Hello all,
I'm trying to do SNP-calling with TASEL. I have 4 fastq.txt.gz files with сhip and line indicators and barcodes key file: H2YJLBCX2_s_2_fastq.txt.gz, H2WYJBCX2_s_1_fastq.txt.gz, H2YJLBCX2_s_1_fastq.txt.gz, H2WYJBCX2_s_2_fastq.txt.gz. I have done successfully FastqToTagCountPlugin, but when I tried to run FastqToTBTPlugin a have following error:
java.lang.NullPointerException
at net.maizegenetics.dna.tag.AbstractTagsByTaxa.getIndexOfTaxaName(AbstractTagsByTaxa.java:54)
at net.maizegenetics.analysis.gbs.FastqToTBTPlugin.matchTagsToTaxa(FastqToTBTPlugin.java:306)
at net.maizegenetics.analysis.gbs.FastqToTBTPlugin.performFunction(FastqToTBTPlugin.java:54)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1915)
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)
Timing process (writing TagsByTaxa file)...
0 tags will be output to H2YJLBCX2_s_2.tbt.byte
My command is:
run_pipeline.pl -fork1 -FastqToTBTPlugin -i fastq/ -k key/GBSkey.txt -e HindIII-NlaIII -o tbt/ -y -t mergedTagCounts/mergednew.cnt -endPlugin -runfork1
It's not possible that i don't have 'good barcod reads'. What do you think? How I can fix it?
Thank you!
