Surpi Base Taxonomy

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8.1 years ago

guipagui ▴ 10

Hello, When i'm try run SURPI (v1.0.22), the script

taxonomy_lookup_embedded.pl
have this error :
DBD::SQLite::db selectrow_arrayref failed: no such table: gi_taxid at ./taxonomy_lookup_embedded.pl line 118.

Have you an idea ? Thanks a lot.

software error • 1.4k views

ADD COMMENT • link updated 8.1 years ago by Pierre Lindenbaum 164k • written 8.1 years ago by guipagui ▴ 10

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Is this for pathogen detection?

ADD REPLY • link 8.1 years ago by Ron ★ 1.2k

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Yes, but this troubleshooting isn't referenced at old post

i haven't solution for the moment. The installation of database with sqlite works without error's message

ADD REPLY • link 8.1 years ago by guipagui ▴ 10

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If you are flexible with using tools,you can try using Kraken https://ccb.jhu.edu/software/kraken/

ADD REPLY • link 8.1 years ago by Ron ★ 1.2k

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Yes, it's a possible issue, but it will better to fix the problem.

ADD REPLY • link 8.1 years ago by guipagui ▴ 10

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