/share/work/biosoft/tassel/latest/lib/ahocorasick-0.2.4.jar:/share/work/biosoft/tassel/latest/lib/biojava-alignment-6.0.4.jar:/share/work/biosoft/tassel/latest/lib/biojava-core-6.0.4.jar:/share/work/biosoft/tassel/latest/lib/biojava-genome-6.0.4.jar:/share/work/biosoft/tassel/latest/lib/biojava-phylo-4.2.12.jar:/share/work/biosoft/tassel/latest/lib/colt-1.2.0.jar:/share/work/biosoft/tassel/latest/lib/commons-codec-1.10.jar:/share/work/biosoft/tassel/latest/lib/commons-io-2.11.0.jar:/share/work/biosoft/tassel/latest/lib/commons-math3-3.4.1.jar:/share/work/biosoft/tassel/latest/lib/ejml-core-0.41.jar:/share/work/biosoft/tassel/latest/lib/ejml-ddense-0.41.jar:/share/work/biosoft/tassel/latest/lib/error_prone_annotations-2.19.1.jar:/share/work/biosoft/tassel/latest/lib/fastutil-8.2.2.jar:/share/work/biosoft/tassel/latest/lib/forester-1.039.jar:/share/work/biosoft/tassel/latest/lib/gs-core-1.3.jar:/share/work/biosoft/tassel/latest/lib/gs-ui-1.3.jar:/share/work/biosoft/tassel/latest/lib/guava-22.0.jar:/share/work/biosoft/tassel/latest/lib/htsjdk-2.24.1.jar:/share/work/biosoft/tassel/latest/lib/ini4j-0.5.4.jar:/share/work/biosoft/tassel/latest/lib/itextpdf-5.1.0.jar:/share/work/biosoft/tassel/latest/lib/jackson-annotations-2.13.2.jar:/share/work/biosoft/tassel/latest/lib/jackson-core-2.13.2.jar:/share/work/biosoft/tassel/latest/lib/jackson-databind-2.13.2.2.jar:/share/work/biosoft/tassel/latest/lib/jackson-module-kotlin-2.13.2.jar:/share/work/biosoft/tassel/latest/lib/javax.json-1.0.4.jar:/share/work/biosoft/tassel/latest/lib/jcommon-1.0.23.jar:/share/work/biosoft/tassel/latest/lib/jfreechart-1.0.19.jar:/share/work/biosoft/tassel/latest/lib/jfreesvg-3.2.jar:/share/work/biosoft/tassel/latest/lib/jhdf5-14.12.5.jar:/share/work/biosoft/tassel/latest/lib/json-simple-1.1.1.jar:/share/work/biosoft/tassel/latest/lib/junit-4.10.jar:/share/work/biosoft/tassel/latest/lib/kotlin-reflect-1.6.10.jar:/share/work/biosoft/tassel/latest/lib/kotlin-stdlib-1.6.10.jar:/share/work/biosoft/tassel/latest/lib/kotlin-stdlib-jdk7-1.6.10.jar:/share/work/biosoft/tassel/latest/lib/kotlin-stdlib-jdk8-1.6.10.jar:/share/work/biosoft/tassel/latest/lib/kotlinx-coroutines-core-jvm-1.6.0.jar:/share/work/biosoft/tassel/latest/lib/log4j-1.2.13.jar:/share/work/biosoft/tassel/latest/lib/mail-1.4.jar:/share/work/biosoft/tassel/latest/lib/phg.jar:/share/work/biosoft/tassel/latest/lib/postgresql-9.4-1201.jdbc41.jar:/share/work/biosoft/tassel/latest/lib/protobuf-java-3.23.0.jar:/share/work/biosoft/tassel/latest/lib/protobuf-java-util-3.23.0.jar:/share/work/biosoft/tassel/latest/lib/protobuf-kotlin-3.23.0.jar:/share/work/biosoft/tassel/latest/lib/scala-library-2.10.1.jar:/share/work/biosoft/tassel/latest/lib/slf4j-api-1.7.10.jar:/share/work/biosoft/tassel/latest/lib/slf4j-simple-1.7.10.jar:/share/work/biosoft/tassel/latest/lib/snappy-java-1.1.8.4.jar:/share/work/biosoft/tassel/latest/lib/sqlite-jdbc-3.39.2.1.jar:/share/work/biosoft/tassel/latest/lib/sshj-0.32.0.jar:/share/work/biosoft/tassel/latest/lib/trove-3.0.3.jar:/share/work/biosoft/tassel/latest/sTASSEL.jar
Memory Settings: -Xms512m -Xmx30G
Tassel Pipeline Arguments: -fork1 -h hapmap.ordered.hmp.txt -fork2 -importGuess /work/my_gwas/data/traits_rice.txt -combine2 -input1 -input2 -intersect -FixedEffectLMPlugin -endPlugin -export hd_GLM
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.90 Date: July 11, 2023
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 27307 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_302
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 56
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel 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.
[main] INFO net.maizegenetics.tassel.TasselLogging -
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Using Library: Practical Haplotype Graph (PHG): Version: 1.6 Date: July 11, 2023
[main] INFO net.maizegenetics.tassel.TasselLogging - PHG Citation: Bradbury PJ, Casstevens T, Jensen SE, Johnson LC, Miller ZR, Monier B, Romay MC, Song B, Buckler ES. The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinformatics. 2022 Aug 2;38(15):3698-3702. doi: 10.1093/bioinformatics/btac410. PMID: 35748708; PMCID: PMC9344836.
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -h, hapmap.ordered.hmp.txt, -fork2, -importGuess, /work/my_gwas/data/traits_rice.txt, -combine2, -input1, -input2, -intersect, -FixedEffectLMPlugin, -endPlugin, -export, hd_GLM]
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Sep 13, 2024 20:33:20
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: Hapmap
sortPositions: false
keepDepth: false
[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: hapmap.ordered.hmp.txt time: Sep 13, 2024 20:33:20
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Sep 13, 2024 20:33:21: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.FileLoadPlugin 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.
[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finished Loading File: hapmap.ordered.hmp.txt time: Sep 13, 2024 20:33:21
Genotype Table Name: hapmap
Number of Taxa: 200
Number of Sites: 15545
Sites x Taxa: 3109000
Chromosomes...
GM01: start site: 0 (86140) last site: 667 (56810228) total: 668
GM02: start site: 668 (30613) last site: 1802 (50305951) total: 1135
GM02_SCAFFOLD_122: start site: 1803 (9676) last site: 1805 (10044) total: 3
GM03: start site: 1806 (359925) last site: 3042 (45589367) total: 1237
GM03_SCAFFOLD_27: start site: 3043 (115765) last site: 3043 (115765) total: 1
GM04: start site: 3044 (661514) last site: 3529 (49129704) total: 486
GM05: start site: 3530 (12184) last site: 3784 (41652928) total: 255
GM06: start site: 3785 (847210) last site: 5252 (50868763) total: 1468
GM06_SCAFFOLD_183: start site: 5253 (12557) last site: 5253 (12557) total: 1
GM06_SCAFFOLD_59: start site: 5254 (78021) last site: 5255 (78139) total: 2
GM07: start site: 5256 (43353) last site: 6016 (44900546) total: 761
GM08: start site: 6017 (1667130) last site: 6307 (46815727) total: 291
GM09: start site: 6308 (50065) last site: 7256 (50390604) total: 949
GM10: start site: 7257 (992185) last site: 7642 (51622515) total: 386
GM10_SCAFFOLD_107: start site: 7643 (9688) last site: 7645 (53829) total: 3
GM11: start site: 7646 (2678) last site: 7999 (39548760) total: 354
GM12: start site: 8000 (50068) last site: 8310 (41042538) total: 311
GM13: start site: 8311 (104310) last site: 8792 (44284132) total: 482
GM14: start site: 8793 (903005) last site: 10346 (49790443) total: 1554
GM14_SCAFFOLD_84: start site: 10347 (72592) last site: 10350 (81948) total: 4
GM15: start site: 10351 (172657) last site: 11907 (53741213) total: 1557
GM15_SCAFFOLD_113: start site: 11908 (10721) last site: 11909 (14964) total: 2
GM16: start site: 11910 (34457) last site: 13063 (37519553) total: 1154
GM17: start site: 13064 (372792) last site: 13533 (41212421) total: 470
GM18: start site: 13534 (76255) last site: 14421 (58124344) total: 888
GM18_SCAFFOLD_54: start site: 14422 (99316) last site: 14425 (99617) total: 4
GM19: start site: 14426 (127937) last site: 14806 (51205675) total: 381
GM20: start site: 14807 (338434) last site: 15415 (47826751) total: 609
SCAFFOLD_103: start site: 15416 (21809) last site: 15425 (24487) total: 10
SCAFFOLD_109: start site: 15426 (37642) last site: 15426 (37642) total: 1
SCAFFOLD_110: start site: 15427 (21339) last site: 15430 (32131) total: 4
SCAFFOLD_125: start site: 15431 (45276) last site: 15431 (45276) total: 1
SCAFFOLD_128: start site: 15432 (11208) last site: 15437 (11539) total: 6
SCAFFOLD_143: start site: 15438 (6831) last site: 15442 (35873) total: 5
SCAFFOLD_157: start site: 15443 (2006) last site: 15445 (6750) total: 3
SCAFFOLD_194: start site: 15446 (26527) last site: 15446 (26527) total: 1
SCAFFOLD_223: start site: 15447 (946) last site: 15450 (12638) total: 4
SCAFFOLD_250: start site: 15451 (731) last site: 15459 (1077) total: 9
SCAFFOLD_26: start site: 15460 (125351) last site: 15477 (231648) total: 18
SCAFFOLD_264: start site: 15478 (18294) last site: 15479 (18302) total: 2
SCAFFOLD_28: start site: 15480 (169887) last site: 15501 (197507) total: 22
SCAFFOLD_31: start site: 15502 (58042) last site: 15505 (162503) total: 4
SCAFFOLD_32: start site: 15506 (21066) last site: 15506 (21066) total: 1
SCAFFOLD_33: start site: 15507 (245743) last site: 15508 (245965) total: 2
SCAFFOLD_330: start site: 15509 (4964) last site: 15511 (4990) total: 3
SCAFFOLD_34: start site: 15512 (33435) last site: 15520 (49150) total: 9
SCAFFOLD_36: start site: 15521 (63695) last site: 15523 (128420) total: 3
SCAFFOLD_39: start site: 15524 (3244) last site: 15524 (3244) total: 1
SCAFFOLD_42: start site: 15525 (49812) last site: 15527 (50070) total: 3
SCAFFOLD_47: start site: 15528 (151582) last site: 15528 (151582) total: 1
SCAFFOLD_56: start site: 15529 (10437) last site: 15533 (44807) total: 5
SCAFFOLD_60: start site: 15534 (1972) last site: 15534 (1972) total: 1
SCAFFOLD_85: start site: 15535 (49434) last site: 15536 (49491) total: 2
SCAFFOLD_88: start site: 15537 (36710) last site: 15542 (67802) total: 6
SCAFFOLD_92: start site: 15543 (39410) last site: 15544 (47115) total: 2
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: Sep 13, 2024 20:33:21
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Sep 13, 2024 20:33:21: progress: 100%