Mercurial > repos > dereeper > sniplay3

annotate MDSplot/test-data/analyse.log @ 24:21d878747ac6 draft default tip

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author dereeper
date Mon, 23 Mar 2015 05:53:20 -0400
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1
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2 @----------------------------------------------------------@
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3 | PLINK! | v1.07 | 10/Aug/2009 |
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4 |----------------------------------------------------------|
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5 | (C) 2009 Shaun Purcell, GNU General Public License, v2 |
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6 |----------------------------------------------------------|
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7 | For documentation, citation & bug-report instructions: |
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8 | http://pngu.mgh.harvard.edu/purcell/plink/ |
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9 @----------------------------------------------------------@
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10
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11 Skipping web check... [ --noweb ]
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12 Writing this text to log file [ analyse.log ]
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13 Analysis started: Tue Jan 20 09:30:56 2015
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14
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15 Options in effect:
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16 --file input
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17 --noweb
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18 --cluster
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19 --matrix
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20 --mds-plot 2
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21 --out analyse
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22
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23 2013 (of 2013) markers to be included from [ input.map ]
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24 93 individuals read from [ input.ped ]
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25 93 individuals with nonmissing phenotypes
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26 Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
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27 Missing phenotype value is also -9
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28 0 cases, 93 controls and 0 missing
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29 93 males, 0 females, and 0 of unspecified sex
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30 Before frequency and genotyping pruning, there are 2013 SNPs
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31 Converting data to SNP-major format
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32 93 founders and 0 non-founders found
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33 Total genotyping rate in remaining individuals is 1
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34 0 SNPs failed missingness test ( GENO > 1 )
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35 0 SNPs failed frequency test ( MAF < 0 )
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36 Converting data to Individual-major format
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37 After frequency and genotyping pruning, there are 2013 SNPs
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38 After filtering, 0 cases, 93 controls and 0 missing
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39 After filtering, 93 males, 0 females, and 0 of unspecified sex
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40
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41 **Warning** this analysis typically requires whole-genome level data
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42 to give accurate results
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43
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44 Clustering individuals based on genome-wide IBS
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45 Merge distance p-value constraint = 0
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46 IBS(g) calculation: 0 of 4278 IBS(g) calculation: 100 of 4278 IBS(g) calculation: 200 of 4278 IBS(g) calculation: 300 of 4278 IBS(g) calculation: 400 of 4278 IBS(g) calculation: 500 of 4278 IBS(g) calculation: 600 of 4278 IBS(g) calculation: 700 of 4278 IBS(g) calculation: 800 of 4278 IBS(g) calculation: 900 of 4278 IBS(g) calculation: 1000 of 4278 IBS(g) calculation: 1100 of 4278 IBS(g) calculation: 1200 of 4278 IBS(g) calculation: 1300 of 4278 IBS(g) calculation: 1400 of 4278 IBS(g) calculation: 1500 of 4278 IBS(g) calculation: 1600 of 4278 IBS(g) calculation: 1700 of 4278 IBS(g) calculation: 1800 of 4278 IBS(g) calculation: 1900 of 4278 IBS(g) calculation: 2000 of 4278 IBS(g) calculation: 2100 of 4278 IBS(g) calculation: 2200 of 4278 IBS(g) calculation: 2300 of 4278 IBS(g) calculation: 2400 of 4278 IBS(g) calculation: 2500 of 4278 IBS(g) calculation: 2600 of 4278 IBS(g) calculation: 2700 of 4278 IBS(g) calculation: 2800 of 4278 IBS(g) calculation: 2900 of 4278 IBS(g) calculation: 3000 of 4278 IBS(g) calculation: 3100 of 4278 IBS(g) calculation: 3200 of 4278 IBS(g) calculation: 3300 of 4278 IBS(g) calculation: 3400 of 4278 IBS(g) calculation: 3500 of 4278 IBS(g) calculation: 3600 of 4278 IBS(g) calculation: 3700 of 4278 IBS(g) calculation: 3800 of 4278 IBS(g) calculation: 3900 of 4278 IBS(g) calculation: 4000 of 4278 IBS(g) calculation: 4100 of 4278 IBS(g) calculation: 4200 of 4278 Writing IBS similarity matrix to [ analyse.mibs ]
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47 Of these, 4278 are pairable based on constraints
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48 Writing cluster progress to [ analyse.cluster0 ]
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49 Writing cluster solution (1) [ analyse.cluster1 ]
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50 Writing cluster solution (2) [ analyse.cluster2 ]
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51 Writing cluster solution (3) [ analyse.cluster3 ]
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52 Writing MDS solution to [ analyse.mds ]
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53 MDS plot of individuals (not clusters)
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54
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55 Analysis finished: Tue Jan 20 09:30:57 2015
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