An error was encountered while running hmmsearch. #692
Description
Environment
- Installed via pip (include the output of
pip list) - Using a conda environment (include the output of
conda list && conda list --revisions) - Using a Docker container (include the
IMAGE IDof the container)
Server information
- CPU:
grep -m 1 "^model name" /proc/cpuinfo && grep -c "^processor" /proc/cpuinfo - RAM:
grep "^MemTotal" /proc/meminfo - OS:
cat /etc/os-release
Debugging information
-
gtdbtk.loghas been included (drag and drop the file to upload). - Genomes have been included (if possible, and there are few).
[2026-03-10 18:10:34] INFO: GTDB-Tk v2.4.0
[2026-03-10 18:10:34] INFO: gtdbtk classify_wf --genome_dir ./ --out_dir ./classify_wf --prefix bin123 --cpus 1 --pplacer_cpus 1 --skip_ani_screen --full_tree --scratch_dir ./
[2026-03-10 18:10:34] INFO: Using GTDB-Tk reference data version r220: /media/home/database/gtdbnew/release220
[2026-03-10 18:10:34] INFO: Identifying markers in 14 genomes with 1 threads.
[2026-03-10 18:10:34] TASK: Running Prodigal V2.6.3 to identify genes.
[2026-03-10 18:16:01] INFO: Completed 14 genomes in 5.45 minutes (2.57 genomes/minute).
[2026-03-10 18:16:01] TASK: Identifying TIGRFAM protein families.
[2026-03-10 18:16:09] ERROR: An error was encountered while running hmmsearch.
[2026-03-10 18:16:09] ERROR: Controlled exit resulting from an unrecoverable error or warning.
Additional comments
I referred to your previous answer and downgraded hmmsearch to version 3.1b2, but I'm still getting the same error. I'm wondering if there's something wrong with my command? My previous command was:
gtdbtk classify_wf --genome_dir ./ --out_dir ./classify_wf --prefix bin123 --cpus 1 --pplacer_cpus 1 --skip_ani_screen --full_tree --scratch_dir ./
The input files are in this format.
