### GTDB-Tk Check Install Command Output Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/check_install.md

This output shows a successful verification of the GTDB-Tk reference data and third-party software. It indicates that all checks passed with 'OK'.

```text
[2025-08-05 17:02:59] INFO: GTDB-Tk v2.5.0
[2025-08-05 17:02:59] INFO: gtdbtk check_install
[2025-08-05 17:02:59] INFO: Using GTDB-Tk reference data version r226: /release226
[2025-08-05 17:02:59] INFO: Running install verification
[2025-08-05 17:02:59] INFO: Checking that all third-party software are on the system path:
[2025-08-05 17:02:59] INFO:          |-- FastTree         OK
[2025-08-05 17:02:59] INFO:          |-- FastTreeMP       OK
[2025-08-05 17:02:59] INFO:          |-- guppy            OK
[2025-08-05 17:02:59] INFO:          |-- hmmalign         OK
[2025-08-05 17:02:59] INFO:          |-- hmmsearch        OK
[2025-08-05 17:02:59] INFO:          |-- pplacer          OK
[2025-08-05 17:02:59] INFO:          |-- prodigal         OK
[2025-08-05 17:02:59] INFO:          |-- skani            OK
[2025-08-05 17:02:59] INFO: Checking integrity of reference package: /release226
[2025-08-05 17:02:59] INFO:          |-- pplacer          OK
[2025-08-05 17:02:59] INFO:          |-- masks            OK
[2025-08-05 17:03:00] INFO:          |-- markers          OK
[2025-08-05 17:03:00] INFO:          |-- radii            OK
[2025-08-05 17:03:05] INFO:          |-- msa              OK
[2025-08-05 17:03:05] INFO:          |-- metadata         OK
[2025-08-05 17:03:05] INFO:          |-- taxonomy         OK
[2025-08-05 17:06:35] INFO:          |-- skani            OK
[2025-08-05 17:06:35] INFO:          |-- mrca_red         OK
[2025-08-05 17:06:35] INFO: Done.
```

--------------------------------

### Decorate Command Output Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/decorate.md

This is an example of the output produced by the decorate command, showing that the functionality is not yet implemented.

```text
[2020-04-14 08:20:51] INFO: GTDB-Tk v1.1.0
[2020-04-14 08:20:51] INFO: gtdbtk decorate --input_tree input.tree --output_tree output.tree
[2020-04-14 08:20:51] INFO: Using GTDB-Tk reference data version r89: /release89
[2020-04-14 08:20:51] WARNING: DECORATE NOT YET IMPLEMENTED!
[2020-04-14 08:20:51] INFO: Done.
```

--------------------------------

### Example pplacer Output

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/pplacer.domain.out.md

This is an example of the raw text output from a pplacer analysis. It shows the progress and status messages during the execution.

```text
Running pplacer v1.1.alpha19-0-g807f6f3 analysis on align_output/align/gtdbtk.ar53.user_msa.fasta...
Didn't find any reference sequences in given alignment file. Using supplied reference alignment.
Pre-masking sequences... sequence length cut from 5124 to 5114.
Determining figs... figs disabled.
Allocating memory for internal nodes... done.
Caching likelihood information on reference tree... done.
Pulling exponents... done.
Preparing the edges for baseball... done.
working on genome_1 (1/3)...
working on genome_2 (2/3)...
working on genome_3 (3/3)...
```

--------------------------------

### Example Mask File

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/trim_msa.md

This is an example of a mask file, where '1' indicates a position to keep and '0' indicates a position to trim.

```text
01011
```

--------------------------------

### GTDB-Tk align command example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/align.md

An example of how to run the gtdbtk align command with specified input and output directories, and number of CPUs.

```bash
gtdbtk align --identify_dir identify_output/ --out_dir align_output --cpus 3
```

--------------------------------

### Decorate Command Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/decorate.md

An example of how to invoke the decorate command with input and output tree files. The output indicates that the decorate functionality is not yet implemented.

```bash
gtdbtk decorate --input_tree input.tree --output_tree output.tree
```

--------------------------------

### Export Archaea MSA Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/export_msa.md

Example of how to export the untrimmed archaeal MSA to a specified output file.

```bash
gtdbtk export_msa --domain arc --output /tmp/msa.faa
```

--------------------------------

### De Novo Workflow Examples

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/de_novo_wf.md

Examples demonstrating how to run the de novo workflow with different configurations, including specifying marker sets, outgroup taxa, and filtering options.

```bash
gtdbtk de_novo_wf --genome_dir genomes/ --outgroup_taxon p__Undinarchaeota --archaea --out_dir de_novo_wf --cpus 3
```

```bash
gtdbtk de_novo_wf --genome_dir genomes/ --outgroup_taxon p__Chloroflexota --bacteria  --taxa_filter p__Firmicutes --out_dir de_novo_output
```

```bash
#Skip GTDB reference genomes ( requires --custom_taxonomy_file for outgrouping)
gtdbtk de_novo_wf --genome_dir genomes/ --outgroup_taxon p__Customphylum --bacteria --custom_taxonomy_file custom_taxonomy.tsv --out_dir de_novo_output
```

```bash
#Use a subset of GTDB reference genomes (p__Firmicutes) and outgroup on a custom Phylum (p__Customphylum)
gtdbtk de_novo_wf --genome_dir genomes/ --taxa_filter p__Firmicutes --outgroup_taxon p__Customphylum --bacteria --custom_taxonomy_file custom_taxonomy.tsv --out_dir de_novo_output
```

--------------------------------

### Example Output of convert_to_itol

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/convert_to_itol.md

This is an example of the log output produced by the convert_to_itol command, showing the version, input/output files, reference data, and completion status.

```text
[2022-06-30 18:44:54] INFO: GTDB-Tk v2.1.0
[2022-06-30 18:44:54] INFO: gtdbtk convert_to_itol --input /tmp/decorated.tree --output new.tree
[2022-06-30 18:44:54] INFO: Using GTDB-Tk reference data version r207: /gtdbtk-data
[2022-06-30 18:44:54] INFO: Convert GTDB-Tk tree to iTOL format
[2022-06-30 18:44:54] INFO: Done.
```

--------------------------------

### Example Input MSA

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/trim_msa.md

This is an example of an input multiple sequence alignment file in FASTA format.

```text
>genome_a
AKLAK
```

--------------------------------

### Classify Workflow Example with Batch File

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/classify_wf.md

An example of running the GTDB-Tk classify_wf command using a batch file to specify genome locations and identifiers. This example also sets the number of CPUs to use for the analysis.

```bash
gtdbtk classify_wf --batchfile genomes/3_batchfile.tsv --out_dir classify_wf_3_genomes --cpus 20
```

--------------------------------

### GTDB-Tk root command output example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/root.md

This is an example of the standard output produced by the gtdbtk root command after successfully rerooting a tree.

```text
[2020-04-14 08:26:53] INFO: GTDB-Tk v1.1.0
[2020-04-14 08:26:53] INFO: gtdbtk root --input_tree input.tree --outgroup_taxon p__Nanoarchaeota --output_tree output.tree
[2020-04-14 08:26:53] INFO: Using GTDB-Tk reference data version r89: /release89
[2020-04-14 08:26:53] INFO: Identifying genomes from the specified outgroup.
[2020-04-14 08:26:53] INFO: Identified 101 outgroup taxa in the tree.
[2020-04-14 08:26:53] INFO: Identified 1151 ingroup taxa in the tree.
[2020-04-14 08:26:53] INFO: Outgroup is monophyletic.
[2020-04-14 08:26:53] INFO: Rerooting tree.
[2020-04-14 08:26:53] INFO: Rerooted tree written to: output.tree
[2020-04-14 08:26:53] INFO: Done.
```

--------------------------------

### FastTree Command and Output Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/tree.log.md

This example shows a typical command used to generate a tree.log file with FastTree and a snippet of the resulting log output, including version information, alignment details, and initial tree construction steps.

```text
Command: FastTree -wag -gamma -log infer_out/infer/intermediate_results/gtdbtk.tree.log msa.faa
FastTree Version 2.1.10 Double precision (No SSE3)
Alignment: msa.faa
Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Whelan-And-Goldman, CAT approximation with 20 rate categories
Read 1 sequences, 5 positions
NJ  (genome_a:0.000000000);
ME_SPR1     (genome_a:0.000000000);
```

--------------------------------

### Example failed_genomes.tsv Content

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/failed_genomes.tsv.md

This example shows the format of the failed_genomes.tsv file, with each line containing a genome identifier and the reason for failure.

```text
GCA_000002165.1,No genes were called by Prodigal
GCA_000002175.1,No genes were called by Prodigal
GCA_000002185.1,No genes were called by Prodigal
GCA_000002195.1,No genes were called by Prodigal
GCA_000002205.1,No genes were called by Prodigal
```

--------------------------------

### GTDB-Tk Reference Data Download and Setup

Source: https://context7.com/ecogenomics/gtdbtk/llms.txt

Instructions for downloading the GTDB-Tk reference data package and setting the `GTDBTK_DATA_PATH` environment variable. This ensures the software uses the correct reference files. The `check_install` command verifies the setup.

```bash
# Download latest reference data
wget https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/auxillary_files/gtdbtk_package/full_package/gtdbtk_data.tar.gz
tar xvzf gtdbtk_data.tar.gz

# Set environment variable (add to ~/.bashrc for persistence)
export GTDBTK_DATA_PATH=/path/to/release_data/

# Verify the reference data version in use
gtdbtk check_install
# [INFO] Using GTDB-Tk reference data version r232: /path/to/release_data/
```

--------------------------------

### Identify Command Output Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/identify.md

This example shows the typical log output from the gtdbtk identify command, detailing the steps performed, versions of tools used, and progress.

```text
[2022-04-11 11:48:59] INFO: GTDB-Tk v2.0.0
[2022-04-11 11:48:59] INFO: gtdbtk identify --genome_dir /tmp/gtdbtk/genomes --out_dir /tmp/gtdbtk/identify --extension gz --cpus 2
[2022-04-11 11:48:59] INFO: Using GTDB-Tk reference data version r207: /srv/db/gtdbtk/official/release207
[2022-04-11 11:48:59] INFO: Identifying markers in 2 genomes with 2 threads.
[2022-04-11 11:48:59] TASK: Running Prodigal V2.6.3 to identify genes.
[2022-04-11 11:49:10] INFO: Completed 2 genomes in 10.94 seconds (5.47 seconds/genome).
[2022-04-11 11:49:10] TASK: Identifying TIGRFAM protein families.
[2022-04-11 11:49:16] INFO: Completed 2 genomes in 5.78 seconds (2.89 seconds/genome).
[2022-04-11 11:49:16] TASK: Identifying Pfam protein families.
[2022-04-11 11:49:16] INFO: Completed 2 genomes in 0.42 seconds (4.81 genomes/second).
[2022-04-11 11:49:16] INFO: Annotations done using HMMER 3.1b2 (February 2015).
[2022-04-11 11:49:16] TASK: Summarising identified marker genes.
[2022-04-11 11:49:16] INFO: Completed 2 genomes in 0.05 seconds (40.91 genomes/second).
[2022-04-11 11:49:16] INFO: Done.
```

--------------------------------

### ani_rep Example Input

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/ani_rep.md

An example of how to run the `ani_rep` command using a batch file for input genomes. Ensure the specified file extension matches your genome files.

```bash
gtdbtk ani_rep --batchfile genomes/500_batchfile.tsv -x fa --out_dir test_ani_reps --cpus 90
```

--------------------------------

### GTDB-Tk infer command output example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/infer.md

Example output from the gtdbtk infer command, showing the progress and information logged during the tree inference process.

```text
[2020-04-14 09:37:55] INFO: GTDB-Tk v1.1.0
[2020-04-14 09:37:55] INFO: gtdbtk infer --msa_file msa.faa --out_dir infer_out
[2020-04-14 09:37:55] INFO: Using GTDB-Tk reference data version r89: /release89
[2020-04-14 09:37:55] INFO: Inferring FastTree (WAG, +gamma, support) using a maximum of 1 CPUs.
[2020-04-14 09:37:55] INFO: FastTree version: 2.1.10
[2020-04-14 09:37:55] INFO: FastTree version: 2.1.10
[2020-04-14 09:37:55] INFO: Done.
```

--------------------------------

### Install GTDB-Tk via pip

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/installing/pip.md

Use this command to install the latest version of GTDB-Tk. It's recommended to do this within a virtual environment.

```bash
python -m pip install gtdbtk
```

--------------------------------

### Example Translation Table Summary

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/translation_table_summary.tsv.md

This is an example of the `translation_table_summary.tsv` file format, showing genome identifiers and their corresponding translation table numbers.

```text
genome_1    11
genome_2    11
genome_3    11
```

--------------------------------

### Test GTDB-Tk Installation

Source: https://github.com/ecogenomics/gtdbtk/wiki/Publishing-GTDB-Tk

Creates a new Conda environment, activates it, and installs the GTDB-Tk package from the generated source distribution for testing purposes.

```bash
conda create -n GTDBTK_TEST --clone gtdbtk-dev
```

```bash
conda activate GTDBTK_TEST
```

```bash
pip install dist/*
```

--------------------------------

### Example RED Values for Taxonomic Ranks

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/red_dictionary.tsv.md

This example shows the typical format of the red_dictionary.tsv file, listing taxonomic ranks and their corresponding median RED values.

```text
Phylum      0.187145401902
Class       0.31012292886
Order       0.514210607301
Family      0.720555789247
Genus       0.905316996783
```

--------------------------------

### Running the GTDB-Tk test command

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/test.md

Example of how to execute the `gtdbtk test` command, specifying an output directory and the number of CPUs to use for the test run.

```bash
gtdbtk test --out_dir /tmp/test --cpus 3
```

--------------------------------

### Example markers_summary.tsv Output

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/markers_summary.tsv.md

This is an example of the markers_summary.tsv file format, showing counts and lists of unique, multiple, and missing genes for different genomes.

```text
name        number_unique_genes     number_multiple_genes   number_multiple_unique_genes    number_missing_genes    list_unique_genes       list_multiple_genes     list_multiple_unique_genes      list_missing_genes
genome_1    120     2       0       0       PF00368.13,PF00410.14,PF00466.15,PF00687.16,PF00827.12,PF00900.15,PF01000.21,PF01015.13,PF01090.14,PF01092.14,PF01157.13,PF01191.14,PF01194.12,PF01198.14,PF01200.13,PF01269.12,PF01280.15,PF01282.14,PF01496.14,PF01655.13,PF01798.13,PF01864.12,PF01866.12,PF01868.11,PF01984.15,PF01990.12,PF02006.11,PF02978.14,PF03874.11,PF04019.7,PF04104.9,PF07541.7,PF13656.1,PF13685.1,TIGR00021,TIGR00037,TIGR00042,TIGR00064,TIGR00111,TIGR00134,TIGR00240,TIGR00264,TIGR00270,TIGR00279,TIGR00283,TIGR00291,TIGR00293,TIGR00307,TIGR00308,TIGR00323,TIGR00324,TIGR00335,TIGR00336,TIGR00337,TIGR00373,TIGR00389,TIGR00392,TIGR00398,TIGR00405,TIGR00408,TIGR00422,TIGR00425,TIGR00432,TIGR00442,TIGR00448,TIGR00456,TIGR00458,TIGR00463,TIGR00468,TIGR00471,TIGR00491,TIGR00501,TIGR00521,TIGR00522,TIGR00549,TIGR00658,TIGR00670,TIGR00729,TIGR00936,TIGR00982,TIGR01008,TIGR01012,TIGR01018,TIGR01020,TIGR01025,TIGR01028,TIGR01038,TIGR01046,TIGR01052,TIGR01060,TIGR01077,TIGR01080,TIGR01213,TIGR01309,TIGR01952,TIGR02076,TIGR02153,TIGR02236,TIGR02258,TIGR02338,TIGR02389,TIGR02390,TIGR02651,TIGR03626,TIGR03627,TIGR03628,TIGR03629,TIGR03636,TIGR03653,TIGR03665,TIGR03670,TIGR03671,TIGR03672,TIGR03673,TIGR03674,TIGR03677,TIGR03680,TIGR03683,TIGR03684,TIGR03722    PF04919.7,TIGR00490
genome_2    108     1       0       13      PF00368.13,PF00410.14,PF00687.16,PF00827.12,PF00900.15,PF01000.21,PF01015.13,PF01090.14,PF01092.14,PF01157.13,PF01191.14,PF01198.14,PF01200.13,PF01269.12,PF01280.15,PF01282.14,PF01496.14,PF01655.13,PF01798.13,PF01864.12,PF01868.11,PF01984.15,PF01990.12,PF02978.14,PF03874.11,PF04019.7,PF04919.7,PF07541.7,PF13656.1,PF13685.1,TIGR00021,TIGR00037,TIGR00042,TIGR00064,TIGR00111,TIGR00134,TIGR00240,TIGR00264,TIGR00270,TIGR00279,TIGR00283,TIGR00291,TIGR00293,TIGR00307,TIGR00308,TIGR00323,TIGR00324,TIGR00335,TIGR00336,TIGR00389,TIGR00392,TIGR00398,TIGR00405,TIGR00408,TIGR00422,TIGR00425,TIGR00442,TIGR00448,TIGR00456,TIGR00463,TIGR00468,TIGR00471,TIGR00490,TIGR00491,TIGR00501,TIGR00521,TIGR00522,TIGR00658,TIGR00670,TIGR00729,TIGR00982,TIGR01008,TIGR01012,TIGR01018,TIGR01020,TIGR01025,TIGR01028,TIGR01038,TIGR01046,TIGR01052,TIGR01060,TIGR01077,TIGR01080,TIGR01213,TIGR01309,TIGR01952,TIGR02076,TIGR02153,TIGR02236,TIGR02258,TIGR02338,TIGR02389,TIGR02651,TIGR03626,TIGR03627,TIGR03628,TIGR03629,TIGR03653,TIGR03665,TIGR03670,TIGR03671,TIGR03672,TIGR03673,TIGR03674,TIGR03677,TIGR03680,TIGR03684,TIGR03722        PF01866.12              PF00466.15,PF01194.12,PF02006.11,PF04104.9,TIGR00337,TIGR00373,TIGR00432,TIGR00458,TIGR00549,TIGR00936,TIGR02390,TIGR03636,TIGR03683
genome_3    92      8       0       22      PF00410.14,PF00466.15,PF00687.16,PF00827.12,PF00900.15,PF01000.21,PF01090.14,PF01092.14,PF01157.13,PF01191.14,PF01194.12,PF01200.13,PF01269.12,PF01282.14,PF01496.14,PF01798.13,PF01864.12,PF01984.15,PF01990.12,PF02006.11,PF03874.11,PF04019.7,PF04104.9,PF04919.7,PF07541.7,TIGR00021,TIGR00037,TIGR00042,TIGR00064,TIGR00134,TIGR00240,TIGR00264,TIGR00270,TIGR00279,TIGR00283,TIGR00291,TIGR00293,TIGR00307,TIGR00308,TIGR00323,TIGR00324,TIGR00335,TIGR00336,TIGR00405,TIGR00408,TIGR00422,TIGR00425,TIGR00432,TIGR00448,TIGR00456,TIGR00463,TIGR00471,TIGR00490,TIGR00491,TIGR00501,TIGR00521,TIGR00522,TIGR00549,TIGR00658,TIGR00670,TIGR00729,TIGR00936,TIGR00982,TIGR01012,TIGR01018,TIGR01028,TIGR01038,TIGR01046,TIGR01060,TIGR01077,TIGR01080,TIGR01213,TIGR01952,TIGR02076,TIGR02153,TIGR02236,TIGR02338,TIGR02389,TIGR02390,TIGR03626,TIGR03627,TIGR03629,TIGR03653,TIGR03665,TIGR03670,TIGR03671,TIGR03672,TIGR03673,TIGR03677,TIGR03680,TIGR03684,TIGR03722    PF00368.13,PF01198.14,PF01866.12,PF13656.1,TIGR00392,TIGR01052,TIGR02651,TIGR03674              PF01015.13,PF01280.15,PF01655.13,PF01868.11,PF02978.14,PF13685.1,TIGR00111,TIGR00337,TIGR00373,TIGR00389,TIGR00398,TIGR00442,TIGR00458,TIGR00468,TIGR01008,TIGR01020,TIGR01025,TIGR01309,TIGR02258,TIGR03628,TIGR03636,TIGR03683
```

--------------------------------

### Tigrfam TSV Output Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/tigrfam.tsv.md

This example shows the structure of the tigrfam.tsv file, detailing sequence information, domain matches, and associated metadata. It is produced by the 'identify' and 'classify_wf' commands.

```text
#                                                               --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name        accession  query name           accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- --------------------- 
NC_013790.1_950      -          TIGR00021            TIGR00021      3e-82  272.2   0.5   3.4e-82  272.0   0.5   1.0   1   0   0   1   1   1   1 # 1219054 # 1219722 # 1 # ID=1_950;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.383
NC_013790.1_1725     -          TIGR00037            TIGR00037    8.2e-50  165.0   0.7   9.2e-50  164.8   0.7   1.0   1   0   0   1   1   1   1 # 2252948 # 2253355 # -1 # ID=1_1725;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.348
NC_013790.1_2080     -          TIGR00042            TIGR00042    4.4e-67  222.0   0.0   4.9e-67  221.8   0.0   1.0   1   0   0   1   1   1   1 # 2740928 # 2741485 # -1 # ID=1_2080;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.360
NC_013790.1_400      -          TIGR00064            TIGR00064   7.6e-102  337.2   5.8  7.6e-102  337.2   5.8   3.4   2   1   2   4   4   1   1 # 571391 # 573106 # 1 # ID=1_400;partial=00;start_type=TTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.382

```

--------------------------------

### GTDB-Tk Log Output Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/gtdbtk.log.md

This snippet shows an example of the console output captured in a GTDB-Tk log file. It includes timestamps, log levels, and GTDB-Tk commands being executed.

```text
[2020-04-14 09:14:44] INFO: GTDB-Tk v1.1.0
[2020-04-14 09:14:44] INFO: gtdbtk align --identify_dir identify_output/ --out_dir align_output --cpus 3
[2020-04-14 09:14:44] INFO: Using GTDB-Tk reference data version r89: /release89
[2020-04-14 09:14:44] INFO: Aligning markers in 3 genomes with 3 threads.
[2020-04-14 09:14:44] INFO: Processing 3 genomes identified as archaeal.
[2020-04-14 09:14:44] INFO: Read concatenated alignment for 1248 GTDB genomes.
[2020-04-14 09:14:49] INFO: Masking columns of multiple sequence alignment using canonical mask.

```

--------------------------------

### Example Output Log

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/trim_msa.md

This log output shows the execution details of the trim_msa command, including version information and the command used.

```text
[2020-04-13 10:25:13] INFO: GTDB-Tk v1.1.0
[2020-04-13 10:25:13] INFO: gtdbtk trim_msa --untrimmed_msa msa.faa --output msa_trim.faa --mask_file mask.txt
[2020-04-13 10:25:13] INFO: Using GTDB-Tk reference data version r89: /release89
[2020-04-13 10:25:13] INFO: Done.
```

--------------------------------

### Run GTDB-Tk Installation Test

Source: https://context7.com/ecogenomics/gtdbtk/llms.txt

Execute the `test` command to run a full `classify_wf` on a small dataset, verifying the installation and functionality of GTDB-Tk and its dependencies. Output can be directed to a specific directory, and CPU usage can be controlled.

```bash
# Run test in a temporary directory (auto-cleaned)
gtdbtk test
```

```bash
# Run test and keep output in a specified directory
gtdbtk test --out_dir test_output/ --cpus 4

# Successful test exits with code 0 and prints:
# [INFO] Test has successfully finished.
# On failure, see: test_output/test_execution.log
```

--------------------------------

### GTDB-Tk Classify Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/classify.md

An example of how to run the `gtdbtk classify` command using a batch file for input genomes, specifying alignment and output directories, and setting the number of CPUs.

```bash
gtdbtk classify --batchfile genomes/3_batchfile.tsv --align_dir 3_align/ --out_dir 3_classify --cpus 50
```

--------------------------------

### Example tree.mapping.tsv Content

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/tree.mapping.tsv.md

This example shows the expected format of the tree.mapping.tsv file, including genome identifiers, classification status, mapped tree class, and the classification rule.

```text
user_genome is_ani_classification   class_tree_mapped       classification_rule
3300006853_26       False   5       Rule 3
```

--------------------------------

### Download Genomes for GTDB-Tk

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/examples/classify_wf.ipynb

Creates a directory and downloads two example genomes from NCBI using wget. Ensure the target directory exists before running.

```python
# Create the directory.
!mkdir -p /tmp/gtdbtk && cd /tmp/gtdbtk

# Obtain the genomes.
!mkdir -p /tmp/gtdbtk/genomes
!wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/947/435/GCF_003947435.1_ASM394743v1/GCF_003947435.1_ASM394743v1_genomic.fna.gz -O /tmp/gtdbtk/genomes/genome_a.fna.gz
!wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/011/125/GCA_002011125.1_ASM201112v1/GCA_002011125.1_ASM201112v1_genomic.fna.gz -O /tmp/gtdbtk/genomes/genome_b.fna.gz
```

--------------------------------

### pplacer JSON Output Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/pplacer.domain.json.md

This JSON structure represents the output of the pplacer tool, including the phylogenetic tree, placement information, metadata, and version.

```json
{
  "tree":
  "((((((((((((((((((((((GB_GCA_002498125.1:0.17454{0}, ...",
  "placements":
  [
    {"p": [[0.00110044638583, 1579, 1, -3185321.84798, 0.00140069377318]],
      "nm": [["genome_2", 1]]
    },
    {"p": [[5.05004882812e-06, 1849, 1, -3541277.48905, 6.11351501465e-06]],
      "nm": [["genome_1", 1]]
    },
    {"p": [[0.00694927704923, 1579, 1, -2665208.65502, 0.0230770193005]],
      "nm": [["genome_3", 1]]
    }
  ], "metadata":
  {"invocation":
    "pplacer -m WAG -j 3 -c \/release89\/pplacer\/gtdb_r89_ar53.refpkg -o classify_output\/classify\/intermediate_results\/pplacer\/pplacer.ar53.json align_output\/align\/gtdbtk.ar53.user_msa.fasta"
  }, "version": 3, "fields":
  ["distal_length", "edge_num", "like_weight_ratio", "likelihood",
    "pendant_length"
  ]
}
```

--------------------------------

### Example FASTA MSA Entry

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/user_msa.fasta.md

This is an example entry from a FASTA file containing a Multiple Sequence Alignment (MSA). It shows a sequence header followed by aligned sequence data, including gaps represented by hyphens.

```text
>genome_3
------------------------------------------DLDAAIKCPKIGVMQGIEDGKAKVM-ANDK...
```

--------------------------------

### Pfam Search Output Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/pfam.tsv.md

This example shows the structure of the pfam.tsv file, which includes sequence identifiers, alignment details, Pfam HMM accessions and names, bit scores, and E-values.

```text
# <seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan>
NC_013790.1_1086     29    400     28    400 PF00368.13  HMG-CoA_red       Family     2   373   373    470.1  5.2e-142   1 No_clan
NC_013790.1_1218     64    245     64    245 PF02006.11  DUF137            Family     1   178   178    232.0   4.3e-70   1 No_clan
NC_013790.1_1352      2    180      1    182 PF00827.12  Ribosomal_L15e    Family     2   182   192    278.4   3.4e-84   1 No_clan
NC_013790.1_1468     19    100     19    102 PF01282.14  Ribosomal_S24e    Family     1    82    84     71.1   7.2e-21   1 No_clan
NC_013790.1_1469     45    165     43    166 PF04019.7   DUF359            Family     3   120   121    117.0   4.3e-35   1 No_clan
NC_013790.1_1475      3    120      1    121 PF01092.14  Ribosomal_S6e     Family     3   126   127    115.1   2.1e-34   1 No_clan
```

--------------------------------

### Example classification_pplacer.tsv Output

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/classification_pplacer.tsv.md

This snippet shows the typical format of the classification_pplacer.tsv file, detailing genome IDs and their taxonomic classifications.

```text
genome_2	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__
genome_3	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__
genome_1	d__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__
```

--------------------------------

### Install GTDB-Tk via pip

Source: https://context7.com/ecogenomics/gtdbtk/llms.txt

Installs GTDB-Tk using pip after ensuring third-party software is installed. The GTDBTK_DATA_PATH environment variable must be set to the location of the reference data package.

```bash
# Install third-party software first (prodigal, hmmalign, hmmsearch, pplacer, guppy, skani, FastTree)
python -m pip install gtdbtk

# Set reference data path
export GTDBTK_DATA_PATH=/path/to/release/package/
```

--------------------------------

### Install GTDB-Tk via Bioconda

Source: https://context7.com/ecogenomics/gtdbtk/llms.txt

Installs GTDB-Tk and dependencies in a dedicated conda environment. Ensure you replace '2.7.1' with the desired version. After installation, activate the environment and download the reference database.

```bash
# Create a dedicated conda environment (replace 2.7.1 with desired version)
mamba create -n gtdbtk-2.7.1 -c conda-forge -c bioconda gtdbtk=2.7.1

conda activate gtdbtk-2.7.1

# Download and extract GTDB reference data (~100 GB)
download-db.sh

# Or download manually and set the environment variable
wget https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/auxillary_files/gtdbtk_package/full_package/gtdbtk_data.tar.gz
tar xvzf gtdbtk_data.tar.gz
conda env config vars set GTDBTK_DATA_PATH="/path/to/unarchived/gtdbtk/data"
```

--------------------------------

### ani_rep Example Output Log

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/ani_rep.md

This is a sample log output from the `ani_rep` command, showing the progress from initialization to completion, including file paths for summary and closest hit results.

```text
[2025-08-05 17:13:33] INFO: GTDB-Tk v2.5.0
[2025-08-05 17:13:33] INFO: gtdbtk ani_rep --batchfile genomes/500_batchfile.tsv -x fa --out_dir test_ani_reps --cpus 90
[2025-08-05 17:13:33] INFO: Using GTDB-Tk reference data version r226: /srv/db/gtdbtk/official/release226
[2025-08-05 17:13:34] INFO: Loading reference genomes.
[2025-08-05 17:13:39] INFO: Calculating all vs all ANI with skani v0.2.1.
[2025-08-05 17:13:40] INFO: Sketching genomes
[2025-08-05 17:15:52] INFO: Sketches done: 2min 11secs
[2025-08-05 17:15:52] INFO: Running comparisons
[2025-08-05 17:21:15] INFO: Comparisons finished, capturing results.
[2025-08-05 17:23:26] INFO: Summary of results saved to: test_ani_reps/gtdbtk.ani_summary.tsv
[2025-08-05 17:23:27] INFO: Closest representative hits saved to: test_ani_reps/gtdbtk.ani_closest.tsv
[2025-08-05 17:23:27] INFO: Done.
```

--------------------------------

### Example filtered.tsv Content

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/filtered.tsv.md

This example shows the typical format of the filtered.tsv file, indicating genomes with insufficient amino acids for MSA.

```text
genome_3	Insufficient number of amino acids in MSA (73.1%)
genome_2	Insufficient number of amino acids in MSA (87.1%)
genome_1	Insufficient number of amino acids in MSA (97.1%)
```

--------------------------------

### Newick Format Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/classify.tree.md

This is an example of the Newick format used for phylogenetic trees. It represents the hierarchical relationships between taxa and branch lengths.

```text
((((((((((((((((((((((GB_GCA_002498125.1:0.17454,UBA10207:0.18672)'1.0:g__UBA52...
```

--------------------------------

### View GTDB-Tk Help Menu

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/index.md

Access the main help documentation for GTDB-Tk. This command provides an overview of available subcommands and general usage.

```bash
gtdbtk -h
```

--------------------------------

### Install GTDB-Tk with Mamba

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/includes/install_block.md

An alternative to conda, mamba can also be used to create an environment and install GTDB-Tk. Replace '2.7.1' with your desired version.

```bash
# using mamba (alternative)
mamba create -n gtdbtk-2.7.1 -c conda-forge -c bioconda gtdbtk=2.7.1
```

--------------------------------

### Decorate Command Usage

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/commands/decorate.md

This shows the basic usage of the decorate command with required input and output tree arguments. Note that the core functionality is not yet implemented.

```bash
usage: gtdbtk decorate --input_tree INPUT_TREE --output_tree OUTPUT_TREE
                       [--gtdbtk_classification_file GTDBTK_CLASSIFICATION_FILE]
                       [--custom_taxonomy_file CUSTOM_TAXONOMY_FILE]
                       [--tmpdir TMPDIR] [--debug] [-h]
```

--------------------------------

### Unrooted Tree Example

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/files/unrooted.tree.md

This is an example of the Newick format used to represent an unrooted phylogenetic tree. It shows a single genome with a branch length.

```text
(genome_a:0.000000000);
```

--------------------------------

### Install GTDB-Tk with Conda

Source: https://github.com/ecogenomics/gtdbtk/blob/master/docs/src/includes/install_block.md

Use this command to create a new conda environment and install GTDB-Tk version 2.7.1. Replace '2.7.1' with your desired version.

```bash
# NOTE: replace 2.7.1 with the version you wish to install

# using conda
conda create -n gtdbtk-2.7.1 -c conda-forge -c bioconda gtdbtk=2.7.1
```