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Trinotate / Trinotate.github.io

web documentation for Trinotate
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sqlite database ok, but report is empty #70

Open matevzl533 opened 5 months ago

matevzl533 commented 5 months ago

Hello,

I used Trinotate to annotate my transcriptome and it finished without an error. The sqlite database is filled out, but the exported Excel file is empty, except the header row. Can you please advise on how to get the data exported into the report or how to proceed?

I am using the latest singularity image t.i. v4.0.2

Best regards,

Matevz

brianjohnhaas commented 5 months ago

Hi,

It sounds like the 'init' step might not have been done, which loads in the target transcript info. Try rerunning that step and then generate the report.

On Fri, Feb 2, 2024 at 2:34 AM matevzl533 @.***> wrote:

Hello,

I used Trinotate to annotate my transcriptome and it finished without an error. The sqlite database is filled out, but the exported Excel file is empty, except the header row. Can you please advise on how to get the data exported into the report or how to proceed?

I am using the latest singularity image t.i. v4.0.2

Best regards,

Matevz

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matevzl533 commented 5 months ago

Thank you for you help. Have redone the step. It does not report any errors, but also it does not report that it was done successfully.

matevzl533 commented 5 months ago

All the checkpoint in the trinotate_data_dir folder say ok. And every other command say that everything is ok. Just the init step does not report anything.

brianjohnhaas commented 5 months ago

So, still no report generation?

Were the blast and pfam searches done against the databases set up in the $TRINOTATE_DATA_DIR/ ? If not, that might explain it.

Otherwise, I'd have to take a look at the sqlite database and see what the issue is. You could privately share it with me via some download site, like dropbox or google drive, and I could check it out.

bhaas at broadinstitute dot org

best,

Brian

On Fri, Feb 2, 2024 at 12:08 PM matevzl533 @.***> wrote:

Have redone the step. It does not report any errors, but also it does not report that it was done successfully.

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matevzl533 commented 5 months ago

Thank you again. I have sent you an email with link to the db and the code I used to generate it.

Best

Matevz

brianjohnhaas commented 5 months ago

Thanks for sending.

So, the Transcript and ORF tables of the database are empty, which means that the 'init' step isn't working for some reason.

Can you send the output from running the init command, which is formatted like so:

Trinotate --db --init \ --gene_trans_map \ --transcript_fasta \ --transdecoder_pep

?

On Fri, Feb 2, 2024 at 12:26 PM matevzl533 @.***> wrote:

Thank you again. I have sent you an email with link to the db and the code I used to generate it.

Best

Matevz

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matevzl533 commented 5 months ago

That's the strange thing - when I run this command, I get no output and no error. If I remember correctly there should be some messages about loading the data into the db? I run the command and it just goes back to prompt: $ $TRINOTATE_HOME/Trinotate --db pwd/Trinotate.sqlite --init \

       --gene_trans_map `pwd`/Trinity.clean.fasta.gene_trans_map \
       --transcript_fasta `pwd`/Trinity.clean.fasta \
       --transdecoder_pep `pwd`/Trinity.clean.fasta.transdecoder.pep

$ All other command t.i. create, the annotations and report export report on progress. But --init does not.

brianjohnhaas commented 5 months ago

very peculiar.

The only thing that comes to mind is to manually type out the command before running it, in case you copied/pasted something - where the characters might look right but they're interpreted differently.

The --init in particular is likely not being recognized as --init and it's being treated as a no-op of some form.

On Fri, Feb 2, 2024 at 5:04 PM matevzl533 @.***> wrote:

That's the strange thing - when I run this command, I get no output and no error. If I remember correctly there should be some messages about loading the data into the db? I run the command and it just goes back to prompt: $ $TRINOTATE_HOME/Trinotate --db pwd/Trinotate.sqlite --init \

   --gene_trans_map `pwd`/Trinity.clean.fasta.gene_trans_map \
   --transcript_fasta `pwd`/Trinity.clean.fasta \
   --transdecoder_pep `pwd`/Trinity.clean.fasta.transdecoder.pep

$ All other command t.i. create, the annotations and report export report on progress. But --init does not.

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matevzl533 commented 5 months ago

Ah, I went to look at the code of the init step and after seeing the first line: my $init_checkpt = "__init.ok"; it was at once clear to me that I overlooked that there was a init_ok flag in the working folder :( After I deleted it the init step works perfectly. I am very sorry that I bothered you with my stupidity. And thank you again for your support.

brianjohnhaas commented 5 months ago

Glad to hear that it's working now!

best,

Brian

On Sat, Feb 3, 2024 at 1:23 AM matevzl533 @.***> wrote:

Ah, I went to look at the code of the init step and after seeing the first line: my $init_checkpt = "__init.ok"; it was at once clear to me that I overlooked that there was a init_ok flag in the working folder :( After I deleted it the init step works perfectly. I am very sorry that I bothered you with my stupidity. And thank you again for your support.

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