Trinotate annotation - sqlite error

[Manu kumar]

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



[B]CMD: /nobackup/users/r01mkg15/softwares/Trinotate-2.0.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl --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/TrinotateSeqLoader.pl line 91.

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

Error, cmd: /nobackup/users/r01mkg15/softwares/Trinotate-2.0.2/util/trinotateSeqLoader/TrinotateSeqLoader.pl --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.

[GenoMax]

For reference cross-posted: https://www.biostars.org/p/176305/

There appears to be a disk I/O error as well. Are you sure the file system you are trying to access is available on the node where you are trying to run this?

[Manu kumar]

The issue is that we do not have sqlite on our cluster, i have installed it locally to my user and all the other databases i need for the execution are stored locally. It seems there is a problem loading sqlite for the execution ??!!!

[GenoMax]

Is that "local" file system available on the node where your are executing the program? Sometimes the local file systems may only be on the head-node but not on workers. Is that a possibility?

[SES]

The database and driver are installed as a single file with the Perl module DBD::SQLite, so if you can load that then it is unlikely a database dependency issue. I agree with the comment above that the "disk I/O error" is the real issue. That could mean a lot of things, out of disk space (for the user quota or the volume) or it could be permissions. If it were me, I'd check that you have space to write that database and permissions, and of course, search for other common causes for the error.

[Manu kumar]

Thank you very much for the suggestions, I believe what you said is right. I have tried installing the software again and running. The same problem persists. I need to consult the HPC cluster staff to check if it is anything pertaining to the access rights and permisssions.

[Manu kumar]

Thank you all, finally figured out.. the problem was with the HPC cluster rights and permissions. I am now able to access the database and populate it with my data. Running successfully... Waiting for my results