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EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes
GNU General Public License v3.0
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Eukcc Failure #16

Closed u15412611 closed 3 years ago

u15412611 commented 3 years ago

Good day Thank you for such a great program I have installed it on a linux system through conda env. I have tried to run it on a set of bins obtained via concoct. I get the following error.

_check before run create directories commit input data soft_mask is in the 'auto' mode. soft_mask was set to: 1000 data report commit training data error, not enough sequnce to run training in file /home/percy/repcontigs/contigs/Eukbins/eukb/workfiles/gmes/data/training.fna (in cleanup) Can't call method "FETCH" on an undefined value at /usr/local/share/perl5/Object/InsideOut.pm line 1953 during global destruction.

please could you assist ?

openpaul commented 3 years ago

Hello, this seems like GeneMark-ES failed. Did you manage to run the minimal example from the documentation? https://eukcc.readthedocs.io/en/latest/install.html#quickstart-and-testing

If GeneMark-ES fails, EukCC also fails. Your current best bet is then to run either GeneMark-ES manually or use some other form of protein prediction for Eukaryotes.

Incomplete bins are often the cause of such failures.

openpaul commented 3 years ago

I will close this for now, please reopen if you could not solve the issue.