I have tried to annotate some HQ MAG data using the EnrichM 0.5.0 software with the enrichm_database_v10.
In my final KO frequency table i only get untill K21032 and I specifically need K21563.
When i look into the database I can see that in KO_IDS.txt and gtdb_ko.tsv, they only contain untill K21032. However, the ko00000.tsv and ko_cutoffs.tsv contains my desired K21563.
The codes i used in a bash terminal (it works, and will be happy to send the full code/error files if needed):
enrichm annotate --genome_directory /my-directory --suffix fa --ko --threads 40 --output /path/file
when the annotation crashes after prodigal:
enrichm annotate --protein_directory /path/genome_proteins --ko --threads 40 --output /path/MGP1000_fa_enrichm_annotate
This gives my desired ko_frequency_table.tsv. However, it cuts of at K21032.
Is there a fix to this or is it on my end, where I "just" need to add the KEGG modules manually to the KO_IDS.txt and/or gtdb_ko.tsv (or other files) or is this a bigger problem than so?
Hello Joel
I have tried to annotate some HQ MAG data using the EnrichM 0.5.0 software with the enrichm_database_v10. In my final KO frequency table i only get untill K21032 and I specifically need K21563. When i look into the database I can see that in KO_IDS.txt and gtdb_ko.tsv, they only contain untill K21032. However, the ko00000.tsv and ko_cutoffs.tsv contains my desired K21563.
The codes i used in a bash terminal (it works, and will be happy to send the full code/error files if needed): enrichm annotate --genome_directory /my-directory --suffix fa --ko --threads 40 --output /path/file when the annotation crashes after prodigal: enrichm annotate --protein_directory /path/genome_proteins --ko --threads 40 --output /path/MGP1000_fa_enrichm_annotate
This gives my desired ko_frequency_table.tsv. However, it cuts of at K21032. Is there a fix to this or is it on my end, where I "just" need to add the KEGG modules manually to the KO_IDS.txt and/or gtdb_ko.tsv (or other files) or is this a bigger problem than so?
Best Regards, Patrick