Command not found iphop add_to_db
Issue #16
resolved
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?
Comments (4)
-
repo owner -
reporter Yeah, that was the issue. I thought I had activated but I was wrong.
Thank you! -
repo owner Great, thanks for letting us know !
-
repo owner - changed status to resolved
Bug fixed
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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” ?