Hi,
I recently worked with MAGs of Gracilibacteria that use a non-standard translation table. I specified the translation table via -g 25 while running prodigal V2.6.3 with -p meta, however, the results I got were the same as when running with -g 11. During troubleshooting I also ran prodigal in single mode, and there I got different results for -g 25 and -g 11, as expected.
Maybe that's intended, but I checked the wiki and the issues and didn't find anything about -g xx not working when -p meta is specified. Also, calling prodigal with both options didn't throw an error or warning to notify me that these parameters are not compatible. This might trick users into believing the selected translation table was used when, in fact, the default was used.
I originally came across this issue when using DRAM, which calls prodigal in meta mode by default yet still allows specification of a translation table... with the same result that the specified translation table is not used.
Best
Hi,
I recently worked with MAGs of Gracilibacteria that use a non-standard translation table. I specified the translation table via
-g 25while running prodigal V2.6.3 with-p meta, however, the results I got were the same as when running with-g 11. During troubleshooting I also ran prodigal in single mode, and there I got different results for-g 25and-g 11, as expected.Maybe that's intended, but I checked the wiki and the issues and didn't find anything about
-g xxnot working when-p metais specified. Also, calling prodigal with both options didn't throw an error or warning to notify me that these parameters are not compatible. This might trick users into believing the selected translation table was used when, in fact, the default was used.I originally came across this issue when using DRAM, which calls prodigal in meta mode by default yet still allows specification of a translation table... with the same result that the specified translation table is not used.
Best