geronimp/graftM

Issues

• Difference between search_otu_table and combined_count_table. Multiple hmm searches.

  #285 opened 2 months ago by robcli
  0

• low number of reads detected

  #284 opened 8 months ago by rzhan186
  0

• An error was found that was difficult to resolve after manually reroot

  #283 opened 9 months ago by Five296
  5

• Issue running graftm create using docker

  #268 opened 4 years ago by erins1
  6

• GraftM graft on big metagenome error

  #277 opened 3 years ago by steff1088
  4

• Getting ZeroDivisionError when running with sample data

  #275 opened 3 years ago by melodymale
  7

• What does 'Root' classification refer to?

  #274 opened 3 years ago by kattweigh
  2

• working with non-gene sequences

  #269 opened 3 years ago by bakeronit
  0

• graftM create failed to root the tree

  #266 opened 4 years ago by x86lu
  9

• error using decoy_database with hmmsearch+diamond

  #267 opened 4 years ago by yboesch
  0

• graftM create error

  #265 opened 4 years ago by adityabandla
  6

• "graftM create" failed with SILVA due to unknown error

  #248 opened 7 years ago by jcmcnch
  13

• Error: TC bit thresholds unavailable on model graftmrzdqhx.aln

  #264 opened 5 years ago by sarah872
  2

• create seems to generate a new HMM even if one is given?

  #177 opened 9 years ago by wwood
  1

• graftM create error while creating package

  #262 opened 5 years ago by ckeuschn
  3

• graft_package_version error on custom GraftM package

  #259 opened 6 years ago by fletchec99
  10

• Can't find FastTreeMP

  #258 opened 6 years ago by alexximalayaunlv
  4

• Combined alignment file intermittently produced

  #254 opened 6 years ago by babakshaban
  15

• search_only mode does not pair reads

  #256 opened 6 years ago by areejalsheikh
  2

• Input Reads or Bins

  #253 opened 6 years ago by colbyga
  3

• KeyError on split sequence?

  #255 opened 6 years ago by maxemil
  0

• LookupError: unknown encoding: utf8

  #252 opened 6 years ago by s4351982
  3

• Install Error using pip install

  #251 opened 6 years ago by colbyga
  0

• graftM create_why error in building tree?

  #249 opened 7 years ago by snmrna
  6

• Missing options on docs for "graft"

  #246 opened 7 years ago by kyclark
  1

• Error with graft command

  #244 opened 7 years ago by SCarrSuperstar
  3

• HMMsearch + DIAMOND

  #236 opened 7 years ago by ljmmm
  3

• Not all temporary files are removed

  #238 opened 7 years ago by wwood
  0

• Cannot specify diamond database when using --search_only option

  #198 opened 7 years ago by geronimp
  3

• graftm tree GreenGenesTaxonomy exceptions are covered up

  #226 opened 7 years ago by wwood
  1

• --reverse help too conservative?

  #163 opened 7 years ago by wwood
  1

• mafft-linsi or similar as default for create alignment

  #218 opened 7 years ago by geronimp
  1

• refactoring of Run

  #199 opened 8 years ago by wwood
  0

• GraftM needs tests for classification

  #200 opened 8 years ago by geronimp
  0

• create does not remove extraneous taxonomy

  #204 opened 8 years ago by wwood
  1

• multijplace

  #211 opened 8 years ago by wwood
  0

• graftm tree decorate not working when given undecorated tree?

  #227 opened 8 years ago by wwood
  0

• taxonomy file empty

  #234 opened 8 years ago by tv195
  0

• rereplication of alignments

  #205 opened 8 years ago by wwood
  1

• logging options repeated in bin/graftM code

  #196 opened 8 years ago by wwood
  0

• taxonomy not extracted correctly from trees with branch lengths?

  #192 opened 8 years ago by wwood
  1

• create chokes when provided an annotated tree and hmm but no alignment

  #191 opened 9 years ago by wwood
  0

• graftm create --graftm_package is a bit picky

  #178 opened 9 years ago by wwood
  1

• Archaea specific models in create

  #186 opened 9 years ago by geronimp
  0

• taxa missing in Krona

  #185 opened 9 years ago by xvazquezc
  2

• resume/continue job

  #182 opened 9 years ago by xvazquezc
  4

• missing output files?

  #184 opened 9 years ago by xvazquezc
  2

• graftm create does not record the taxonomy of sequences that are deduplicated

  #180 opened 9 years ago by wwood
  1

• graftm create --graftm_package TypeError

  #179 opened 9 years ago by wwood
  0

• decorate uses taxonomy embedded in tree even when an input taxonomy is given

  #176 opened 9 years ago by wwood
  4