biobakery/phylophlan

Issues

• FastTreeMP returned non-zero exit status 1.

  #102 opened 2 years ago by gabridinosauro
  8

• What is the difference between "phylophlan" database and "SGB.XXX"?

  #116 opened a year ago by augfranco93
  2

• no inputs found, please check your params and inputs file extensions error

  #78 opened 3 years ago by nishu92
  8

• RAxML can't parse alignments for which there are sequences made entirely of undetermined characters

  #113 opened 2 years ago by RyanCook94
  1

• Phylophlan Error

  #103 opened 2 years ago by afedynak
  3

• Running partial workflow

  #121 opened a year ago by AroneyS
  1

• Trouble running example 2 - Tree of Life

  #120 opened a year ago by sierra-smith
  0

• The generated phylogenetic tree is missing MAGs at the leaf nodes.

  #119 opened a year ago by ylei14
  0

• Reducing number of RAxML threads to 20, as it appears to underperform with more threads

  #117 opened a year ago by ylei14
  2

• broken link on wiki

  #118 opened a year ago by jorondo1
  0

• Where are the bootstrap values in RAxML trees?

  #70 opened 3 years ago by liuyuwen1
  2

• [e] gene_markers_identification crashed

  #115 opened a year ago by kaw97
  1

• Mapping with Diamond v2 seems slow

  #110 opened 2 years ago by ganiatgithub
  1

• Can not download the phylophlan database

  #114 opened a year ago by jiaojiaoguan
  0

• Does Phylophlan support genome multiple alignment of samples as multiple contigs?

  #86 opened 2 years ago by ne1al
  3

• phylophlan_metagenomic.py - offline usage

  #112 opened 2 years ago by fahad3li
  1

• UnboundLocalError: cannot access local variable 'uniprotkb2uniref90' where it is not associated with a value

  #111 opened 2 years ago by chennyhui
  0

• Restart from checkpoint function available

  #107 opened 2 years ago by ganiatgithub
  1

• [e] No alignments found to concatenate

  #104 opened 2 years ago by jwkkang
  1

• RAxML bad base

  #91 opened 3 years ago by nicholascdove
  6

• maybee update taxa2core_cpa* to recent uniprot release

  #109 opened 2 years ago by EricDeveaud
  0

• Diamond error

  #79 opened 3 years ago by LisaCarraro
  5

• [BUG] `phylophlan_configs` folder does not exists

  #73 opened 3 years ago by Mxrcon
  18

• How can I use my own database?

  #106 opened 2 years ago by EdderDaniel
  2

• [e] mapping file (--maas) not specified

  #105 opened 2 years ago by IRSINGH27
  2

• [error] Command: raxmlHPC-PTHREADS-SSE3' returned non-zero exit status 255.

  #77 opened 3 years ago by Jimmyeric94
  5

• Bootstrap error obtained. zsh: killed

  #97 opened 2 years ago by pavlo888
  1

• mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')

  #101 opened 2 years ago by PabloArrow
  1

• Seems unable to find input faa files

  #100 opened 2 years ago by ganiatgithub
  1

• uniprot database differing number of markers

  #93 opened 3 years ago by pavlo888
  4

• Error: returned non-zero exit status 2

  #99 opened 2 years ago by GriffyGe
  1

• set.py long description file name variation

  #95 opened 3 years ago by erinpnewcomer
  1

• UnboundLocalError: local variable 'uniprotkb2uniref90' referenced before assignment

  #98 opened 2 years ago by llk578496
  8

• [Enhancement] Future plans for fungi

  #94 opened 2 years ago by llk578496
  2

• AttributeError: module 'collections' has no attribute 'MutableMapping'

  #96 opened 2 years ago by Guan06
  2

• Error while running S aureus example

  #92 opened 3 years ago by rajneeshdadwal
  1

• Error when running for Enterococcus faecium

  #82 opened 3 years ago by llk578496
  2

• where is the log file

  #90 opened 3 years ago by pavlo888
  3

• Error running Phylophlan

  #88 opened 3 years ago by rybioinf
  3

• The download of reference genomes

  #84 opened 3 years ago by lipumpkin
  2

• Feature proposal: `tqdm` progressbar during execution of `phylophlan`

  #85 opened 3 years ago by valentynbez
  0

• Problem running phylophlan

  #83 opened 3 years ago by itiago
  1

• Strains resolution

  #80 opened 3 years ago by LisaCarraro
  2

• Mutation Rate Table output

  #81 opened 3 years ago by LisaCarraro
  2

• [e] substitution matrix "pfasum60" not found in "phylophlan_substitution_matrices/"

  #76 opened 3 years ago by linss123
  5

• Need help for understanding how phylophlan works

  #75 opened 3 years ago by RunJiaJi
  2

• Can't seem to execute Phylophlan successfully!!

  #74 opened 3 years ago by redekarnr
  8

• number of genomes to download in phylophlan_get_reference

  #72 opened 3 years ago by fancyge
  2

• Generate the same tree

  #71 opened 3 years ago by Biofarmer
  2

• AttributeError: 'NoneType' object has no attribute 'replace'

  #69 opened 4 years ago by TonyMane
  1