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zhangrengang / TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
https://doi.org/10.1093/hr/uhac017
GNU General Public License v3.0
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Add -f for hmmpress #5

Closed oushujun closed 4 years ago

oushujun commented 4 years ago

I updated from the last version and use sh build_database.sh to rebuild hmm profiles. I got the following information and yet TEsorter still asked me to rebuid hmm profiles. So I think it would be good to use the -f option for hmmpress to overwrite any prebuilt libraries.

# hmmpress :: prepare an HMM database for faster hmmscan searches # HMMER 3.2.1 (June 2018); http://hmmer.org/ # Copyright (C) 2018 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Usage: hmmpress [-options]

Options: -h : show brief help on version and usage -f : force: overwrite any previous pressed files SSI index file database/GyDB2.hmm.h3i already exists; Delete old hmmpress indices first SSI index file database/REXdb_protein_database_metazoa_v3.hmm.h3i already exists; Delete old hmmpress indices first SSI index file database/REXdb_protein_database_viridiplantae_v3.0.hmm.h3i already exists; Delete old hmmpress indices first SSI index file database/REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm.h3i already exists; Delete old hmmpress i

Best, Shujun

zhangrengang commented 4 years ago

I have fixed it.