Ecogenomics / GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

https://ecogenomics.github.io/GTDBTk/

Ecogenomics/GTDBTk Issues

Add environment variable for mash database
Updated 3 days ago2
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
Updated 3 days ago1
it also hang on during "Identifying TIGRFAM protein families." gtdbtk-2.3.2
Updated 3 days ago3
database error
Closed 4 days ago1
Troubleshooting GTDB-Tk Database Installation and Environment Configuration
Updated 5 days ago4
How can we construct a phylogenetic tree that includes both bacteria and archaea?
Updated 16 days ago2
Skani external command error
Updated 16 days ago2
FastTree returned a non-zero exit code
Updated a month ago1
A failure of the classification of a reference genome
Updated 2 months ago1
GTDB-Tk/2.4.0 - Spirochaetota clustering far from other bacteria from the same phylum
Updated 2 months ago6
Using classify_wf with low completeness genomes
Updated 2 months ago1
Difference between fastani_ani and closest_placement_ani
Updated 2 months ago1
ANI values for the MAGs
Updated 2 months ago2
GTDB-Tk 2.4.0: Prodigal returned a non-zero exit code
Closed 2 months ago1
How to Interpret and Change IDs in Phylogenetic Trees Generated by GTDB-Tk?
Closed 2 months ago
Check install showing Hash Mismatch even though database MD5 checks
Closed 4 months ago3
Using gtdb_to_ncbi_majority_vote.py script to convert gtbd taxonomy to SILVA taxonomy
Closed 4 months ago2
Bacterial GTDB-Tk classification file does not exist error when using gtdb_to_ncbi_majority_vote.py
Updated 4 months ago1
No sequence results for archaea in the align folder of classify_wf
Closed 4 months ago2
Is the lasted GTDB database version220 missing files?
Closed 4 months ago4
The GTDB-Tk reference data does not exist or is corrupted.
Closed 5 months ago4
Error from skani
Closed 5 months ago2
classify_wf errors out when all inputs are unclassified
Closed 5 months ago
Attempting to add duplicate row
Closed 5 months ago4
Specify in documentation that the `--genes` parameter requires proteins as input.
Closed 5 months ago
Small (mock) reference data
Closed 5 months ago3
pydantic.dev/2.6/v/missing
Closed 5 months ago1
relative evolutionary divergence (RED) values and median RED values
Closed 5 months ago3
How to get a tree containing all my MAGs
Closed 5 months ago1
Cannot open classify.tree file in Dendroscope
Closed 5 months ago2
Do I need a network to run classify_wf
Closed 5 months ago1
def TypedDict(typename, fields=_marker,/, *, total=True, closed=False, **kwargs): SyntaxError: invalid syntax
Closed 5 months ago3
Is the lasted GTDB database version220 missing files?
Closed 6 months ago
GTDB-tk has given confliction results for two genomes using different command
Closed 6 months ago2
Total genome counter in log is off (warning message)
Updated 6 months ago1
Inquiry on the error "libgsl.so.25"
Closed 6 months ago1
Error running Prodigal on genome
Updated 6 months ago4
gtdbtk.exceptions.ProdigalException: An exception was caught while running Prodigal: Prodigal returned a non-zero exit code.
Closed 7 months ago6
The annotation results of gtdbtk are inconsistent with the Phylogenetic position.
Closed 7 months ago4
Uncontrolled exit resulting from an unexpected error.
Closed 7 months ago4
How to understand RELATIVE EVOLUTIONARY DIVERSION (RED)?
Closed 7 months ago4
Getting the GTDB version used from GTDB-Tk
Closed 7 months ago2
Decorate command issue
Closed 8 months ago1
de_novo_wf fails to parse gtdb classification file
Closed 8 months ago1
RED value and classification results
Closed a year ago4
Error occured using gtdbtk de_novo_wf for bins
Closed a year ago5
gtdbtk: error: unrecognized arguments: --mash_db
Closed a year ago1
failed to process sequence file "gzip.baggzipfile: not a gzipped file (b'>k')" and prodigal non-zero exit code
Closed a year ago4
Not all genomes identified
Closed a year ago1
gtdb_to_ncbi_majority_vote and Unclassified Bacteria
Closed a year ago2