gbouras13/phold

Issues

• Phold proteins-predict ends prematurely with large input files

  #79 opened a month ago by shiraz-shah
  0

• Core dependencies versions

  #78 opened a month ago by deminatanja
  1

• Stop codons in ORFs

  #77 opened a month ago by deminatanja
  3

• Phage genome annotations for GenBank submission

  #76 opened 2 months ago by vdruelle
  0

• gbk file - 1 nucleotide shift in CDS region printing

  #75 opened 3 months ago by viralnomad
  0

• phold.features.predict_3Di:get_embeddings:592 - prediction has length 0

  #74 opened 3 months ago by mikenada
  9

• ProstT5 issue: iteration over a 0-d array

  #47 opened 6 months ago by vdruelle
  7

• ValueError during Processing Foldseek output

  #42 opened 5 months ago by acvill
  6

• Inquiry on protein annotation

  #54 opened 6 months ago by songmj86
  12

• anti-CRISPR proteins get assigned the phrog cluster "acr" instead of a number

  #71 opened 4 months ago by Fabian-Bastiaanssen
  1

• using phold plot

  #70 opened 4 months ago by r4carson
  1

• [Request] GFF Output

  #69 opened 4 months ago by MJNT1999
  2

• phold memory usage

  #66 opened 5 months ago by shiraz-shah
  6

• long ids > 54 characters in genbank input introduce space

  #67 opened 5 months ago by gbouras13
  0

• PermissionError in `phold plot`

  #36 opened 9 months ago by Ulthran
  6

• `phold proteins-predict` will silently fail if .gbk given as input

  #57 opened 5 months ago by gbouras13
  0

• Add gff output

  #58 opened 5 months ago by gbouras13
  1

• phold.features.predict_3Di:get_embeddings:441 - Using models in half-precision

  #59 opened 5 months ago by emmaosei
  3

• phold run error

  #56 opened 6 months ago by ChaoXianSen
  1

• [BUG] Limit CPU usage for 3Di prediction

  #60 opened 5 months ago by valentynbez
  2

• Error running `phold run` in Colab Notebook

  #55 opened 6 months ago by Noonanav
  3

• models--Rostlab--ProstT5_fp16 error with Downloading

  #43 opened 6 months ago by CynthiaChibani
  3

• phold install gets killed. Manually downloading the ProstT5 database doesn't fix the issue

  #50 opened 6 months ago by LSHillary
  2

• Add .cif support to Phold

  #48 opened 6 months ago by gbouras13
  0

• Foldseek Version checking -

  #39 opened 6 months ago by gbouras13
  1

• Running Phold offline

  #44 opened 6 months ago by aponsero
  3

• Phold crashes when the start position is 0

  #49 opened 6 months ago by konstytucja
  2

• Problem with using custom phold database

  #45 opened 6 months ago by rozwalak
  0

• KeyError when analyzing pharokka output

  #41 opened 7 months ago by mesti90
  2

• OSError on phold install

  #40 opened 8 months ago by jonbakerlab
  5

• ValueError: Columns must be same length as key

  #37 opened 9 months ago by kayanac
  7

• Questions regarding the proper use of phold

  #33 opened 9 months ago by bhagavadgitadu22
  3

• KeyError: 'transl_table' when writing genbank output

  #31 opened 9 months ago by btemperton
  2

• Add opacity for probabilistic annotation

  #22 opened 10 months ago by gbouras13
  0