Matthew Eldridge wrote:
> 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
> net.sf.basedb.core.BaseException: Item not found: Feature[Feature
> ID=0004280546] doesn't exist on array design when inserting spot 0004280546
> 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)
> ... 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 BeadSummaryImporter.java 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: http://baseplugins.thep.lu.se/ticket/121
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