hExtendedRangeQuery: table xenoRefGene doesn't exist in xyz database, or hFindTableInfoWithConn failed

[Stephen Turner]

Good morning.

We recently set up a local/private mirror (after purchasing an enterprise license). I'm loading genomes that are either private or aren't in annotation hub. I'm running into issues when I load the browser:

hExtendedRangeQuery: table xenoRefGene doesn't exist in XYZ database, or hFindTableInfoWithConn failed
hExtendedRangeQuery: table cpgIslandExtUnmasked doesn't exist in XYZ database, or hFindTableInfoWithConn failed
hExtendedRangeQuery: table simpleRepeat doesn't exist in XYZ database, or hFindTableInfoWithConn failed

When I look at the trackDb.ra file for this organism, all the paths to the data, html, searchtrix, are all present at the path specified.

track xenoRefGene
shortLabel RefSeq mRNAs
longLabel RefSeq mRNAs mapped to this assembly
group rna
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl /mnt/db/gbdb/XYZ/bbi/XYZ.2_ORGANISMX.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix /mnt/db/gbdb/XYZ/ixIxx/XYZ.2_ORGANISMX.xenoRefGene.ix
html /mnt/db/gbdb/XYZ/html/XYZ.2_ORGANISMX.xenoRefGene.html

I'm creating the trackDb table in that organism's directory with:

hgTrackDb XYZ XYZ trackDb /mnt/db/kent/src/hg/lib/trackDb.sql ./

...and this seems to be successful:

Loaded 27 track descriptions total
Loaded database XYZ

But I'm still getting the errors on the browser page. 

I'm following the directions at https://genomewiki.ucsc.edu/index.php?title=Building_a_new_genome_database to build a new genome.

I've looked through the mailing list here and the public genome google group messages, and I've looked through the documentation below, and can't seem to find anything.

• Building a new genome database - genomewiki - https://genomewiki.ucsc.edu/index.php?title=Building_a_new_genome_database
• Local tracks at mirror sites - genomewiki - https://genomewiki.ucsc.edu/index.php/Local_tracks_at_mirror_sites
• Genome Browser Manual Installation Adding a new, custom (non-UCSC) genome to the browser https://genome.ucsc.edu/goldenPath/help/mirrorManual.html#adding-a-new-custom-non-ucsc-genome-to-the-browser
• UCSC Genome Browser Public Support - Google Groups - https://groups.google.com/a/soe.ucsc.edu/g/genome
• UCSC Genome Browser Mirror-Specific Support - Google Groups - https://groups.google.com/a/soe.ucsc.edu/g/genome-mirror

Thanks for pointing me in the right direction!

Stephen

[Gerardo Perez]

Hello, Stephen.

To get a better understanding of what is going on with the hExtendedRangeQuery issue, can you share what the apache error log (/usr/local/apache/logs/error_log) file outputs? The issue may be due to special code looking for tables by those names when the track exists. You can try renaming those tracks, for example, you can rename “xenoRefGene” to “otherRefGene”. You would also rename the “cpgIslandExtUnmasked” and “simpleRepeat” to a different name that doesn't trigger the code's expectation of SQL tables.

I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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