Error biostudio- genedesign

01 January 1970 1 9K Report

I am trying to run BioStudio and GeneDesign to design a chromosome. When running any of the BioStudio scripts (for example, BS_PCRTagger), I encounter the following error:

DBD::SQLite::db prepare_cached failed: no such table: locationlist at /usr/local/share/perl/5.34.0/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1807.

-------------------- EXCEPTION --------------------

MSG: no such table: locationlist

STACK Bio::DB::SeqFeature::Store::DBI::mysql::_prepare /usr/local/share/perl/5.34.0/Bio/DB/SeqFeature/Store/DBI/mysql.pm:1807

STACK Bio::DB::SeqFeature::Store::DBI::SQLite::_offset_boundary /usr/local/share/perl/5.34.0/Bio/DB/SeqFeature/Store/DBI/SQLite.pm:606

STACK Bio::DB::SeqFeature::Store::DBI::SQLite::_fetch_sequence /usr/local/share/perl/5.34.0/Bio/DB/SeqFeature/Store/DBI/SQLite.pm:562

STACK Bio::DB::SeqFeature::Store::seq /usr/local/share/perl/5.34.0/Bio/DB/SeqFeature/Store.pm:2054

STACK Bio::DB::SeqFeature::Store::fetch_sequence /usr/local/share/perl/5.34.0/Bio/DB/SeqFeature/Store.pm:1289

STACK Bio::BioStudio::Chromosome::sequence /usr/local/share/perl/5.34.0/Bio/BioStudio/Chromosome.pm:390

STACK toplevel /usr/local/bin/BS_PCRTagger.pl:88

I would appreciate any help to resolve this issue.

Abdoulaye Balde

# 1. First, reset the BioStudio database

rm -f biostudio.db

BS-BuildDB.pl your_genome_file.gb

# 2. Install required prerequisites

cpan Bio::DB::SeqFeature::Store

cpan DBD::SQLite

# 3. Set correct permissions

chmod -R 755 .

chmod 666 biostudio.db # If file exists

# 4. Debug SQLite database (if needed)

sqlite3 biostudio.db

.tables # View existing tables

.schema # View database structure

# If still encountering: "DBD::SQLite::db prepare-cached failed: no such table: sitelist" error:

# 5. Verify file paths and database initialization:

# - Check if BioStudio is properly installed

# - Ensure GenBank file is valid

# - Check write permissions in working directory

# - Make sure Bio::DB::SeqFeature::Store is properly initialized

# 6. If problem persists, try clean reinstall:

cpanm --force Bio::BioStudio # Force reinstall BioStudio

cpanm --force Bio::DB::SeqFeature::Store # Force reinstall SeqFeature Store

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