Hello,
I'm having trouble in creating bead summary files from bead level
files on BASE 2.9.2
using the Illumina plugin package version 1.2.
I created the array designs, imported the features and the reporters.
Then I created a
new raw bioassay and added two beadlevel files as they were supplied
to me. When
activating the bead summary importer, I get the following error
(pasted from the log):
Failed: Can't find start of data in file: File[id=386;
name=4449817059_A_1.txt] on line
101 in file 4449817059_A_1.txt
net.sf.basedb.core.BaseException: Can't find start of data in file:
File[id=386;
name=4449817059_A_1.txt] on line 101 in file 4449817059_A_1.txt
at
net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(BeadSummaryImporter.java:738)
at
net.sf.basedb.illumina.plugins.BeadSummaryImporter.run(BeadSummaryImporter.java:284)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:106)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:504)
at java.lang.Thread.run(Thread.java:619)
Caused by: net.sf.basedb.core.InvalidDataException: Can't find start
of data in file:
File[id=386; name=4449817059_A_1.txt]
at
net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(BeadSummaryImporter.java:677)
... 4 more
I don't know why line 101, as it does not matter what it is on that
line (I made a backup
of the bead level file and removed the offending line just to make
sure, since apparently
setting "skip" as option in case of errors has no effect).
I noticed that the header in my bead level data is different than what
the README
indicates, namely it is
Code,Grn,GrnX,GrnY
Also, the file is tab-separated, rather than comma-separated (but
substituting tabs to
commas does not fix the problem). Is there a way to work around this
problem, is it a
plugin limitation, or am I just doing things in the wrong way?
Thanks in advance.
P.S.: Apologies if it comes in multiple copies - my institution web
mail had some trouble.
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