Matthew Eldridge wrote:
> Hi,
> I’ve been loading some Illumina Bead Summary (IBS) data into Base 2.7.0 
> using the illumina-plugins-1.1 package and got the following error when 
> it tries to match up the Illumina ID, or Illumicode, with a 
> corresponding feature ID read from the Illumina-supplied BGX annotation 
> file.
> net.sf.basedb.core.BaseException: Item not found: Feature[Feature 
> ID=0004280546] doesn't exist on array design when inserting spot 0004280546
> at 
> net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(
> at 
> at 
> net.sf.basedb.core.PluginExecutionRequest.invoke(
> at 
> net.sf.basedb.core.InternalJobQueue$
> at
> Caused by: net.sf.basedb.core.ItemNotFoundException: Item not found: 
> Feature[Feature ID=0004280546] doesn't exist on array design
> at net.sf.basedb.core.RawDataBatcher.doInsert(
> at net.sf.basedb.core.RawDataBatcher.insert(
> at 
> net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(
> ... 4 more
> The BeadSummaryImporter class is left-padding with zeros the Illumina 
> ID, presumably because in most BGX files the Array_Address_ID values are 
> left-padded in this way and read into Base2 as such. However, for the 
> BGX file I downloaded from Illumina’s web site, 
> MouseWG-6_V1_1_R3_11234304_A.bgx, the IDs are not padded hence the error 
> message. From what I can tell, this appears to be an isolated case 
> affecting just the MouseWG-6_V1_1_R[0-3]_11234304.bgx files.

Somehow, this is not surprising... Illumina file formats has a history 
of being unstable. Thanks for reporting this to us.

> As a quick and dirty fix, I edited and removed 
> the MD5.leftPad function call in importScandata, rebuilt the plugin and 
> redeployed and that worked. 

I guess that after this "fix" the plug-in only works with that file and 
not with the others that have the 0-padding.

 > But I thought I should alert the plugin
> developers to a potential inconsistency in the Illumina annotation 
> files. Perhaps an alternative approach might be to strip zeros from 
> Illumina feature IDs when read in from the BGX file?

This will not work, since it would cause already imported data that has 
the 0-padding to be unusable. The only possible solution I can see is to 
let the BGX-importer do the 0-padding of Array_Address_ID values if this 
is missing in the first place.

I have added this as a ticket:


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