--trans_table parameter not working as expected

[m-taubert]

Hi,

I recently wanted to use DRAM to annotate genomes of Gracilibacteria that use a non-standard translation table. I specified the translation table via DRAM.py annotate [...] --trans_table 25, however, the results I got were still based on the standard (table 11). By doing some troubleshooting with running prodigal alone, I found out that prodigal ignores the specified translation table when the meta mode is specified.

So, this seems to be a prodigal issue rather than a DRAM issue. However, DRAM calls prodigal in meta mode by default and still allows a selection of a translation table via --trans_table (which won't be used). This will trick users into believing a non-default translation table was used, when in fact, it wasn't. Hence I think it's worth highlighting it here. The obvious work-around is to run DRAM with --prodigal_mode single (which has the downside of not using contigs below 3 kb).

Best