ProductionSNPCallerPluginV2: Total batches to process: 4
size of all positions in snpPosition table=207913
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 -
The target HDF5 file:
GBSPVdUnifiedResultsOpen.h5
does not exist. A new HDF5 file of that name will be created
to hold the genotypes from this run.
size of all positions in snpPosition table=207913
size of all alleles in allele table=448635
Start processing batch 1
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:457862 rate:24251 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:355967 rate:25569 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1344680 rate:23773 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:972443 rate:24187 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1778118 rate:23815 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1563205 rate:23919 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2200560 rate:23740 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:1191682 rate:23275 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:2752463 rate:23568 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:3880803 rate:23409 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:10000000 Reads with barcode and cut site overhang:2674223 rate:23502 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:1900567 rate:23298 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3833741 rate:23501 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5201645 rate:23512 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:3231738 rate:23511 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:3530582 rate:23463 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:4685876 rate:23483 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:973045 rate:23256 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:6672919 rate:23435 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:2733492 rate:23251 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:4581295 rate:23393 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:7181609 rate:23408 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:5913254 rate:23372 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:6523548 rate:23429 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:735177 rate:23195 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:6532646 rate:23373 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:8618174 rate:23387 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:7435389 rate:23423 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:773478 rate:23060 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:3399119 rate:23294 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:5943837 rate:23401 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:9097058 rate:23414 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:7820241 rate:23471 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:854402 rate:23148 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:6536063 rate:23329 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:10067312 rate:23350 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:8604244 rate:23733 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:928973 rate:23103 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:10542200 rate:23381 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:9027936 rate:23745 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:7169019 rate:23321 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:11010456 rate:23362 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:9452773 rate:23709 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24853605
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=996511
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=1329705
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 575985.78029 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:4301317 rate:23188 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:7483275 rate:23284 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:11487748 rate:23314 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:9820938 rate:23599 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:26000000 Reads with barcode and cut site overhang:11979666 rate:23219 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:4653863 rate:22989 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:12476830 rate:23105 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:8980369 rate:23113 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:10595427 rate:23367 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=27627572
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=9091237
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=17031715
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 636573.333103 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:8813457 rate:22764 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:13480408 rate:22777 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:30000000 Reads with barcode and cut site overhang:14012618 rate:22584 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:31000000 Reads with barcode and cut site overhang:14537767 rate:22438 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:31000000 Reads with barcode and cut site overhang:12273199 rate:22631 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:32000000 Reads with barcode and cut site overhang:5528102 rate:22214 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:32000000 Reads with barcode and cut site overhang:15021858 rate:22285 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=33746558
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=2175514
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3679143
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 740182.597661 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:34000000 Reads with barcode and cut site overhang:13447593 rate:22127 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:35000000 Reads with barcode and cut site overhang:6033507 rate:21698 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:35000000 Reads with barcode and cut site overhang:16522229 rate:21755 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:36000000 Reads with barcode and cut site overhang:14131112 rate:21696 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:11793207 rate:21339 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:17554205 rate:21345 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:14536094 rate:21495 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:12162279 rate:21173 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:18046706 rate:21179 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:40000000 Reads with barcode and cut site overhang:19076200 rate:20854 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=41312418
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1581938
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=2293559
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 846532.673444 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:41000000 Reads with barcode and cut site overhang:13303120 rate:20681 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:42000000 Reads with barcode and cut site overhang:7221841 rate:20439 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:42000000 Reads with barcode and cut site overhang:20114831 rate:20474 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:43000000 Reads with barcode and cut site overhang:20645538 rate:20261 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:43000000 Reads with barcode and cut site overhang:14102184 rate:20262 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:45000000 Reads with barcode and cut site overhang:21548355 rate:19875 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:46000000 Reads with barcode and cut site overhang:21738510 rate:19702 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:46000000 Reads with barcode and cut site overhang:17955285 rate:19791 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:47000000 Reads with barcode and cut site overhang:7967367 rate:19508 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:48000000 Reads with barcode and cut site overhang:22786244 rate:19367 ns/read
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=48312799
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=8188613
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=10941481
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 932124.786952 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:49000000 Reads with barcode and cut site overhang:18995509 rate:19229 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:50000000 Reads with barcode and cut site overhang:23803607 rate:18953 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:51000000 Reads with barcode and cut site overhang:24334846 rate:18756 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:52000000 Reads with barcode and cut site overhang:24746362 rate:18561 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:52000000 Reads with barcode and cut site overhang:20010857 rate:18620 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:17722888 rate:18371 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:20432779 rate:18431 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:54000000 Reads with barcode and cut site overhang:18116004 rate:18193 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:55000000 Reads with barcode and cut site overhang:26328801 rate:18029 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:58000000 Reads with barcode and cut site overhang:27878848 rate:17545 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=58322655
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=28039733
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=29202212
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 1020589.631942 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:59000000 Reads with barcode and cut site overhang:20062764 rate:17358 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:20455709 rate:17169 ns/read
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:22689065 rate:17206 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:61000000 Reads with barcode and cut site overhang:20853728 rate:16984 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:62000000 Reads with barcode and cut site overhang:21303005 rate:16804 ns/read
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62268079
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=21409214
[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=39011508
[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 1043383.062723 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62500553
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=23400053
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=36210925
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 1045124.194128 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R2_fastq.fastq
Finished processing batch 1
Start processing batch 2
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R1_fastq.fastq: Quality score base:33
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1237352 rate:23676 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2481349 rate:23456 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:1859802 rate:24036 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2502398 rate:24057 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:2974952 rate:23635 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:2290845 rate:24042 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:3448523 rate:23462 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:2674408 rate:23849 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:3254462 rate:21912 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:3897921 rate:23736 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:10000000 Reads with barcode and cut site overhang:4341823 rate:23427 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3991434 rate:21843 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=12158498
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=4421065
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=6049864
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 265867.889974 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_2_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5267137 rate:23212 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:4036890 rate:23428 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:5754364 rate:23030 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:4400103 rate:23278 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:6746524 rate:22810 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:7222387 rate:22681 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:6286185 rate:22394 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:1124955 rate:21973 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:9042387 rate:22243 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:6578340 rate:22262 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:9490519 rate:22016 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:6871289 rate:22139 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:9977484 rate:22028 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:7423653 rate:21989 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:10945502 rate:21794 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24404610
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=11174187
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=12657479
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 534010.823697 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:11429298 rate:21697 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=25527073
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=11697787
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=13299901
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 551577.135421 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=25527073
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=8107465
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=15775883
[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 553715.934882 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol4-1-TGACCA_L008-R2_fastq.fastq
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:1120859 rate:20430 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:31000000 Reads with barcode and cut site overhang:1574244 rate:19807 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=32237757
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1596704
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=4074794
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 628453.729928 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=38230971
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=958481
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=2220064
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 681493.856418 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R2_fastq.fastq
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=38230971
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1450705
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=1851100
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 681956.032733 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol010-1-TAGCTT_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=49082144
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=2501488
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3314516
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-4] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 714497.493646 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R1_fastq.fastq
Finished processing batch 2
Start processing batch 3
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R1_fastq.fastq: Quality score base:33
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:316918 rate:21181 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:2000000 Reads with barcode and cut site overhang:884867 rate:23388 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1409334 rate:22264 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1324425 rate:23563 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:5000000 Reads with barcode and cut site overhang:1359588 rate:22915 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:5000000 Reads with barcode and cut site overhang:1937673 rate:23978 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2577156 rate:23436 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:2657535 rate:23716 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:8000000 Reads with barcode and cut site overhang:3064269 rate:23565 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:4243878 rate:21735 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:2723615 rate:23127 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:10000000 Reads with barcode and cut site overhang:3780435 rate:23550 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:5177053 rate:21815 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3311839 rate:23225 ns/read
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=12158498
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=5713902
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=5164922
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-6] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 264397.969293 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/GBSPVD_1_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5150971 rate:23237 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:4556625 rate:23304 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:5605011 rate:23024 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:13000000 Reads with barcode and cut site overhang:4958895 rate:23125 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:14000000 Reads with barcode and cut site overhang:6052820 rate:22860 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:14000000 Reads with barcode and cut site overhang:5389819 rate:22918 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:5840279 rate:22720 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:7070172 rate:22505 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:6337652 rate:22545 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:7569794 rate:22427 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:7285975 rate:22305 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:8075230 rate:22330 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:5631460 rate:22135 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:8575747 rate:22245 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:597887 rate:21886 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:1377496 rate:21923 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:5917778 rate:22031 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:9034543 rate:22142 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:9953503 rate:21936 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:8998935 rate:21967 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:1579063 rate:21708 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:9901670 rate:21845 ns/read
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24404610
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=6986692
[ForkJoinPool.commonPool-worker-3] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=15624016
[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 530056.571209 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol3-1-TTAGGC_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:10327496 rate:21697 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:11380193 rate:21726 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:26000000 Reads with barcode and cut site overhang:10715627 rate:21546 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:12328287 rate:21433 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:1914714 rate:21110 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:12825961 rate:21267 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:11600288 rate:21277 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:13317062 rate:21116 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:12073805 rate:21126 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:30000000 Reads with barcode and cut site overhang:12563912 rate:20985 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:32000000 Reads with barcode and cut site overhang:14837633 rate:20771 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=32237757
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=2171977
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3682205
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 665281.582289 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol009-1-GATCAG_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=33746558
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1433058
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=4219957
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 688732.100247 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol011-1-GGCTAC_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:34000000 Reads with barcode and cut site overhang:15832741 rate:20380 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:34000000 Reads with barcode and cut site overhang:14348269 rate:20392 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:36000000 Reads with barcode and cut site overhang:15088785 rate:19893 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:36000000 Reads with barcode and cut site overhang:16815573 rate:19907 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:37000000 Reads with barcode and cut site overhang:15555884 rate:19675 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:16026525 rate:19461 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:40000000 Reads with barcode and cut site overhang:16886694 rate:19081 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=41312418
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1094894
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=2654430
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 773970.71309 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol007-1-CAGATC_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:41000000 Reads with barcode and cut site overhang:19335695 rate:18895 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:43000000 Reads with barcode and cut site overhang:18154165 rate:18415 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:47000000 Reads with barcode and cut site overhang:19958871 rate:17595 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:48000000 Reads with barcode and cut site overhang:22808719 rate:17407 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=49082144
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=1807034
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=3838814
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 841932.735109 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol012-1-CTTGTA_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:51000000 Reads with barcode and cut site overhang:21548499 rate:16769 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:25000735 rate:16357 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:53000000 Reads with barcode and cut site overhang:22383514 rate:16357 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:54000000 Reads with barcode and cut site overhang:22862918 rate:16161 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:56000000 Reads with barcode and cut site overhang:26424926 rate:15792 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:57000000 Reads with barcode and cut site overhang:26930617 rate:15615 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:59000000 Reads with barcode and cut site overhang:27990444 rate:15283 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:28522015 rate:15126 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:60000000 Reads with barcode and cut site overhang:25082888 rate:15126 ns/read
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:61000000 Reads with barcode and cut site overhang:28981366 rate:14973 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:61000000 Reads with barcode and cut site overhang:25523782 rate:14974 ns/read
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62268079
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=25825559
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=32192312
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-8] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 921142.937374 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol1-1-ATCACG_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=62500553
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=29775658
[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=31632914
[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 921829.248553 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol6-1-GCCAAT_L008-R1_fastq.fastq
Finished processing batch 3
Start processing batch 4
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
Enzyme: ApeKI
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R1_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R2_fastq.fastq: Quality score base:33
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R2_fastq.fastq: Quality score base:33
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:1000000 Reads with barcode and cut site overhang:415271 rate:11160 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:2000000 Reads with barcode and cut site overhang:814889 rate:11291 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:3000000 Reads with barcode and cut site overhang:1207316 rate:11419 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1605974 rate:11450 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:4000000 Reads with barcode and cut site overhang:1437704 rate:11661 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:6000000 Reads with barcode and cut site overhang:2423622 rate:11484 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:7000000 Reads with barcode and cut site overhang:890161 rate:11634 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:9000000 Reads with barcode and cut site overhang:2971903 rate:11571 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:11000000 Reads with barcode and cut site overhang:3612099 rate:11590 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:5153809 rate:11548 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:12000000 Reads with barcode and cut site overhang:3931257 rate:11607 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:14000000 Reads with barcode and cut site overhang:4743413 rate:11619 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:15000000 Reads with barcode and cut site overhang:5199355 rate:11579 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:2068821 rate:11561 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:16000000 Reads with barcode and cut site overhang:5628864 rate:11593 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:17000000 Reads with barcode and cut site overhang:7534051 rate:11548 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:18000000 Reads with barcode and cut site overhang:6438060 rate:11602 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:8494581 rate:11562 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:19000000 Reads with barcode and cut site overhang:6783122 rate:11599 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:8983660 rate:11554 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:20000000 Reads with barcode and cut site overhang:2584410 rate:11572 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:21000000 Reads with barcode and cut site overhang:652002 rate:11802 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:9758533 rate:11560 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:22000000 Reads with barcode and cut site overhang:2843322 rate:11575 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:2989576 rate:11569 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:23000000 Reads with barcode and cut site overhang:8291684 rate:11590 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:24000000 Reads with barcode and cut site overhang:8616788 rate:11589 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:3295271 rate:11578 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:25000000 Reads with barcode and cut site overhang:8969613 rate:11587 ns/read
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=24853605
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=716748
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=1530844
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-13] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 293209.451315 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol008-1-ACTTGA_L008-R2_fastq.fastq
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:12157192 rate:11384 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:3553818 rate:11397 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:27000000 Reads with barcode and cut site overhang:9715171 rate:11406 ns/read
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=27627572
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=12473904
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=14636326
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-15] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 312754.31718 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol5-1-ACAGTG_L008-R1_fastq.fastq
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:28000000 Reads with barcode and cut site overhang:3684489 rate:11260 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:29000000 Reads with barcode and cut site overhang:10495434 rate:11072 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:35000000 Reads with barcode and cut site overhang:4539563 rate:10170 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:38000000 Reads with barcode and cut site overhang:13552955 rate:9830 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:39000000 Reads with barcode and cut site overhang:13866086 rate:9727 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:40000000 Reads with barcode and cut site overhang:14231978 rate:9630 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:42000000 Reads with barcode and cut site overhang:5236201 rate:9446 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:44000000 Reads with barcode and cut site overhang:15632588 rate:9281 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:45000000 Reads with barcode and cut site overhang:15902867 rate:9205 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:46000000 Reads with barcode and cut site overhang:16290239 rate:9131 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:47000000 Reads with barcode and cut site overhang:16581236 rate:9062 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:48000000 Reads with barcode and cut site overhang:16911506 rate:8994 ns/read
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=48312799
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=5643335
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=12704945
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[ForkJoinPool.commonPool-worker-9] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 433386.048592 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol013-1-AGTCAA_L008-R2_fastq.fastq
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:50000000 Reads with barcode and cut site overhang:17615397 rate:8766 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:54000000 Reads with barcode and cut site overhang:18772604 rate:8332 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total Reads:55000000 Reads with barcode and cut site overhang:19159328 rate:8234 ns/read
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of reads in lane=58322655
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of good barcoded reads=19952138
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Total number of low quality reads=35196217
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Timing process (sorting, collapsing, and writing TagCount to file).
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Process took 462507.370558 milliseconds for file /home/facon/GBS_PVd_unified_analysis/./AllFastqFiles/PVd-Pol2-1-CGATGT_L008-R2_fastq.fastq
Finished processing batch 4
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 -
Writing ReadsPerSample log file...
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - ReadsPerSample log file: /home/facon/GBS_PVd_unified_analysis/GBS_PVd_unifiedfile_ReadsPerSample.log
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 -
Total number of SNPs processed with minimum quality score 20 was 2200875.
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - ...done
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2: time: Dec 18, 2015 20:26:12
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2: time: Dec 18, 2015 20:26:12: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 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.