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Trinotate / Trinotate.github.io

web documentation for Trinotate
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Unable to locate SQLite Database file #43

Closed williamsonjpa closed 3 years ago

williamsonjpa commented 3 years ago

Hi there,

I am running Trinotate v3.2.1 and am trying to initialise the SQLite database to load in my BLAST and HMMSCAN results.

I have downloaded the Trinotate.sqlite file using the Build_Trinotate_Boilerplate_SQLite_db.pl script.

When I run the Trinotate init command I get the error 'Error, cannot locate --sqlite database file. Be sure it's in your current directory. at /data/home/btx225/.conda/envs/trinotate/bin/Trinotate line 53.'

This is regardless of where my .sqlite database is.

My code is Trinotate --sqlite Trinotate.sqlite init -gene_trans_map /data/scratch/btx225/rna_seq/annotation2/data/gene_trans_maps/CR/CR_gene_trans_map --transcript_fasta /data/scratch/btx225/rna_seq/annotation2/data/cdhit/CR_out --transdecoder_pep /data/scratch/btx225/rna_seq/annotation2/data/long_orfs_cdhit/CR/longest_orfs.pep

Any help would be much appreciated.

Regards,

Joe

brianjohnhaas commented 3 years ago

Hi Joe,

For that step, there's no --sqlite parameter. Just list the database name as the first parameter after Trinotate.

best,

~b

On Wed, Oct 14, 2020 at 11:34 AM williamsonjpa notifications@github.com wrote:

Hi there,

I am running Trinotate v3.2.1 and am trying to initialise the SQLite database to load in my BLAST and HMMSCAN results.

I have downloaded the Trinotate.sqlite file using the Build_Trinotate_Boilerplate_SQLite_db.pl script.

When I run the Trinotate init command I get the error 'Error, cannot locate --sqlite database file. Be sure it's in your current directory. at /data/home/btx225/.conda/envs/trinotate/bin/Trinotate line 53.'

This is regardless of where my .sqlite database is.

My code is Trinotate --sqlite Trinotate.sqlite init -gene_trans_map /data/scratch/btx225/rna_seq/annotation2/data/gene_trans_maps/CR/CR_gene_trans_map --transcript_fasta /data/scratch/btx225/rna_seq/annotation2/data/cdhit/CR_out --transdecoder_pep /data/scratch/btx225/rna_seq/annotation2/data/long_orfs_cdhit/CR/longest_orfs.pep

Any help would be much appreciated.

Regards,

Joe

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williamsonjpa commented 3 years ago

Hi Brian,

Many thanks, that is now running. It didnt like me renaming the script as something else either, so reverting back to Trinotate.sqlite rather than CR.sqlite as I had called it.

Cheers,

Joe

brianjohnhaas commented 3 years ago

glad that it's running now. I didn't expect it to require the sqlite database to have special file naming here, though. That's curious.

On Thu, Oct 15, 2020 at 7:14 AM williamsonjpa notifications@github.com wrote:

Hi Brian,

Many thanks, that is now running. It didnt like me renaming the script as something else either, so reverting back to Trinotate.sqlite rather than CR.sqlite as I had called it.

Cheers,

Joe

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/43#issuecomment-709207827, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX6PVLMNPIBJFWKMG6LSK3KQJANCNFSM4SQYUTAA .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas