Making our own database error

[daniel251994]

I have followed the steps exactly as described for making our own database using Abricate. In my case, i am making a database of arcobacter that contains 46 sequences, and the database name assigned is "arcodb" while the sequence file in fasta format is named as "sequences.fa". However after this step : makeblastdb -in sequences.fa -title arcodb -dbtype nucl -hash_index, the database arcodb is not listed after the "abricate --list" command, even after the database is created successfully. I am currently using abricate through conda. I kindly request you to help me with this issue.

[buihoangphuc412]

I think you should delete the format .fa of sequences.fa into sequences only when make your own databases. Since abricate cannot identify sequences.fa in db.

[daniel251994]

Ok i will try that soon, Thank you very much for your reply.

[daniel251994]

I did remove the format .fa but i got the same results.

[buihoangphuc412]

I see. I usually do not use the hash_index argument but I think it is no problem. Did you try command? abricate --setupdb It will add your own databse into the database list!

[daniel251994]

Yes, before running the makeblastdb, i already ran abricate --setupdb but arcodb wasn't added so i went for makeblastdb.

[buihoangphuc412]

After you makeblastdb, you should type this command, not before!

[daniel251994]

ok i will check . Thank you once again

[daniel251994]

It still didn't work. But I was able to avoid this issue by not using conda, in other words I have install abricate separately from source outside conda and everything went fine.