Trinotate : No output for eggnog, gene_ontology_blast, kegg

[Urmi Trivedi]

Hello,

I am using trinotate v3.1.1 for annotation of a transcriptome generated by Trinity. My annotation report show no entries for gene_ontology_blast, kegg or eggnog. Following other threads, I realise that people do have these problems if the latest version of trinotate is not used or if the boilerplate is not built from scratch. But none of these are true in my case. When I try to run runMe.sh on the sample_data I get following error:

pulling swissprot resource db from ftp site

--2018-05-01 10:32:10--  https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz

Resolving data.broadinstitute.org (data.broadinstitute.org)... 69.173.92.29

Connecting to data.broadinstitute.org (data.broadinstitute.org)|69.173.92.29|:443... connected.

HTTP request sent, awaiting response... 404 Not Found

2018-05-01 10:32:11 ERROR 404: Not Found. 

But when I run "$TRINOTATE/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate", it finishes without any errors and generates Trinotate.sqlite. I am confused where the problem lies. Please could anyone help? 

Many thanks,

Urmi

[Brian Haas]

Hi Urmi,

I had relocated the database used by the sample data set. I just restored the link so it should work fine for you now.   If you want to explore the sample data set, you'd have to use the database that's tailored to it instead of using the boilerplate db you constructed yourself.  This is because the pfam and swissprot accessions point to earlier releases.

best,

~b

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[Urmi]

Thanks for your prompt response, Brian. sample dataset is working fine now and I do have kegg and gene_ontoloty_blast columns in the report. 

Just to clarify, my question was more for my dataset than the sample data. I was exploring sample dataset just to check if that produces the desired output. Do you have any suggestions on why my dataset would be missing the kegg, gene_ontology_blast and eggnog columns in the final trinotate report? 

Cheers,

Urmi

On Tue, May 1, 2018 at 12:00 PM, Brian Haas <bh...@broadinstitute.org> wrote:

Hi Urmi,

I had relocated the database used by the sample data set. I just restored the link so it should work fine for you now.   If you want to explore the sample data set, you'd have to use the database that's tailored to it instead of using the boilerplate db you constructed yourself.  This is because the pfam and swissprot accessions point to earlier releases.

best,

~b

On Tue, May 1, 2018 at 5:37 AM, Urmi Trivedi <urm...@gmail.com> wrote:

Hello,

I am using trinotate v3.1.1 for annotation of a transcriptome generated by Trinity. My annotation report show no entries for gene_ontology_blast, kegg or eggnog. Following other threads, I realise that people do have these problems if the latest version of trinotate is not used or if the boilerplate is not built from scratch. But none of these are true in my case. When I try to run runMe.sh on the sample_data I get following error:

pulling swissprot resource db from ftp site

--2018-05-01 10:32:10--  https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz

Resolving data.broadinstitute.org (data.broadinstitute.org)... 69.173.92.29

Connecting to data.broadinstitute.org (data.broadinstitute.org)|69.173.92.29|:443... connected.

HTTP request sent, awaiting response... 404 Not Found

2018-05-01 10:32:11 ERROR 404: Not Found. 

But when I run "$TRINOTATE/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate", it finishes without any errors and generates Trinotate.sqlite. I am confused where the problem lies. Please could anyone help? 

Many thanks,

Urmi

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[Brian Haas]

Hi Urmi,

Did you search the version of swissprot and pfam that were downloaded and prepped as part of building the boilerplate database?

If the exact same databases weren't searched, then this would cause a mismatch between the boilerplate and the blast results.

best,

~b