Question: Trinotate Sqlite db error
gravatar for manukumar.fgb13-15
3.9 years ago by
manukumar.fgb13-150 wrote:

Hi all,

Am using trinotate to annotate a transcriptome, everything went fine till I started uploading my data into sqlite database. Am pretty new to trinotate and the field of transcriptome annotation. I am facing an error when I try uploading my data into sqlite which I am not able to understand. The error displayed is as follows


CMD: /nobackup/users/r01mkg15/softwares/Trinotate-2.0.2/util/trinotateSeqLoader/ --sqlite Trinotate.sqlite --gene_trans_map trinity.panto.fasta.gene_trans_map --transcript_fasta trinity.panto.fasta --transdecoder_pep transdecoder.pep --bulk_load

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

DBD::SQLite::db do failed: disk I/O error at /nobackup/users/r01mkg15/softwares/Trinotate-2.0.2/util/trinotateSeqLoader/ line 91.

Function not implemented at /nobackup/users/r01mkg15/softwares/Trinotate-2.0.2/util/trinotateSeqLoader/ line 91.

Error, cmd: /nobackup/users/r01mkg15/softwares/Trinotate-2.0.2/util/trinotateSeqLoader/ --sqlite Trinotate.sqlite --gene_trans_map trinity.panto.fasta.gene_trans_map --transcript_fasta trinity.panto.fasta --transdecoder_pep transdecoder.pep --bulk_load died with ret 9728 at /users/r01mkg15/sharedscratch/softwares/Trinotate-2.0.2/Trinotate line 112.  


This seems to be persistent even after I reinstalled the sqlite module in perl and i have download the new the new database of trinotate.sqlite database. nothing seems to work. please guide me with this. Am working on a HPC cluster without root user access. 


Thanks in advance, looking forward for uaa helps and suggestions.


assembly software error • 2.3k views
ADD COMMENTlink written 3.9 years ago by manukumar.fgb13-150

Which version of SQLite are you using? Maybe it is old you need a newer one - just a guess.

ADD REPLYlink written 3.9 years ago by h.mon29k

sqlite3 is the version in our cluster at the moment

ADD REPLYlink written 3.9 years ago by manukumar.fgb13-150


sqlite3 -version

If it is old, try installing a newer one on your area and prepend it to the PATH. Anyway, Trinity / Trinotate has a mailing list where the developers are very active and helpful, it would be a good idea to ask there if my suggestion doesn't help.

ADD REPLYlink written 3.9 years ago by h.mon29k

I reinstalled the sqlite db all over again and found that the same problem persists. I feel its something to do with our HPC cluster, there might be some issues with the rights and permissions for the user to access the database. I will work with that issue and get in touch.

Thank you very much for the suggestions 

ADD REPLYlink written 3.9 years ago by manukumar.fgb13-150

I meet same problem.Have you fixed it yet?

ADD REPLYlink written 15 months ago by harrypotterandsbt70
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