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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 56eb8eaa7ffcdd9a4de1b9c7fb6459a049c7a416
author iuc
date Fri, 16 May 2025 18:50:59 +0000
parents ab97b3b44590
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
iuc
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diff changeset
1 beagle.29Oct24.c8e.jar (version 5.4)
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
iuc
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2 Copyright (C) 2014-2022 Brian L. Browning
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
iuc
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3 Enter "java -jar beagle.29Oct24.c8e.jar" to list command line argument
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
iuc
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4 Start time: 10:39 PM CEST on 02 May 2025
0
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5
2
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
iuc
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6 Command line: java -Xmx1024m -jar beagle.29Oct24.c8e.jar
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
iuc
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7 gt=/home/elmedjadji/Documents/newgal/galaxy/database/objects/4/3/b/dataset_43be6aa5-2515-4fff-be35-4cbf54b2842f.dat
0
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 Study markers: 223
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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34
2
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
iuc
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35 Burnin iteration 1: 0 seconds
0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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36 Burnin iteration 2: 0 seconds
2
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
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37 Burnin iteration 3: 0 seconds
0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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38
2
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
iuc
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39 Estimated ne: 333498
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
iuc
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40 Estimated err: 2.0e-03
0
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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41
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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42 Phasing iteration 1: 0 seconds
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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43 Phasing iteration 2: 0 seconds
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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44 Phasing iteration 3: 0 seconds
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45 Phasing iteration 4: 0 seconds
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46 Phasing iteration 5: 0 seconds
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47 Phasing iteration 6: 0 seconds
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48 Phasing iteration 7: 0 seconds
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49 Phasing iteration 8: 0 seconds
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50 Phasing iteration 9: 0 seconds
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51 Phasing iteration 10: 0 seconds
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52 Phasing iteration 11: 0 seconds
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53 Phasing iteration 12: 0 seconds
2
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
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54 Low frequency phasing: 0 seconds
0
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55
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56 Cumulative Statistics:
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57
117d42db0a30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8"
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58 Study markers: 223
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59
2
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
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60 Haplotype phasing time: 1 second
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
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61 Total time: 2 seconds
0
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62
2
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
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63 End time: 10:39 PM CEST on 02 May 2025
ab97b3b44590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 607e1d083ce036edde6f0ddb66871608c0ff7ca8
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64 beagle.29Oct24.c8e.jar finished