brianjohnhaas
commented
3 years ago hi,
I've sometimes come across this sort of thing when I've had different versions of perl available on my system, and the module installation was done for one and not the other.
Try
which perl
and then run that version of perl like so:
/path/to/this/perl -MCPAN -e shell install DBD::SQLite exit
if that goes well, then try running Trinotate again and hopefully it's fine.
best,
~b
On Fri, Apr 23, 2021 at 11:47 AM Brent-Saylor-Canopy < @.***> wrote:
Hi,
I am trying to install Trinotate on my system and I'm having a problem running the Build_Trinotate_Boilerplate_SQLite_db.pl script.
I get the following error: `/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate -- Skipping CMD: wget " ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz", checkpoint exists. -- Skipping CMD: /opt/Trinotate-Trinotate-v3.2.2/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate, checkpoint exists. -- Skipping CMD: mv uniprot_sprot.dat.gz.pep uniprot_sprot.pep, checkpoint exists.
- Running CMD: /opt/Trinotate-Trinotate-v3.2.2/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create CMD: /opt/Trinotate-Trinotate-v3.2.2/admin/util/init_Trinotate_sqlite_db.pl --sqlite Trinotate.sqlite install_driver(SQLite) failed: Can't locate DBD/SQLite.pm in @inc https://github.com/inc (you may need to install the DBD::SQLite module) @.*** https://github.com/inc contains: /opt/Trinotate-Trinotate-v3.2.2/admin/util/../../PerlLib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at (eval 6) line 3. Perhaps the DBD::SQLite perl module hasn't been fully installed, or perhaps the capitalisation of 'SQLite' isn't right. Available drivers: DBM, ExampleP, File, Gofer, Mem, Proxy, Sponge, mysql. at /opt/Trinotate-Trinotate-v3.2.2/admin/util/init_Trinotate_sqlite_db.pl line 53. Error, cmd: /opt/Trinotate-Trinotate-v3.2.2/admin/util/init_Trinotate_sqlite_db.pl --sqlite Trinotate.sqlite died with ret 512 at /opt/Trinotate-Trinotate-v3.2.2/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl line 145. Error, cmd: /opt/Trinotate-Trinotate-v3.2.2/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create died with ret 512 at /opt/Trinotate-Trinotate-v3.2.2/admin/../PerlLib/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0x557e1bc87b88)) called at ./Build_Trinotate_Boilerplate_SQLite_db.pl line 120 ` I have tried reinstalling both SQLite and DBD:SQLite (via both cpan and conda) and it doesn't seem to help. I also tried aliasing my sqlite command (sqlite3) to sqlite and SQLite to see if the capatilization was the issue, but that did't work either.
Can you provide any assistance?
Thanks, Brent
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Brent-Saylor-Canopy
matevzl533
Hi,
I am trying to install Trinotate on my system and I'm having a problem running the Build_Trinotate_Boilerplate_SQLite_db.pl script.
I get the following error: `/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate -- Skipping CMD: wget "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz", checkpoint exists. -- Skipping CMD: /opt/Trinotate-Trinotate-v3.2.2/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate, checkpoint exists. -- Skipping CMD: mv uniprot_sprot.dat.gz.pep uniprot_sprot.pep, checkpoint exists.
Can you provide any assistance?
Thanks, Brent