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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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mob_typer running error? #130

Closed sekhwal closed 1 year ago

sekhwal commented 1 year ago

I installed the pipeline using conda. However, when I run it, it shows the following error.

(mob_env)U:~/mob.suite_run$ mob_typer --infile node2.fasta --out_file re.txt

2023-02-18 21:55:12,219 mob_suite.mob_typer INFO: Running Mob-typer version 3.1.4 [in /home/anaconda3/envs/mob_env/lib/python3.8/site-packages/mob_suite/mob_typer.py:173] 2023-02-18 21:55:12,219 mob_suite.mob_typer INFO: Processing fasta file node2.fasta [in /home/anaconda3/envs/mob_env/lib/python3.8/site-packages/mob_suite/mob_typer.py:175] 2023-02-18 21:55:12,219 mob_suite.mob_typer INFO: SUCCESS: Found program blastn at /home/anaconda3/envs/mob_env/bin/blastn [in /home/anaconda3/envs/mob_env/lib/python3.8/site-packages/mob_suite/utils.py:592] 2023-02-18 21:55:12,219 mob_suite.mob_typer INFO: SUCCESS: Found program makeblastdb at /home/anaconda3/envs/mob_env/bin/makeblastdb [in /home/anaconda3/envs/mob_env/lib/python3.8/site-packages/mob_suite/utils.py:592] 2023-02-18 21:55:12,219 mob_suite.mob_typer INFO: SUCCESS: Found program tblastn at /home/anaconda3/envs/mob_env/bin/tblastn [in /home/anaconda3/envs/mob_env/lib/python3.8/site-packages/mob_suite/utils.py:592] 2023-02-18 21:55:12,219 mob_suite.mob_typer INFO: Warning! Needed database missing "/home/anaconda3/envs/mob_env/lib/python3.8/site-packages/mob_suite/databases/ncbi_plasmid_full_seqs.fas.msh" [in /home/anaconda3/envs/mob_env/lib/python3.8/site-packages/mob_suite/mob_typer.py:321] usage: mob_typer [-h] [-d DATABASE_DIRECTORY] [-v] [-V] mob_typer: error: unrecognized arguments: --infile node2.fasta --out_file re.txt

jrober84 commented 1 year ago

The error here is pointing a missing database. You need to download and initialize the various databases using mob_init. Please run mob_init and see if that resolves the issue.