run_pipeline.pl -fork1 -GBSSeqToTagDBPlugin -e ApeKI -i data -k sample_key.txt -o gbsV2db -mxTagL 64 -mnTagL 20 -mnQS 20 -endPlugin -runfork1
Error in Reading Annotated Taxon File:sample_key.txtjava.lang.IndexOutOfBoundsException: Index: 1, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:653) at java.util.ArrayList.get(ArrayList.java:429) at net.maizegenetics.taxa.TaxaListIOUtils.readTaxaAnnotationFile(TaxaListIOUtils.java:277) at net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin.processData(GBSSeqToTagDBPlugin.java:93) at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:94) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1444) 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)
TomatoBC2F6_NoIndex_L001_R1_001.fastq.gz
TomatoBC2F6_NoIndex_L001_R2_001.fastq.gz
Flowcell Lane Barcode Sample PlateName Row Column LibraryPrepIDBC5YCLACXX 1 CTCC 8_S_1001 TomatoBC2F6 A 1 1100BC5YCLACXX 1 TGCA 12_S_1798 TomatoBC2F6 A 2 1101BC5YCLACXX 1 ACTA BC2F6_9057 TomatoBC2F6 A 3 1102BC5YCLACXX 1 CAGA BC2F6_9058 TomatoBC2F6 A 4 1103BC5YCLACXX 1 AACT BC2F6_9060 TomatoBC2F6 A 5 1104BC5YCLACXX 1 GCGT BC2F6_9061 TomatoBC2F6 A 6 1105BC5YCLACXX 1 TGCGA BC2F6_9062 TomatoBC2F6 A 7 1106BC5YCLACXX 1 CGAT BC2F6_9064 TomatoBC2F6 A 8 1107BC5YCLACXX 1 CGCTT BC2F6_9065 TomatoBC2F6 A 9 1108
when I run first step in GBSv2 pipeline, I encountered this error.
The command I used:
run_pipeline.pl -fork1 -GBSSeqToTagDBPlugin-e ApeKI-i data -k sample_key.txt -o gbsV2db -mxTagL 64-mnTagL 20-mnQS 20-endPlugin -runfork1
exerpt from error:
BC5YCLACXX 1CGCTT BC2F6_9065TomatoBC2F6 A9 1108
Any help would be appreciated!
Thanks!
For example,
BC2F6_9058:1103
The angle brackets <> are meant to indicate that the value is up to the user to supply.
Best,
Jeff
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