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web documentation for Trinotate
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Error when running Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate #3

Closed madkimball23 closed 6 years ago

madkimball23 commented 6 years ago
brianjohnhaas commented 6 years ago

It doesn't seem to like the directory name including /mnt/c/Program Files (x86)/

You can create a shortcut to it that doesn't have spaces or parenthesis, and call the software via this other path.

hope this helps,

~b

On Thu, Aug 16, 2018 at 12:37 PM madkimball23 notifications@github.com wrote:

  • Running CMD: /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate sh: 1: Syntax error: "(" unexpected Error, cmd: /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate died with ret 512 at /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0x2351b70)) called at ./Build_Trinotate_Boilerplate_SQLite_db.pl line 118

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madkimball23 commented 6 years ago

Thank you!

I moved it so that it's just in the "C" folder, but now I'm getting this error:

Error, cmd: /mnt/c/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --uniprot_index Trinotate.UniprotIndex died with ret 32512 at /mnt/c/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0xddeb50)) called at ./Build_Trinotate_Boilerplate_SQLite_db.pl line 118

On Thu, Aug 16, 2018 at 12:41 PM, Brian Haas notifications@github.com wrote:

It doesn't seem to like the directory name including /mnt/c/Program Files (x86)/

You can create a shortcut to it that doesn't have spaces or parenthesis, and call the software via this other path.

hope this helps,

~b

On Thu, Aug 16, 2018 at 12:37 PM madkimball23 notifications@github.com wrote:

  • Running CMD: /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate sh: 1: Syntax error: "(" unexpected Error, cmd: /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate died with ret 512 at /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0x2351b70)) called at ./Build_Trinotate_Boilerplate_SQLite_db.pl line 118

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brianjohnhaas commented 6 years ago

Is there an error message earlier on in the log that's more informative?

best

~b

On Thu, Aug 16, 2018 at 1:06 PM madkimball23 notifications@github.com wrote:

Thank you!

I moved it so that it's just in the "C" folder, but now I'm getting this error:

Error, cmd:

/mnt/c/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --uniprot_index Trinotate.UniprotIndex died with ret 32512 at /mnt/c/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0xddeb50)) called at ./Build_Trinotate_Boilerplate_SQLite_db.pl line 118

On Thu, Aug 16, 2018 at 12:41 PM, Brian Haas notifications@github.com wrote:

It doesn't seem to like the directory name including /mnt/c/Program Files (x86)/

You can create a shortcut to it that doesn't have spaces or parenthesis, and call the software via this other path.

hope this helps,

~b

On Thu, Aug 16, 2018 at 12:37 PM madkimball23 notifications@github.com wrote:

  • Running CMD: /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate sh: 1: Syntax error: "(" unexpected Error, cmd: /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate died with ret 512 at /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0x2351b70)) called at ./Build_Trinotate_Boilerplate_SQLite_db.pl line 118

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madkimball23 commented 6 years ago

This is the all of the output:

-- Skipping CMD: wget " ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz", checkpoint exists. -- Skipping CMD: /mnt/c/Trinotate-Trinotate-v3.1.1/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. -- Skipping CMD: /mnt/c/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --create, checkpoint exists.

Thanks,

Madison

On Thu, Aug 16, 2018 at 2:13 PM, Brian Haas notifications@github.com wrote:

Is there an error message earlier on in the log that's more informative?

best

~b

On Thu, Aug 16, 2018 at 1:06 PM madkimball23 notifications@github.com wrote:

Thank you!

I moved it so that it's just in the "C" folder, but now I'm getting this error:

Error, cmd:

/mnt/c/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_datto Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --uniprot_index Trinotate.UniprotIndex died with ret 32512 at /mnt/c/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0xddeb50)) called at ./Build_Trinotate_Boilerplate_SQLite_db.pl line 118

On Thu, Aug 16, 2018 at 12:41 PM, Brian Haas notifications@github.com wrote:

It doesn't seem to like the directory name including /mnt/c/Program Files (x86)/

You can create a shortcut to it that doesn't have spaces or parenthesis, and call the software via this other path.

hope this helps,

~b

On Thu, Aug 16, 2018 at 12:37 PM madkimball23 < notifications@github.com> wrote:

  • Running CMD: /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate sh: 1: Syntax error: "(" unexpected Error, cmd: /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate died with ret 512 at /mnt/c/Program Files (x86)/Trinotate-Trinotate-v3.1.1/admin/../PerlLib/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0x2351b70)) called at ./Build_Trinotate_Boilerplate_SQLite_db.pl line 118

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brianjohnhaas commented 6 years ago

Thanks. This is the problem:

sh: 5: sqlite3: not found

You'll need to install sqlite3

https://sqlite.org/index.html

best,

~brian

madkimball23 commented 6 years ago

Thank you!!

On Thu, Aug 16, 2018 at 2:16 PM, Brian Haas notifications@github.com wrote:

Thanks. This is the problem:

sh: 5: sqlite3: not found

You'll need to install sqlite3

https://sqlite.org/index.html

best,

~brian

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