[] are not present in the input list of genome to process

[anatmaozcrispr]

running: gtdbtk de_novo_wf --batchfile run_genomes.txt --bacteria --outgroup_taxon p__Chloroflexota --out_dir gtdb -x fa --cpus 10 --force --debug [2023-09-20 18:41:24] ERROR: [] are not present in the input list of genome to process. [2023-09-20, 21:41:24 IDT] {pod_manager.py:382} INFO - [2023-09-20 18:41:24] ERROR: Controlled exit resulting from an unrecoverable error or warning. there are 11 bacteria that Prodigal cannot find genes for. BUT de_novo_wf throws an exception instead of continuing with the rest. I thought "--force" would take care of it.

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 ID of 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.log has been included (drag and drop the file to upload).
• [ ] Genomes have been included (if possible, and there are few).

Additional comments

[anatmaozcrispr]

anyone knows why "--force" does not do anything?

[pchaumeil]

Hello, Seems like an issue with Tk Are you getting this error when you run --force on a new output_directory? or an existing one with data already in it?