gem-pasteur/macsyfinder

Issues

• [BUG] miscalculation of alignment coverage

  #76 opened 3 months ago by jpjarnoux
  2

• [HELP] unordered vs ordered_replicon with TXSS models and the inter-gene-max-space parameter

  #75 opened 3 months ago by gabepen
  1

• FAA files do not always reflect the real order of the genes

  #64 opened a year ago by najwataib
  2

• [BUG]GA bit thresholds unavailable on profile T6SSiii_tssO/Q. Switch to e-value threshold (-E 0.100000)

  #74 opened 3 months ago by goldenmole1
  4

• [FEAT] New release to fix bugs in package manager installations

  #70 opened 5 months ago by LucasPaoli
  8

• GA score threshold missing in some CasFinder profile [HELP]

  #72 opened 5 months ago by jpjarnoux
  1

• [FEAT] supress duplicated log messages

  #66 opened 5 months ago by bneron
  0

• [BUG]How to get rid of github API throttling？

  #67 opened 5 months ago by Revolution233
  0

• Generating results.macsyfinder.json file for MacSyView!

  #71 opened 5 months ago by NabilAsyraf98
  1

• [BUG] timeout parameter is missing/not povided in parallel_macsyfinder.nf

  #73 opened 5 months ago by bryan-brancotte
  1

• [BUG] `_scan_profiles` strips `h` and `m` from profile name

  #69 opened a year ago by ezherman
  4

• [FEAT] Should we use pyhmmer ?

  #65 opened a year ago by jeanrjc
  3

• [FEAT] Enable MacSyFinder to run on zipped FASTA files

  #63 opened a year ago by saphia
  3

• [HELP] Maxyfinder fails to run

  #68 opened a year ago by sujeetpowar
  3

• Something is wrong with the operation

  #56 opened 2 years ago by tu1120
  5

• [HELP] macsydata install TXSS

  #59 opened 2 years ago by plasminogene
  2

• [BUG] TXSScan + macsyfinder extremely long on some genomes

  #62 opened 2 years ago by NelleV
  0

• [FEAT] Add a `--force` option to remove the folder in which macsyfinder writes results

  #61 opened 2 years ago by NelleV
  0

• [BUG] Macsyfinder with python subprocess kill main process on error

  #60 opened 2 years ago by celliern
  0

• [BUG] test_extract_concurent fail with "cannot join current thread"

  #58 opened 2 years ago by nileshpatra
  3

• Gembase format

  #55 opened 2 years ago by mozammel47
  2

• Whether it is possible to run the singularity version for the Conjugation models?

  #35 opened 2 years ago by biofuture
  3

• Models compatible with version 1

  #37 opened 2 years ago by sarah872
  2

• conda installation?

  #33 opened 2 years ago by cschu
  6

• [HELP] .json file

  #47 opened 2 years ago by cpeduzzi
  1

• [HELP] error when installing models

  #46 opened 2 years ago by schmittel
  3

• [Question] Why using --cpu 0 in hmmer ?

  #54 opened 2 years ago by jeanrjc
  0

• [BUG] MacSyFinder does not deal well when a replicon has a single protein.

  #53 opened 2 years ago by jeanrjc
  5

• [HELP]

  #49 opened 2 years ago by Aluminio-visto
  3

• [HELP] OSError: [Errno 39] Directory not empty when installing models

  #50 opened 2 years ago by ShailNair
  4

• [HELP] Error parsing models

  #52 opened 2 years ago by alexweisberg
  4

• unrecognized argument in test run

  #51 opened 2 years ago by usr2
  1

• Error using the docker gempasteur/macsyfinder:2.0rc7

  #48 opened 3 years ago by yuxiangtan
  10

• how to use models

  #45 opened 3 years ago by bneron
  1

• change genes order in xml definition

  #44 opened 3 years ago by bneron
  2

• How can I get the modle from the macsyfinder v2.0?

  #34 opened 3 years ago by lkj66666
  9

• Problem when running macsyfinder 2.0 for TXSS identification

  #43 opened 3 years ago by zhangyumeng1sjtu
  2

• I can't install macsyfinder(v2.0rcl) sucessfully.

  #36 opened 3 years ago by lkj66666
  8

• crash when no mandatory/accessory/neutral genes are found

  #39 opened 3 years ago by cschu
  4

• FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/share/macsyfinder/data/models'

  #41 opened 3 years ago by dineshkumarsrk
  0

• "summary_best_solution" takes too long for large inputs

  #42 opened 3 years ago by apcamargo
  1

• AttributeError: module 'colorlog' has no attribute 'logging'

  #40 opened 3 years ago by dineshkumarsrk
  2

• Latest colorlog release breaks macsydata on fresh macsyfinder installs

  #38 opened 3 years ago by Alexandre-Herve
  2

• Where can I find the Python3 port

  #29 opened 4 years ago by tillea
  8

• Installation test error.

  #28 opened 4 years ago by OmarCabrero
  0

• Incompatibility with BLAST+ 2.10.0

  #30 opened 4 years ago by ilnamkang
  1

• Proper input format

  #32 opened 4 years ago by liangcmu
  1

• Input sequence

  #31 opened 4 years ago by liangcmu
  1

• sudo python setup.py install: "build/scripts-2.7/macsyview: No such file or directory"

  #27 opened 5 years ago by vbrover
  2

• Cannot install: python error

  #26 opened 5 years ago by vbrover
  1