/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/colt-1.2.0.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/snappy-java-1.1.1.6.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/biojava-core-4.0.0.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/jfreechart-1.0.19.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/ahocorasick-0.2.4.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/commons-codec-1.10.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/slf4j-simple-1.7.10.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/guava-22.0.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/sqlite-jdbc-3.8.5-pre1.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/mail-1.4.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/biojava-phylo-4.0.0.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/itextpdf-5.1.0.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/jcommon-1.0.23.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/htsjdk-2.19.0.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/biojava-alignment-4.0.0.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/slf4j-api-1.7.10.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/ejml-0.23.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/trove-3.0.3.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/javax.json-1.0.4.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/jhdf5-14.12.5.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/jfreesvg-3.2.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/json-simple-1.1.1.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/log4j-1.2.13.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/forester-1.038.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/jfxrt.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/ini4j-0.5.4.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/je-6.0.11.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/commons-math3-3.4.1.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/junit-4.10.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/avro-1.8.1.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/lib/postgresql-9.4-1201.jdbc41.jar:/Analysis/PFY2021N10GBS1156_Dr.S.N.Jena_new/tas/tassel5-src/dist/sTASSEL.jar Memory Settings: -Xms514g -Xmx754g Tassel Pipeline Arguments: -debug -fork1 -GBSSeqToTagDBPlugin -e MluCI -i . -db GBS_BM_MluCI.db -k fakebarcodes_key_MluCI.tsv -c 3 -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 100000000 -endPlugin -runfork1 [main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.73 Date: June 23, 2021 [main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 686308 MB [main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_265 [main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux [main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 192 [main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -GBSSeqToTagDBPlugin, -e, MluCI, -i, ., -db, GBS_BM_MluCI.db, -k, fakebarcodes_key_MluCI.tsv, -c, 3, -kmerLength, 64, -minKmerL, 20, -mnQS, 20, -mxKmerNum, 100000000, -endPlugin, -runfork1] net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: Aug 6, 2021 10:33:0 [pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null java.lang.NullPointerException at net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin.postProcessParameters(GBSSeqToTagDBPlugin.java:150) at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:107) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2017) at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Usage: GBSSeqToTagDBPlugin -i : Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name. (required) -k : Key file listing barcodes distinguishing the samples (required) -e : Enzyme used to create the GBS library, if it differs from the one listed in the key file (required) -kmerLength : Specified length for each kmer to process (Default: 64) -minKmerL : Minimum kmer Length after second cut site is removed (Default: 20) -c : Minimum kmer count (Default: 10) -db : Output Database File (required) -mnQS : Minimum quality score within the barcode and read length to be accepted (Default: 0) -mxKmerNum : Maximum number of kmers (Default: 50000000) -batchSize : Number of flow cells being processed simultaneously (Default: 8) -deleteOldData : Delete existing SNP quality data from db tables (Default: true) [pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - null