[Hello!] L casei 12A.zip

I'm new at MetaDraft. I was trying to build my own template by: 1-convert my SBML level 2 to level 3 FBC v3 2-create a template with a Genbank file + my converted SBML file.

In both of these steps anaconda finds an "Unhandled Python exception" and shuts down MetaDraft. I'm using the anaconda prompt with python v3.8.5. Interestingly, after step 1 I did receive a converted SBML and after step 2 (using the converted SBML from step 1) I received a .xlsx file. However my template is not shown in the "select the target network(s)" window.

Any idea how to solve this? Best,

1st update:the same problem happens with other files. 2nd update: I tried using python 3.6. I then managed to upgrade the sbml version and to build templates, but didn't manage to create metaproteome, python shutted down again. I tried installing python 2.7 and cbmpy 0.7.5 (that only needs biopython 1.7.6., more recent versions would require a more updated python) but then libsbml was missing. I could only install libsbml with "pip install python-libsbml-experimental" .

Now the error is that no QtGui is defined, which I solved by installing PyQT4. However then there is a conflict with PyQT5, which makes me think that the QtGui was not missing. Any ideas how to proceed?

Hi,

While trying to run metadraft.py after okay from systemtest.py i got the message: '2' after showing the icon, this was while running on python 2.7 using PyQt4. I did update to PyQt5, however I then got an error message showing that no module named sip was available, this module dropped support for python versions below v3.5 as stated on their website.

Kind regards, Bas

Edit: i also get the 2 using python 3.5

Hi!

I'm trying to build a template model using Trypanosoma cruzi. However, I'm gettin an error:
NITDB: connecting geneDB INITDB: connecting notesDB [('iIS312', 'iIS312.gbff', 'iIS312.xml')] /media/alexranieri/Data/Trypanosoma/metadraft/Tbrucei/reference_model /media/alexranieri/Data/Trypanosoma/metadraft/Tbrucei/reference_model Processing: iIS312 iIS312.gbff iIS312.xml INITDB: connecting geneDB INFO: addGeneInformationToDB committed 0 new records FBC version: 2 M.getNumReactions: 519 M.getNumSpecies: 606 FBC.getNumObjectives: 1 FBC.getNumParameters: 3 FBC.getNumGeneProducts: 312 Zero dimension compartment detected: c Zero dimension compartment detected: e Zero dimension compartment detected: x Zero dimension compartment detected: m Zero dimension compartment detected: n Zero dimension compartment detected: r FluxBounds process1: 0.01 INFO: Active objective: obj Adding objective: obj FluxBounds process2: 0.01

SBML3 load time: 0.57

CheckModelLocusTags is processing: /media/alexranieri/Data/Trypanosoma/metadraft/Tbrucei/reference_model/iIS312.gbff INFO: Multiple sequences encountered in file: /media/alexranieri/Data/Trypanosoma/metadraft/Tbrucei/reference_model/iIS312.gbff Traceback (most recent call last): File "/home/alexranieri/metadraft/cbmpy-metadraft/libpython/qtmetadraft.py", line 1615, in bp_createSeqPlusProcess compress_output=self.CREATE_TEMPLATE_ZIP) File "/home/alexranieri/metadraft/cbmpy-metadraft/libpython/biotools.py", line 946, in createSeqplusModel ) = checkModelLocusTags(fmod, fgb) File "/home/alexranieri/metadraft/cbmpy-metadraft/libpython/biotools.py", line 215, in checkModelLocusTags 'isDescribedBy', 'PubMed', r_.pubmed_id File "/home/alexranieri/anaconda3/envs/metadraft3/lib/python3.7/site-packages/cbmpy/CBModel.py", line 771, in addMIRIAMannotation self.miriam.addMIRIAMannotation(qual, entity, mid) File "/home/alexranieri/anaconda3/envs/metadraft3/lib/python3.7/site-packages/cbmpy/CBDataStruct.py", line 380, in addMIRIAMannotation if self.checkId(E, mid): File "/home/alexranieri/anaconda3/envs/metadraft3/lib/python3.7/site-packages/cbmpy/CBDataStruct.py", line 333, in checkId if self.checkEntityPattern(entity): File "/home/alexranieri/anaconda3/envs/metadraft3/lib/python3.7/site-packages/cbmpy/CBDataStruct.py", line 316, in checkEntityPattern if type(self.MIRIAM[entity]['pattern']) == re._pattern_type: AttributeError: module 're' has no attribute '_pattern_type' Aborted (core dumped)

The model I'm using is: http://bigg.ucsd.edu/models/iIS312 And its genbank: https://sra-download.ncbi.nlm.nih.gov/traces/wgs03/wgs_aux/AY/LP/AYLP01/AYLP01.1.gbff.gz

Is it a problem in the model, genbank or both?

I need to look into how complex GPR's are added, also add GPR string as annotation for comparison. Comparative testing using set 3 should get most patterns

Hello,

I'm trying to install and run MetaDraft, I've run the following commands:

$ conda env create -f environment.yml (for installation)

$ conda activate metadraft3

(metadraft3) $ python systemtest.py

Which gives me:

System check results:

Java test passed: True Perl test passed: True Perl XML test passed: True BLAST test passed: True Python dependency test passed: True

Congratulations you are ready to run MetaDraft! (python metadraft.py)

However, when I run:

(metadraft3) $ sh ./run.sh

I get the following error:

Traceback (most recent call last): File "metadraft.py", line 62, in import libpython.qtmetadraft File "/scr/k61san/natasha/matomic/metadraft/cbmpy-metadraft-0.9.5/libpython/qtmetadraft.py", line 40, in import sip ModuleNotFoundError: No module named 'sip'

Even though sip is installed

(metadraft3) $ pip install sip

Requirement already satisfied: sip in /homes/brauerei/natasha/miniconda3/envs/metadraft3/lib/python3.8/site-packages (6.5.1) Requirement already satisfied: setuptools in /homes/brauerei/natasha/miniconda3/envs/metadraft3/lib/python3.8/site-packages (from sip) (60.9.3) Requirement already satisfied: toml in /homes/brauerei/natasha/miniconda3/envs/metadraft3/lib/python3.8/site-packages (from sip) (0.10.2) Requirement already satisfied: packaging in /homes/brauerei/natasha/miniconda3/envs/metadraft3/lib/python3.8/site-packages (from sip) (21.3) Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /homes/brauerei/natasha/miniconda3/envs/metadraft3/lib/python3.8/site-packages (from packaging->sip) (3.0.7)

Please, can you help me? What can I do to run metadraft ?

Thanks in advance

When one follows the installation instructions of the README and tries to run a BLAST, one can end up with messages like this:

Starting first BLAST pass for IN - IN on 05/09/2021sh: 1: blastall: not found

no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110.

Starting second BLAST pass for IN - IN on 
Starting first BLAST pass for IN - DB on 05/09/202105/09/2021sh: 1: blastall: not found

no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110.

Starting second BLAST pass for IN - DB on 
Starting first BLAST pass for DB - IN on 05/09/202105/09/2021sh: 1: blastall: not found

no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110.

Starting second BLAST pass for DB - IN on 
Starting first BLAST pass for DB - DB on 05/09/202105/09/2021sh: 1: blastall: not found

no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110.

On a Linux system, one can easily solve it by installing the missing modules like this:

sudo apt-get install ncbi-blast+-legacy

Might be good to add it to the README (in case I overlooked it somewhere, my apologies for the noise).

I am using the genbank file from here and blast it against the Bigg1 version of Hpylori (just for testing purposes).

I built the metaproteome and then click BLAST. I then get the expected output in the terminal:

2
4278 sequences in file IN
335 sequences in file DB
Trying to run BLAST now - this may take several hours ... or days in worst case!
Formatting BLAST databases


Building a new DB, current time: 05/09/2021 13:45:56
New DB name:   /stuff/cbmpy-metadraft/data_blast/1620560756/IN
New DB title:  IN
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 4278 sequences in 0.0583789 seconds.


Building a new DB, current time: 05/09/2021 13:45:56
New DB name:   /stuff/cbmpy-metadraft/data_blast/1620560756/DB
New DB title:  DB
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 335 sequences in 0.0046699 seconds.
Done formatting
Starting BLAST searches...

Starting first BLAST pass for IN - IN on 05/09/2021Warning: [blastp] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output

Starting second BLAST pass for IN - IN on 05/09/2021

Building a new DB, current time: 05/09/2021 13:47:10
New DB name:   /stuff/cbmpy-metadraft/data_blast/1620560756/tmpd
New DB title:  ./tmpd
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 4 sequences in 0.000277996 seconds.
Warning: [blastp] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output


Building a new DB, current time: 05/09/2021 13:47:10
New DB name:   /stuff/cbmpy-metadraft/data_blast/1620560756/tmpd
New DB title:  ./tmpd
Sequence type: Protein
Deleted existing Protein BLAST database named /stuff/cbmpy-metadraft/data_blast/1620560756/tmpd
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 5 sequences in 0.000389099 seconds.
Warning: [blastp] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output

I get a lot of the messages as shown here starting from the second Blast; is there a way to not show these but only the "important" ones like "Starting second BLAST pass for IN - IN on 05/09/2021" and then - once finished

Output saved to file Output.IN-DB
HTML output saved to orthologs.IN-DB.html
Table output saved to table.IN-DB
mysql output saved to sqltable.IN-DB

The messages inbetween make it hard to follow in which round of blasting metadraft is currently.

Thanks!

I just installed Metadraft following the instructions in the README (on Ubuntu).

When I execute

sh ./run.sh

I receive

Using Qt5 - the next generation
You are using BioPython 1.78
Traceback (most recent call last):
  File "metadraft.py", line 62, in <module>
    import libpython.qtmetadraft
  File "/stuff/cbmpy-metadraft/libpython/qtmetadraft.py", line 169, in <module>
    from . import biotools
  File "/stuff/cbmpy-metadraft/libpython/biotools.py", line 61, in <module>
    import cbmpy
  File "/stuff/anaconda3/envs/metadraft3/lib/python3.7/site-packages/cbmpy/__init__.py", line 48, in <module>
    from . import CBSolver
  File "/stuff/anaconda3/envs/metadraft3/lib/python3.7/site-packages/cbmpy/CBSolver.py", line 40, in <module>
    from . import CBGLPK
  File "/stuff/anaconda3/envs/metadraft3/lib/python3.7/site-packages/cbmpy/CBGLPK.py", line 38, in <module>
    and int(sympy.__version__.split('.')[2]) >= 4
IndexError: list index out of range

Reason is that Sympy 1.8 gets installed, therefore int(sympy.__version__.split('.')[2] is undefined.

A quick fix is to just run

conda install sympy=1.7.1

but I guess ideally it can be solved on code level.