Trinotate error DBD::SQLite::db do failed: no such table:

Question

[biologo]

hello: Dear all, i am doing the genome annotation now, and we have RNA-seq data, so i did the trinity assembly, and use Trinotate do the annotation, but after i generate several results and need to import into Trinotate.sqlite, i got the error.

that is my code: Trinotate ./Trinotate.sqlite init --gene_trans_map trinity_unigene_clean.fa.gene_trans_map --transcript_fasta trinity_unigene_clean.fa --transdecoder_pep longest_orfs.pep

and the error here: DBD::SQLite::db do failed: no such table: Transcript(1) at dbdimp.c line 271 at /share_bio/disk8/software/Trinotate-3.0.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl line 93.

waiting for your help and thank you so much

[h.mon]

Did you download (and unpacked) or created ($TRINOTATE_HOME/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate) a boilerplate db?

[biologo]

yes, thank you for your suggestion, because at that time i can no create the database through Build_Trinotate_Boilerplate_SQLite_db.pl, so i built it by myself and it still did not work and finally i change the version of perl and it works.

Answer 1

[biomonte]

The TRINOTATE software provides a boilerplate SQLite database that comes pre-populated with a lot of generic data about SwissProt records and Pfam domains. Please make sure that you downloaded the TRINOTATE pre-generated SQLite database and decompress it:

wget https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz -O Trinotate.sqlite.gz
gunzip Trinotate.sqlite.gz

[biologo]

yes, i find it for a long time, and thank you for your link

[Pranavathiyani G]

The command shows the resource doesn't exist now. From where I can download the Trinotate.sqlite.gz??

[h.mon]

You are asking a question, as a comment, on a 10-month old post - you should not, you should open a new post.

Even better: read my comment above, or Trinotate page, and create a new boilerplate database:

$TRINOTATE_HOME/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate