gwajnberg@gwajnberg-ThinkPad-E560:~/RSEQREP$ sh run-pre-processing.sh
Performing sanity checks on configuration options
Parsing Analysis Configuration
Parsing Sample Metadata
Parsing Workflow Configuration
mkdir: cannot create directory ‘/home/gwajnberg/.ncbi’: File exists
cd /home/rseqrepuser/pre-processing
perl /home/gwajnberg/RSEQREP/source/perl/preprocess-rnaseq.pl /home/rseqrepuser/pre-processing/preprocess_config.csv /home/rseqrepuser/pre-processing/sample_metadata.csv
install_driver(SQLite) failed: Can't load '/usr/lib/x86_64-linux-gnu/perl5/5.26/auto/DBD/SQLite/SQLite.so' for module DBD::SQLite: /usr/lib/x86_64-linux-gnu/perl5/5.26/auto/DBD/SQLite/SQLite.so: undefined symbol: sqlite3_column_table_name at /usr/lib/x86_64-linux-gnu/perl/5.26/DynaLoader.pm line 187, <$cfg> line 19.
at (eval 6) line 3.
Compilation failed in require at (eval 6) line 3, <$cfg> line 19.
Perhaps a required shared library or dll isn't installed where expected
at /home/gwajnberg/RSEQREP/source/perl/preprocess-rnaseq.pl line 82.
EorgeKit
commented
1 year ago
gwajnberg@gwajnberg-ThinkPad-E560:~/RSEQREP$ sh run-pre-processing.sh Performing sanity checks on configuration options Parsing Analysis Configuration Parsing Sample Metadata Parsing Workflow Configuration mkdir: cannot create directory ‘/home/gwajnberg/.ncbi’: File exists cd /home/rseqrepuser/pre-processing perl /home/gwajnberg/RSEQREP/source/perl/preprocess-rnaseq.pl /home/rseqrepuser/pre-processing/preprocess_config.csv /home/rseqrepuser/pre-processing/sample_metadata.csv install_driver(SQLite) failed: Can't load '/usr/lib/x86_64-linux-gnu/perl5/5.26/auto/DBD/SQLite/SQLite.so' for module DBD::SQLite: /usr/lib/x86_64-linux-gnu/perl5/5.26/auto/DBD/SQLite/SQLite.so: undefined symbol: sqlite3_column_table_name at /usr/lib/x86_64-linux-gnu/perl/5.26/DynaLoader.pm line 187, <$cfg> line 19. at (eval 6) line 3. Compilation failed in require at (eval 6) line 3, <$cfg> line 19. Perhaps a required shared library or dll isn't installed where expected at /home/gwajnberg/RSEQREP/source/perl/preprocess-rnaseq.pl line 82.
config.xlsx
I used the work study config file ....I run first the setup.sh and after some errors, I could run everything and created all files