AuReMe/metage2metabo

Issues

• IScope Issue

  #65 opened 3 months ago by ggmirandac
  2

• M2M workflow and mincom

  #64 opened 4 months ago by ggmirandac
  2

• mpwt could not find the version of Pathway Tools

  #52 opened a year ago by Choaro
  1

• Non optimal powergraph visualisation

  #39 opened 2 years ago by ArnaudBelcour
  2

• UnicodeDecodeError when running m2m_analysis with Singularity

  #25 opened 10 months ago by cfrioux
  2

• "Can't connect to X11 window server using..." m2m_analysis

  #24 opened 10 months ago by cfrioux
  2

• m2m_analysis : ignore unproducible targets

  #23 opened 10 months ago by cfrioux
  3

• m2m_analysis - deal with empty last row when reading taxon_id

  #22 opened 10 months ago by cfrioux
  1

• Create a list of targets for the content of the community metabolic potential

  #21 opened 10 months ago by cfrioux
  3

• Producibility_targets.json does not include essential and alterative symbiont list

  #19 opened 10 months ago by cfrioux
  1

• When using `--pwt-xml`, the xml files extracted from Pathway Tools can be incompatible with python-libsbml.

  #60 opened 10 months ago by ArnaudBelcour
  1

• Producibility_targets file is not created when `m2m mincom` is called

  #20 opened a year ago by cfrioux
  1

• Sanitize use of tarfile extractall.

  #55 opened a year ago by ArnaudBelcour
  1

• Do not allow abbreviation in command arguments.

  #54 opened a year ago by ArnaudBelcour
  1

• Install metage2metabo problem

  #50 opened a year ago by LiZhihua1982
  5

• Individual scopes include seeds even if non producible or absent from the GSMNs

  #53 opened a year ago by cfrioux
  3

• gff file format problem while running m2m recon

  #56 opened a year ago by gpchoupichou
  1

• [Question] Where can I find seed files?

  #48 opened a year ago by jolespin
  4

• No /home/chencong/.ncbirc file, please fix it before using the program

  #47 opened a year ago by ChenCongZ
  5

• How to prepare inputs for metage2metabo

  #51 opened a year ago by LiZhihua1982
  3

• CRITICAL:metage2metabo.m2m.reconstruction:Something went wrong running Pathway Tools. See the log file in /home/chencong/output3/pgdb_log/log_error.txt

  #46 opened 2 years ago by ChenCongZ
  6

• m2m_analysis - deal with powergrasp config file creation when launching multiple runs

  #26 opened 3 years ago by ArnaudBelcour
  0

• A better focus on the host metabolism when a host is provided

  #36 opened 3 years ago by cfrioux
  1

• m2m recon not working with gbff file inputs

  #43 opened 2 years ago by alsmadin01
  4

• Error with analysis graph when using taxon_id

  #45 opened 2 years ago by KDeaton
  5

• Issue with pathway tools API limitation and PGDB entries verification

  #37 opened 2 years ago by Adifo
  4

• m2m_analysis powergraph not working as expected

  #41 opened 2 years ago by alsmadin01
  27

• Compute deadend and orphan metabolites

  #38 opened 2 years ago by ArnaudBelcour
  0

• Multiple errors when running test data

  #35 opened 3 years ago by DafniGi
  7

• I have the following problems when running the t2d_m2m_target_producers.R file:

  #34 opened 3 years ago by ChenCongZ
  8

• A few process questions

  #32 opened 3 years ago by KDeaton
  4

• I'm terribly sorry, but I can't solve it by trying many methods. I'm looking for your help.

  #31 opened 3 years ago by ChenCongZ
  0

• Progress problem

  #30 opened 3 years ago by ChenCongZ
  4

• Error for teste with PathoLogic subprocess, return code: 255

  #13 opened 3 years ago by Lucas-Maciel
  8

• Hi，I'm trying to run your pipeline but I had an error. Do you have any idea how can I solve this? I'm leaving here the input and outputs.Thank you very much

  #29 opened 3 years ago by ChenCongZ
  0

• Hi

  #28 opened 3 years ago by ChenCongZ
  0

• Help with creating seed file

  #18 opened 3 years ago by choon-sim
  4

• Error during recon: XML not well formed

  #17 opened 3 years ago by KDeaton
  2

• Oog.jar no longer available at link

  #14 opened 4 years ago by WShorrock
  4

• New GenBank file format

  #16 opened 3 years ago by KDeaton
  1

• metabolic objective

  #15 opened 4 years ago by choon-sim
  2

• Powergraph labels

  #12 opened 4 years ago by aassie
  3

• Issue during installation with Python 3.8.

  #11 opened 4 years ago by ArnaudBelcour
  1

• KeyError 'Producible' when running test data

  #10 opened 4 years ago by DennyPopp
  5

• Ugly exit when target sbml file has empty metabolites

  #9 opened 4 years ago by cfrioux
  0

• Error running iscope -- Something went wrong running Menetools

  #8 opened 5 years ago by aassie
  14

• Non-caught error in mincom if target sbml is not ok

  #7 opened 5 years ago by cfrioux
  3

• Error with test data.

  #4 opened 5 years ago by ArnaudBelcour
  1

• Singularity recipe uses python3.5 while clyngor requires a more recent version

  #5 opened 5 years ago by cfrioux
  0

• Issue with pyasp.

  #2 opened 6 years ago by ArnaudBelcour
  1