Mercurial > repos > dereeper > sniplay3
comparison MDSplot/test-data/analyse.log @ 21:50bd37c444ac draft
Uploaded
| author | dereeper |
|---|---|
| date | Mon, 23 Mar 2015 05:35:48 -0400 |
| parents | a0a95688cf17 |
| children |
comparison
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| 20:13cff72ec2d3 | 21:50bd37c444ac |
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| 1 | |
| 2 @----------------------------------------------------------@ | |
| 3 | PLINK! | v1.07 | 10/Aug/2009 | | |
| 4 |----------------------------------------------------------| | |
| 5 | (C) 2009 Shaun Purcell, GNU General Public License, v2 | | |
| 6 |----------------------------------------------------------| | |
| 7 | For documentation, citation & bug-report instructions: | | |
| 8 | http://pngu.mgh.harvard.edu/purcell/plink/ | | |
| 9 @----------------------------------------------------------@ | |
| 10 | |
| 11 Skipping web check... [ --noweb ] | |
| 12 Writing this text to log file [ analyse.log ] | |
| 13 Analysis started: Tue Jan 20 09:30:56 2015 | |
| 14 | |
| 15 Options in effect: | |
| 16 --file input | |
| 17 --noweb | |
| 18 --cluster | |
| 19 --matrix | |
| 20 --mds-plot 2 | |
| 21 --out analyse | |
| 22 | |
| 23 2013 (of 2013) markers to be included from [ input.map ] | |
| 24 93 individuals read from [ input.ped ] | |
| 25 93 individuals with nonmissing phenotypes | |
| 26 Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) | |
| 27 Missing phenotype value is also -9 | |
| 28 0 cases, 93 controls and 0 missing | |
| 29 93 males, 0 females, and 0 of unspecified sex | |
| 30 Before frequency and genotyping pruning, there are 2013 SNPs | |
| 31 Converting data to SNP-major format | |
| 32 93 founders and 0 non-founders found | |
| 33 Total genotyping rate in remaining individuals is 1 | |
| 34 0 SNPs failed missingness test ( GENO > 1 ) | |
| 35 0 SNPs failed frequency test ( MAF < 0 ) | |
| 36 Converting data to Individual-major format | |
| 37 After frequency and genotyping pruning, there are 2013 SNPs | |
| 38 After filtering, 0 cases, 93 controls and 0 missing | |
| 39 After filtering, 93 males, 0 females, and 0 of unspecified sex | |
| 40 | |
| 41 **Warning** this analysis typically requires whole-genome level data | |
| 42 to give accurate results | |
| 43 | |
| 44 Clustering individuals based on genome-wide IBS | |
| 45 Merge distance p-value constraint = 0 | |
| 46 IBS(g) calculation: 0 of 4278 | |
| 47 IBS(g) calculation: 100 of 4278 | |
| 48 IBS(g) calculation: 200 of 4278 | |
| 49 IBS(g) calculation: 300 of 4278 | |
| 50 IBS(g) calculation: 400 of 4278 | |
| 51 IBS(g) calculation: 500 of 4278 | |
| 52 IBS(g) calculation: 600 of 4278 | |
| 53 IBS(g) calculation: 700 of 4278 | |
| 54 IBS(g) calculation: 800 of 4278 | |
| 55 IBS(g) calculation: 900 of 4278 | |
| 56 IBS(g) calculation: 1000 of 4278 | |
| 57 IBS(g) calculation: 1100 of 4278 | |
| 58 IBS(g) calculation: 1200 of 4278 | |
| 59 IBS(g) calculation: 1300 of 4278 | |
| 60 IBS(g) calculation: 1400 of 4278 | |
| 61 IBS(g) calculation: 1500 of 4278 | |
| 62 IBS(g) calculation: 1600 of 4278 | |
| 63 IBS(g) calculation: 1700 of 4278 | |
| 64 IBS(g) calculation: 1800 of 4278 | |
| 65 IBS(g) calculation: 1900 of 4278 | |
| 66 IBS(g) calculation: 2000 of 4278 | |
| 67 IBS(g) calculation: 2100 of 4278 | |
| 68 IBS(g) calculation: 2200 of 4278 | |
| 69 IBS(g) calculation: 2300 of 4278 | |
| 70 IBS(g) calculation: 2400 of 4278 | |
| 71 IBS(g) calculation: 2500 of 4278 | |
| 72 IBS(g) calculation: 2600 of 4278 | |
| 73 IBS(g) calculation: 2700 of 4278 | |
| 74 IBS(g) calculation: 2800 of 4278 | |
| 75 IBS(g) calculation: 2900 of 4278 | |
| 76 IBS(g) calculation: 3000 of 4278 | |
| 77 IBS(g) calculation: 3100 of 4278 | |
| 78 IBS(g) calculation: 3200 of 4278 | |
| 79 IBS(g) calculation: 3300 of 4278 | |
| 80 IBS(g) calculation: 3400 of 4278 | |
| 81 IBS(g) calculation: 3500 of 4278 | |
| 82 IBS(g) calculation: 3600 of 4278 | |
| 83 IBS(g) calculation: 3700 of 4278 | |
| 84 IBS(g) calculation: 3800 of 4278 | |
| 85 IBS(g) calculation: 3900 of 4278 | |
| 86 IBS(g) calculation: 4000 of 4278 | |
| 87 IBS(g) calculation: 4100 of 4278 | |
| 88 IBS(g) calculation: 4200 of 4278 | |
| 89 Writing IBS similarity matrix to [ analyse.mibs ] | |
| 90 Of these, 4278 are pairable based on constraints | |
| 91 Writing cluster progress to [ analyse.cluster0 ] | |
| 92 Writing cluster solution (1) [ analyse.cluster1 ] | |
| 93 Writing cluster solution (2) [ analyse.cluster2 ] | |
| 94 Writing cluster solution (3) [ analyse.cluster3 ] | |
| 95 Writing MDS solution to [ analyse.mds ] | |
| 96 MDS plot of individuals (not clusters) | |
| 97 | |
| 98 Analysis finished: Tue Jan 20 09:30:57 2015 | |
| 99 |