brianjohnhaas
commented
5 years ago This is peculiar. Try giving the full path to the Trinotate sqlite database in the command. This should help in case it's not finding it.
-via googleFi
On Wed, Apr 17, 2019, 1:35 AM gdamasco notifications@github.com wrote:
Dear Brian I am getting the following error message at the very last step of trinotate to write the annotation report. Would you mind helping me out?
I am running the exact codes you have avialable in github in a HPC.
CMD: /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/Trinotate_report_writer.pl --sqlite Trinotate.sqlite -E 1e-5 --pfam_cutoff DNC DBD::SQLite::db prepare failed: no such table: RNAMMERdata at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/../PerlLib/Sqlite_connect.pm line 77. DBD::SQLite::db prepare failed: no such table: RNAMMERdata at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/../PerlLib/Sqlite_connect.pm line 77. at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/../PerlLib/Sqlite_connect.pm line 108. Sqlite_connect::do_sql_2D('DBI::db=HASH(0x198da48)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_DN11686_c0_g1_i1') called at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x198da48)', 'TRINITY_DN11686_c0_g1_i1') called at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x198da48)', 'TRINITY_DN11686_c0_g1_i1') called at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/Trinotate_report_writer.pl line 139 Error, cmd: /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/Trinotate_report_writer.pl --sqlite Trinotate.sqlite -E 1e-5 --pfam_cutoff DNC died with ret 512 at ./Trinotate line 126.
— 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/17, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVXyZG_9bLmEZhRserJ7KbSpeFdw8aks5vhrKrgaJpZM4c0Oq- .
gdamasco
Dear Brian I am getting the following error message at the very last step of trinotate to write the annotation report. Would you mind helping me out?
I am running the exact codes you have avialable in github in a HPC.
CMD: /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/Trinotate_report_writer.pl --sqlite Trinotate.sqlite -E 1e-5 --pfam_cutoff DNC DBD::SQLite::db prepare failed: no such table: RNAMMERdata at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/../PerlLib/Sqlite_connect.pm line 77. DBD::SQLite::db prepare failed: no such table: RNAMMERdata at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/../PerlLib/Sqlite_connect.pm line 77. at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/../PerlLib/Sqlite_connect.pm line 108. Sqlite_connect::do_sql_2D('DBI::db=HASH(0x198da48)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_DN11686_c0_g1_i1') called at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x198da48)', 'TRINITY_DN11686_c0_g1_i1') called at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x198da48)', 'TRINITY_DN11686_c0_g1_i1') called at /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/Trinotate_report_writer.pl line 139 Error, cmd: /global/scratch/damasco/SRA/trinotate/trinotate3.1.1/util/Trinotate_report_writer.pl --sqlite Trinotate.sqlite -E 1e-5 --pfam_cutoff DNC died with ret 512 at ./Trinotate line 126.