Rory M Flynn
Rory M Flynn
Just want to add my vote for this feature!
You will want to increase your memory, as mmseqs has likely been killed by your memory management system, [As in this issue](https://github.com/soedinglab/MMseqs2/issues/431). Heed this warning from the README. "NOTE: Setting...
Memory remains the biggest stumbling block to dram, but I will not be able to fix this today.
This may be a problem best answered by @shafferm, but while he is unavailable, here are some things you could try (in order of most to least likely to help)...
The problem does look to be specific to the Zenodo data. I can confirm that that profile is missing from the kofam_ko_list.tsv, and it only exists in the kofam_profiles.hmm from...
The solution may be as simple at `DRAM-setup.py export_config --output_file fix_me.txt ` then open fix_me.text find `"kofam": "/None_h"` and `"uniref": "/None_h"` make them `"kofam": null` and `"uniref": null` then save...
Let me know if you have problems after that, and I will address them!
Sorry tipo in the commands above, when you use `DRAM-setup.py export_config --output_file fix_me.txt` what are the contents of the `fix_me.txt` file?
Try replacing it with this `{"kegg": null, "kofam": "/home/user/wmg_tools/annotation/DRAM_data/kofam_profiles.hmm", "kofam_ko_list": "/home/user/wmg_tools/annotation/DRAM_data/kofam_ko_list.tsv", "uniref": null, "pfam": "/home/user/wmg_tools/annotation/DRAM_data/pfam.mmspro", "dbcan": "/home/user/wmg_tools/annotation/DRAM_data/dbCAN-HMMdb-V10.txt", "viral": "/home/user/wmg_tools/annotation/DRAM_data/refseq_viral.20220221.mmsdb", "peptidase": "/home/user/wmg_tools/annotation/DRAM_data/peptidases.20220221.mmsdb", "vogdb": "/home/user/wmg_tools/annotation/DRAM_data/vog_latest_hmms.txt", "pfam_hmm_dat": "/home/user/wmg_tools/annotation/DRAM_data/Pfam-A.hmm.dat.gz", "dbcan_fam_activities": "/home/user/wmg_tools/annotation/DRAM_data/CAZyDB.07292021.fam-activities.txt", "vog_annotations": "/home/user/wmg_tools/annotation/DRAM_data/vog_annotations_latest.tsv.gz", "genome_summary_form":...
It can't be `None` it must be `null`, it looks like a python dict, but it is not.