SemiBin2 runs prodigal even when --prodigal-output-faa is provided

[jolespin]

I've added SemiBin2 as one of the default prokaryotic binning algorithms in VEBA v2.4.0 to replace some of the more dated binning algorithms (e.g., MaxBin2). I'm trying to decrease redundancies in my workflow since I want to be able to scale VEBA up to thousands of samples. Since the prokaryotic binning module runs iteratively there is a good amount of redundant compute by performing gene calls each time.

When I run btop, I can see that prodigal is running in the backend tied back to the SemiBin2 process (I forgot to screenshot it but noticed it a few times. I can rerun if needed).

Here's my command:

SemiBin2 --version
2.1.0

SemiBin2 single_easy_bin -i scaffolds.fasta --depth-metabat2 ../Analysis/veba_output/binning/prokaryotic/S1/intermediate/1__coverage/coverage_metabat.tsv -o ../Analysis/veba_output/binning/prokaryotic/S1/intermediate/6__binning_semibin2/intermediate -m 1500 -p 16 --environment global --prodigal-output-faa ../Analysis/veba_output/binning/prokaryotic/S1/intermediate/2__pyrodigal/gene_models.faa --minfasta-kbs 200 --random-seed 1 --verbose --tmpdir ../Analysis/veba_output/binning/prokaryotic/S1/intermediate/6__binning_semibin2/intermediate/tmp --engine auto --compression none --tag-output bin --sequencing-type short_read

Is there any way you can look into this?