We have DRAM (1.4.6) set up with the full KEGG database, which has been working ok. But I recently wanted to run some viral contigs using kofam instead of full KEGG via DRAM-v.py annotate --low_mem_mode. The annotate step completed, but then DRAM-v.py distill gave the error: KeyError: 'vogdb_categories'
Checking annotation.tsv, vogdb_categories is indeed missing. But a similar run without --low_mem_mode did have vogdb_categories (and that worked with distill).
I tracked down this section in database_handler.py, where the --low_mem_mode settings are applied:
if low_mem_mode:
if ("kofam_hmm" not in self.config.get("search_databases")) or (
"kofam_ko_list" not in self.config.get("search_databases")
):
raise ValueError(
"To run in low memory mode KOfam must be configured for use in DRAM"
)
dbs_to_use = [i for i in dbs_to_use if i not in ("uniref", "kegg", "vogdb")]
So, evidently (based on the last line above) --low_mem_mode always excludes vogdb as well as uniref and kegg (although the help message only notes the latter two), but vogdb is required for DRAM-v's version of distill.
Is it possible to have --low_mem_mode behave differently for DRAM.py and DRAM-v.py, so that the latter doesn't exclude vogdb? Or alternatively, remove vogdb from that --low_mem_mode exclusion list above, but add an additional --exclude_vogdb option seperately?
Hi there,
We have DRAM (1.4.6) set up with the full KEGG database, which has been working ok. But I recently wanted to run some viral contigs using kofam instead of full KEGG via
DRAM-v.py annotate --low_mem_mode. The annotate step completed, but thenDRAM-v.py distillgave the error:KeyError: 'vogdb_categories'Checking annotation.tsv, vogdb_categories is indeed missing. But a similar run without
--low_mem_modedid have vogdb_categories (and that worked with distill).I tracked down this section in
database_handler.py, where the--low_mem_modesettings are applied:So, evidently (based on the last line above)
--low_mem_modealways excludes vogdb as well as uniref and kegg (although the help message only notes the latter two), but vogdb is required for DRAM-v's version of distill.Is it possible to have
--low_mem_modebehave differently for DRAM.py and DRAM-v.py, so that the latter doesn't exclude vogdb? Or alternatively, remove vogdb from that--low_mem_modeexclusion list above, but add an additional--exclude_vogdboption seperately?Cheers! Mike.