Error in the add_to_db step. Cannot create the file Host_genomes.nal

[Apoorva Prabhu]

Thank you for the useful tool, we have installed iphop_1.3.3 and downloaded the latest db Aug23. At first I created a new database with 2,459 genomes and ran the iphop predict, and in the results the blast steps doesn’t run ( I have no blast results in the output). The log file indicates I have no index file found for nucleotide database in search path. I noticed that in the new database (new_db/db/Host_genomes), the file Host_genome.nal is not created and this is an error during the add_to_db step. Would there be something wrong with my command? Or something to be fixed? For the --db_dir, I provided an absolute path, but symlinked the directory.

All other db seems to work fine, just the blast one.

[Apoorva Prabhu]

Just to add to this, I get this error even when testing : BLAST Database error: Cannot memory map /srv/db/iphop/Aug_2023_pub_rw/db/Host_Genomes/Host_Genomes.nal. Number of files opened: 0 . I also tested with older sept2021 db, and it seems to work fine.

[Simon Roux]

Hi,

I don’t think something is wrong with your command, but something definitely need to be fixed. The first step would probably be to verify that the download of the database worked as expected. Could you try:

$ iphop download --db_dir /path/to/Aug_2023_pub_rw/ --full_verify

This should make sure that all the relevant files are present and have the expected content. If this is the case, then we’ll have to look into the nal file because these are text files that should not cause major issues, typically.