/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._ahocorasick-0.2.4.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._biojava-alignment-4.0.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._biojava-core-4.0.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._biojava-phylo-4.0.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._colt-1.2.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._commons-codec-1.10.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._commons-math3-3.4.1.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._ejml-0.23.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._fastutil-8.2.2.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._forester-1.038.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._gs-core-1.3.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._gs-ui-1.3.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._guava-22.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._htsjdk-2.19.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._itextpdf-5.1.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._javax.json-1.0.4.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/biojava-alignment-4.0.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/biojava-core-4.0.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/biojava-phylo-4.0.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/colt-1.2.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/commons-codec-1.10.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/commons-math3-3.4.1.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/ejml-0.23.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/fastutil-8.2.2.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/forester-1.038.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/gs-core-1.3.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/gs-ui-1.3.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/guava-22.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/htsjdk-2.19.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/itextpdf-5.1.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/javax.json-1.0.4.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/jcommon-1.0.23.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._jfreechart-1.0.19.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._jfreesvg-3.2.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._jhdf5-14.12.5.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._json-simple-1.1.1.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._junit-4.10.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._kotlin-stdlib-1.3.50.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._kotlinx-coroutines-core-1.3.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._log4j-1.2.13.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._mail-1.4.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._phg.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._postgresql-9.4-1201.jdbc41.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._scala-library-2.10.1.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._slf4j-api-1.7.10.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._slf4j-simple-1.7.10.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._snappy-java-1.1.1.6.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._sqlite-jdbc-3.8.5-pre1.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._trove-3.0.3.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/jfreesvg-3.2.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/jhdf5-14.12.5.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/json-simple-1.1.1.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/junit-4.10.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/kotlin-stdlib-1.3.50.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/kotlinx-coroutines-core-1.3.0.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/log4j-1.2.13.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/mail-1.4.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/phg.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/postgresql-9.4-1201.jdbc41.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/scala-library-2.10.1.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/slf4j-api-1.7.10.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/slf4j-simple-1.7.10.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/snappy-java-1.1.1.6.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/sqlite-jdbc-3.8.5-pre1.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/trove-3.0.3.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/._jcommon-1.0.23.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/ahocorasick-0.2.4.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/lib/jfreechart-1.0.19.jar:/media/user/22CE5BE378448A49/tassel_5_standalone/sTASSEL.jar
Memory Settings: -Xms512m -Xmx50g
Tassel Pipeline Arguments: -fork1 -h /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0.0012.hmp.txt -excludeTaxa N0203,N0204,N0205,N0206 -export /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0.0012_remove_four_samples.hapmap.txt -exportType Hapmap
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.57  Date: October 10, 2019
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 45511 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_152-release
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 36
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -h, /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0.0012.hmp.txt, -excludeTaxa, N0203,N0204,N0205,N0206, -export, /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0.0012_remove_four_samples.hapmap.txt, -exportType, Hapmap]
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: 四月 20, 2022 10:41:11
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - 
FileLoadPlugin Parameters
format: Hapmap
sortPositions: false
keepDepth: true

[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0.0012.hmp.txt time: 四月 20, 2022 10:41:11
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: 四月 20, 2022 10:41:12: progress: 14%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: 四月 20, 2022 10:41:12: progress: 28%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: 四月 20, 2022 10:41:12: progress: 42%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: 四月 20, 2022 10:41:12: progress: 57%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: 四月 20, 2022 10:41:12: progress: 71%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: 四月 20, 2022 10:41:12: progress: 85%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: 四月 20, 2022 10:41:12: 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: /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0.0012.hmp.txt time: 四月 20, 2022 10:41:13
Genotype Table Name: sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0
Number of Taxa: 189
Number of Sites: 256796
Sites x Taxa: 48534444
Chromosomes...
1: start site: 0 (6636) last site: 66837 (258393651) total: 66838
2: start site: 66838 (11367) last site: 127840 (224503884) total: 61003
3: start site: 127841 (23259) last site: 145396 (70575666) total: 17556
4: start site: 145397 (4253) last site: 161866 (67224618) total: 16470
5: start site: 161867 (43) last site: 174569 (49302137) total: 12703
6: start site: 174570 (2296) last site: 183709 (39318297) total: 9140
7: start site: 183710 (2605) last site: 193151 (36990581) total: 9442
8: start site: 193152 (7563) last site: 202330 (35903490) total: 9179
9: start site: 202331 (12358) last site: 209535 (30510483) total: 7205
10: start site: 209536 (1665) last site: 216752 (29490562) total: 7217
11: start site: 216753 (1974) last site: 222450 (25711335) total: 5698
12: start site: 222451 (1254) last site: 229130 (26352854) total: 6680
13: start site: 229131 (6680) last site: 234904 (25494014) total: 5774
14: start site: 234905 (96) last site: 240687 (22073335) total: 5783
15: start site: 240688 (1513) last site: 245714 (20632913) total: 5027
16: start site: 245715 (5254) last site: 250080 (16675199) total: 4366
17: start site: 250081 (2267) last site: 252956 (11213396) total: 2876
18: start site: 252957 (5595) last site: 255679 (9947664) total: 2723
19: start site: 255680 (6166) last site: 256795 (4656409) total: 1116

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: 四月 20, 2022 10:41:13
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin: time: 四月 20, 2022 10:41:13
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - 
FilterTaxaBuilderPlugin Parameters
filterName: Filter
minNotMissing: 0.0
minHeterozygous: 0.0
maxHeterozygous: 1.0
includeTaxa: false
taxaList: [N0203, N0204, N0205, N0206]

Genotype Table Name: sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0_Filter
Number of Taxa: 185
Number of Sites: 256796
Sites x Taxa: 47507260
Chromosomes...
1: start site: 0 (6636) last site: 66837 (258393651) total: 66838
2: start site: 66838 (11367) last site: 127840 (224503884) total: 61003
3: start site: 127841 (23259) last site: 145396 (70575666) total: 17556
4: start site: 145397 (4253) last site: 161866 (67224618) total: 16470
5: start site: 161867 (43) last site: 174569 (49302137) total: 12703
6: start site: 174570 (2296) last site: 183709 (39318297) total: 9140
7: start site: 183710 (2605) last site: 193151 (36990581) total: 9442
8: start site: 193152 (7563) last site: 202330 (35903490) total: 9179
9: start site: 202331 (12358) last site: 209535 (30510483) total: 7205
10: start site: 209536 (1665) last site: 216752 (29490562) total: 7217
11: start site: 216753 (1974) last site: 222450 (25711335) total: 5698
12: start site: 222451 (1254) last site: 229130 (26352854) total: 6680
13: start site: 229131 (6680) last site: 234904 (25494014) total: 5774
14: start site: 234905 (96) last site: 240687 (22073335) total: 5783
15: start site: 240688 (1513) last site: 245714 (20632913) total: 5027
16: start site: 245715 (5254) last site: 250080 (16675199) total: 4366
17: start site: 250081 (2267) last site: 252956 (11213396) total: 2876
18: start site: 252957 (5595) last site: 255679 (9947664) total: 2723
19: start site: 255680 (6166) last site: 256795 (4656409) total: 1116

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin: time: 四月 20, 2022 10:41:13
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.ExportPlugin: time: 四月 20, 2022 10:41:13
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - 
ExportPlugin Parameters
saveAs: /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_01
format: Hapmap
keepDepth: true
includeTaxaAnnotations: true

[pool-1-thread-1] INFO net.maizegenetics.analysis.data.ExportPlugin - performFunction: wrote dataset: sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_0_Filter to file: /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_01.hmp.txt
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.ExportPlugin: time: 四月 20, 2022 10:41:16
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.ExportPlugin: time: 四月 20, 2022 10:41:16
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - 
ExportPlugin Parameters
saveAs: /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_02
format: Hapmap
keepDepth: true
includeTaxaAnnotations: true

[pool-1-thread-1] INFO net.maizegenetics.analysis.data.ExportPlugin - performFunction: wrote dataset: Filter to file: /media/user/18T/sample_all_joint_variant_SNPs_filtered_bqsr_snps_subset_02.json.gz
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.ExportPlugin: time: 四月 20, 2022 10:41:16
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin: time: 四月 20, 2022 10:41:16: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: 四月 20, 2022 10:41:16: progress: 100%