[Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.25 Date: April 28, 2016 [Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 7282 MB [Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_40 [Thread-6] INFO net.maizegenetics.tassel.TasselLogging - OS: Mac OS X [Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 4 [Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.tassel.TasselLogging: time: mai 28, 2016 21:20:29 [Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.tassel.TasselLogging Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635. [Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2: time: mai 28, 2016 21:20:38 Enzyme: ApekI [Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin - ProductionSNPCallerPluginV2 Parameters i: /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data k: /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/key_file_sorghoBCNAMpop.txt e: ApekI db: /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/GBSv2standalone/SbBCNAM_GBS5.2.24stane.sqlite o: /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/GBSv2standalone/sbBCNAM_SNP5.2.24stane3.vcf eR: 0.01 d: 0 ko: false do: true kmerLength: 64 minPosQS: 0.0 batchSize: 8 mnQS: 0 size of all tags in tag table=201571 size of all tissues in tissue table=0 size of all tags in mappingApproach table=2 size of all taxa in taxa table=74 ProductionSNPCallerPluginV2: Total batches to process: 2 size of all positions in snpPosition table=81078 [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Output VCF file: /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/GBSv2standalone/sbBCNAM_SNP5.2.24stane3.vcf created for genotypes from this run. size of all positions in snpPosition table=81078 size of all alleles in allele table=167244 Start processing batch 1 Enzyme: ApekI Enzyme: ApekI Enzyme: ApekI Enzyme: ApekI [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_18_fastq.txt.gz: Quality score base:33 [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_14_fastq.txt.gz: Quality score base:33 [ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_4_fastq.txt.gz: Quality score base:33 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_13_fastq.txt.gz: Quality score base:33 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=170882 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=170738 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=0 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file). [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 2294.796456 milliseconds for file /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_13_fastq.txt.gz Enzyme: ApekI [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_12_fastq.txt.gz: Quality score base:33 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=417230 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=416884 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=0 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file). [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 3383.321474 milliseconds for file /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_12_fastq.txt.gz Enzyme: ApekI [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_15_fastq.txt.gz: Quality score base:33 [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=704408 [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=703984 [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=0 [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file). [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 6542.878182 milliseconds for file /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_14_fastq.txt.gz Enzyme: ApekI [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_1_fastq.txt.gz: Quality score base:33 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=82532 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=82483 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=0 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file). [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 699.81464 milliseconds for file /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_15_fastq.txt.gz Enzyme: ApekI [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_16_fastq.txt.gz: Quality score base:33 [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:999073 rate:9259 ns/read [ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:998846 rate:9916 ns/read [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=1490684 [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1489273 [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=0 [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file). [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 13798.019173 milliseconds for file /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_18_fastq.txt.gz [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=867460 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=866802 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=0 [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file). [ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 7971.890935 milliseconds for file /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_16_fastq.txt.gz [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:998935 rate:8369 ns/read [ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:2000000 Reads with barcode and cut site overhang:1997596 rate:8758 ns/read [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:2000000 Reads with barcode and cut site overhang:1997901 rate:6941 ns/read [ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:2996368 rate:7659 ns/read [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:2996867 rate:6317 ns/read [ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=3868808 [ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=3864097 [ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=0 [ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file). [ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 27321.926254 milliseconds for file /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_4_fastq.txt.gz [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:3995773 rate:5820 ns/read [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:5000000 Reads with barcode and cut site overhang:4994708 rate:5449 ns/read [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:5993707 rate:5212 ns/read [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=6877005 [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=6869804 [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=0 [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file). [ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 34736.882123 milliseconds for file /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/SorghoBCNAM_1_fastq.txt.gz Finished processing batch 1 Start processing batch 2 Enzyme: ApekI [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/test384plex_1_fastq.txt.gz: Quality score base:33 [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:998186 rate:3811 ns/read [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:2000000 Reads with barcode and cut site overhang:1996397 rate:3740 ns/read [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=2052871 [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=2049177 [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=0 [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file). [Thread-7] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 7648.804418 milliseconds for file /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/bioinfo/TD_Tassel/run_tassel5GBSv2/00_raw_data/test384plex_1_fastq.txt.gz Finished processing batch 2 java.lang.ArrayIndexOutOfBoundsException: 1 at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:650) at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:216) at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2.processData(ProductionSNPCallerPluginV2.java:280) at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631) at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29) [Thread-7] DEBUG net.maizegenetics.plugindef.AbstractPlugin - Error writing VCF file: /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/GBSv2standalone/sbBCNAM_SNP5.2.24stane3.vcf: 1 java.lang.IllegalArgumentException: Error writing VCF file: /Users/SIDIBEBOCS/Documents/Communication/OtherDoc/Formation/enseignant/CERAAS/2016/GBSv2standalone/sbBCNAM_SNP5.2.24stane3.vcf: 1 at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:677) at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:216) at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2.processData(ProductionSNPCallerPluginV2.java:280) at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631) at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)