gbouras13/pharokka

Issues

• Add validation if out directory exists

  #271 opened a year ago
  1

• Plotter inclusive of AMR genes and VFs?

  #270 opened a year ago
  3

• Fixed GBK translation when non-11 coding tables used

  #268 opened a year ago
  3

• Sequences (contigs) ids should be equal in gff's table and fasta section

  #267 opened a year ago
  2

• MMSeqs2 error on PHROG database

  #266 opened a year ago
  1

• --label_hypotheticals

  #263 opened a year ago
  3

• specify in documentation that --terminase_start requires strand-specific coordinate

  #261 opened 2 years ago
  1

• pharokka_plotter.py v1.3.1 bug

  #255 opened 2 years ago
  1

• Error in tRNAscan-SE step

  #252 opened a year ago
  11

• No *cds_functions.tsv in the output file

  #251 opened 2 years ago
  3

• curl and tar are not in the conda recipe

  #250 opened 2 years ago
  2

• Adding custom databases

  #249 opened a year ago
  3

• Phanotate does not work properly

  #244 opened 2 years ago
  3

• empty VFDB and CARD counts in functions.tsv despite hits to both in top_hits_[].tsv

  #243 opened 2 years ago
  3

• Add error checking to threads - ensure an integer is passed

  #242 opened 2 years ago
  2

• Pharokka Database Install Failed.

  #241 opened 2 years ago
  3

• pharokka's default mash version error

  #240 opened 2 years ago
  2

• Issue with PHAROKKA 1.1.0 or 1.2.0 intsallation

  #238 opened 2 years ago
  4

• Add pharokka as a toot to galaxy

  #237 opened a year ago
  2

• Problems using the database.

  #236 opened 2 years ago
  1

• Running crashed due to ""IndexError: list index out of range"

  #235 opened a year ago
  20

• add circular plot for single phage contigs

  #230 opened 2 years ago
  2

• Replace Prodigal with Pyrodigal

  #228 opened 2 years ago
  1

• If the contig header is an integer - leads to 0's in pharokka_cds_functions.tsv

  #224 opened 2 years ago
  0

• MMseqs2 v 14-7e284 Error - Pharokka Hanging at database steps.

  #222 opened 2 years ago
  1

• pharokka.tbl files are empty for conda install v1.0.0

  #204 opened 2 years ago
  3

• ModuleNotFoundError: No module named 'Bio'

  #200 opened 2 years ago
  7

• Add Module to Check Databases Installed upon running Pharokka

  #199 opened 2 years ago
  1

• Other features to add

  #186 opened 2 years ago
  1

• documentation of use

  #184 opened 2 years ago
  0

• Pharokka crashes if no mmseqs2 matches found

  #179 opened 2 years ago
  1

• Bug in tmRNA output processing

  #178 opened 2 years ago
  0

• [hhsuite] cluster consensus error

  #149 opened 2 years ago
  6

• No trna scans in pharokka_cds_functions.tsv but tRNAs found in the off

  #141 opened 2 years ago
  0

• An error after proccesing after processing hhsuite

  #140 opened 2 years ago
  4

• Add prodigal as a gene prediction option

  #135 opened 3 years ago
  0

• Add locus tag option

  #127 opened 3 years ago
  0

• Conversion to string failed - and a couple of additional observation.

  #122 opened 3 years ago
  2

• some gff genes are blank

  #120 opened 2 years ago
  1

• Phrokka gff contig name

  #103 opened 2 years ago
  1

• phrokka

  #102 opened 3 years ago
  1

• Phrokka Error in post_processing

  #101 opened 3 years ago
  0

• Phrokka Databases Don't Download

  #100 opened 3 years ago
  0

• add --prefix

  #95 opened 3 years ago
  1

• phrokka thread usage

  #91 opened 3 years ago
  0

• trnascan-SE pseudogene

  #90 opened 3 years ago
  0

• Long fasta headers raise errors

  #89 opened 3 years ago
  2

• Initial Update

  #1 opened 3 years ago
  1