track hub error - unsupported file type

[HARDING Simon]

Dear UCSC

We have a track hub set up for the GUDMAP project at

http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/hub.txt

Until recently it has been functioning fine, but now we see this error when trying to load it.

ERROR: Unsupported type '13156_CM4G.bam' in hub http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/hub.txt genome mm9 track 13156_CM4G

Running hubCheck gives:

./hubCheck.exe hub.txt
Found 2 problems:
Unsupported type '13156_CM4G.bam' in hub hub.txt genome mm9 track 13156_CM4G
Unsupported type '21814_accepted_hits.bam' in hub hub.txt genome mm10 track E14_5_DRG_(10ng,_high_volume)


The directories that hold those BAM files contain index (.bai) files and they are accessible. The site documentation still says BAM is supported. Can you advise on what might be happening here and how to resolve?

Many thanks

--
Simon D. Harding, PhD.
MRC HGU
MRC IGMM at University of Edinburgh
Crewe Road, EDINBURGH, EH4 2XU


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The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[Brian Lee]

Dear Simon,

Thank you for using the UCSC Genome Browser and the Track Hub feature and your question regarding an error about unsupported type.

The error is arising from a line in your trackDb.txt where instead of "type bam" there is some additional metadata that should be trimmed from "type 21814_accepted_hits.bam" to be only "type bam". That information might be better placed in the "track uniqueTrackName" line such as "track name_metadata", for example, "track uniqueTrackName_21814_accepted_hits". While you suggest it was working previously, it should not have worked, for more details see this trackDb statement link:http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#commonSettings

If you change all these "type metadata.bam" lines to only be "type bam" it should correct the issue. If it does not fix the issue, please respond with more information.

curl -s "http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/mm10/trackDb_out_mm10.txt" | grep type
curl -s "http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/mm9/trackDb_out_mm9.txt" | grep type

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead togeno...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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