Error running Prodigal on genome

fhdbqr commented 9 months ago

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: Intel(R) Xeon(R) CPU E5-4657L v2 @ 2.40GHz 48
RAM: 792598980 kB
OS: Ubuntu 20.04.4 LTS

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

Hello everyone, I've come across an error while running 'classify_wf' or 'identify' modules': 'Error running Prodigal on the genome, free(): invalid pointer. This genome is skipped.' However, there were no details in 'gtdbtk.failed_genomes.tsv'. Interestingly, when I individually run Prodigal V2.6.3 with these bins, no errors arise. Any suggestions on how to resolve this? gtdbtk.log gtdbtk.failed_genomes.txt

pchaumeil commented 5 months ago

Hello, Apologies for the very late reply. Do you still have an issue with Prodigal?

fhdbqr commented 5 months ago

Hello, Yes, this error occurred during the execution of certain MAGs; however, the overall process was successfully completed.

pchaumeil commented 5 months ago

Could you please send few MAGS generating this error? Thanks, Pierre

fhdbqr commented 5 months ago

I'm sorry for the delay. Here's an example where the aforementioned problem might occur. It contains a 'binning' file and an output folder from GTDBTk. example.tar.gz

Ecogenomics / GTDBTk