Hi,
I¹ve 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(BeadSummar
yImporter.java:611)
at
net.sf.basedb.illumina.plugins.BeadSummaryImporter.run(BeadSummaryImporter.j
ava:225)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java
:108)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:505)
at java.lang.Thread.run(Thread.java:619)
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(RawDataBatcher.java:581)
at net.sf.basedb.core.RawDataBatcher.insert(RawDataBatcher.java:525)
at
net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(BeadSummar
yImporter.java:589)
... 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 Illumina¹s 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.
As a quick and dirty fix, I edited BeadSummaryImporter.java and removed the
MD5.leftPad function call in importScandata, rebuilt the plugin and
redeployed and that worked. 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?
Cheers,
Matt
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