corason
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nselem
Remove Docker dependency
Hello,
I'd like to use Corason on a Google Colab virtual machine, but sadly they don't support Docker and have no plans to do so (https://github.com/googlecolab/colabtools/issues/299). Unlike most packages that only use Docker for installation (e.g., BiG-SCAPE), I see that Corason actually uses Docker in its execution (e.g., docker run ... in run_corason). Would it be very difficult to modify the scripts so that they can run without Docker?
Thanks!
Hello Other packages has a cover script that writes de docker run instruction for you, but it canot be just the instalation, because docker is a container to run software and its dependencies inside it. CORASON is a set of perl scripts, with dependencies on blast, muscle, gblocks newick utilities and fasttree. It does not need docker in its execution, docker is just the container. You would need to install those dependencies in the paths indicated in the dockerfile, it could be troublesome. I think easiest way is to get accesion to a LINUX machine, for example in Amazon Web Services. Sorry, these are not the best news for you.
I see, then perhaps I have some confusion. In the installation instructions for BiG-SCAPE under "Manual installation," there's no dependency on Docker, and I install the other dependencies via Conda, which works great in Google Colab. Since you said that CORASON also doesn't depend on Docker, is a similar "manual installation" possible for CORASON, and how could I do it? Currently when I clone the GutHub repo and run run_corason, I get the error: /usr/local/envs/CORASON/corason/run_corason: line 42: docker: command not found
CCing @jorgecnavarrom in case he has some tips
Its because BiG-SCAPE has two possible instalation forms, one is with conda and another one with docker, since CORASON is not python it has not the option to use conda. It will be hard to run a manual installation, for the dependencies, that is why conda and docker are valuable resources. For CORASON you need a linux or mac machine in order tat docker runs. Nevertheless I can run your data for you, If you whish.
CORASON is a set of perl scripts, with dependencies on blast, muscle, gblocks newick utilities and fasttree
So in principle if those dependencies are installed (perhaps even through conda) it should be possible to run the CORASON perl scripts right? (e.g. https://github.com/nselem/corason/blob/master/CORASON/corason.pl)
Yup that's what I'm thinking, and fortunately Conda does support Perl. I'll post some code for how to install those dependencies in a Perl virtual environment via Conda, but there will need to be a few changes to the master script that calls the others, right?
Yes, we can try, the paths would be what we must change, but it would be great to have CORASON in CONDA too.
This sounds great, and I don't think it should be too hard.
After installing Conda, you can run the following commands in terminal:
# Add channels to look for packages in
conda config --add channels bioconda
conda config --add channels conda-forge
# Create virtual environment for CORASON
conda create -y --prefix /usr/local/envs/CORASON
# Install dependencies into virtual environment
conda install -y --name CORASON perl perl-bioperl perl-app-cpanminus fasttree quicktree blast muscle newick_utils biopython gblocks vim
# Clone CORASON from Git and install in virtual environment
cd /usr/local/envs/CORASON
git clone https://github.com/nselem/corason.git
chmod a+x /usr/local/envs/CORASON/corason/run_corason
# Install cpan modules in virtual environment
conda activate CORASON
cpanm SVG
## I'm not sure if you need to install these from cpan or if they're included in the perl-bioperl module above
cpanm Bio::SeqIO
cpanm Bio::SeqFeature::Generic
cpanm Bio::Seq
conda deactivate
# Check that everything was installed correctly
conda activate CORASON
bash /usr/local/envs/CORASON/corason/run_corason --help
conda deactivate
This should get you started, but let me know if you run into any Conda problems. Do you also need to install any cpan packages? If so I can give you code for that.
Ok, I will try, give me some days. :) Yes we need svg from cpan, basically, all needs are in the Dockerfile of the github repo.
Ok, I just edited the above to include that. The code above should work, but if you run into any problems with cpan in conda, you can look here for troubleshooting
You may need to put these two lines at the top of Perl scripts you want to run, but I'm not sure--it might just be enough to do conda activate CORASON in terminal before calling the Perl script, as above.
module load anaconda
source activate CORASON
Please do let me know if I can help more with the Conda stuff. I know others use Conda + Perl a lot, so I'm sure we can get it working, and I think that would be great for users.
Hi @nselem, Just wanted to check in to see how this is going and if there's anything I can do to help--just let me know.
Hello @rchurt,
This sounds great, and I don't think it should be too hard.
After installing Conda, you can run the following commands in terminal:
# Add channels to look for packages in conda config --add channels bioconda conda config --add channels conda-forge # Create virtual environment for CORASON conda create -y --prefix /usr/local/envs/CORASON # Install dependencies into virtual environment conda install -y --name CORASON perl perl-bioperl perl-app-cpanminus fasttree quicktree blast muscle newick_utils biopython gblocks vim # Clone CORASON from Git and install in virtual environment cd /usr/local/envs/CORASON git clone https://github.com/nselem/corason.git chmod a+x /usr/local/envs/CORASON/corason/run_corason # Install cpan modules in virtual environment conda activate CORASON cpanm SVG ## I'm not sure if you need to install these from cpan or if they're included in the perl-bioperl module above cpanm Bio::SeqIO cpanm Bio::SeqFeature::Generic cpanm Bio::Seq conda deactivate # Check that everything was installed correctly conda activate CORASON bash /usr/local/envs/CORASON/corason/run_corason --help conda deactivateThis should get you started, but let me know if you run into any Conda problems. Do you also need to install any
cpanpackages? If so I can give you code for that
I can try this as well, would love to have this tool in Conda.
I followed these steps am at the point where I can actually run CORASON. Of note, the program run_corason points to docker, so, according to some documentation I found, instead we should be using corason.pl.
Unfortunately, I am working with proprietary bacterial genomes and am not able to upload them to RAST for annotation. For my own research, I may have to build phylogenetic trees from the Big-Scape network data instead.
Doesn't seem like I'll be able to test CORASON because the paremeters for "run_corason" and "corason.pl" are different, and I can't run corason.pl without RAST IDs. Is there a way to run it without RAST IDs? I'm trying to use the example dataset from the website. @nselem
Hello jc, sorry, Im late with conda version, let me keep trying, you can use gbks. We can set a meeting next week and try do it togheter
Hey @nselem, just wanted to see how this is going--did you manage to get it to work in Conda without Docker?
Hello Curt If fact, I got good news, Now it works for conda, (not for windows). I will update the code today with a small example
Hello, here how you can use it with conda. (only tested with Rast files for now, gbk will be next step to be tried)
git clone https://github.com/nselem/corason.git
cd corason
conda env create -f corason.yml
conda activate corason
tar -xvzf EXAMPLE.tar.gz
mv EXAMPLE/* .
CORASON/corason.pl -q ctg2_515.query -rast_ids Example.Ids -s 501926 -conda
firefox ctg2_515.query-output/Joined.svg
That's great news! I tried it out--below is my code and the output. It worked, but in the ctg2_515.query-output directory there are no files named Contextos.svg or Joined.svg. The only SVG in that directory is ctg2_515.query_tree.svg. Have you seen this before?
# Create virtual environment for CORASON
conda create -y --prefix /usr/local/envs/CORASON
# Install dependencies into virtual environment
conda install -y --name CORASON perl fasttree quicktree blast muscle newick_utils biopython gblocks
# Clone CORASON from Git and install in virtual environment directory
cd /usr/local/envs/CORASON
git clone https://github.com/nselem/corason.git
# Check that everything was installed correctly
conda activate CORASON
corason/CORASON/corason.pl --help -conda
conda deactivate
conda activate CORASON
# load example data
cd /usr/local/envs/CORASON/corason
tar -xvzf EXAMPLE.tar.gz
mv EXAMPLE/* .
# run example
CORASON/corason.pl -q ctg2_515.query -rast_ids Example.Ids -s 501926 -conda
conda deactivate
Full output:
EXAMPLE/GENOMES/501966.txt
EXAMPLE/GENOMES/501890.txt
EXAMPLE/GENOMES/501954.faa
EXAMPLE/GENOMES/501936.faa
EXAMPLE/GENOMES/501926.faa
EXAMPLE/GENOMES/501938.txt
EXAMPLE/GENOMES/501936.txt
EXAMPLE/GENOMES/501926.txt
EXAMPLE/GENOMES/501888.txt
EXAMPLE/GENOMES/
EXAMPLE/GENOMES/501879.faa
EXAMPLE/GENOMES/501938.faa
EXAMPLE/GENOMES/501879.txt
EXAMPLE/GENOMES/501861.faa
EXAMPLE/GENOMES/501861.txt
EXAMPLE/GENOMES/501933.faa
EXAMPLE/ctg2_515.query
EXAMPLE/GENOMES/501933.txt
EXAMPLE/Example.Ids
EXAMPLE/GENOMES/501888.faa
EXAMPLE/
EXAMPLE/GENOMES/501890.faa
EXAMPLE/GENOMES/501966.faa
EXAMPLE/GENOMES/501954.txt
special org: 501926
rast=Example.Ids special=501926
##########################################################
Welcome to CORASON
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/ /___ / /_/ / / / /_/ /_(__ )/ /_/ / / / /
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Y
CORASON-BGC
CORe Analysis of Syntenic Orthologs Natural Product-Biosynthetic Gene Cluster
##########################################################
Your current directory is /usr/local/envs/CORASON/corason, local path corason
You will use antiSMASH file none
I must check ctg2_515.query is a fasta file
Your cluster is located on organism number 501926
Default e-value=1E-15
Your bitscore is set to 0, you can use a positive bitscore to reduce your hunchs
the radio of your cluster is 10
Minimal e-value to be consider an homologous of a cluster member is: 1E-3
Minimal e-value for ortho groups in core 1E-3
You are rescaling gene size by a factor: 85000
Your rast ids file is Example.Ids
All genomes would be procesed
You will explore 10 genomes
CORASON/CoreCluster.pl -q ctg2_515.query -s 501926 -e_value 1E-15 -b 0 -cluster_radio 10 -e_core 1E-3 -e_cluster 1E-3 -rescale 85000 -l 501861,501879,501888,501890,501926,501933,501936,501938,501954,501966 -num 10 -rast_ids Example.Ids -antismash none -conda 1
Searching sequences from query (CORASON/1_Context_text.pl)
CORASON/1_Context_text.pl -q ctg2_515.query -s 501926 -e_value 1E-15 -b 0 -cluster_radio 10 -e_cluster 1E-3 -r 85000 -l 501861,501879,501888,501890,501926,501933,501936,501938,501954,501966 -n 10 -rast_ids Example.Ids -type prots -makedb -antismash none -conda 1
mkdir: cannot create directory ‘ctg2_515.query-output’: File exists
I will search homologous genes in organisms
I will create a Database with selected genomes
prots type
Aminoacid data will be analized
CORASON/header.pl GENOMES Example.Ids ctg2_515.query-output
pause before makeDB
`makeblastdb -in ctg2_515.query-output/TempConcatenados.faa -dbtype prot -out ctg2_515.query-output/temDatabase.db`Protein db was created
Looking for hits
homologous gene search finished
Searching for homologous gene in clusters
16 gen were found surrounding query, cluster radio can not exceed this radio.
I have colored genes according to homology
Now I will produce the *.input file
Sequences search finished
Analizing cluster with hits according to the query sequence
Can't exec "1": No such file or directory at CORASON/ReadingInputs.pl line 17.
Can't locate Bio/SeqFeature/Generic.pm in @INC (you may need to install the Bio::SeqFeature::Generic module) (@INC contains: /usr/local/lib/perl5/site_perl/5.20.3 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at CORASON/GbkCreator.pl line 4.
BEGIN failed--compilation aborted at CORASON/GbkCreator.pl line 4.
Can't locate Bio/SeqFeature/Generic.pm in @INC (you may need to install the Bio::SeqFeature::Generic module) (@INC contains: /usr/local/lib/perl5/site_perl/5.20.3 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at CORASON/GbkCreator.pl line 4.
BEGIN failed--compilation aborted at CORASON/GbkCreator.pl line 4.
Can't locate Bio/SeqFeature/Generic.pm in @INC (you may need to install the Bio::SeqFeature::Generic module) (@INC contains: /usr/local/lib/perl5/site_perl/5.20.3 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at CORASON/GbkCreator.pl line 4.
BEGIN failed--compilation aborted at CORASON/GbkCreator.pl line 4.
Can't locate Bio/SeqFeature/Generic.pm in @INC (you may need to install the Bio::SeqFeature::Generic module) (@INC contains: /usr/local/lib/perl5/site_perl/5.20.3 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at CORASON/GbkCreator.pl line 4.
BEGIN failed--compilation aborted at CORASON/GbkCreator.pl line 4.
Can't locate Bio/SeqFeature/Generic.pm in @INC (you may need to install the Bio::SeqFeature::Generic module) (@INC contains: /usr/local/lib/perl5/site_perl/5.20.3 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at CORASON/GbkCreator.pl line 4.
BEGIN failed--compilation aborted at CORASON/GbkCreator.pl line 4.
Can't locate Bio/SeqFeature/Generic.pm in @INC (you may need to install the Bio::SeqFeature::Generic module) (@INC contains: /usr/local/lib/perl5/site_perl/5.20.3 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at CORASON/GbkCreator.pl line 4.
BEGIN failed--compilation aborted at CORASON/GbkCreator.pl line 4.
Can't locate Bio/SeqFeature/Generic.pm in @INC (you may need to install the Bio::SeqFeature::Generic module) (@INC contains: /usr/local/lib/perl5/site_perl/5.20.3 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at CORASON/GbkCreator.pl line 4.
BEGIN failed--compilation aborted at CORASON/GbkCreator.pl line 4.
Can't locate Bio/SeqFeature/Generic.pm in @INC (you may need to install the Bio::SeqFeature::Generic module) (@INC contains: /usr/local/lib/perl5/site_perl/5.20.3 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at CORASON/GbkCreator.pl line 4.
BEGIN failed--compilation aborted at CORASON/GbkCreator.pl line 4.
Can't locate Bio/SeqFeature/Generic.pm in @INC (you may need to install the Bio::SeqFeature::Generic module) (@INC contains: /usr/local/lib/perl5/site_perl/5.20.3 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at CORASON/GbkCreator.pl line 4.
BEGIN failed--compilation aborted at CORASON/GbkCreator.pl line 4.
There are 9 similar clusters
Creating query hits tree, without considering the core-clusters
Aligning Sequences
Shaving alignments with Gblocks
9 sequences and 193 positions in the first alignment file:
ctg2_515.query-output/PrincipalHits.muscle
ctg2_515.query-output/PrincipalHits.muscle
Original alignment: 193 positions
Gblocks alignment: 150 positions (77 %) in 1 selected block(s)
FastTree Version 2.1.10 Double precision (No SSE3)
Alignment: ctg2_515.query-output/RightNamesPrincipalHits.txt
Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories
Initial topology in 0.00 seconds
Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
Total branch-length 0.232 after 0.00 sec
ML-NNI round 1: LogLk = -685.444 NNIs 2 max delta 1.77 Time 0.04
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.698 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
ML-NNI round 2: LogLk = -666.025 NNIs 0 max delta 0.00 Time 0.09
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 3: LogLk = -666.025 NNIs 0 max delta 0.00 Time 0.13 (final)
Optimize all lengths: LogLk = -666.025 Time 0.14
Total time: 0.17 seconds Unique: 8/9 Bad splits: 0/5
Searching genetic core on selected clusters
CORASON/2_OrthoGroups.pl -e_core 1E-3 -list 501861_5412,501879_708,501888_3244,501890_57,501926_231,501933_4070,501938_4339,501954_3632,501966_1760 -num 9 -rast_ids Example.Ids -outname ctg2_515.query-output -conda 1
I will run allvsall with blast ctg2_515.query-output/Corecorason.blast
You want ortho groups of the following genomes
501861_5412 501879_708 501888_3244 501890_57 501926_231 501933_4070 501938_4339 501954_3632 501966_1760
Now finding Best Bidirectional Hits List
Selecting List that contains orthologs from all desired genomes
Starting Star groups
num 9
list 501861_5412,501879_708,501888_3244,501890_57,501926_231,501933_4070,501938_4339,501954_3632,501966_1760
Starting stars
CORASON/SearchAminoacidsFromCore.pl 501861_5412,501879_708,501888_3244,501890_57,501926_231,501933_4070,501938_4339,501954_3632,501966_1760 ctg2_515.query-output
Done!
CORASON/ReadReaction 501861_5412,501879_708,501888_3244,501890_57,501926_231,501933_4070,501938_4339,501954_3632,501966_1760 9 ctg2_515.query-output
rm: cannot remove 'ctg2_515.query-output/CORASON/FUNCTION': No such file or directory
Core finished!
There is a core with at least two genes on this cluster
Best cluster ctg2_515.query-output/501926_231
Best cluster ctg2_515.query-output
cut -f1,2 ctg2_515.query-output/CORASON/FUNCTION/501926_231.core.function
Aligning...
ctg2_515.query-output/CORASON
&align 1,9,ctg2_515.query-output/CORASON,501861_5412 501879_708 501888_3244 501890_57 501926_231 501933_4070 501938_4339 501954_3632 501966_1760
9 sequences and 383 positions in the first alignment file:
ctg2_515.query-output/CORASON/ALIGNMENTS_GB/1.orden.muscle
ctg2_515.query-output/CORASON/ALIGNMENTS_GB/1.orden.muscle
Original alignment: 383 positions
Gblocks alignment: 93 positions (24 %) in 1 selected block(s)
&align 2,9,ctg2_515.query-output/CORASON,501861_5412 501879_708 501888_3244 501890_57 501926_231 501933_4070 501938_4339 501954_3632 501966_1760
9 sequences and 193 positions in the first alignment file:
ctg2_515.query-output/CORASON/ALIGNMENTS_GB/2.orden.muscle
ctg2_515.query-output/CORASON/ALIGNMENTS_GB/2.orden.muscle
Original alignment: 193 positions
Gblocks alignment: 150 positions (77 %) in 1 selected block(s)
&align 3,9,ctg2_515.query-output/CORASON,501861_5412 501879_708 501888_3244 501890_57 501926_231 501933_4070 501938_4339 501954_3632 501966_1760
9 sequences and 369 positions in the first alignment file:
ctg2_515.query-output/CORASON/ALIGNMENTS_GB/3.orden.muscle
ctg2_515.query-output/CORASON/ALIGNMENTS_GB/3.orden.muscle
Original alignment: 369 positions
Gblocks alignment: 339 positions (91 %) in 2 selected block(s)
Gblocks and muscle have finished
Sequences were aligned
Creating aminoacid core cluster matrix..
directory ctg2_515.query-output/CORASON/ALIGNMENTS_GB will be open
Se abrio el directorio ctg2_515.query-output/CORASON/ALIGNMENTS_GB con los archivos numericos
2.orden.muscle-gb
Se escribio archivo de salida 2
3.orden.muscle-gb
Se escribio archivo de salida 3
1.orden.muscle-gb
Se escribio archivo de salida 1
CORASON/Rename_Ids_Star_Tree.pl Example.Ids ctg2_515.query-output
rm: cannot remove 'ctg2_515.query-output/RightNames.txt': No such file or directory
Formating matrix..
FastTree Version 2.1.10 Double precision (No SSE3)
Alignment: ctg2_515.query-output/RightNames.txt
Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories
Initial topology in 0.00 seconds
Refining topology: 13 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
Total branch-length 0.390 after 0.02 sec
ML-NNI round 1: LogLk = -3061.915 NNIs 1 max delta 6.10 Time 0.18
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.737 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
ML-NNI round 2: LogLk = -2934.581 NNIs 2 max delta 1.65 Time 0.39
ML-NNI round 3: LogLk = -2932.177 NNIs 1 max delta 2.39 Time 0.46
ML-NNI round 4: LogLk = -2932.177 NNIs 0 max delta 0.00 Time 0.51
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 5: LogLk = -2932.174 NNIs 0 max delta 0.00 Time 0.65 (final)
Optimize all lengths: LogLk = -2932.174 Time 0.69
Total time: 0.80 seconds Unique: 9/9 Bad splits: 0/6
nw_topology -b -IL ctg2_515.query-output/ctg2_515.query_BGC.tre | nw_display -b 'opacity:0' -v 40 -s - >ctg2_515.query-output/ctg2_515.query_tree.svgI will draw SVG clusters with concatenated tree order
Draw
Now SVG file will be generated with inputs: 501926_231.input,501890_57.input,501861_5412.input,501966_1760.input,501888_3244.input,501954_3632.input,501879_708.input,501938_4339.input,501933_4070.input
CORASON/3_Draw.pl 85000 501926_231.input,501890_57.input,501861_5412.input,501966_1760.input,501888_3244.input,501954_3632.input,501879_708.input,501938_4339.input,501933_4070.input ctg2_515.query-output ctg2_515.queryCan't locate SVG.pm in @INC (you may need to install the SVG module) (@INC contains: /usr/local/lib/perl5/site_perl/5.20.3 /usr/local/lib/perl5/site_perl/5.20.3 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at CORASON/3_Draw.pl line 3.
BEGIN failed--compilation aborted at CORASON/3_Draw.pl line 3.
SVG file generated
mv: cannot stat 'ctg2_515.query-output/Contextos.svg': No such file or directory
Cleaning temporary files
rm: cannot remove 'ctg2_515.query-output/CORASON_GENOMES': No such file or directory
mv ctg2_515.query /home/output/Done
Have a nice day
Can you show me the content of ctg2_515.query-output directory. Perhaps is the svg perl module (that I already have in my computer). Are the input files such as 501890_57.input empty or do they have some content?. If they have content, then we are only missing the drawing, that is the last step run by CORASON/3_Draw.pl.
In fact your output shows BEGIN failed--compilation aborted at CORASON/3_Draw.pl line 3.
So it may be The Bangshee : #!/usr/bin/perl -I/usr/local/lib/perl5/site_perl/5.20.3
or the modules SVG;, Getopt::Long; or Cwd;
Great, that worked. I had to manually install SVG and change the first line of 3_Draw.pl to #!/usr/bin/perl -I/usr/local/envs/CORASON/lib/site_perl/5.26.2. Since that's the default install location for SVG via Conda, should we just change that line in the 3_Draw.pl script? Otherwise each user will have to change it manually.
Here's my code: https://colab.research.google.com/github/rchurt/rchurt.github.io/blob/master/CORASON.ipynb
Glad it worked for you. Next step will be to making it work directly with gbk files. I dont know how to change SVG location without affecting docker users, it also worries me that the perl version that conda writes now 5.26.2 may change in future, and then users would need to change it any way.
Hi, all, I really appreciate the effort to make CORASON available through conda, thanks!! Are there any updates on whether the conda-installed CORASON works with gbk files? I have followed @rchurt's instructions, but I only have gbk files and I cannot make it work :( I have previously run CORASON from docker in my laptop, but my dataset has grown and I can no longer run it locally comfortably. But from those runs, I have the automatically produced Corason_Rast.IDs. Does that help? I have tried to pass this file, but the program still fails.
Alternatively, are there any instructions to make it run in Singularity? I have never used it before, but it seems to work to run docker images.
Any help is greatly appreciated!
Hello, YIf you have run CORASON gbk mode before in your laptop you can use the Corason_Rast.IDs files and the faa and txt genomes that were also generated. This files are in RAST format, so you can use them for the conda mode. Try, and If you cant, send me anemail and I can help you by zoom. Unfortunatly it does not work on singularity. I have plans to a full conda version but until next semester !
Nelly