GTDBTk

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Starting pplacer.pplacer: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed

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## Environment - [x] Using a conda environment (include the output of `conda list && conda list --revisions`) conda list ``` # packages in environment at /mnt/mibi_ngs/keerthi/miniconda3/envs/gtdbtk-2.1.0: # # Name...

sannareddyk

Hanging on classify_wf and TIGRFam

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## Environment - [ ] Installed via pip (include the output of `pip list`) - [X] Using a conda environment (include the output of `conda list && conda list --revisions`)...

cjfields

error Mask and alignment length do not match.

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Dear, Can you help me? Please see below: The first error was that several Tigrfam and pfam files (markers) were missing from the gtdbk r207 database. So I include them,...

mattoslmp

maker not found

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Hi @donovan-parks! I just ran into an error while running the gtdbtk classify_wf command. My command was: **gtdbtk classify_wf --genome_dir /lustre/rsharma/FLOOR-METAGENOME-NOVASEQ/ASSEMBLY/MAXBIN_REZ/GOOD_QUALITY_BINS/GBINS/ --out_dir /lustre/rsharma/FLOOR-METAGENOME-NOVASEQ/GTDBTK_REZ/** Terminal output:  ERROR:...

saras224

Add a line in the log file listing how many genomes have a warning. Similar to `[2022-07-12 12:00:00] WARNING: 10 out of 100 genomes ( 10% ) have a warning,...

pchaumeil

Number of classified reads

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I would like to ask that how we suppose to know how much reads or percentage of reads were classified? I would like to compare it to other analysis method.

natchaphon602

Subroutines for classify

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I had some bad experiences with gtdb-tk classify which I run on large datasets. - For example, It passed all the steps but then failed because the symlinked files already...

SilasK

Flag to allow genomes to be supplied as called genes

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It would be good if users could supply genomes as called genes in amino acid space. Basically just a flag (--genes) to indicate the FASTA file contains genes and then...

donovan-h-parks

NCBI Taxonomy Names in output

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Thanks for the great tool! This suggestion is definitely not critical, but something I think could be useful. I definitely like that on the GTDB website you can search for...

elizabethmcd

Hi there I used GTDB-tk (v1.4) to generate MSA and then used it to construct a phylogenetic tree. However, IQ-tree reported that some of the sequences have >50% gaps/ambiguity. As...

TianyiChang