AstrobioMike/GToTree

Issues

• Save downloaded genomes from NCBI

  #95 opened 5 months ago by jmtsuji
  2

• Alignment file empty

  #94 opened 5 months ago by aelbehery
  5

• adding taxonomy info not working when run in nucleotide mode

  #91 opened 6 months ago by AstrobioMike
  2

• Using gtt-data-locations set with singularity image

  #93 opened 6 months ago by nandan75
  3

• gtt-hmms only reports info for pre-built hmms

  #92 opened 6 months ago by AstrobioMike
  0

• remove doubling of genus if requesting genus and species

  #90 opened 6 months ago by AstrobioMike
  0

• file name spacing issue with gtt-get-accessions-from-gtdb

  #89 opened 7 months ago by AstrobioMike
  0

• GTDB metadata URL change

  #88 opened 7 months ago by ThinkPad254
  2

• getting a `CERTIFICATE_VERIFY_FAILED` when running `gtt-get-accessions-from-GTDB`

  #87 opened 7 months ago by ctb
  3

• Add check for input genome file not having line return after last input genome (renamed by Mike)

  #75 opened 2 years ago by Calvin2077
  4

• can't seem to find a place to store startup environmental variables

  #86 opened 8 months ago by nandan75
  6

• Error with pfam_counting.py

  #85 opened 9 months ago by SandersonHaley
  3

• pfamA.txt.gz missing from ftp?

  #84 opened 9 months ago by SandersonHaley
  2

• GTDB Download - Latest path file extensions changed

  #82 opened 10 months ago by gdangelo8
  5

• Unable to continue after **NOTICE**

  #83 opened a year ago by ReneKat
  2

• Bad metadata URLs in gtt-check-or-setup-GTDB-files

  #81 opened a year ago by jmtsuji
  2

• Connection issue?

  #78 opened a year ago by corkdagga
  15

• wiki fix

  #79 opened a year ago by hyphaltip
  1

• Alignment file missing

  #76 opened a year ago by morgansobol
  4

• Create a nucleotide alignment

  #77 opened a year ago by Sidduppal
  6

• current version fails downloads with openssl / curl errors

  #74 opened 2 years ago by spleonard1
  6

• Xs in alignment, Error codes in "Finished aligning and formatting gene-set steps"

  #53 opened 3 years ago by gkatahon
  2

• provide protein sequence or hmm for searching in lieu of pfam

  #73 opened 2 years ago by spleonard1
  2

• Failed to make temporary directory

  #46 opened 2 years ago by susheelbhanu
  10

• HTTP error with downloading and parsing archaeal and bacteria metadata tables from GTDB

  #72 opened 2 years ago by oduwoleiyanu
  7

• Bioconda recipe

  #68 opened 2 years ago by vinisalazar
  9

• Issue with using GTDB

  #71 opened 2 years ago by Ahmed-Shibl
  4

• Construct the tree of Virus and searching the metabolic genes

  #70 opened 2 years ago by Tsingsjeen
  3

• Table with location(s) of SCG markers

  #69 opened 2 years ago by gkatahon
  1

• Test run error

  #67 opened 2 years ago by asuria25
  4

• Problem downloading the Actinobacteria.hmm

  #66 opened 2 years ago by oduwoleiyanu
  3

• need to update pfam searching now that it's hosted by interpro

  #65 opened 2 years ago by AstrobioMike
  2

• Same as closed issue #29 - runs successfully but .tre file is empty when using -m flag

  #64 opened 2 years ago by kellikmullane
  4

• Feature request: subset-GTDB-accession options at family/genus/species level

  #63 opened 2 years ago by gabriellerocap
  6

• Problem using -D to add GTDB lineage info to genome labels

  #62 opened 2 years ago by gabriellerocap
  3

• Alphaproteobacteria (0 targets)

  #56 opened 2 years ago by ebervilla
  5

• restarting GToTree

  #60 opened 2 years ago by nicholascdove
  5

• Is this tool suitable for rodents?

  #61 opened 2 years ago by kuangzhuoran
  2

• Muscle Thread Usage

  #59 opened 2 years ago by raufs
  2

• Trimal shows errors when prodigal amino acid file is provided to GToTree

  #58 opened 2 years ago by brymerr921
  1

• Cleaning Trees with TreeShrink

  #54 opened 3 years ago by joshuakirsch
  1

• GTDB database update today

  #57 opened 3 years ago by Tsingsjeen
  2

• duplicate entries

  #55 opened 3 years ago by Tsingsjeen
  2

• Is this gzip step necessary?

  #52 opened 3 years ago by joshuakirsch
  3

• Alignment for 'Bacteria' SCG set is only 169 AA long

  #51 opened 3 years ago by emily-ebel
  9

• new muscle support

  #48 opened 3 years ago by jianshu93
  5

• hmmsearch issue with large target sequence

  #50 opened 3 years ago by gavinmdouglas
  5

• An option to prevent database version check

  #45 opened 3 years ago by felixeye
  5

• Alignment not loaded error during Aligning, trimming, and inserting gap-sequences step

  #47 opened 3 years ago by MiAiM
  4

• fasta file has duplicate entries

  #44 opened 3 years ago by ReneKat
  2