Hi I am trying to filter out the snps from my dataset following this command line:
/usr/local/bin/tassel-5-standalone/
run_pipeline.pl -Xmx400G -fork1 -h5 /nobackup/data7/jose/GBSv2/MedicagoGenotypes_KO.h5 -filterAlign -filterAlignExtInd -export /nobackup/data7/jose/GBSv2/MedicagoGenotypes_KO_NoIndels.h5 -runfork1 | tee GBSv2logfile.txt
java.lang.UnsupportedOperationException
at net.maizegenetics.analysis.filter.FilterAlignmentPlugin.processDatum(FilterAlignmentPlugin.java:190)
at net.maizegenetics.analysis.filter.FilterAlignmentPlugin.performFunction(FilterAlignmentPlugin.java:82)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1490)
at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1397)
at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:216)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1490)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Aug 28, 2015 13:37:44: progress: 100%