Problem with Trinotate.sqlite database

[jt...@tongji.edu.cn]

Hi,

I am learning the tutorial of Trinity and move to the step to using Trinotate to annotate.

The first step is to load data into Trinotate.squlite. So I should excute the script below as requied by tutorial:

%  $TRINOTATE_HOME/Trinotate ../Trinotate.sqlite init \

     --gene_trans_map ../trinity_out_dir/Trinity.fasta.gene_trans_map \

     --transcript_fasta ../trinity_out_dir/Trinity.fasta \

     --transdecoder_pep Trinity.fasta.transdecoder.pep

I got the path of Trinotate progam which is '/home/apps/Trinotate-3.0.2' and database 'Trinotate.sqlite' is '/home/apps/Trinotate-3.0.2/admin', So I use the following script to run:

/home/apps/Trinotate-3.0.2/Trinotate /home/apps/Trinotate-3.0.2/admin/Trinotate.sqlite init --gene_trans_map ../trinity_out_dir/Trinity.fasta.gene_trans_map --transcript_fasta ../trinity_out_dir/Trinity.fasta --transdecoder_pep Trinity.fasta.transdecoder.pep 

It just worked for a couple of steps and then died with the returns below:

CMD: /home/apps/Trinotate-3.0.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite /home/apps/Trinotate-3.0.2/admin/Trinotate.sqlite --gene_trans_map ../trinity_out_dir/Trinity.fasta.gene_trans_map --transcript_fasta ../trinity_out_dir/Trinity.fasta --transdecoder_pep Trinity.fasta.transdecoder.pep --bulk_load

-parsing gene/trans map file.... done.

DBD::SQLite::db do failed: attempt to write a readonly database at /home/apps/Trinotate-3.0.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl line 93.

No such file or directory at /home/apps/Trinotate-3.0.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl line 93.

Error, cmd: /home/apps/Trinotate-3.0.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite /home/apps/Trinotate-3.0.2/admin/Trinotate.sqlite --gene_trans_map ../trinity_out_dir/Trinity.fasta.gene_trans_map --transcript_fasta ../trinity_out_dir/Trinity.fasta --transdecoder_pep Trinity.fasta.transdecoder.pep --bulk_load died with ret 512 at /home/apps/Trinotate-3.0.2/Trinotate line 126.

I checked all the input files are at thier right pathes. 

Do you think where the problem come from? 

Thank you very much and sorry for the disturbing again.

Regards,

Jiangtao

[Brian Haas]

Hi Jiangtaou,

You'll need to build a boilerplate database in your local workspace, as per:

http://trinotate.github.io/

2. Sequence Databases Required

Trinotate relies heavily on SwissProt and Pfam, and custom protein files are generated as described below to be specifically used with Trinotate. You can obtain the protein database files by running this Trinotate build process. This step will download several data resources including the latest version of swissprot, pfam, and other companion resources, create and populate a Trinotate boilerplate sqlite database (Trinotate.sqlite), and yield uniprot_sprot.pep file to be used with BLAST, and the Pfam-A.hmm.gz file to be used for Pfam searches. Run the build process like so:

$TRINOTATE_HOME/admin/Build_Trinotate_Boilerplate_SQLite_db.pl  Trinotate

and once it completes, it will provide to you:

Trinotate.sqlite
uniprot_sprot.pep
Pfam-A.hmm.gz

Prepare the protein database for blast searches by:

makeblastdb -in uniprot_sprot.pep -dbtype prot

Uncompress and prepare the Pfam database for use with hmmscan like so:

gunzip Pfam-A.hmm.gz
hmmpress Pfam-A.hmm




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Brian J. Haas
The Broad Institute
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[Adriana Romero]

I'm trying to build the boilerplate database and I keep getting this mistake.

844 $ /data/apps/trinotate/3.0.2/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate

-- Skipping CMD: wget "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz", checkpoint exists.

* Running CMD: /data/apps/trinotate/3.0.2/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate

/usr/bin/perl: symbol lookup error: /data/apps/perl/5.16.2/lib/site_perl/5.16.2/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_xs_apiversion_bootcheck

Error, cmd: /data/apps/trinotate/3.0.2/admin/util/EMBL_swissprot_parser.pl uniprot_sprot.dat.gz Trinotate died with ret 32512 at /data/apps/trinotate/3.0.2/admin/../PerlLib/Pipeliner.pm line 102.

        Pipeliner::run('Pipeliner=HASH(0x62eba0)') called at /data/apps/trinotate/3.0.2/admin/Build_Trinotate_Boilerplate_SQLite_db.pl line 117

What should I do? 

Thanks! 

[Adriana Romero]

Ok, I ended up downloading everything separately and it works 

Instructions here: https://github.com/harvardinformatics/website/blob/master/content/trinotate_example.optional.md