Running gtdbtk classify_wf resulted in only an archaeal output, bacterial output was not created. I am wondering if it is a error in how the database was downloaded, the quality of my input data (which is quite good actually), or using the --skip_ani_screen flag.
Here is the code used (after the database was downloaded):
#Activate your needed conda environment using source activate {path}/env
source activate {path}/GTDB_new_env
export GTDBTK_DATA_PATH={path}/share/gtdbtk-2.3.0/db
gtdbtk classify_wf --genome_dir {path}/contigs --out_dir {path}/output --skip_ani_screen
Here is the logfile:
[2024-04-19 16:18:54] INFO: GTDB-Tk v2.3.2
[2024-04-19 16:18:54] INFO: gtdbtk classify_wf --genome_dir {path}/contigs --out_dir {path}/output --skip_ani_screen
[2024-04-19 16:18:54] INFO: Using GTDB-Tk reference data version r214: {path}/gtdbtk-2.3.0/db
[2024-04-19 16:18:54] INFO: Identifying markers in 1 genomes with 1 threads.
[2024-04-19 16:18:54] TASK: Running Prodigal V2.6.3 to identify genes.
[2024-04-19 16:31:57] INFO: Completed 1 genome in 13.04 minutes (13.04 minutes/genome).
[2024-04-19 16:31:57] TASK: Identifying TIGRFAM protein families.
[2024-04-19 16:40:32] INFO: Completed 1 genome in 8.58 minutes (8.58 minutes/genome).
[2024-04-19 16:40:32] TASK: Identifying Pfam protein families.
[2024-04-19 16:40:52] INFO: Completed 1 genome in 20.39 seconds (20.39 seconds/genome).
[2024-04-19 16:40:52] INFO: Annotations done using HMMER 3.4 (Aug 2023).
[2024-04-19 16:40:52] TASK: Summarising identified marker genes.
[2024-04-19 16:40:58] INFO: Completed 1 genome in 6.38 seconds (6.38 seconds/genome).
[2024-04-19 16:40:58] INFO: Done.
[2024-04-19 16:41:02] INFO: Aligning markers in 1 genomes with 1 CPUs.
[2024-04-19 16:41:02] INFO: Processing 1 genomes identified as archaeal.
[2024-04-19 16:41:02] INFO: Read concatenated alignment for 4,416 GTDB genomes.
[2024-04-19 16:41:02] TASK: Generating concatenated alignment for each marker.
[2024-04-19 16:41:05] INFO: Completed 1 genome in 3.11 seconds (3.11 seconds/genome).
[2024-04-19 16:41:05] TASK: Aligning 14 identified markers using hmmalign 3.4 (Aug 2023).
[2024-04-19 16:41:06] INFO: Completed 14 markers in 0.44 seconds (31.89 markers/second).
[2024-04-19 16:41:06] TASK: Masking columns of archaeal multiple sequence alignment using canonical mask.
[2024-04-19 16:41:10] INFO: Completed 4,417 sequences in 3.90 seconds (1,131.46 sequences/second).
[2024-04-19 16:41:10] INFO: Masked archaeal alignment from 13,540 to 10,135 AAs.
[2024-04-19 16:41:10] INFO: 0 archaeal user genomes have amino acids in <10.0% of columns in filtered MSA.
[2024-04-19 16:41:10] INFO: Creating concatenated alignment for 4,417 archaeal GTDB and user genomes.
[2024-04-19 16:41:12] INFO: Creating concatenated alignment for 1 archaeal user genomes.
[2024-04-19 16:41:12] INFO: Done.
[2024-04-19 16:41:12] TASK: Placing 1 archaeal genomes into reference tree with pplacer using 1 CPUs (be patient).
[2024-04-19 16:41:12] INFO: pplacer version: v1.1.alpha19-0-g807f6f3
[2024-04-19 16:42:04] INFO: Calculating RED values based on reference tree.
[2024-04-19 16:42:05] TASK: Traversing tree to determine classification method.
[2024-04-19 16:42:05] INFO: Completed 1 genome in 0.00 seconds (276.10 genomes/second).
[2024-04-19 16:42:05] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2024-04-19 16:42:05] WARNING: 1 of 1 genome has a warning (see summary file).
[2024-04-19 16:42:05] INFO: Note that Tk classification mode is insufficient for publication of new taxonomic designations. New designations should be based on one or more de novo trees, an example of which can be produced by Tk in de novo mode.
[2024-04-19 16:42:05] INFO: Done.
[2024-04-19 16:42:05] INFO: Removing intermediate files.
[2024-04-19 16:42:05] INFO: Intermediate files removed.
[2024-04-19 16:42:05] INFO: Done.