geronimp/graftM issues and pull requests

#285 - Difference between search_otu_table and combined_count_table. Multiple hmm searches.

Issue - State: open - Opened by robcli 3 months ago

#284 - low number of reads detected

Issue - State: open - Opened by rzhan186 9 months ago

#283 - An error was found that was difficult to resolve after manually reroot

Issue - State: closed - Opened by Five296 11 months ago - 5 comments

#282 - CVE-2007-4559 Patch

Pull Request - State: closed - Opened by TrellixVulnTeam about 2 years ago

#281 - Remove unnessary conda dependencies

Pull Request - State: closed - Opened by AroneyS over 2 years ago

#280 - Remove backports.tempfile dependency

Pull Request - State: closed - Opened by AroneyS over 2 years ago - 3 comments

#279 - Fix diamond tests failing with each new version

Pull Request - State: closed - Opened by AroneyS over 2 years ago - 6 comments

#278 - Update conda env yaml

Pull Request - State: closed - Opened by AroneyS over 2 years ago

#277 - GraftM graft on big metagenome error

Issue - State: open - Opened by steff1088 over 2 years ago - 4 comments

#276 - account for no hits by non-decoy diamond db

Pull Request - State: closed - Opened by AroneyS almost 3 years ago

#275 - Getting ZeroDivisionError when running with sample data

Issue - State: closed - Opened by MelodyMale about 3 years ago - 7 comments

#274 - What does 'Root' classification refer to?

Issue - State: closed - Opened by kattweigh about 3 years ago - 2 comments

#273 - fix create no-tree flag

Pull Request - State: closed - Opened by AroneyS about 3 years ago

#272 - add create no-tree flags

Pull Request - State: closed - Opened by AroneyS about 3 years ago - 1 comment

#271 - Update README.md

Pull Request - State: closed - Opened by AroneyS over 3 years ago

#270 - Create no tree

Pull Request - State: closed - Opened by AroneyS over 3 years ago

#269 - working with non-gene sequences

Issue - State: open - Opened by bakeronit over 3 years ago

#268 - Issue running graftm create using docker

Issue - State: open - Opened by erins1 about 4 years ago - 6 comments

#267 - error using decoy_database with hmmsearch+diamond

Issue - State: open - Opened by yboesch over 4 years ago

#266 - graftM create failed to root the tree

Issue - State: closed - Opened by x86lu over 4 years ago - 9 comments

#265 - graftM create error

Issue - State: open - Opened by adityabandla over 4 years ago - 6 comments

#264 - Error: TC bit thresholds unavailable on model graftmrzdqhx.aln

Issue - State: open - Opened by sarah872 almost 5 years ago - 2 comments

#263 - accept interleaved input

Pull Request - State: closed - Opened by jmeppley over 5 years ago - 6 comments

#262 - graftM create error while creating package

Issue - State: closed - Opened by ckeuschn over 5 years ago - 3 comments

#261 - Split challenge

Pull Request - State: closed - Opened by geronimp over 5 years ago - 1 comment

#260 - Geronimp jplace missing orfm names

Pull Request - State: closed - Opened by geronimp over 5 years ago

#259 - graft_package_version error on custom GraftM package

Issue - State: open - Opened by fletchec99 over 5 years ago - 10 comments

#258 - Can't find FastTreeMP

Issue - State: closed - Opened by alexximalayaunlv almost 6 years ago - 4 comments

#257 - Fixes dec2018

Pull Request - State: closed - Opened by wwood almost 6 years ago - 2 comments

#256 - search_only mode does not pair reads

Issue - State: closed - Opened by areejalsheikh about 6 years ago - 2 comments

#255 - KeyError on split sequence?

Issue - State: open - Opened by maxemil over 6 years ago

#254 - Combined alignment file intermittently produced

Issue - State: closed - Opened by babakshaban over 6 years ago - 15 comments

#253 - Input Reads or Bins

Issue - State: open - Opened by colbyga over 6 years ago - 3 comments

#252 - LookupError: unknown encoding: utf8

Issue - State: closed - Opened by s4351982 over 6 years ago - 3 comments

#251 - Install Error using pip install

Issue - State: closed - Opened by colbyga over 6 years ago

#250 - update: Add option to regenerate diamond databases.

Pull Request - State: closed - Opened by wwood over 6 years ago

#249 - graftM create_why error in building tree?

Issue - State: open - Opened by snmrna over 6 years ago - 6 comments

#248 - "graftM create" failed with SILVA due to unknown error

Issue - State: closed - Opened by jcmcnch over 6 years ago - 13 comments

#247 - graft: Use specified --input_sequence_type.

Pull Request - State: closed - Opened by wwood over 6 years ago - 1 comment

#246 - Missing options on docs for "graft"

Issue - State: closed - Opened by kyclark over 6 years ago - 1 comment

#245 - Remove seqmagick

Pull Request - State: closed - Opened by wwood almost 7 years ago - 1 comment

#244 - Error with graft command

Issue - State: closed - Opened by SCarrSuperstar almost 7 years ago - 3 comments

#243 - GraftM can now take >7 taxonomy ranks when creating a graftM package

Pull Request - State: closed - Opened by geronimp almost 7 years ago

#242 - setup.py: Restrict seqmagick version to <0.7.0.

Pull Request - State: closed - Opened by wwood almost 7 years ago - 1 comment

#241 - Leftover tempfiles

Pull Request - State: closed - Opened by wwood over 7 years ago

#240 - Geromimp renaming hmmer

Pull Request - State: closed - Opened by geronimp over 7 years ago - 2 comments

#239 - Bug fix for issue 198

Pull Request - State: closed - Opened by geronimp over 7 years ago

#238 - Not all temporary files are removed

Issue - State: closed - Opened by wwood over 7 years ago

#237 - Diamond 0.9

Pull Request - State: closed - Opened by wwood over 7 years ago

#236 - HMMsearch + DIAMOND

Issue - State: open - Opened by ljmmm over 7 years ago - 3 comments
Labels: bug

#235 - Changed default dereplication level to 0

Pull Request - State: closed - Opened by geronimp over 7 years ago - 1 comment

#234 - taxonomy file empty

Issue - State: open - Opened by tv195 over 7 years ago
Labels: bug

#233 - update graftM help

Pull Request - State: closed - Opened by geronimp over 7 years ago

#232 - v0.10.0

Pull Request - State: closed - Opened by geronimp almost 8 years ago

#231 - test: Update diamond DBs to a post 0.7.9 format.

Pull Request - State: closed - Opened by wwood almost 8 years ago - 2 comments

#230 - updated README and replaced old gpkg store link to the new ACE ftp li…

Pull Request - State: closed - Opened by geronimp about 8 years ago

#229 - Too short sequences catching

Pull Request - State: closed - Opened by wwood about 8 years ago - 1 comment

#228 - Updated License information and added SILVA license

Pull Request - State: closed - Opened by geronimp about 8 years ago - 1 comment

#227 - graftm tree decorate not working when given undecorated tree?

Issue - State: open - Opened by wwood about 8 years ago
Labels: bug

#226 - graftm tree GreenGenesTaxonomy exceptions are covered up

Issue - State: closed - Opened by wwood about 8 years ago - 1 comment
Labels: bug

#225 - Final skbio removal

Pull Request - State: closed - Opened by wwood about 8 years ago - 1 comment

#224 - Geronimp remove skbio from reroot

Pull Request - State: closed - Opened by geronimp about 8 years ago - 12 comments

#223 - Add graft --decoy_database.

Pull Request - State: closed - Opened by wwood about 8 years ago - 5 comments

#222 - geronimp-placement_cutoff_error

Pull Request - State: closed - Opened by geronimp about 8 years ago - 2 comments

#221 - Skbio removal

Pull Request - State: closed - Opened by wwood over 8 years ago - 2 comments

#220 - Improved GraftM help

Pull Request - State: closed - Opened by geronimp over 8 years ago - 5 comments

#219 - Create examples

Pull Request - State: closed - Opened by wwood over 8 years ago

#218 - mafft-linsi or similar as default for create alignment

Issue - State: closed - Opened by geronimp over 8 years ago - 1 comment
Labels: enhancement

#217 - Geronimp update mode2

Pull Request - State: closed - Opened by geronimp over 8 years ago - 4 comments

#216 - removed incorrect file suffix

Pull Request - State: closed - Opened by geronimp over 8 years ago - 1 comment

#215 - Geronimp make merge reads default

Pull Request - State: closed - Opened by geronimp over 8 years ago - 1 comment

#214 - rename bootstrap expand_search

Pull Request - State: closed - Opened by geronimp over 8 years ago - 3 comments

#213 - Geronimp remove no clustering and rereplicate alignments

Pull Request - State: closed - Opened by geronimp over 8 years ago - 4 comments

#212 - test_graft: add test for --no_clustering

Pull Request - State: closed - Opened by wwood over 8 years ago

#211 - multijplace

Issue - State: open - Opened by wwood over 8 years ago
Labels: enhancement

#210 - graftm_package: add is_protein_package method

Pull Request - State: closed - Opened by wwood over 8 years ago - 4 comments

#209 - create: Actually use '10 sequences' file when testing

Pull Request - State: closed - Opened by wwood over 8 years ago

#208 - Create tweaks

Pull Request - State: closed - Opened by wwood over 8 years ago - 2 comments

#207 - create: Update logging info

Pull Request - State: closed - Opened by wwood over 8 years ago

#206 - Dendropy reannotator

Pull Request - State: closed - Opened by wwood over 8 years ago - 5 comments

#205 - rereplication of alignments

Issue - State: open - Opened by wwood over 8 years ago - 1 comment

#204 - create does not remove extraneous taxonomy

Issue - State: open - Opened by wwood over 8 years ago - 1 comment
Labels: bug

#203 - reannotator: add failing unit test

Pull Request - State: closed - Opened by wwood over 8 years ago - 3 comments

#202 - Bugfix: Do not attempt to re-create the alignment HMM when not all se…

Pull Request - State: closed - Opened by geronimp over 8 years ago - 1 comment

#201 - Geronimp investigating pplacer issue rereplicate jplace files

Pull Request - State: closed - Opened by geronimp over 8 years ago - 2 comments

#200 - GraftM needs tests for classification

Issue - State: open - Opened by geronimp over 8 years ago
Labels: enhancement

#199 - refactoring of Run

Issue - State: open - Opened by wwood over 8 years ago
Labels: enhancement

#198 - Cannot specify diamond database when using --search_only option

Issue - State: closed - Opened by geronimp over 8 years ago - 3 comments

#193 - taxonomy_extractor: add test for branch lengths, ref #192.

Pull Request - State: closed - Opened by wwood over 8 years ago - 2 comments

#189 - Geronimp investigating pplacer issue

Pull Request - State: closed - Opened by geronimp over 8 years ago - 9 comments

#181 - Neater, more understandable, and hopefully bugfree code for GraftM tr…

Pull Request - State: open - Opened by geronimp almost 9 years ago - 2 comments

#177 - create seems to generate a new HMM even if one is given?

Issue - State: open - Opened by wwood almost 9 years ago - 1 comment

#174 - decorate: Add ability to decorate trees with <7 levels of taxonomy.

Pull Request - State: closed - Opened by wwood almost 9 years ago - 11 comments

#172 - Geronimp jplace improvements

Pull Request - State: open - Opened by geronimp almost 9 years ago - 3 comments

#171 - geronimp-slash_error patch

Pull Request - State: open - Opened by geronimp almost 9 years ago - 17 comments

#165 - add failing test_input_sequence_near_duplication

Pull Request - State: closed - Opened by wwood almost 9 years ago - 5 comments

#163 - --reverse help too conservative?

Issue - State: closed - Opened by wwood almost 9 years ago - 1 comment

#155 - Geronimp alignment as input

Pull Request - State: open - Opened by geronimp almost 9 years ago - 1 comment

#154 - add failing test for input sequence with gaps

Pull Request - State: closed - Opened by wwood almost 9 years ago - 17 comments

#146 - Can now update contents file within a graftM package

Pull Request - State: open - Opened by geronimp almost 9 years ago - 3 comments

GitHub / geronimp/graftM issues and pull requests