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Issues list

Using classify_wf with low completeness genomes
#597 opened Aug 12, 2024 by lingrongjin
1
Add checkpointing enhancement Proposed feature or change to GTDB-Tk.
#207 opened Dec 12, 2019 by aaronmussig
Establish novelty of user genomes enhancement Proposed feature or change to GTDB-Tk.
#233 opened Mar 13, 2020 by donovan-h-parks
Unnecessary computation in de novo workflow enhancement Proposed feature or change to GTDB-Tk.
#243 opened Apr 20, 2020 by donovan-h-parks
Subroutines for classify enhancement Proposed feature or change to GTDB-Tk.
#358 opened Nov 8, 2021 by SilasK
1
Write debug file on exception enhancement Proposed feature or change to GTDB-Tk.
#432 opened Sep 11, 2022 by aaronmussig
Use Pyrodigal as Prodigal alternative enhancement Proposed feature or change to GTDB-Tk.
#456 opened Dec 5, 2022 by lfenske-93
2
Slow download speed v214
#522 opened Jun 2, 2023 by kafker
20
Use type strains for GTDB to NCBI taxonomy translation
#552 opened Oct 16, 2023 by fplazaonate
2
Error running Prodigal on genome error Help required for a GTDB-Tk error.
#566 opened Dec 20, 2023 by fhdbqr
2 tasks
4
Total genome counter in log is off (warning message) error Help required for a GTDB-Tk error.
#585 opened Apr 26, 2024 by GabeAl
1
Bacterial GTDB-Tk classification file does not exist error when using gtdb_to_ncbi_majority_vote.py error Help required for a GTDB-Tk error.
#595 opened Jun 22, 2024 by schmittel
1
Non-parametric bootstraps enhancement Proposed feature or change to GTDB-Tk.
#116 opened Apr 17, 2019 by donovan-h-parks
Troubleshooting GTDB-Tk Database Installation and Environment Configuration error Help required for a GTDB-Tk error.
#596 opened Jul 16, 2024 by soojunglee98
3 tasks
4
GTDB-Tk/2.4.0 - Spirochaetota clustering far from other bacteria from the same phylum
#598 opened Aug 13, 2024 by ValterAlmeida
6
ANI values for the MAGs
#599 opened Aug 21, 2024 by saras224
2
Difference between fastani_ani and closest_placement_ani
#602 opened Aug 28, 2024 by saras224
1
A failure of the classification of a reference genome error Help required for a GTDB-Tk error.
#603 opened Sep 14, 2024 by biotengwk
1
FastTree returned a non-zero exit code error Help required for a GTDB-Tk error.
#604 opened Oct 1, 2024 by esraagithub
1 task
1
How can we construct a phylogenetic tree that includes both bacteria and archaea?
#605 opened Oct 10, 2024 by qbdong122
2
Skani external command error error Help required for a GTDB-Tk error.
#606 opened Oct 14, 2024 by magicprotoss
2
Add environment variable for mash database
#607 opened Oct 18, 2024 by fplazaonate
3
it also hang on during "Identifying TIGRFAM protein families." gtdbtk-2.3.2 error Help required for a GTDB-Tk error.
#608 opened Oct 22, 2024 by Caiyulu-818
3
Hello, what is the reason for this problem? runing: gtdbtk classify_wf --genome_dir new_genome_data/ --skip_ani_screen --out_dir classify_wf_out --cpus 16
#610 opened Oct 27, 2024 by huzongde
1
GTDB for large number of genomes (1.3M)
#611 opened Nov 5, 2024 by intikhab
6
ProTip! Adding no:label will show everything without a label.