Regarding usage, installing CPLEX & CarveMe

[ShailNair]

Hi, The package seems to be interesting, and would like to give a shot on my data. I have a sweet of prokaryotic MAGs and would like to run the GEM pipeline on it without starting from assembly and MAG generation. Is it possible to do so?

[franciscozorrilla]

Hi Shail,

Absolutely! Since metaGEM is implemented as a series of Snakemake rules, it is possible to use the pipeline in a modular fashion. You can simply begin with the bash metaGEM.sh --task carveme command, which will use the CarveMe tool for generating your metabolic models.

Please note that you will need to obtain a free academic license and manually install the CPLEX solver to use CarveMe. You can use CarveMe as a standalone tool or through the metaGEM pipeline. If you run CarveMe through metaGEM, note that the Snakefile will identify your MAGs by searching for files with extension .faa under the protein_bins subfolder. Also note that CarveMe takes as input ORF annotated protein fasta files, so you may need to run prodigal or similar software if you are starting from DNA MAGs.

Finally, if your MAGs come from short-read data and you have the time/resources, I would encourage you to try using metaGEM for MAG reconstruction to see if it yields better quality MAGs. You may also find this tutorial useful to see how metaGEM can be used. Let me know if you have any further questions and thank you for your interest in the pipeline!

Best wishes,
Francisco

[wupeng1998]

Hi, I also have a well-boxed macro-genomic data and have built the model using CarveMe. I input the colony macrogenomic data and only one model is output and this model has an empty output file when Smetana simulates the colony metabolite exchange.
this is my code in carveme: carve D:\AS\ST_third.faa --output YL_model.xml

and an code in smetana:python smetana D:\jupyternotebook\Y_YL_model\YL_model.xml -v -d --molweight --zeros

Is there any error in this step?

[franciscozorrilla]

Hi wupeng, just to clarify, by "colony macrogenomic" do you mean shotgun metagenomic reads?
The CarveMe input should be a single genome (e.g. metagenome assembled genome), annotated for open reading frames (ORFs), and translated to protein.
You should generate one model per genome.
For some example commands and files you may want to check out this repo tutorial
If you provide SMETANA with only a single genome, then indeed there should be no interactions predicted 👍
Please let me know if this answers your question, and feel free to open a new issue or discussion and provide more details 💎

[wupeng1998]

Ok, thanks for your answer, I think I know where the mistake is. But now I have a new question - can SMETANA's input model be from another library? For example modelseed, the ID in the modelseed model is not the same as on bigg.

[franciscozorrilla]

By "library" I assume you mean genome-scale metabolic model reconstruction tool? In that case, I would recommend you to use CarveMe models for SMETANA simulations. I have never tried using modelseed, I always use CarveMe models for SMETANA simulation. Feel free to try the modelseed GEMs and see what happens, only one way to find out!

Also check out the SMETANA github repo issues section, you may be interested in the following:
cdanielmachado/smetana#36
cdanielmachado/smetana#21
cdanielmachado/smetana#12

[wupeng1998]

okay，thank you very much，i will try

[ShailNair]

Thanks. i will try to set it up and run

[ShailNair]

Hi, unfortunately, my request to obtain a free academic license was rejected (even though my the university is eligible for the program). I tried with another colleague and same response for him also.

[franciscozorrilla]

Hi Shail, sorry to hear that. I think the link I had in the README file was broken, is this the portal where you tried to get the license from? Did they give a reason for rejecting your request?

[ShailNair]

Yes. i saw the previous link was not correct. I used this link. Unfortunately, it seems my university is not a registered member to avail IBM academic initiative program. Is there any other way, because to register is a long process and has to go through university officials.

[franciscozorrilla]

That is a shame, I hope your university can register successfully. If you have access to a high performance computer cluster you could check if CPLEX is installed and loadable as a module, or you could ask your cluster support people if they are able to install CPLEX on the cluster for you. Alternatively you could try using the gurobi solver instead of CPLEX, as discussed in this issue from the CarveMe repository, although I have never tried using gurobi with CarveMe and it seems like it may not give you the same results.

[ShailNair]

Thanks. unfortunately, CPLEX isnt installed on my lab server. I did manage to get gurobi solver license. So if am not wrong,
I followed the manual method:
i first create conda enve and install metaGEM
already have metawrap (with CheckM)
create and install prokka-roary

Activate metagem env. and install gurobi solver.

Is that correct?

[franciscozorrilla]

Glad you could get the gurobi solver. Your installation procedure sounds correct to me, although you do not need the prokka-roary environment to run CarveMe. Try activating the metagem environment and run the command carve to check if CarveMe is installed successfully able to locate/use the gurobi solver. If you dont get any errors then you can try running CarveMe on a test MAG to see if it generates a model successfully:

carve -g M3 -v --mediadb /path/to/media_db.tsv --fbc2 -o test_MAG_output.xml test_MAG_input.faa

If you cloned the github repo then the media_db file should be under the Scripts folder. M3 is complete media, but you can use any media in the database or even create your own custom media based on BiGG metabolite IDs.

[ShailNair]

CarveMe cannot locate the gurobi solver and throws error saying Solver cplex not available

carve -g M3 -v --mediadb /home/mcs/soft/metaGEM/Scripts/media_db.tsv --fbc2 -o /home/mcs/miniconda3/envs/metagem/test_MAG_output.xml /home/mcs/miniconda3/envs/metagem/SN_MAG_00001-contigs.faa
Traceback (most recent call last):
File "/home/mcs/.local/bin/carve", line 5, in
from carveme.cli.carve import main
File "/home/mcs/.local/lib/python3.8/site-packages/carveme/init.py", line 14, in
set_default_solver(config.get('solver', 'default_solver'))
File "/home/mcs/.local/lib/python3.8/site-packages/reframed/solvers/init.py", line 60, in set_default_solver
raise RuntimeError(f"Solver {solvername} not available.")
RuntimeError: Solver cplex not available.

[kunaljaani]

Hi!

I could see the installed version of the cplex but still I am getting the "Solver cplex not available" error.

ubuntu@kv-metagenome:/DATA/janik/metaGEM$ python -c 'import cplex; print(cplex.version)'
20.1.0.0

Creating temporary directory /DATA/janik/metaGEM/SCRATCH/GEMs/M_bin.19.p ...
Begin carving GEM ...
Traceback (most recent call last):
File "/home/ubuntu/.local/bin/carve", line 5, in
from carveme.cli.carve import main
File "/home/ubuntu/.local/lib/python3.8/site-packages/carveme/init.py", line 14, in
set_default_solver(config.get('solver', 'default_solver'))
File "/home/ubuntu/.local/lib/python3.8/site-packages/reframed/solvers/init.py", line 60, in set_default_solver
raise RuntimeError(f"Solver {solvername} not available.")
RuntimeError: Solver cplex not available.

could you please suggest some fix.

Thanks a lot.
Kunal

[franciscozorrilla]

Hi Kunal,

Regarding your first comment:

smetanaSolver: /opt/gurobi/linux64 in the metagem config.yaml is correct?

No, this config parameter is a string that gets passed to the SMETANA call (see SMETANA documentation), it should not be a path to your solver. As you can see here, the allowable options are cplex or gurobi.

Regarding your second comment:

RuntimeError: Solver cplex not available.

After installing CPLEX, have you also installed the CPLEX python API as described in the CarveMe documentation?

I hope this helps!

Best wishes,
Francisco

[kunaljaani]

Hi Francisco,

Thanks a lot for your input and clarification. I will make the suggested changes.

Thanks again for your time.
Kunal

[kunaljaani]

#UPDATE

Hi Francisco,

Thank you very much for your help. It finally worked!
After installing an academic version of CPLEX followed the steps for CPLEX python API.

ubuntu@#####:$ cd /opt/ibm/ILOG/CPLEX_Studio201/cplex/python/3.8/x86-64_linux/
ubuntu@#####:$ python setup.py install
ubuntu@#####:$ python setup.py install --home /home/ubuntu/.local/lib/python3.8/site-packages/cplex
ubuntu@#####:$ export PYTHONPATH=/opt/ibm/ILOG/CPLEX_Studio201/cplex/python/3.8/x86-64_linux

Thanks again!
Kunal

[LiZhihua1982]

Hi Francisco,
(metagem) lizhihua@lizhihua-T640:/opt/ibm/ILOG/CPLEX_Studio201/cplex/python/3.8/x86-64_linux$ sudo python setup.py install
[sudo] password for lizhihua:
Traceback (most recent call last):
File "setup.py", line 91, in
main()
File "setup.py", line 72, in main
check_version()
File "setup.py", line 49, in check_version
expected_major, expected_minor, actual_major, actual_minor))
Exception: this 'cplex' package (version 20.1.0.0) is not compatible with this version of Python: expected 3.8 but got 2.7
(metagem) lizhihua@lizhihua-T640:/opt/ibm/ILOG/CPLEX_Studio201/cplex/python/3.7/x86-64_linux$ sudo python setup.py install
Traceback (most recent call last):
File "setup.py", line 91, in
main()
File "setup.py", line 72, in main
check_version()
File "setup.py", line 49, in check_version
expected_major, expected_minor, actual_major, actual_minor))
Exception: this 'cplex' package (version 20.1.0.0) is not compatible with this version of Python: expected 3.7 but got 2.7

This seems we need python 2.7

(metagem) lizhihua@lizhihua-T640:/opt/ibm/ILOG/CPLEX_Studio129/cplex/python/2.7/x86-64_linux$ sudo python2 setup.py install
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/cplex
copying cplex/model_info.py -> build/lib.linux-x86_64-2.7/cplex
copying cplex/paramset.py -> build/lib.linux-x86_64-2.7/cplex
copying cplex/callbacks.py -> build/lib.linux-x86_64-2.7/cplex
copying cplex/six.py -> build/lib.linux-x86_64-2.7/cplex
copying cplex/aborter.py -> build/lib.linux-x86_64-2.7/cplex
copying cplex/init.py -> build/lib.linux-x86_64-2.7/cplex
creating build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_parameters_auto.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_matrices.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_constantsenum.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_pycplex_platform.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_procedural.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_subinterfaces.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_list_array_utils.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_solutionstrategyenum.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_aux_functions.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_callbackinfoenum.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_multiobjsoln.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_pycplex.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_pwl.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_ostream.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_anno.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_constants.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_parameter_hierarchy.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_baseinterface.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_parameter_classes.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/_multiobj.py -> build/lib.linux-x86_64-2.7/cplex/_internal
copying cplex/_internal/init.py -> build/lib.linux-x86_64-2.7/cplex/_internal
creating build/lib.linux-x86_64-2.7/cplex/exceptions
copying cplex/exceptions/errors.py -> build/lib.linux-x86_64-2.7/cplex/exceptions
copying cplex/exceptions/error_codes.py -> build/lib.linux-x86_64-2.7/cplex/exceptions
copying cplex/exceptions/init.py -> build/lib.linux-x86_64-2.7/cplex/exceptions
copying cplex/_internal/py27_cplex1290.so -> build/lib.linux-x86_64-2.7/cplex/_internal
running install_lib
creating /usr/local/lib/python2.7/dist-packages/cplex
copying build/lib.linux-x86_64-2.7/cplex/model_info.py -> /usr/local/lib/python2.7/dist-packages/cplex
copying build/lib.linux-x86_64-2.7/cplex/paramset.py -> /usr/local/lib/python2.7/dist-packages/cplex
creating /usr/local/lib/python2.7/dist-packages/cplex/exceptions
copying build/lib.linux-x86_64-2.7/cplex/exceptions/errors.py -> /usr/local/lib/python2.7/dist-packages/cplex/exceptions
copying build/lib.linux-x86_64-2.7/cplex/exceptions/error_codes.py -> /usr/local/lib/python2.7/dist-packages/cplex/exceptions
copying build/lib.linux-x86_64-2.7/cplex/exceptions/init.py -> /usr/local/lib/python2.7/dist-packages/cplex/exceptions
copying build/lib.linux-x86_64-2.7/cplex/callbacks.py -> /usr/local/lib/python2.7/dist-packages/cplex
copying build/lib.linux-x86_64-2.7/cplex/six.py -> /usr/local/lib/python2.7/dist-packages/cplex
copying build/lib.linux-x86_64-2.7/cplex/aborter.py -> /usr/local/lib/python2.7/dist-packages/cplex
copying build/lib.linux-x86_64-2.7/cplex/init.py -> /usr/local/lib/python2.7/dist-packages/cplex
creating /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_parameters_auto.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_matrices.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_constantsenum.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_pycplex_platform.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_procedural.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_subinterfaces.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_list_array_utils.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_solutionstrategyenum.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_aux_functions.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_callbackinfoenum.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_multiobjsoln.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_pycplex.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/py27_cplex1290.so -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_pwl.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_ostream.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_anno.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_constants.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_parameter_hierarchy.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_baseinterface.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_parameter_classes.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/_multiobj.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
copying build/lib.linux-x86_64-2.7/cplex/_internal/init.py -> /usr/local/lib/python2.7/dist-packages/cplex/_internal
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/model_info.py to model_info.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/paramset.py to paramset.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/exceptions/errors.py to errors.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/exceptions/error_codes.py to error_codes.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/exceptions/init.py to init.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/callbacks.py to callbacks.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/six.py to six.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/aborter.py to aborter.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/init.py to init.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_parameters_auto.py to _parameters_auto.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_matrices.py to _matrices.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_constantsenum.py to _constantsenum.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_pycplex_platform.py to _pycplex_platform.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_procedural.py to _procedural.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_subinterfaces.py to _subinterfaces.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_list_array_utils.py to _list_array_utils.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_solutionstrategyenum.py to _solutionstrategyenum.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_aux_functions.py to _aux_functions.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_callbackinfoenum.py to _callbackinfoenum.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_multiobjsoln.py to _multiobjsoln.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_pycplex.py to _pycplex.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_pwl.py to _pwl.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_ostream.py to _ostream.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_anno.py to _anno.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_constants.py to _constants.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_parameter_hierarchy.py to _parameter_hierarchy.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_baseinterface.py to _baseinterface.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_parameter_classes.py to _parameter_classes.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/_multiobj.py to _multiobj.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/cplex/_internal/init.py to init.pyc
running install_egg_info
Writing /usr/local/lib/python2.7/dist-packages/cplex-12.9.0.0.egg-info
It is OK, however,
(metagem) lizhihua@lizhihua-T640:/opt/ibm/ILOG/CPLEX_Studio129/cplex/python/2.7/x86-64_linux$ carve
Traceback (most recent call last):
File "/home/lizhihua/.local/bin/carve", line 5, in
from carveme.cli.carve import main
File "/home/lizhihua/.local/lib/python3.8/site-packages/carveme/init.py", line 14, in
set_default_solver(config.get('solver', 'default_solver'))
File "/home/lizhihua/.local/lib/python3.8/site-packages/reframed/solvers/init.py", line 60, in set_default_solver
raise RuntimeError(f"Solver {solvername} not available.")
RuntimeError: Solver cplex not available.

Would you help me? Thank you!

[ShailNair]

It worked after changing the default solver to gurobi in CarveME config.cfg file. the output is a .tsv file and an XML file. How to visualize this data into a graphical model.

SN_MAG_00001-contigs.tsv.txt
test_MAG_output.xml.txt

what is --fbc2 in the above carve command?
Is Species metabolic coupling analysis with SMETANA which is mentioned as [in progress] ready to be used?

Similarly, how to build a custom media_db.tsv file (for say I want to construct a model outputting ammonia production and the associated organisms within the metagenome)

[franciscozorrilla]

Good to hear that you are able to get CarveMe running. The tsv file you can ignore as it is an intermediate file, your output model is the .xml file.

How to visualize this data into a graphical model.

Since metaGEM is designed to reconstruct thousands of genome scale metabolic models from metagenomes I did not include any visualization of individual models. Instead, after generating many models you can run the bash metaGEM.sh -t modelVis command to get an overall idea of the distribution of genes, reactions, and metabolites (see unseenbio demo section 7). Beware that this command works under the assumption that your models are labeled according to the following scheme: {sampleID}_{binNumber}.xml. You could also create a summary file with number of metabolites, number of reactions, and number of genes by running the following bash code (taken from modelVis Snakefile rule, see line 1181) from within the folder where your models are stored and assuming that they end with the .xml extension:

while read model;do
    id=$(echo $(basename $model)|sed 's/.xml//g');
    mets=$(less $model| grep "species id="|cut -d ' ' -f 8|sed 's/..$//g'|sort|uniq|wc -l);
    rxns=$(less $model|grep -c 'reaction id=');
    genes=$(less $model|grep 'fbc:geneProduct fbc:id='|grep -vic spontaneous);
    echo "Model: $id has $mets mets, $rxns reactions, and $genes genes ... "
    echo "$id $mets $rxns $genes" >> GEMs.stats;
done< <(find . -name "*.xml")

This should generate the GEMs.stats file, which you can visualize yourself or using the modelVis.R script.

For quick individual model visualization I can recommend the fluxer webtool. You may also find the memote webtool useful for quick inspection of individual models.

what is --fbc2 in the above carve command?

As described in the documentation, the --fbc2 flag tells CarveMe to output the model in sbml fbc2 (flux balance constraint v2) instead of using the default old COBRA format.

Is Species metabolic coupling analysis with SMETANA which is mentioned as [in progress] ready to be used?

Yes, SMETANA is already implemented into the metaGEM workflow, the [in progress] refers only to the unseen bio demonstration results which I plan to finish soon. Beware that SMETANA also uses the CPLEX solver by default, but you may be able to use the gurobi sovler by setting the --solver flag as described in the documentation.

how to build a custom media_db.tsv file

I have not tried creating my own media recipes yet, and this is something you will need to do manually. For example if you want to create a new medium called M42 with metabolites leucine, glucose, and tryptophan then you would add to the end of the media_db.tsv file the following lines:

M42	M42	leu__L	leu__L
M42	M42	glc__D	glc__D
M42	M42	trp__L	trp__L

[ShailNair]

Thanks. I tried a single model with fluxer and it works nicely. will try modelvis once I run the pipeline on all MAGs.

You said the M3 is a complete media, does it mean that it encompasses all the metabolic reactions of prokaryotes?
What is the cut off for assigning a metabolite to a protein. I see in the intermediate TSV file different protein are assigned to a metabolite/reaction at different cut-off.

[franciscozorrilla]

You said the M3 is a complete media, does it mean that it encompasses all the metabolic reactions of prokaryotes?

I am not sure what you mean by encompassing all metabolic reactions of prokaryotes. If you mean that this media should support the growth of prokaryotes then yes, although there are of course prokaryotes that are not presently cultivable due to unknown growth conditions/physiology. You can look into the media_db.tsv file and search for M3 to see which metabolites are present, and to get an overview of what is in M3 you can also look at Fig. 1 panel D of this paper:

What is the cut off for assigning a metabolite to a protein?

Since I am not intimately familiar with the implementation details I encourage you to look at the methods/supplementary sections of the CarveMe paper.

Sorry for the late response, hope it helps!

[franciscozorrilla]

Closing this due to lack of activity but please re-open if you have any follow up questions.
Best,
Francisco

[LiZhihua1982]

Hi,It seems I have installed the cplex,but "RuntimeError: Solver cplex not available."
(metagem) lizhihua@lizhihua-T640:/media/lizhihua/software/metaGEM_tem/GEMs/GJ2_bin.10.s$ carve
Traceback (most recent call last):
File "/home/lizhihua/.local/bin/carve", line 5, in
from carveme.cli.carve import main
File "/home/lizhihua/.local/lib/python3.8/site-packages/carveme/init.py", line 14, in
set_default_solver(config.get('solver', 'default_solver'))
File "/home/lizhihua/.local/lib/python3.8/site-packages/reframed/solvers/init.py", line 60, in set_default_solver
raise RuntimeError(f"Solver {solvername} not available.")
RuntimeError: Solver cplex not available.
It seems I have installed the cplex as below:

---

Tue Nov 29 05:55:12 CST 2022

Free Memory: 6343 kB
Total Memory: 25472 kB

2 Command Line Args:
0: -m
1: CONSOLE

java.class.path:
/tmp/install.dir.22111/InstallerData
/tmp/install.dir.22111/InstallerData/installer.zip

ZGUtil.CLASS_PATH:
/tmp/install.dir.22111/InstallerData
/tmp/install.dir.22111/InstallerData/installer.zip

sun.boot.class.path:
/tmp/install.dir.22111/Linux/resource/jre/lib/amd64/compressedrefs/jclSC180/vm.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/se-service.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/cuda4j.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/math.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmorb.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmorbapi.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmcfw.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmpkcs.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmcertpathfw.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmjgssfw.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmjssefw.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmsaslfw.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmjcefw.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmjgssprovider.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmjsseprovider2.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/ibmcertpathprovider.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/xmldsigfw.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/xml.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/charsets.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/resources.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/rt.jar
/tmp/install.dir.22111/Linux/resource/jre/lib/dataaccess.jar

java.ext.dirs:
/tmp/install.dir.22111/Linux/resource/jre/lib/ext

java.version == 1.8.0_144 (Java 1)
java.vm.name == IBM J9 VM
java.vm.vendor == IBM Corporation
java.vm.version == 2.9
java.vm.specification.name == Java Virtual Machine Specification
java.vm.specification.vendor == Oracle Corporation
java.vm.specification.version == 1.8
java.specification.name == Java Platform API Specification
java.specification.vendor == Oracle Corporation
java.specification.version == 1.8
java.vendor == IBM Corporation
java.vendor.url == http://www.ibm.com/
java.class.version == 52.0
java.library.path == /tmp/install.dir.22111/Linux/resource/jre/lib/amd64/compressedrefs:/tmp/install.dir.22111/Linux/resource/jre/lib/amd64:/usr/lib64:/usr/lib
java.compiler == j9jit29
java.home == /tmp/install.dir.22111/Linux/resource/jre
java.io.tmpdir == /tmp
os.name == Linux
os.arch == amd64
os.version == 4.15.0-197-generic
path.separator == :
file.separator == /
file.encoding == UTF-8
user.name == root
user.home == /root
user.dir == /tmp/install.dir.22111
user.language == en
user.region == null

---

Installed Feature(s) Application, Help of IBM ILOG CPLEX Enterprise Server 12.8.0

Install Begin: NOVEMBER 29, 2022 5:49:23 PM CST
Install End: NOVEMBER 29, 2022 5:50:28 PM CST

Installed by InstallAnywhere 18.0 Premier Build 5608

User Interactions

#Indicate whether the license agreement been accepted
#----------------------------------------------------
LICENSE_ACCEPTED=TRUE

#Choose Install Folder
#---------------------
USER_INSTALL_DIR=/media/lizhihua/software/metaGEM/envs/metagem/bin

#Install
#-------
-fileOverwrite_/media/lizhihua/software/metaGEM/envs/metagem/bin/README.html=Yes
-fileOverwrite_/media/lizhihua/software/metaGEM/envs/metagem/bin/REDIST.txt=Yes
-fileOverwrite_/media/lizhihua/software/metaGEM/envs/metagem/bin/Uninstall/Uninstall.lax=Yes
-fileOverwrite_/media/lizhihua/software/metaGEM/envs/metagem/bin/Uninstall/symlinks-aix-ppc64.sh=Yes
-fileOverwrite_/media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Studio/README.html=Yes

Summary

Installation: Successful null

223 Successes
1 Warnings
0 NonFatalErrors
0 FatalErrors

Action Notes:

None

Install Log Detail:

Check Disk Space: /opt/IBM/ILOG/CPLEX_Enterprise_Server128
Status: SUCCESSFUL
Additional Notes: NOTE - Required Disk Space:1,982,442,639 Bytes Free Disk Space:417,136,685,056 Bytes

Check Disk Space: /opt/ibm/ILOG/CPLEX_Enterprise_Server128
Status: SUCCESSFUL
Additional Notes: NOTE - Required Disk Space:1,982,442,639 Bytes Free Disk Space:417,136,709,632 Bytes

Check Disk Space: /media/lizhihua/software/metaGEM/envs/metagem/bin
Status: SUCCESSFUL
Additional Notes: NOTE - Required Disk Space:1,982,442,639 Bytes Free Disk Space:417,136,693,248 Bytes

Check Disk Space: /media/lizhihua/software/metaGEM/envs/metagem/bin
Status: SUCCESSFUL
Additional Notes: NOTE - Required Disk Space:1,982,442,639 Bytes Free Disk Space:417,136,693,248 Bytes

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/
Status: SUCCESSFUL
Additional Notes: NOTE - Directory already existed

Custom Action: com.ibm.lex.lap.ia.LAFiles_IA
Status: SUCCESSFUL

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/license/
Status: SUCCESSFUL
Additional Notes: NOTE - Directory already existed

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/license/notices.txt
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/README.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/REDIST.txt
Status: SUCCESSFUL

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/README/
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/README/README_de.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/README/README_en.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/README/README_es.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/README/README_fr.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/README/README_ja.html
Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/README/README_pt_BR.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/README/README_ru.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/README/README_tr.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/README/README_zh_CN.html
Status: SUCCESSFUL

Copy File: Destination: /media/lizhihua/software/metaGEM/envs/metagem/bin/README_en.html
Status: SUCCESSFUL

Delete Folder: Source:README
Status: SUCCESSFUL

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/Uninstall/
Status: SUCCESSFUL
Additional Notes: NOTE - Directory already existed

Install Uninstaller: IBM ILOG CPLEX Enterprise Server 12.8.0(Install All Uninstaller Components)
Status: SUCCESSFUL

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/jre
Status: SUCCESSFUL
Additional Notes: NOTE - Directory already existed

Install JRE: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/jre
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/Uninstall/Uninstall.lax
Status: SUCCESSFUL

Install Uninstaller: IBM ILOG CPLEX Enterprise Server 12.8.0(Install All Uninstaller Components)
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/Uninstall/symlinks-aix-ppc64.sh
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/swidtag/ibm.com_IBM_ILOG_CPLEX_Enterprise_Server-12.8.0.swidtag
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/swidtag/ILMT/Tags.zip
Status: SUCCESSFUL

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/
Status: SUCCESSFUL
Additional Notes: NOTE - Directory already existed

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/
Status: SUCCESSFUL
Additional Notes: NOTE - Directory already existed

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/allclasses-frame.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/allclasses-noframe.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/Application.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/CplexServer.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/CplexServerFactory.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/ApplicationAlreadyDeployedException.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/ArchiveNotDeployedException.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/ForbiddenException.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/IllegalJobStatusException.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/NotValidProjectException.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/package-frame.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/package-summary.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/package-tree.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/ServerConnectionException.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/UnknownJobAttachmentException.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/exception/UnknownJobException.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/Job.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/Job.LogType.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/Job.Status.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/JobSummary.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/CumulFunction.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Element.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Element.Type.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/exception/ObjectiveValueNotAvailableException.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/exception/package-frame.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/exception/package-summary.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/exception/package-tree.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Function.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Interval.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Map.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/package-frame.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/package-summary.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/package-tree.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Range.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Sequence.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Set.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Solution.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Solution.Type.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/StateFunction.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/opl/element/Tuple.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/OplApplicationPackager.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/package-frame.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/package-summary.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/package-tree.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/com/ibm/ilog/optim/server/client/Result.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/constant-values.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/deprecated-list.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/help-doc.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/index-all.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/index.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/overview-frame.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/overview-summary.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/overview-tree.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/package-list
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/resources/background.gif
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/resources/tab.gif
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/resources/titlebar.gif
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/resources/titlebar_end.gif
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/serialized-form.html
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/doc/en-US/html/stylesheet.css
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/examples/build.xml
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/examples/src/com/ibm/ilog/optim/server/client/OplCplexServer/OplCplexServer.java
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/examples/src/com/ibm/ilog/optim/server/client/OplCPServer/OplCPServer.java
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/lib/axis2-client.jar
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/lib/cplexserver-client.jar
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/lib/icu4j.jar
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/client/lib/lpgruntime.jar
Status: SUCCESSFUL

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/server/
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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/server/doc/en-US/pdf/CPLEX_Enterprise_Server_InstallV12.8.0_Installation_Guide.pdf
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/server/ears/cplexserver-processor-ear-x86-64_linux.ear
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/server/ears/odme-application-mgmt-ear.ear
Status: SUCCESSFUL

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server/server/ears/optimserver-mgmt-ear-x86-64_linux.ear
Status: SUCCESSFUL

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Studio/
Status: SUCCESSFUL
Additional Notes: NOTE - Directory already existed

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Studio/doc/
Status: SUCCESSFUL
Additional Notes: NOTE - Directory already existed

Install File: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Studio/README.html
Status: SUCCESSFUL

Install Directory: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Studio/README/
Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

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Status: SUCCESSFUL

Copy File: Destination: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Studio/README_en.html
Status: SUCCESSFUL

Delete Folder: Source:README
Status: SUCCESSFUL

Copy Folder: Destination: /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Server
Status: WARNING
Additional Notes: WARNING - There was a problem copying /media/lizhihua/software/metaGEM/envs/metagem/bin/CPLEX_Studio/opl/ant

Execute Command: chmod a+x /media/lizhihua/software/metaGEM/envs/metagem/bin//bin//.
Status: SUCCESSFUL

Execute Command: chmod a+x /media/lizhihua/software/metaGEM/envs/metagem/bin//bin//*
Status: SUCCESSFUL

[franciscozorrilla]

Li, please read the discussion above. The solution to your problem is directly answered in this comment, looks like you probably didnt install the CPLEX python api.