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gbouras13 / pharokka

fast phage annotation program
MIT License
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database error #309

Closed mengyuan09876 closed 7 months ago

mengyuan09876 commented 7 months ago

Description

“2023-12-07 15:51:55.033 | INFO | main:main:105 - Starting Pharokka v1.5.1 2023-12-07 15:51:55.034 | INFO | main:main:106 - Command executed: Namespace(infile='./finalVir/0_101.fasta', outdir='./pharokka_virus3/', database='Default', threads='20', force=False, prefix='Default', locustag='Default', gene_predictor='phanotate', meta=False, split=False, coding_table='11', evalue='1E-05', fast=False, mmseqs2_only=False, meta_hmm=False, dnaapler=False, custom_hmm='', genbank=False, terminase=False, terminase_strand='nothing', terminase_start='nothing', skip_extra_annotations=False, skip_mash=False, citation=False) 2023-12-07 15:51:55.034 | INFO | main:main:107 - Repository homepage is https://github.com/gbouras13/pharokka 2023-12-07 15:51:55.034 | INFO | main:main:108 - Written by George Bouras: george.bouras@adelaide.edu.au 2023-12-07 15:51:55.034 | INFO | main:main:110 - Checking database installation in /home/bioinfo/bin/anaconda/envs/pharokka/bin/pharokka.py/../databases/. 2023-12-07 15:51:55.034 | INFO | databases:check_db_installation:213 - PHROGs Databases are missing. 2023-12-07 15:51:55.034 | INFO | databases:check_db_installation:220 - VFDB Databases are missing. 2023-12-07 15:51:55.035 | INFO | databases:check_db_installation:227 - CARD Databases are missing. 2023-12-07 15:51:55.035 | INFO | databases:check_db_installation:233 - PHROGs Annotation File is missing. 2023-12-07 15:51:55.035 | INFO | databases:check_db_installation:239 - INPHARED Mash Annotation File is missing. 2023-12-07 15:51:55.035 | INFO | databases:check_db_installation:245 - INPHARED Mash Sketch File is missing. 2023-12-07 15:51:55.035 | ERROR | main:main:115 - The database directory was unsuccessfully checked. Please run install_databases.py.”

What I Did

I use bioconda installed pharokka and database, after I run install_databases.py,this problem still there.

gbouras13 commented 7 months ago

Hi @mengyuan09876 ,

I'd try install and running pharokka with a specific database directory specified with -d:

install_databases.py -o my_pharokka_database_directory

pharokka.py -i  finalVir/0_101.fasta' -o pharokka_virus3 -d my_pharokka_database_directory -t 20

George

mengyuan09876 commented 7 months ago

hi, thanks for your reply, it started working when I specified the path

George Bouras @.***> 于2023年12月7日周四 23:51写道：

Hi @mengyuan09876 https://github.com/mengyuan09876 ,

I'd try install and running pharokka with a specific database directory specified with -d:

install_databases.py -o my_pharokka_database_directory

pharokka.py -i finalVir/0_101.fasta' -o pharokka_virus3 -d my_pharokka_database_directory -t 20

George

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