Vaneet Lotay
2015-03-30 18:06:22 UTC
Hello,
We seem to be having trouble creating a new GBrowse database in MySQL for a brand new track or so it would seem as I'm not sure what exactly is going wrong. We have a FASTA file and GFF3 file, we created a new GBrowse database and followed the tutorial (http://cpansearch.perl.org/src/LDS/GBrowse-2.43/htdocs/tutorial/tutorial.html#mysql) except to change user names and database names relevant to us. We used the following command as in the tutorial and it loads successfully (replacing volvox of course):
bp_seqfeature_load.pl -c -f -a DBI::mysql -d volvox volvox_all.fa volvox_all.gff3
We checked the database after to verify that the sequence and features are loaded properly with matching sequence IDs to link them and it's all there. However when we go to our test server we get a 'Not found' error as if it can't find those tables in the database. Doing some gene searches eventually gets another common error "Chromosome/contig not found". It actually reveals in the detailed message the correct gene name in our attributes column as well as the correct scaffold ID yet it says not defined in the database.
We created a very simplistic subset of the FASTA and GFF3 file containing only one scaffold sequence and one gene/mRNA with 1 exon and 1 CDS from the original files. We created a brand new database and loaded these small files and it still comes up with the same error. Just wondering what we can be doing wrong as we've really changed a lot of small minor things that might be causing this disconnection but to no avail. I attached these small subset files as well as the configuration file and you can visit our test server for this new database here:
http://gbrowse-test.xenbase.org/fgb2/gbrowse/xl_wt1_0/
In the context of these new files, after you visit this test server page, you'll notice if you search for LOC which is the first 3 letters of the actual gene name (LOC100489), it comes up with the 'contig not found' message and shows this detail underneath which I stated before indicates that it at least found the GFF3 file and possibly the Chr01 sequence but still won't display them for some reason:
Cannot display LOC100489 because the chromosome/contig named Chr01 is not defined in the database.
Please help if you know what initial steps might be going wrong.
Thanks,
Vaneet
Vaneet Lotay
Xenbase Bioinformatician
724 ICT Building - University of Calgary
2500 University Drive NW
Calgary AB T2N 1N4
CANADA
We seem to be having trouble creating a new GBrowse database in MySQL for a brand new track or so it would seem as I'm not sure what exactly is going wrong. We have a FASTA file and GFF3 file, we created a new GBrowse database and followed the tutorial (http://cpansearch.perl.org/src/LDS/GBrowse-2.43/htdocs/tutorial/tutorial.html#mysql) except to change user names and database names relevant to us. We used the following command as in the tutorial and it loads successfully (replacing volvox of course):
bp_seqfeature_load.pl -c -f -a DBI::mysql -d volvox volvox_all.fa volvox_all.gff3
We checked the database after to verify that the sequence and features are loaded properly with matching sequence IDs to link them and it's all there. However when we go to our test server we get a 'Not found' error as if it can't find those tables in the database. Doing some gene searches eventually gets another common error "Chromosome/contig not found". It actually reveals in the detailed message the correct gene name in our attributes column as well as the correct scaffold ID yet it says not defined in the database.
We created a very simplistic subset of the FASTA and GFF3 file containing only one scaffold sequence and one gene/mRNA with 1 exon and 1 CDS from the original files. We created a brand new database and loaded these small files and it still comes up with the same error. Just wondering what we can be doing wrong as we've really changed a lot of small minor things that might be causing this disconnection but to no avail. I attached these small subset files as well as the configuration file and you can visit our test server for this new database here:
http://gbrowse-test.xenbase.org/fgb2/gbrowse/xl_wt1_0/
In the context of these new files, after you visit this test server page, you'll notice if you search for LOC which is the first 3 letters of the actual gene name (LOC100489), it comes up with the 'contig not found' message and shows this detail underneath which I stated before indicates that it at least found the GFF3 file and possibly the Chr01 sequence but still won't display them for some reason:
Cannot display LOC100489 because the chromosome/contig named Chr01 is not defined in the database.
Please help if you know what initial steps might be going wrong.
Thanks,
Vaneet
Vaneet Lotay
Xenbase Bioinformatician
724 ICT Building - University of Calgary
2500 University Drive NW
Calgary AB T2N 1N4
CANADA