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(BeadSummaryImporter.java:611) > at > net.sf.basedb.illumina.plugins.BeadSummaryImporter.run(BeadSummaryImporter.java: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(BeadSummaryImporter.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 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 /Nicklas ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
