gbouras13/pharokka

Issues

• Database issues

  #346 opened 7 months ago by ZoseJapata
  10

• has solved

  #355 opened 6 months ago by ChaoXianSen
  0

• Inquiry on error for running protein annotation

  #354 opened 6 months ago by songmj86
  2

• While using --genbank Pharokka still counts from 0 instead of 1

  #353 opened 6 months ago by konstytucja
  0

• ValueError: invalid literal for int() with base 10: 'Traceback (most recent call last):\n File "/home/resistance/miniconda3/envs/pharokkaENV/bin/phanotate

  #332 opened 6 months ago by yzhong005
  6

• getting consistent error with pharokka_multiplotter

  #337 opened 6 months ago by JEMINA-JOHN
  1

• Issues with pharokka_multiplotter.py: IndexError: index -1 is out of bounds for axis 0 with size 0

  #348 opened 6 months ago by aryehjc
  1

• issues parsing genbank files produced by Pharokka

  #339 opened 6 months ago by vmkhot
  4

• Error with Phanotate (return code 1)

  #350 opened 6 months ago by Norina28
  5

• Google Colab error

  #349 opened 6 months ago by CristianUNR
  3

• pharokka protein crashed after completing mmseqs searches

  #300 opened a year ago by luisalbertoc95
  9

• UnsatisfiableError when installing with conda

  #343 opened 8 months ago by fluhus
  4

• Inquiry on Pharokka

  #342 opened 8 months ago by songmj86
  3

• Libgsl error from mash - cant run

  #341 opened 8 months ago by raw937
  1

• Linear genome plot?

  #338 opened 9 months ago by raw937
  3

• Number-like sequence ID would generate invalid genbank files.

  #334 opened 10 months ago by shenwei356
  1

• question about pharokka_plotter.py and multi-contig .fasta

  #326 opened 10 months ago by nsvarona
  3

• Error with some sequences

  #335 opened 10 months ago by Sudaraka88
  2

• Replace `hmmscan` with `hmmsearch`

  #330 opened a year ago by valentynbez
  0

• Alphabet error while annotating phage

  #331 opened a year ago by Fabian-Bastiaanssen
  1

• Wrong attribute - PyHMMER module

  #328 opened a year ago by valentynbez
  2

• Pharokka stuck at running mmseqs search

  #325 opened a year ago by quocviet0908
  7

• Mash issue in upgrade

  #315 opened a year ago by raw937
  3

• KeyError: 'Name contig'

  #327 opened a year ago by SergeyBaikal
  4

• PHAROKKA introducing dataframe and its dtype into NCBI Feature Table (.tbl) in each Loop.

  #303 opened a year ago by deinotoxazumab
  5

• Missing lot of databases

  #313 opened a year ago by ala98412
  8

• tRNAs are not being included in tbl file.

  #323 opened a year ago by hmontenegro
  1

• pharokka failure due to missing BioPython function

  #320 opened a year ago by leahfa
  6

• External tools Fine parameter tuning

  #299 opened a year ago by iferres
  4

• dropped contigs

  #316 opened a year ago by k6logc
  5

• Prodigal-gv and Prodigal issue

  #317 opened a year ago by raw937
  1

• Cannot get pharokka databases installed

  #304 opened a year ago by Jlee795
  8

• phannote issues?

  #307 opened a year ago by raw937
  2

• Pharokka fails on large dataset

  #308 opened a year ago by nelsonruth11
  4

• Prodigal not working Pharokka v1.4.1

  #314 opened a year ago by raw-lab
  2

• wrong Aragorn version

  #319 opened a year ago by ZaeemBIo
  0

• ERROR | __main__:main:115 - The database directory was unsuccessfully checked. Please run install_databases.py.

  #318 opened a year ago by ZaeemBIo
  0

• Bioconda version is out of date

  #310 opened a year ago by marade
  2

• database links incorrect

  #311 opened a year ago by marade
  2

• database error

  #309 opened a year ago by mengyuan09876
  2

• FR: add a pharokka_plotter.py argument to select the contig to be plotted in case more than one contig in the assembly

  #305 opened a year ago by splaisan
  2

• what gene should we use to put at +1 in a Stx-phage assembly

  #306 opened a year ago by splaisan
  4

• Pharokka fails when contig input file ends in .fa, runs when file ends in .fasta

  #301 opened a year ago by nelsonruth11
  1

• AttributeError: module 'pyrodigal' has no attribute 'OrfFinder'

  #297 opened a year ago by gbouras13
  2

• Quick question

  #285 opened a year ago by r4carson
  2

• Error calling tRNAscan-SE

  #290 opened a year ago by asierFernandezP
  19

• Expanding initial checks for user friendliness

  #293 opened a year ago by thauptfeld
  0

• Pharokka doesn't look for the good file in meta mode

  #286 opened a year ago by rdenise
  3

• VFDB databases are missing

  #291 opened a year ago by sallybyers
  6

• install_databases.py downloads unneeded hidden files

  #274 opened a year ago by jowodo
  2