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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
author iuc
date Sun, 22 Jan 2023 12:42:30 +0000
parents 117d42db0a30
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
iuc
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1 beagle.21Apr21.304.jar (version 5.2)
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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2 Copyright (C) 2014-2021 Brian L. Browning
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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3 Enter "java -jar beagle.21Apr21.304.jar" to list command line argument
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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4 Start time: 08:46 PM GMT on 26 Jun 2021
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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5
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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6 Command line: java -Xmx989m -jar beagle.21Apr21.304.jar
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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7 gt=/tmp/tmpoahokk9w/files/e/9/3/dataset_e93c5cb3-373e-4432-80ab-47ff1068bc9f.dat
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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8 chrom=22:100-
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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9 ne=1000000
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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10 window=40.0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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11 overlap=2.0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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12 seed=1
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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13 err=0.02
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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14 burnin=3
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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15 iterations=12
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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16 phase-states=280
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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17 impute=true
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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18 imp-states=1600
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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19 imp-segment=6.0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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20 imp-step=0.1
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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21 cluster=0.005
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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22 ap=false
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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23 gp=false
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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24 out=out
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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25 nthreads=1
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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26
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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27 No genetic map is specified: using 1 cM = 1 Mb
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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28
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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29 Reference samples: 0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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30 Study samples: 191
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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31
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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32 Window 1 [22:20000086-20016908]
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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33 Reference markers: 223
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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34 Study markers: 223
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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35
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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36 Burnin iteration 1: 1 second
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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37
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38 Burnin iteration 2: 0 seconds
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39
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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40 Burnin iteration 3: 0 seconds
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42 Phasing iteration 1: 0 seconds
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44 Phasing iteration 2: 0 seconds
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46 Phasing iteration 3: 0 seconds
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48 Phasing iteration 4: 0 seconds
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50 Phasing iteration 5: 0 seconds
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52 Phasing iteration 6: 0 seconds
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54 Phasing iteration 7: 0 seconds
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56 Phasing iteration 8: 0 seconds
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58 Phasing iteration 9: 0 seconds
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60 Phasing iteration 10: 0 seconds
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62 Phasing iteration 11: 0 seconds
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64 Phasing iteration 12: 0 seconds
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66 Cumulative Statistics:
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68 Study markers: 223
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69
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70 Haplotype phasing time: 2 seconds
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71 Total time: 3 seconds
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72
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73 End time: 08:46 PM GMT on 26 Jun 2021
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74 beagle.21Apr21.304.jar finished