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[] are not present in the input list of genome to process #549

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anatmaozcrispr opened this issue Sep 21, 2023 · 2 comments
Closed
5 tasks

[] are not present in the input list of genome to process #549

anatmaozcrispr opened this issue Sep 21, 2023 · 2 comments
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error Help required for a GTDB-Tk error. next version Upcoming feature/fix in staging branch.

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@anatmaozcrispr
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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 anatmaozcrispr added the error Help required for a GTDB-Tk error. label Sep 21, 2023
@anatmaozcrispr
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anyone knows why "--force" does not do anything?

@pchaumeil
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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?

pchaumeil added a commit that referenced this issue Nov 23, 2023
This commit is to fix few bugs:
- #540 : The empty files are skip during the sketch step of Mash,
they are then catch in the prodigal step and are returned as Unclassified
- #549 : `--force` has been modified to deal with #540
- Prodigal wasn't returning the empty files as failed genomes, it was only skipping them.
These genomes are now returned in the summary file and flagged as Unclassified.
@pchaumeil pchaumeil added the next version Upcoming feature/fix in staging branch. label Nov 24, 2023
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Labels
error Help required for a GTDB-Tk error. next version Upcoming feature/fix in staging branch.
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