions.py - /home/linuxbrew/.linuxbrew/bin/fasta_generate_regions.py
[02:57:32] Found vcfstreamsort - /home/linuxbrew/.linuxbrew/bin/vcfstreamsort
[02:57:32] Found vcfuniq - /home/linuxbrew/.linuxbrew/bin/vcfuniq
[02:57:32] Found vcffirstheader - /home/linuxbrew/.linuxbrew/bin/vcffirstheader
[02:57:32] Found vcf-consensus - /home/linuxbrew/.linuxbrew/bin/vcf-consensus
[02:57:32] Found snippy-vcf_to_tab - /home/linuxbrew/.linuxbrew/Cellar/snippy/3.1/bin/snippy-vcf_to_tab
[02:57:32] Found snippy-vcf_report - /home/linuxbrew/.linuxbrew/Cellar/snippy/3.1/bin/snippy-vcf_report
[02:57:32] Found snippy-vcf_filter - /home/linuxbrew/.linuxbrew/Cellar/snippy/3.1/bin/snippy-vcf_filter
[02:57:32] Using reference: /home/ubuntu/efn/reference_new_EcoliUMN206.fasta
[02:57:32] Treating reference as ‘fasta’ format.
[02:57:32] Will use 4 CPU cores.
[02:57:32] Using read file: /home/ubuntu/efn/concat_reads/nullarbor_run08Apr2018/580-1/R1.fq.gz
[02:57:32] Using read file: /home/ubuntu/efn/concat_reads/nullarbor_run08Apr2018/580-1/R2.fq.gz
[02:57:32] Creating folder: 580-1/580-1
[02:57:32] Changing working directory: 580-1/580-1
[02:57:32] Creating reference folder: reference
[02:57:32] Extracting FASTA and GFF from reference.
[02:57:33] Wrote 1 sequences to ref.fa
[02:57:33] Wrote 0 features to ref.gff
[02:57:33] Freebayes will process 16 chunks of 330554 bp, 4 chunks at a time.
[02:57:33] Using BAM RG (Read Group) ID: snps
[02:57:33] Running: samtools faidx reference/ref.fa 2>> snps.log
[02:57:33] Running: bwa index reference/ref.fa 2>> snps.log
[02:57:37] Running: mkdir reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[02:57:37] Running: mkdir reference/ref && bgzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[02:57:37] Running: (bwa mem -v 2 -M -R ‘@RG ID:snps SM:snps’ -t 4 reference/ref.fa /home/ubuntu/efn/concat_reads/nullarbor_run08Apr2018/580-1/R1.fq.gz /home/ubuntu/efn/concat_reads/nullarbor_run08Apr2018/580-1/R2.fq.gz | samtools view -@ 4 -F 3844 -q 60 -S -b -u -T reference/ref.fa - | samtools sort -O bam -o snps.bam -@ 4 -) 2>> snps.log
[02:57:37] Running: samtools index snps.bam 2>> snps.log
[02:57:37] Running: samtools depth -q 20 snps.bam | bgzip > snps.depth.gz 2>> snps.log
[02:57:37] Running: tabix -s 1 -b 2 -e 2 snps.depth.gz 2>> snps.log
[02:57:37] Running: fasta_generate_regions.py reference/ref.fa.fai 330554 > reference/ref.txt 2>> snps.log
[02:57:37] Error running command, check 580-1/580-1/snps.log
Makefile:33: recipe for target ‘580-1/580-1/snps.tab’ failed
make: *** [580-1/580-1/snps.tab] Error 2
make: Leaving directory ‘/home/ubuntu/efn/concat_reads/nullarbor_run08Apr2018’
ubuntu@ebenn:~/efn/concat_reads$
Your kind assistance is greatly appreciated as always 
Here’s the content of 580-1/580-1/snps.log please:
ubuntu@ebenn:~/efn/concat_reads/nullarbor_run08Apr2018/580-1/580-1$ cat snps.log
[bwa_index] Pack FASTA… 0.07 sec
[bwa_index] Construct BWT for the packed sequence…
[bwa_index] 2.52 seconds elapse.
[bwa_index] Update BWT… 0.04 sec
[bwa_index] Pack forward-only FASTA… 0.03 sec
[bwa_index] Construct SA from BWT and Occ… 0.96 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index reference/ref.fa
[main] Real time: 3.886 sec; CPU: 3.628 sec
[E::bwa_set_rg] the read group line contained literal characters – replace with escaped tabs: \t
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], " ")?
(end of snp.log content)
Thx
Ebenn
The way that print function is called changed between Python 2 and 3. The error below is caused by trying to run a program written in Python 2 (fasta_generate_regions.py) using the Python 3 interpreter.
I suspect that conda is still interfering with your environment. The default miniconda3 python interpreter is currently something like version 3.6.4, and the default Ubuntu 16.04 interpreter is something like version 2.7.12.
If you used the automatic miniconda installer, it gives you the option to prepend the miniconda bin directory to the PATH by writing the following to the end ~/.bashrc:
# added by Miniconda3 installer
export PATH="/home/ubuntu/miniconda3/bin:$PATH"
I suspect that you will need to comment out this line then logout and log back in to your VM for the changes to take effect to fix this problem.
You can check python interpreter your session is using with:
which python
python --version
For nullarbor to run smoothly, you want a Python version of 2.x.x.
I’d suggest that if you want to use miniconda, it need to be the sole package manager installed, or at least only using software from inside the environment, not system and linuxbrew packages.
I suspect that you’ll get on better using miniconda on a clean Ubuntu 16.04 install, rather than GVL.
Hi Matt,
You’re right, my python version is 3.6.4. I changed directory to /home/ubuntu/efn/miniconda3/bin/.bashrc and added 'export PATH="/home/ubuntu/miniconda3/bin:$PATH", rebooted my VM and tried to resume nullarbor, but the error persists.
Please can you guide me through a “clean ubunt 16.04 install” ? I have no idea how to proceed.
Thx,
Ebenn
The problem is with the file:
/home/ubuntu/.bashrc
It has a line at the bottom which reads:
export PATH="/home/ubuntu/miniconda3/bin:$PATH"
Please use nano, to edit this file with the following command:
nano /home/ubuntu/.bashrc
and replace the line that reads:
export PATH="/home/ubuntu/miniconda3/bin:$PATH"
with:
#export PATH="/home/ubuntu/miniconda3/bin:$PATH"
When you have done that, and pressed Ctrl+X and followed the prompts to save the file and exit nano, disconnect and reconnect to your VM.
Thx Matt,
This is done, and nullarbor resumed again. But I’m afraid there is an error about creating the core.aln. Here is what it says:
–aformat=s Output alignment format: nexus fasta phylip maf clustalw … (default ‘fasta’).
Makefile:2302: recipe for target ‘core.aln’ failed
make: *** [core.aln] Error 1
make: Leaving directory ‘/home/ubuntu/efn/concat_reads/nullarbor_run08Apr2018’
ubuntu@ebenn:~/efn/concat_reads$ ls
Any idea what might this be please?
Thx,
Ebenn
I suspect that the problem is this:
But its difficult to say exactly because this run has stopped and started so many times. I suggest that you install the latest version of snippy (v3.2):
brew upgrade snippy
Then completely remove the output directory from your nullarbor run and start it again fresh.
Thx Matt!
I have upgraded snippy, but it gave several warnings! Please see below:
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!
Warning: Calling ‘depends_on … => :perl’ is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/abricate.rb:14:in `class:Abricate’
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/abricate.rb:15:in `class:Abricate’
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/abricate.rb:16:in `class:Abricate’
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/abricate.rb:17:in `class:Abricate’
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/snippy.rb:12:in `class:Snippy’
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/snippy.rb:13:in `class:Snippy’
Please report this to the tseemann/bioinformatics-linux tap!
==> Upgrading 1 outdated package, with result:
tseemann/bioinformatics-linux/snippy 3.1 -> 3.2
Error: No available formula with the name “vcflib” (dependency of tseemann/bioinformatics-linux/snippy)
Not sure if it’s ok to proceed?
Thx,
Ebenn
The warnings aren’t a problem, but you’ll need these two taps before you can upgrade snippy:
brew tap brewsci/science
brew tap brewsci/bio
Then you can run:
brew upgrade snippy
Ignoring the warnings.
Hi Matt,
Good morning!
Nullarbor completed successfully!
Most grateful for your patience and kind assistance!
Cheers
Ebenn
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