Command not found iphop add_to_db

[Christina Pavloudi]

Hello!
I have already ran iphop predict, with the latest host database, and it worked fine.

Now I want to run it add my MAGs to the host database using the command
iphop add_to_db --fna_dir /virus_analysis/bins/ --gtdb_dir /virus_analysis/gtdb-tk_out/ --out_dir iphop_hosts/ --db_dir /christina/iphop_db/Sept_2021_pub/ -t 32

but I got the error
/cm/local/apps/slurm/var/spool/job2125194/slurm_script: line 16: iphop: command not found

Do you have any idea why this might be happening?

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[Simon Roux]

Hi,

“iphop: command not found” looks like the conda environment (assuming you installed through conda) was not properly loaded. Can you check in the slurm script whether the proper environment is loaded prior to “iphop add_to_db” ?

[Christina Pavloudi]

Yeah, that was the issue. I thought I had activated but I was wrong.
Thank you!

[Simon Roux]

Great, thanks for letting us know !

[Simon Roux]

Bug fixed