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gbouras13 / pharokka

fast phage annotation program
MIT License
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Can't use the downloaded db #358

Closed AnneliektH closed 1 month ago

AnneliektH commented 1 month ago

Hey! Trying to use pharokka, but in order to do so I am trying to get the databases: Tried the following: 

install_databases.py -o /home/amhorst/databases/pharokka

PHROGs Databases are missing. Pharokka Database Will be Downloaded
VFDB Databases are missing. Pharokka Database Will be Downloaded
CARD Databases are missing. Pharokka Database Will be Downloaded
PHROGs Annotation File Needs to be Downloaded
Downloading Pharokka Database
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   295  100   295    0     0    511      0 --:--:-- --:--:-- --:--:--   511

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

Using -d gives the same error

Also tried downloading the db using command line, then untar it which seems to have worked: In the database folder:

1Aug2023_data.tsv             aro_index.tsv                       phrogs_profile_db_seq.dbtype
1Aug2023_genomes.fa.msh       phrog_annot_v4.tsv                  phrogs_profile_db_seq.index
CARD                          phrogs_db                           phrogs_profile_db_seq_h
CARD.dbtype                   phrogs_db.dbtype                    phrogs_profile_db_seq_h.index
CARD.index                    phrogs_db.index                     vfdb
CARD.lookup                   phrogs_profile_db                   vfdb.dbtype
CARD.source                   phrogs_profile_db.dbtype            vfdb.index
CARD_h                        phrogs_profile_db.index             vfdb.lookup
CARD_h.dbtype                 phrogs_profile_db_consensus         vfdb.source
CARD_h.index                  phrogs_profile_db_consensus.dbtype  vfdb_h
VFDB_setB_pro.fas.gz          phrogs_profile_db_consensus.index   vfdb_h.dbtype
VFDBclusterRes_cluster.tsv    phrogs_profile_db_h                 vfdb_h.index
VFDBclusterRes_rep_seq.fasta  phrogs_profile_db_h.index
all_phrogs.h3m                phrogs_profile_db_seq

When running pharokka pointing to db location I get the following error:

pharokka.py -i vir_23.fa -o ./pharokka -d /home/amhorst/databases/pharokka_v1.4.0_databases/ -t 1 -p vir_23 

Starting pharokka v1.1.0
Checking database installation
VFDB Databases are missing. Pharokka Database Will be Downloaded

The database directory was unsuccessfully checked. Please run install_databases.py

What am I doing wrong?

AnneliektH commented 1 month ago

Nevermind just saw the closed issue, will try different version!