Ecogenomics GTDBTk issues

Ecogenomics / GTDBTk

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

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

GNU General Public License v3.0

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issues

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ERROR: An error was encountered while running hmmsearch.

#612 J-Weijie98 opened 4 days ago
0
GTDB for large number of genomes (1.3M)

#611 intikhab opened 2 weeks ago
6
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 huzongde opened 3 weeks ago
1
database error

#609 jianshu93 closed 3 weeks ago
1
it also hang on during "Identifying TIGRFAM protein families." gtdbtk-2.3.2

#608 Caiyulu-818 opened 1 month ago
3
Add environment variable for mash database

#607 fplazaonate opened 1 month ago
3
Skani external command error

#606 magicprotoss opened 1 month ago
2
How can we construct a phylogenetic tree that includes both bacteria and archaea?

#605 qbdong122 opened 1 month ago
2
FastTree returned a non-zero exit code

#604 esraagithub opened 1 month ago
1
A failure of the classification of a reference genome

#603 biotengwk closed 4 days ago
2
Difference between fastani_ani and closest_placement_ani

#602 saras224 opened 2 months ago
1
How to Interpret and Change IDs in Phylogenetic Trees Generated by GTDB-Tk?

#601 kuttibiotech2009 closed 2 months ago
0
GTDB-Tk 2.4.0: Prodigal returned a non-zero exit code

#600 Nura7177 closed 2 months ago
1
ANI values for the MAGs

#599 saras224 opened 3 months ago
2
GTDB-Tk/2.4.0 - Spirochaetota clustering far from other bacteria from the same phylum

#598 ValterAlmeida opened 3 months ago
6
Using classify_wf with low completeness genomes

#597 lingrongjin opened 3 months ago
1
Troubleshooting GTDB-Tk Database Installation and Environment Configuration

#596 soojunglee98 opened 4 months ago
4
Bacterial GTDB-Tk classification file does not exist error when using gtdb_to_ncbi_majority_vote.py

#595 schmittel opened 5 months ago
1
Check install showing Hash Mismatch even though database MD5 checks

#594 ErikLHendrickson closed 4 months ago
3
No sequence results for archaea in the align folder of classify_wf

#593 Liuhanlin22 closed 4 months ago
2
Error from skani

#592 jehaab closed 6 months ago
2
Do I need a network to run classify_wf

#591 zhaoxuetong closed 6 months ago
1
Is the lasted GTDB database version220 missing files?

#590 changhaozhou closed 4 months ago
4
Is the lasted GTDB database version220 missing files?

#589 changhaozhou closed 6 months ago
0
The GTDB-Tk reference data does not exist or is corrupted.

#588 vichy123 closed 5 months ago
4
GTDB-tk has given confliction results for two genomes using different command

#587 quliping closed 6 months ago
2
Inquiry on the error "libgsl.so.25"

#586 songmj86 closed 6 months ago
1
Total genome counter in log is off (warning message)

#585 GabeAl opened 7 months ago
1
Merge Staging for release of 2.4.0

#584 pchaumeil closed 7 months ago
0
def TypedDict(typename, fields=_marker,/, *, total=True, closed=False, **kwargs): SyntaxError: invalid syntax

#583 zhaoxuetong closed 6 months ago
3
feat(fix of #576):

#582 pchaumeil closed 7 months ago
0
Rename summary fields

#581 pchaumeil closed 7 months ago
0
fix(fixing of issue #573):

#580 pchaumeil closed 7 months ago
0
Skani branch

#579 pchaumeil closed 7 months ago
0
Getting the GTDB version used from GTDB-Tk

#578 wwood closed 8 months ago
2
Merge master to Staging

#577 pchaumeil closed 8 months ago
0
classify_wf errors out when all inputs are unclassified

#576 Zach-Sisson-1 closed 6 months ago
0
Using gtdb_to_ncbi_majority_vote.py script to convert gtbd taxonomy to SILVA taxonomy

#575 tarunaaggarwal closed 4 months ago
2
Decorate command issue

#574 Nura7177 closed 8 months ago
1
Attempting to add duplicate row

#573 liu-congcong closed 6 months ago
4
Small (mock) reference data

#572 bernt-matthias closed 6 months ago
3
Specify in documentation that the `--genes` parameter requires proteins as input.

#571 LeeBergstrand closed 6 months ago
0
de_novo_wf fails to parse gtdb classification file

#570 adityabandla closed 9 months ago
1
pydantic.dev/2.6/v/missing

#569 WUD2018 closed 6 months ago
1
relative evolutionary divergence (RED) values and median RED values

#568 Julboteroc closed 6 months ago
3
How to get a tree containing all my MAGs

#567 Sh1von closed 6 months ago
1
Error running Prodigal on genome

#566 fhdbqr opened 11 months ago
4
fix(setup.py): use ~= to constrain major version

#565 Artoria2e5 closed 7 months ago
1
RED value and classification results

#564 rusanovaA closed 11 months ago
4
Cannot open classify.tree file in Dendroscope

#563 lewhiteside closed 6 months ago
2