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Error with Build_Trinotate_Boilerplate_SQLite_db.pl #16

Closed nadeaue closed 5 years ago

nadeaue commented 5 years ago

I'm having trouble getting the SwissProt and Pfam databases. When I cd into my Programs directory that contains Trinotate and the other programs, I write this: "$Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate"

It runs for a bit and says it successfully gets uniprot_sprot.dat.gz, but fails after moving on. It gives me this error: " Running CMD: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate [559000] Running CMD: mv uniprot_sprot.dat.gz.pep uniprot_sprot.pep *Running CMD: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create CMD: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl --sqlite Trinotate.sqlite install_driver(SQLite) failed: Can't locate DBD/SQLite.pm in @INC (@INC contains: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/../../PerlLib /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at (eval 7) 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, Proxy, Sponge. at /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl line 53 Error, cmd: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl --sqlite Trinotate.sqlite died with ret 512 at /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl line 145. Error, cmd: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create died with ret 512 at /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102 Pipeliner::run('Pipeliner=HASH(0x1cc0370)') called at Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl line 119"

I can't get past this error and am not sure what I'm doing wrong. Could I just wget the SwissProt ad Pfam files instead?

brianjohnhaas commented 5 years ago

Hi,

There's a perl module you'll need to install:

https://metacpan.org/pod/DBD::SQLite

and then it should hopefully work.

best,

~b

On Wed, Apr 10, 2019 at 1:12 PM nadeaue notifications@github.com wrote:

I'm having trouble getting the SwissProt and Pfam databases. When I cd into my Programs directory that contains Trinotate and the other programs, I write this: "$Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate"

It runs for a bit and says it successfully gets uniprot_sprot.dat.gz, but fails after moving on. It gives me this error: " Running CMD: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate [559000] Running CMD: mv uniprot_sprot.dat.gz.pep uniprot_sprot.pep *Running CMD: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create CMD: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/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 (@inc https://github.com/inc contains: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/../../PerlLib /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at (eval 7) 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, Proxy, Sponge. at /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl line 53 Error, cmd: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl --sqlite Trinotate.sqlite died with ret 512 at /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl line 145. Error, cmd: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create died with ret 512 at /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102 Pipeliner::run('Pipeliner=HASH(0x1cc0370)') called at Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl line 119"

I can't get past this error and am not sure what I'm doing wrong. Could I just wget the SwissProt ad Pfam files instead?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/16, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVX4excC_1jCgqZ1x7lC-Rf274IW8Tks5vfhtmgaJpZM4cn1kl .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

nadeaue commented 5 years ago

Hi Brian, How do I install the module on my cluster? I downloaded the SQLite.pm file and sent that to my cluster in the Trinotate directory, but I'm still getting the same error. I can't do a sudo cpan install, which is what I saw on the "known bugs" portion of GitHub. If I try to just do "cpan install DBD::SQLite module" I'm told I don't have permission for that.  Thanks,Emily On Wednesday, April 10, 2019, 3:19:16 PM EDT, Brian Haas notifications@github.com wrote:

Hi,

There's a perl module you'll need to install:

https://metacpan.org/pod/DBD::SQLite

and then it should hopefully work.

best,

~b

On Wed, Apr 10, 2019 at 1:12 PM nadeaue notifications@github.com wrote:

I'm having trouble getting the SwissProt and Pfam databases. When I cd into my Programs directory that contains Trinotate and the other programs, I write this: "$Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate"

It runs for a bit and says it successfully gets uniprot_sprot.dat.gz, but fails after moving on. It gives me this error: " Running CMD: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate [559000] Running CMD: mv uniprot_sprot.dat.gz.pep uniprot_sprot.pep *Running CMD: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create CMD: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/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 (@inc https://github.com/inc contains: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/../../PerlLib /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at (eval 7) 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, Proxy, Sponge. at /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl line 53 Error, cmd: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl --sqlite Trinotate.sqlite died with ret 512 at /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl line 145. Error, cmd: /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create died with ret 512 at /home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102 Pipeliner::run('Pipeliner=HASH(0x1cc0370)') called at Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl line 119"

I can't get past this error and am not sure what I'm doing wrong. Could I just wget the SwissProt ad Pfam files instead?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/16, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVX4excC_1jCgqZ1x7lC-Rf274IW8Tks5vfhtmgaJpZM4cn1kl .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

brianjohnhaas commented 5 years ago

I think there's a way to install it as a user and not requiring it to be centrally installed, but if you have an IT person that can do the central install for you, that would probably be best.

The way I typically install perl modules is:

perl -MCPAN -e shell install DBD::SQLite exit or quit

If it complains about not being able to install because you don't have root privileges, and doesn't enable a user-level installation, then another method will be needed. Google is your friend there. If it still isn't working out, let me know and I'll have some other suggestions.

hope this helps,

~b

On Wed, Apr 10, 2019 at 5:08 PM nadeaue notifications@github.com wrote:

Hi Brian, How do I install the module on my cluster? I downloaded the SQLite.pm file and sent that to my cluster in the Trinotate directory, but I'm still getting the same error. I can't do a sudo cpan install, which is what I saw on the "known bugs" portion of GitHub. If I try to just do "cpan install DBD::SQLite module" I'm told I don't have permission for that. Thanks,Emily On Wednesday, April 10, 2019, 3:19:16 PM EDT, Brian Haas < notifications@github.com> wrote:

Hi,

There's a perl module you'll need to install:

https://metacpan.org/pod/DBD::SQLite

and then it should hopefully work.

best,

~b

On Wed, Apr 10, 2019 at 1:12 PM nadeaue notifications@github.com wrote:

I'm having trouble getting the SwissProt and Pfam databases. When I cd into my Programs directory that contains Trinotate and the other programs, I write this:

"$Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate"

It runs for a bit and says it successfully gets uniprot_sprot.dat.gz, but fails after moving on. It gives me this error: "* Running CMD:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate [559000] Running CMD: mv uniprot_sprot.dat.gz.pep uniprot_sprot.pep Running CMD:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create CMD:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/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 (@inc https://github.com/inc contains:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/../../PerlLib /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at (eval 7) 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, Proxy, Sponge. at

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl line 53 Error, cmd:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl --sqlite Trinotate.sqlite died with ret 512 at

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl line 145. Error, cmd:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create died with ret 512 at

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102 Pipeliner::run('Pipeliner=HASH(0x1cc0370)') called at Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl line 119"

I can't get past this error and am not sure what I'm doing wrong. Could I just wget the SwissProt ad Pfam files instead?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/16, or mute the thread < https://github.com/notifications/unsubscribe-auth/AHMVX4excC_1jCgqZ1x7lC-Rf274IW8Tks5vfhtmgaJpZM4cn1kl

.

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/16#issuecomment-481866035, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVX9hxNPVvmGGdnxR4X4YVraLfnLpLks5vflLBgaJpZM4cn1kl .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

nadeaue commented 5 years ago

Hi Brian,

I've attempted to run the Build_Trinotate_Boilerplate step multiple times with no luck. I was wondering if there was another way I could get the uniprot_sprot.pep and Pfam-A.hmm.gz files. I'm following a pipeline where the author uses wget to pull these off of the Broad Institute website, but the links she uses are no longer working. She also uses wget to download Trinotate.sqlite.gz. She was able to complete her annotation without the Boilerplate step. Are you familiar with doing it this way?  Thanks,Emily On Wednesday, April 10, 2019, 7:00:07 PM EDT, Brian Haas notifications@github.com wrote:

I think there's a way to install it as a user and not requiring it to be centrally installed, but if you have an IT person that can do the central install for you, that would probably be best.

The way I typically install perl modules is:

perl -MCPAN -e shell install DBD::SQLite exit or quit

If it complains about not being able to install because you don't have root privileges, and doesn't enable a user-level installation, then another method will be needed. Google is your friend there. If it still isn't working out, let me know and I'll have some other suggestions.

hope this helps,

~b

On Wed, Apr 10, 2019 at 5:08 PM nadeaue notifications@github.com wrote:

Hi Brian, How do I install the module on my cluster? I downloaded the SQLite.pm file and sent that to my cluster in the Trinotate directory, but I'm still getting the same error. I can't do a sudo cpan install, which is what I saw on the "known bugs" portion of GitHub. If I try to just do "cpan install DBD::SQLite module" I'm told I don't have permission for that. Thanks,Emily On Wednesday, April 10, 2019, 3:19:16 PM EDT, Brian Haas < notifications@github.com> wrote:

Hi,

There's a perl module you'll need to install:

https://metacpan.org/pod/DBD::SQLite

and then it should hopefully work.

best,

~b

On Wed, Apr 10, 2019 at 1:12 PM nadeaue notifications@github.com wrote:

I'm having trouble getting the SwissProt and Pfam databases. When I cd into my Programs directory that contains Trinotate and the other programs, I write this:

"$Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate"

It runs for a bit and says it successfully gets uniprot_sprot.dat.gz, but fails after moving on. It gives me this error: "* Running CMD:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate [559000] Running CMD: mv uniprot_sprot.dat.gz.pep uniprot_sprot.pep Running CMD:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create CMD:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/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 (@inc https://github.com/inc contains:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/../../PerlLib /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at (eval 7) 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, Proxy, Sponge. at

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl line 53 Error, cmd:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl --sqlite Trinotate.sqlite died with ret 512 at

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl line 145. Error, cmd:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create died with ret 512 at

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102 Pipeliner::run('Pipeliner=HASH(0x1cc0370)') called at Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl line 119"

I can't get past this error and am not sure what I'm doing wrong. Could I just wget the SwissProt ad Pfam files instead?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/16, or mute the thread < https://github.com/notifications/unsubscribe-auth/AHMVX4excC_1jCgqZ1x7lC-Rf274IW8Tks5vfhtmgaJpZM4cn1kl

.

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/16#issuecomment-481866035, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVX9hxNPVvmGGdnxR4X4YVraLfnLpLks5vflLBgaJpZM4cn1kl .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

brianjohnhaas commented 5 years ago

Hi,

The best thing to do is to download the latest version of the software and follow the instructions from the wiki: https://github.com/Trinotate/Trinotate.github.io/wiki

If it gives you any trouble, just post the error messages and I'll give you some pointers.

best,

~b

On Mon, Apr 15, 2019 at 2:38 PM nadeaue notifications@github.com wrote:

Hi Brian,

I've attempted to run the Build_Trinotate_Boilerplate step multiple times with no luck. I was wondering if there was another way I could get the uniprot_sprot.pep and Pfam-A.hmm.gz files. I'm following a pipeline where the author uses wget to pull these off of the Broad Institute website, but the links she uses are no longer working. She also uses wget to download Trinotate.sqlite.gz. She was able to complete her annotation without the Boilerplate step. Are you familiar with doing it this way? Thanks,Emily On Wednesday, April 10, 2019, 7:00:07 PM EDT, Brian Haas < notifications@github.com> wrote:

I think there's a way to install it as a user and not requiring it to be centrally installed, but if you have an IT person that can do the central install for you, that would probably be best.

The way I typically install perl modules is:

perl -MCPAN -e shell install DBD::SQLite exit or quit

If it complains about not being able to install because you don't have root privileges, and doesn't enable a user-level installation, then another method will be needed. Google is your friend there. If it still isn't working out, let me know and I'll have some other suggestions.

hope this helps,

~b

On Wed, Apr 10, 2019 at 5:08 PM nadeaue notifications@github.com wrote:

Hi Brian, How do I install the module on my cluster? I downloaded the SQLite.pm file and sent that to my cluster in the Trinotate directory, but I'm still getting the same error. I can't do a sudo cpan install, which is what I saw on the "known bugs" portion of GitHub. If I try to just do "cpan install DBD::SQLite module" I'm told I don't have permission for that. Thanks,Emily On Wednesday, April 10, 2019, 3:19:16 PM EDT, Brian Haas < notifications@github.com> wrote:

Hi,

There's a perl module you'll need to install:

https://metacpan.org/pod/DBD::SQLite

and then it should hopefully work.

best,

~b

On Wed, Apr 10, 2019 at 1:12 PM nadeaue notifications@github.com wrote:

I'm having trouble getting the SwissProt and Pfam databases. When I cd into my Programs directory that contains Trinotate and the other programs, I write this:

"$Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl

Trinotate"

It runs for a bit and says it successfully gets uniprot_sprot.dat.gz, but fails after moving on. It gives me this error: "* Running CMD:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl

uniprot_sprot.dat.gz Trinotate [559000] Running CMD: mv uniprot_sprot.dat.gz.pep uniprot_sprot.pep Running CMD:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl

--sqlite Trinotate.sqlite --create CMD:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/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 (@inc https://github.com/inc contains:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/../../PerlLib

/usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at (eval 7) 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, Proxy, Sponge. at

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl

line 53 Error, cmd:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/init_Trinotate_sqlite_db.pl

--sqlite Trinotate.sqlite died with ret 512 at

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl

line 145. Error, cmd:

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl

--sqlite Trinotate.sqlite --create died with ret 512 at

/home/eana226/Programs/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm

line 102 Pipeliner::run('Pipeliner=HASH(0x1cc0370)') called at

Trinotate-Trinotate-v3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl line 119"

I can't get past this error and am not sure what I'm doing wrong. Could I just wget the SwissProt ad Pfam files instead?

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