Mercurial > repos > iuc > structureharvester
changeset 0:8a7390c4d6bf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/structureharvester.xml Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,81 @@ +<tool id="structureharvester" name="structureHarvester" version="0.6.94"> + <description>for parsing STRUCTURE outputs and for performing the Evanno method</description> + <requirements> + <requirement type="package" version="0.6.94">structureharvester</requirement> + </requirements> + <version_command><![CDATA[ + structureHarvester.py --version + ]]></version_command> + <command detect_errors="exit_code"><![CDATA[ + mkdir inputs && + #for $input in $inputs + ln -s '$input' 'inputs/$input.element_identifier' && + #end for + structureHarvester.py --dir inputs/ --out . $evanno $clumpp && + mv summary.txt '$summary' + #if $evanno + && mv evanno.txt $evanno + #end if + #if $clumpp + && mkdir clumpp_indfile clumpp_popfile + && mv *.indfile clumpp_indfile/ + && mv *.popfile clumpp_popfile/ + #end if + ]]></command> + <inputs> + <param name="inputs" type="data" format="txt" multiple="true" label="STRUCTURE outputs" /> + <param argument="--evanno" type="boolean" checked="false" truevalue="--evanno" falsevalue="" label="If possible, performs the Evanno 2005 method." help="You must test at least 3 values of K. K values must be sequential. The number of replicates per K > 1."/> + <param argument="--clumpp" type="boolean" checked="false" truevalue="--clumpp" falsevalue="" label="Generates one K*.indfile for each value of K run, for use with CLUMPP." /> + </inputs> + <outputs> + <data name="summary" format="txt" label="Structure Harvester summary"/> + <data name="evanno" format="txt" label="Evann method output"> + <filter>evanno</filter> + </data> + <collection name="clumpp_indfile" type="list" label="Clumpp K*.indfile"> + <filter>clumpp</filter> + <discover_datasets pattern="__name__" format="txt" directory="clumpp_indfile" /> + </collection> + <collection name="clumpp_popfile" type="list" label="Clumpp K*.popfile"> + <filter>clumpp</filter> + <discover_datasets pattern="__name__" format="txt" directory="clumpp_popfile" /> + </collection> + </outputs> + <tests> + <test> + <param name="inputs" value="example_harvester_archive/Admix_run_001_f,example_harvester_archive/Admix_run_002_f,example_harvester_archive/Admix_run_004_f,example_harvester_archive/Admix_run_005_f,example_harvester_archive/Admix_run_007_f,example_harvester_archive/Admix_run_008_f,example_harvester_archive/K1ReRun_run_1_f,example_harvester_archive/K1ReRun_run_2_f" /> + <param name="evanno" value="false" /> + <param name="clumpp" value="true" /> + <output name="summary"> + <assert_contents> + <has_line line="1	2	-4329.950000	0.070711" /> + <has_line line="4	2	-2773.550000	0.212132" /> + <has_line line="K1ReRun_run_2_f	2	1	-4330.0	-4300.2	59.7" /> + <has_line line="Admix_run_008_f	008	4	-2773.4	-2678.8	189.2" /> + <has_line line="Core version: vA.2 July 2014" /> + </assert_contents> + </output> + <output_collection name="clumpp_indfile" type="list"> + <element name="K1.indfile" value="clumpp_indfile/K1.indfile" /> + <element name="K4.indfile" value="clumpp_indfile/K4.indfile" /> + </output_collection> + <output_collection name="clumpp_popfile" type="list"> + <element name="K1.popfile" value="clumpp_popfile/K1.popfile" /> + <element name="K4.popfile" value="clumpp_popfile/K4.popfile" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ + +Structure_Harvester_ is a program for parsing the output of Pritchard's STRUCTURE_ and for performing the Evanno method. + +.. _Structure_Harvester: http://taylor0.biology.ucla.edu/structureHarvester/ +.. _STRUCTURE: http://web.stanford.edu/group/pritchardlab/structure.html + + ]]></help> + <citations> + <citation type="doi">10.1007/s12686-011-9548-7</citation> + <citation type="doi">10.1111/j.1365-294X.2005.02553.x</citation> + <citation type="doi">10.1093/bioinformatics/btm233</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clumpp_indfile/K1.indfile Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,192 @@ + 1 1 (0) 1 : 1.000 + 2 2 (0) 1 : 1.000 + 3 3 (0) 1 : 1.000 + 4 4 (0) 1 : 1.000 + 5 5 (0) 1 : 1.000 + 6 6 (0) 1 : 1.000 + 7 7 (0) 2 : 1.000 + 8 8 (0) 2 : 1.000 + 9 9 (0) 2 : 1.000 + 10 10 (0) 2 : 1.000 + 11 11 (0) 2 : 1.000 + 12 12 (0) 2 : 1.000 + 13 13 (0) 3 : 1.000 + 14 14 (0) 3 : 1.000 + 15 15 (0) 3 : 1.000 + 16 16 (0) 3 : 1.000 + 17 17 (0) 3 : 1.000 + 18 18 (0) 3 : 1.000 + 19 19 (0) 4 : 1.000 + 20 20 (0) 4 : 1.000 + 21 21 (0) 4 : 1.000 + 22 22 (0) 4 : 1.000 + 23 23 (0) 4 : 1.000 + 24 24 (0) 4 : 1.000 + 25 25 (0) 5 : 1.000 + 26 26 (0) 5 : 1.000 + 27 27 (0) 5 : 1.000 + 28 28 (0) 5 : 1.000 + 29 29 (0) 5 : 1.000 + 30 30 (0) 5 : 1.000 + 31 31 (0) 6 : 1.000 + 32 32 (0) 6 : 1.000 + 33 33 (0) 6 : 1.000 + 34 34 (0) 6 : 1.000 + 35 35 (0) 6 : 1.000 + 36 36 (0) 6 : 1.000 + 37 37 (0) 7 : 1.000 + 38 38 (0) 7 : 1.000 + 39 39 (0) 7 : 1.000 + 40 40 (0) 7 : 1.000 + 41 41 (0) 7 : 1.000 + 42 42 (0) 7 : 1.000 + 43 43 (0) 8 : 1.000 + 44 44 (0) 8 : 1.000 + 45 45 (0) 8 : 1.000 + 46 46 (0) 8 : 1.000 + 47 47 (0) 8 : 1.000 + 48 48 (0) 8 : 1.000 + 49 49 (0) 9 : 1.000 + 50 50 (0) 9 : 1.000 + 51 51 (0) 9 : 1.000 + 52 52 (0) 9 : 1.000 + 53 53 (0) 9 : 1.000 + 54 54 (0) 9 : 1.000 + 55 55 (0) 10 : 1.000 + 56 56 (0) 10 : 1.000 + 57 57 (0) 10 : 1.000 + 58 58 (0) 10 : 1.000 + 59 59 (0) 10 : 1.000 + 60 60 (0) 10 : 1.000 + 61 61 (0) 11 : 1.000 + 62 62 (0) 11 : 1.000 + 63 63 (0) 11 : 1.000 + 64 64 (0) 11 : 1.000 + 65 65 (0) 11 : 1.000 + 66 66 (0) 11 : 1.000 + 67 67 (0) 12 : 1.000 + 68 68 (0) 12 : 1.000 + 69 69 (0) 12 : 1.000 + 70 70 (0) 12 : 1.000 + 71 71 (0) 12 : 1.000 + 72 72 (0) 12 : 1.000 + 73 73 (0) 13 : 1.000 + 74 74 (0) 13 : 1.000 + 75 75 (0) 13 : 1.000 + 76 76 (0) 13 : 1.000 + 77 77 (0) 13 : 1.000 + 78 78 (0) 13 : 1.000 + 79 79 (0) 14 : 1.000 + 80 80 (0) 14 : 1.000 + 81 81 (0) 14 : 1.000 + 82 82 (0) 14 : 1.000 + 83 83 (0) 14 : 1.000 + 84 84 (0) 14 : 1.000 + 85 85 (5) 15 : 1.000 + 86 86 (5) 15 : 1.000 + 87 87 (5) 15 : 1.000 + 88 88 (5) 15 : 1.000 + 89 89 (5) 15 : 1.000 + 90 90 (5) 15 : 1.000 + 91 91 (5) 16 : 1.000 + 92 92 (5) 16 : 1.000 + 93 93 (5) 16 : 1.000 + 94 94 (5) 16 : 1.000 + 95 95 (5) 16 : 1.000 + + 1 1 (0) 1 : 1.000 + 2 2 (0) 1 : 1.000 + 3 3 (0) 1 : 1.000 + 4 4 (0) 1 : 1.000 + 5 5 (0) 1 : 1.000 + 6 6 (0) 1 : 1.000 + 7 7 (0) 2 : 1.000 + 8 8 (0) 2 : 1.000 + 9 9 (0) 2 : 1.000 + 10 10 (0) 2 : 1.000 + 11 11 (0) 2 : 1.000 + 12 12 (0) 2 : 1.000 + 13 13 (0) 3 : 1.000 + 14 14 (0) 3 : 1.000 + 15 15 (0) 3 : 1.000 + 16 16 (0) 3 : 1.000 + 17 17 (0) 3 : 1.000 + 18 18 (0) 3 : 1.000 + 19 19 (0) 4 : 1.000 + 20 20 (0) 4 : 1.000 + 21 21 (0) 4 : 1.000 + 22 22 (0) 4 : 1.000 + 23 23 (0) 4 : 1.000 + 24 24 (0) 4 : 1.000 + 25 25 (0) 5 : 1.000 + 26 26 (0) 5 : 1.000 + 27 27 (0) 5 : 1.000 + 28 28 (0) 5 : 1.000 + 29 29 (0) 5 : 1.000 + 30 30 (0) 5 : 1.000 + 31 31 (0) 6 : 1.000 + 32 32 (0) 6 : 1.000 + 33 33 (0) 6 : 1.000 + 34 34 (0) 6 : 1.000 + 35 35 (0) 6 : 1.000 + 36 36 (0) 6 : 1.000 + 37 37 (0) 7 : 1.000 + 38 38 (0) 7 : 1.000 + 39 39 (0) 7 : 1.000 + 40 40 (0) 7 : 1.000 + 41 41 (0) 7 : 1.000 + 42 42 (0) 7 : 1.000 + 43 43 (0) 8 : 1.000 + 44 44 (0) 8 : 1.000 + 45 45 (0) 8 : 1.000 + 46 46 (0) 8 : 1.000 + 47 47 (0) 8 : 1.000 + 48 48 (0) 8 : 1.000 + 49 49 (0) 9 : 1.000 + 50 50 (0) 9 : 1.000 + 51 51 (0) 9 : 1.000 + 52 52 (0) 9 : 1.000 + 53 53 (0) 9 : 1.000 + 54 54 (0) 9 : 1.000 + 55 55 (0) 10 : 1.000 + 56 56 (0) 10 : 1.000 + 57 57 (0) 10 : 1.000 + 58 58 (0) 10 : 1.000 + 59 59 (0) 10 : 1.000 + 60 60 (0) 10 : 1.000 + 61 61 (0) 11 : 1.000 + 62 62 (0) 11 : 1.000 + 63 63 (0) 11 : 1.000 + 64 64 (0) 11 : 1.000 + 65 65 (0) 11 : 1.000 + 66 66 (0) 11 : 1.000 + 67 67 (0) 12 : 1.000 + 68 68 (0) 12 : 1.000 + 69 69 (0) 12 : 1.000 + 70 70 (0) 12 : 1.000 + 71 71 (0) 12 : 1.000 + 72 72 (0) 12 : 1.000 + 73 73 (0) 13 : 1.000 + 74 74 (0) 13 : 1.000 + 75 75 (0) 13 : 1.000 + 76 76 (0) 13 : 1.000 + 77 77 (0) 13 : 1.000 + 78 78 (0) 13 : 1.000 + 79 79 (0) 14 : 1.000 + 80 80 (0) 14 : 1.000 + 81 81 (0) 14 : 1.000 + 82 82 (0) 14 : 1.000 + 83 83 (0) 14 : 1.000 + 84 84 (0) 14 : 1.000 + 85 85 (5) 15 : 1.000 + 86 86 (5) 15 : 1.000 + 87 87 (5) 15 : 1.000 + 88 88 (5) 15 : 1.000 + 89 89 (5) 15 : 1.000 + 90 90 (5) 15 : 1.000 + 91 91 (5) 16 : 1.000 + 92 92 (5) 16 : 1.000 + 93 93 (5) 16 : 1.000 + 94 94 (5) 16 : 1.000 + 95 95 (5) 16 : 1.000 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clumpp_indfile/K2.indfile Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,192 @@ + 1 1 (0) 1 : 0.005 0.995 + 2 2 (0) 1 : 0.005 0.995 + 3 3 (0) 1 : 0.009 0.991 + 4 4 (0) 1 : 0.005 0.995 + 5 5 (0) 1 : 0.006 0.994 + 6 6 (0) 1 : 0.005 0.995 + 7 7 (0) 2 : 0.005 0.995 + 8 8 (0) 2 : 0.005 0.995 + 9 9 (0) 2 : 0.005 0.995 + 10 10 (0) 2 : 0.006 0.994 + 11 11 (0) 2 : 0.004 0.996 + 12 12 (0) 2 : 0.006 0.994 + 13 13 (0) 3 : 0.004 0.996 + 14 14 (0) 3 : 0.004 0.996 + 15 15 (0) 3 : 0.004 0.996 + 16 16 (0) 3 : 0.005 0.995 + 17 17 (0) 3 : 0.004 0.996 + 18 18 (0) 3 : 0.004 0.996 + 19 19 (0) 4 : 0.004 0.996 + 20 20 (0) 4 : 0.011 0.989 + 21 21 (0) 4 : 0.007 0.993 + 22 22 (0) 4 : 0.016 0.984 + 23 23 (0) 4 : 0.014 0.986 + 24 24 (0) 4 : 0.037 0.963 + 25 25 (0) 5 : 0.017 0.983 + 26 26 (0) 5 : 0.019 0.981 + 27 27 (0) 5 : 0.006 0.994 + 28 28 (0) 5 : 0.009 0.991 + 29 29 (0) 5 : 0.006 0.994 + 30 30 (0) 5 : 0.019 0.981 + 31 31 (0) 6 : 0.009 0.991 + 32 32 (0) 6 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clumpp_indfile/K3.indfile Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,192 @@ + 1 1 (0) 1 : 0.002 0.997 0.001 + 2 2 (0) 1 : 0.002 0.997 0.001 + 3 3 (0) 1 : 0.002 0.997 0.001 + 4 4 (0) 1 : 0.002 0.997 0.001 + 5 5 (0) 1 : 0.002 0.996 0.001 + 6 6 (0) 1 : 0.002 0.997 0.001 + 7 7 (0) 2 : 0.002 0.997 0.001 + 8 8 (0) 2 : 0.002 0.997 0.001 + 9 9 (0) 2 : 0.002 0.997 0.001 + 10 10 (0) 2 : 0.002 0.996 0.002 + 11 11 (0) 2 : 0.002 0.996 0.002 + 12 12 (0) 2 : 0.002 0.997 0.001 + 13 13 (0) 3 : 0.002 0.997 0.001 + 14 14 (0) 3 : 0.002 0.997 0.001 + 15 15 (0) 3 : 0.001 0.997 0.001 + 16 16 (0) 3 : 0.002 0.997 0.001 + 17 17 (0) 3 : 0.002 0.997 0.001 + 18 18 (0) 3 : 0.002 0.997 0.001 + 19 19 (0) 4 : 0.001 0.997 0.001 + 20 20 (0) 4 : 0.003 0.996 0.001 + 21 21 (0) 4 : 0.002 0.996 0.002 + 22 22 (0) 4 : 0.006 0.993 0.002 + 23 23 (0) 4 : 0.003 0.996 0.001 + 24 24 (0) 4 : 0.003 0.995 0.001 + 25 25 (0) 5 : 0.004 0.994 0.002 + 26 26 (0) 5 : 0.004 0.994 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clumpp_indfile/K4.indfile Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,192 @@ + 1 1 (0) 1 : 0.994 0.002 0.003 0.001 + 2 2 (0) 1 : 0.995 0.001 0.003 0.001 + 3 3 (0) 1 : 0.981 0.007 0.010 0.001 + 4 4 (0) 1 : 0.995 0.002 0.002 0.001 + 5 5 (0) 1 : 0.994 0.002 0.003 0.001 + 6 6 (0) 1 : 0.989 0.002 0.008 0.002 + 7 7 (0) 2 : 0.992 0.002 0.005 0.001 + 8 8 (0) 2 : 0.995 0.001 0.003 0.001 + 9 9 (0) 2 : 0.991 0.002 0.006 0.001 + 10 10 (0) 2 : 0.984 0.003 0.010 0.003 + 11 11 (0) 2 : 0.985 0.002 0.011 0.002 + 12 12 (0) 2 : 0.993 0.002 0.004 0.001 + 13 13 (0) 3 : 0.996 0.001 0.002 0.001 + 14 14 (0) 3 : 0.995 0.001 0.002 0.001 + 15 15 (0) 3 : 0.995 0.001 0.002 0.001 + 16 16 (0) 3 : 0.995 0.002 0.002 0.001 + 17 17 (0) 3 : 0.995 0.001 0.002 0.001 + 18 18 (0) 3 : 0.995 0.001 0.003 0.001 + 19 19 (0) 4 : 0.989 0.001 0.007 0.002 + 20 20 (0) 4 : 0.990 0.002 0.006 0.001 + 21 21 (0) 4 : 0.988 0.002 0.008 0.003 + 22 22 (0) 4 : 0.975 0.007 0.016 0.002 + 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clumpp_popfile/K1.popfile Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,34 @@ + 1: 1.000 6 + 2: 1.000 6 + 3: 1.000 6 + 4: 1.000 6 + 5: 1.000 6 + 6: 1.000 6 + 7: 1.000 6 + 8: 1.000 6 + 9: 1.000 6 + 10: 1.000 6 + 11: 1.000 6 + 12: 1.000 6 + 13: 1.000 6 + 14: 1.000 6 + 15: 1.000 6 + 16: 1.000 5 + + 1: 1.000 6 + 2: 1.000 6 + 3: 1.000 6 + 4: 1.000 6 + 5: 1.000 6 + 6: 1.000 6 + 7: 1.000 6 + 8: 1.000 6 + 9: 1.000 6 + 10: 1.000 6 + 11: 1.000 6 + 12: 1.000 6 + 13: 1.000 6 + 14: 1.000 6 + 15: 1.000 6 + 16: 1.000 5 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clumpp_popfile/K2.popfile Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,34 @@ + 1: 0.006 0.994 6 + 2: 0.005 0.995 6 + 3: 0.004 0.996 6 + 4: 0.015 0.985 6 + 5: 0.013 0.987 6 + 6: 0.091 0.909 6 + 7: 0.007 0.993 6 + 8: 0.024 0.976 6 + 9: 0.638 0.362 6 + 10: 0.485 0.515 6 + 11: 0.995 0.005 6 + 12: 0.996 0.004 6 + 13: 0.996 0.004 6 + 14: 0.995 0.005 6 + 15: 0.004 0.996 6 + 16: 0.005 0.995 5 + + 1: 0.001 0.999 6 + 2: 0.002 0.998 6 + 3: 0.001 0.999 6 + 4: 0.002 0.998 6 + 5: 0.002 0.998 6 + 6: 0.003 0.997 6 + 7: 0.001 0.999 6 + 8: 0.001 0.999 6 + 9: 0.002 0.998 6 + 10: 0.005 0.995 6 + 11: 0.001 0.999 6 + 12: 0.002 0.998 6 + 13: 0.002 0.998 6 + 14: 0.002 0.998 6 + 15: 0.999 0.001 6 + 16: 0.998 0.002 5 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clumpp_popfile/K3.popfile Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,34 @@ + 1: 0.002 0.997 0.001 6 + 2: 0.002 0.997 0.002 6 + 3: 0.002 0.997 0.001 6 + 4: 0.003 0.996 0.001 6 + 5: 0.003 0.995 0.002 6 + 6: 0.016 0.981 0.003 6 + 7: 0.002 0.996 0.001 6 + 8: 0.004 0.994 0.002 6 + 9: 0.038 0.961 0.002 6 + 10: 0.082 0.913 0.005 6 + 11: 0.995 0.004 0.001 6 + 12: 0.997 0.002 0.001 6 + 13: 0.997 0.002 0.001 6 + 14: 0.997 0.002 0.001 6 + 15: 0.001 0.001 0.998 6 + 16: 0.002 0.001 0.997 5 + + 1: 0.001 0.997 0.002 6 + 2: 0.002 0.997 0.002 6 + 3: 0.001 0.997 0.002 6 + 4: 0.001 0.996 0.003 6 + 5: 0.002 0.995 0.003 6 + 6: 0.003 0.981 0.016 6 + 7: 0.001 0.996 0.002 6 + 8: 0.002 0.994 0.004 6 + 9: 0.002 0.960 0.038 6 + 10: 0.005 0.913 0.081 6 + 11: 0.001 0.004 0.995 6 + 12: 0.001 0.002 0.997 6 + 13: 0.001 0.002 0.996 6 + 14: 0.001 0.002 0.997 6 + 15: 0.998 0.001 0.001 6 + 16: 0.997 0.001 0.002 5 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clumpp_popfile/K4.popfile Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,34 @@ + 1: 0.991 0.003 0.005 0.001 6 + 2: 0.990 0.002 0.006 0.002 6 + 3: 0.995 0.001 0.002 0.001 6 + 4: 0.968 0.003 0.027 0.002 6 + 5: 0.212 0.003 0.783 0.002 6 + 6: 0.104 0.015 0.878 0.003 6 + 7: 0.991 0.002 0.006 0.001 6 + 8: 0.022 0.002 0.974 0.002 6 + 9: 0.003 0.006 0.989 0.001 6 + 10: 0.036 0.021 0.940 0.004 6 + 11: 0.002 0.988 0.009 0.001 6 + 12: 0.002 0.995 0.002 0.001 6 + 13: 0.002 0.994 0.003 0.001 6 + 14: 0.002 0.995 0.002 0.001 6 + 15: 0.001 0.001 0.001 0.997 6 + 16: 0.001 0.002 0.002 0.995 5 + + 1: 0.003 0.005 0.991 0.001 6 + 2: 0.002 0.006 0.990 0.002 6 + 3: 0.001 0.002 0.995 0.001 6 + 4: 0.003 0.027 0.968 0.002 6 + 5: 0.003 0.784 0.211 0.002 6 + 6: 0.016 0.877 0.104 0.003 6 + 7: 0.002 0.006 0.991 0.001 6 + 8: 0.003 0.974 0.021 0.002 6 + 9: 0.006 0.989 0.003 0.002 6 + 10: 0.021 0.940 0.035 0.004 6 + 11: 0.988 0.009 0.002 0.001 6 + 12: 0.995 0.002 0.002 0.001 6 + 13: 0.994 0.003 0.002 0.001 6 + 14: 0.995 0.002 0.002 0.001 6 + 15: 0.001 0.001 0.001 0.997 6 + 16: 0.002 0.002 0.001 0.995 5 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evanno.txt Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,22 @@ +# This document produced by structureHarvester.py v0.6.94 July 2014 core vA.2 July 2014 +# http://www.structureharvester.com/ +# https://github.com/dentearl/structureHarvester/ +# http://taylor0.biology.ucla.edu/structureHarvester +# http://users.soe.ucsc.edu/~dearl/software/structureHarvester +# Written by Dent Earl, dearl (a) soe ucsc edu. +# CITATION: +# Earl, Dent A. and vonHoldt, Bridgett M. (2012) +# STRUCTURE HARVESTER: a website and program for visualizing +# STRUCTURE output and implementing the Evanno method. +# Conservation Genetics Resources 4(2) 359-361. DOI: 10.1007/s12686-011-9548-7 +# Stand-alone version: v0.6.94 July 2014 +# Core version: vA.2 July 2014 +# File generated at 2017-Dec-06 15:30:18 CET +# + +########## +# K Reps Mean LnP(K) Stdev LnP(K) Ln'(K) |Ln''(K)| Delta K +1 3 -4330.0667 0.2082 NA NA NA +2 3 -3636.9333 8.2887 693.133333 77.133333 9.305789 +3 3 -3020.9333 0.2309 616.000000 368.833333 1597.095182 +4 3 -2773.7667 0.4041 247.166667 NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/Admix_run_001_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,384 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + Code by J.K. Pritchard + Modified by Daniel Falush to + incorporate recombination breakpoints + Version 2.0 (July 2001) +---------------------------------------------------- + + + +Command line arguments: bin/structure.exe -m \mainparams -e \extraparams +Input File: \project_data + +Run parameters: + 95 individuals + 18 loci + 2 populations assumed + 50000 Burn-in period + 500000 Reps + + +-------------------------------------------- +Proportion of membership of each pre-defined + population in each of the 2 clusters + +Given Inferred Clusters Number of + Pop 1 2 Individuals + + 1: 0.001 0.999 6 + 2: 0.002 0.998 6 + 3: 0.001 0.999 6 + 4: 0.002 0.998 6 + 5: 0.002 0.998 6 + 6: 0.003 0.997 6 + 7: 0.001 0.999 6 + 8: 0.001 0.999 6 + 9: 0.002 0.998 6 + 10: 0.005 0.995 6 + 11: 0.001 0.999 6 + 12: 0.002 0.998 6 + 13: 0.002 0.998 6 + 14: 0.002 0.998 6 + 15: 0.999 0.001 6 + 16: 0.998 0.002 5 +-------------------------------------------- + +Allele-freq. divergence among pops (Kullback-Leibler distance), +computed using point estimates of P. + + 1 2 + 1 - 2.67 + 2 2.10 - +-------------------------------------------- +Estimated Ln Prob of Data = -3646.5 +Mean value of ln likelihood = -3597.1 +Variance of ln likelihood = 98.8 +Mean value of alpha = 0.0254 + +Mean value of Fst_1 = 0.5120 +Mean value of Fst_2 = 0.0523 + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters + 1 A01 (0) 1 : 0.001 0.999 + 2 A02 (0) 1 : 0.002 0.998 + 3 A03 (0) 1 : 0.001 0.999 + 4 A04 (0) 1 : 0.001 0.999 + 5 A05 (0) 1 : 0.002 0.998 + 6 A24 (0) 1 : 0.001 0.999 + 7 B466 (0) 2 : 0.001 0.999 + 8 B479 (0) 2 : 0.001 0.999 + 9 B480 (0) 2 : 0.001 0.999 + 10 B482 (0) 2 : 0.002 0.998 + 11 B484 (0) 2 : 0.003 0.997 + 12 B485 (0) 2 : 0.001 0.999 + 13 C02 (0) 3 : 0.001 0.999 + 14 C05 (0) 3 : 0.001 0.999 + 15 C14 (0) 3 : 0.001 0.999 + 16 C30 (0) 3 : 0.001 0.999 + 17 C31 (0) 3 : 0.001 0.999 + 18 C40 (0) 3 : 0.001 0.999 + 19 D08 (0) 4 : 0.002 0.998 + 20 D09 (0) 4 : 0.001 0.999 + 21 D13 (0) 4 : 0.003 0.997 + 22 D21 (0) 4 : 0.002 0.998 + 23 D25 (0) 4 : 0.001 0.999 + 24 D30 (0) 4 : 0.001 0.999 + 25 E01 (0) 5 : 0.003 0.997 + 26 E02 (0) 5 : 0.003 0.997 + 27 E03 (0) 5 : 0.001 0.999 + 28 E04 (0) 5 : 0.002 0.998 + 29 E05 (0) 5 : 0.002 0.998 + 30 E06 (0) 5 : 0.002 0.998 + 31 F03 (0) 6 : 0.010 0.990 + 32 F05 (0) 6 : 0.001 0.999 + 33 F08 (0) 6 : 0.002 0.998 + 34 F14 (0) 6 : 0.001 0.999 + 35 F25 (0) 6 : 0.001 0.999 + 36 F35 (0) 6 : 0.001 0.999 + 37 B360 (0) 7 : 0.001 0.999 + 38 B365 (0) 7 : 0.001 0.999 + 39 B367 (0) 7 : 0.001 0.999 + 40 B370 (0) 7 : 0.001 0.999 + 41 B371 (0) 7 : 0.001 0.999 + 42 B372 (0) 7 : 0.001 0.999 + 43 B341 (0) 8 : 0.002 0.998 + 44 B342 (0) 8 : 0.001 0.999 + 45 B343 (0) 8 : 0.001 0.999 + 46 B345 (0) 8 : 0.001 0.999 + 47 B346 (0) 8 : 0.001 0.999 + 48 B349 (0) 8 : 0.001 0.999 + 49 B121 (0) 9 : 0.002 0.998 + 50 B122 (0) 9 : 0.001 0.999 + 51 B125 (0) 9 : 0.003 0.997 + 52 B127 (0) 9 : 0.001 0.999 + 53 B128 (0) 9 : 0.002 0.998 + 54 B129 (0) 9 : 0.003 0.997 + 55 B306 (0) 10 : 0.016 0.984 + 56 B310 (0) 10 : 0.001 0.999 + 57 B312 (0) 10 : 0.002 0.998 + 58 B313 (0) 10 : 0.004 0.996 + 59 B317 (0) 10 : 0.001 0.999 + 60 B318 (0) 10 : 0.005 0.995 + 61 G19 (0) 11 : 0.001 0.999 + 62 G20 (0) 11 : 0.001 0.999 + 63 G21 (0) 11 : 0.001 0.999 + 64 G22 (0) 11 : 0.001 0.999 + 65 G23 (0) 11 : 0.002 0.998 + 66 G24 (0) 11 : 0.001 0.999 + 67 H01 (0) 12 : 0.001 0.999 + 68 H02 (0) 12 : 0.002 0.998 + 69 H03 (0) 12 : 0.001 0.999 + 70 H04 (0) 12 : 0.002 0.998 + 71 H05 (0) 12 : 0.002 0.998 + 72 H12 (0) 12 : 0.002 0.998 + 73 I20 (0) 13 : 0.002 0.998 + 74 I21 (0) 13 : 0.001 0.999 + 75 I23 (0) 13 : 0.002 0.998 + 76 I24 (0) 13 : 0.002 0.998 + 77 I25 (0) 13 : 0.002 0.998 + 78 I26 (0) 13 : 0.002 0.998 + 79 J02 (0) 14 : 0.002 0.998 + 80 J04 (0) 14 : 0.001 0.999 + 81 J05 (0) 14 : 0.001 0.999 + 82 J08 (0) 14 : 0.001 0.999 + 83 J09 (0) 14 : 0.002 0.998 + 84 J10 (0) 14 : 0.001 0.999 + 85 K20 (5) 15 : 0.999 0.001 + 86 K33 (5) 15 : 0.999 0.001 + 87 K34 (5) 15 : 0.999 0.001 + 88 K35 (5) 15 : 0.999 0.001 + 89 K53 (5) 15 : 0.999 0.001 + 90 K56 (5) 15 : 0.999 0.001 + 91 L04 (5) 16 : 0.999 0.001 + 92 L07 (5) 16 : 0.999 0.001 + 93 L14 (5) 16 : 0.996 0.004 + 94 L26 (5) 16 : 0.999 0.001 + 95 L27 (5) 16 : 0.999 0.001 + + +Estimated Allele Frequencies in each population +First column gives estimated ancestral frequencies + + +Locus 1 : L1 +7 alleles +0.0% missing data + 118 (0.478) 0.020 0.670 + 127 (0.104) 0.004 0.080 + 130 (0.081) 0.484 0.024 + 114 (0.069) 0.003 0.034 + 122 (0.119) 0.005 0.103 + 110 (0.107) 0.005 0.086 + 135 (0.042) 0.478 0.004 + +Locus 2 : L2 +15 alleles +0.0% missing data + 228 (0.091) 0.004 0.111 + 222 (0.099) 0.004 0.133 + 225 (0.119) 0.005 0.178 + 234 (0.043) 0.002 0.015 + 219 (0.111) 0.005 0.161 + 213 (0.147) 0.006 0.250 + 204 (0.037) 0.002 0.009 + 216 (0.058) 0.002 0.038 + 195 (0.042) 0.002 0.015 + 231 (0.052) 0.002 0.027 + 210 (0.051) 0.002 0.027 + 240 (0.037) 0.002 0.009 + 207 (0.047) 0.002 0.021 + 198 (0.034) 0.915 0.003 + 185 (0.033) 0.045 0.003 + +Locus 3 : L3 +3 alleles +0.0% missing data + 266 (0.873) 0.037 0.961 + 272 (0.079) 0.003 0.035 + 278 (0.048) 0.959 0.005 + +Locus 4 : L4 +19 alleles +0.0% missing data + 164 (0.081) 0.003 0.121 + 173 (0.146) 0.006 0.357 + 182 (0.066) 0.003 0.076 + 170 (0.043) 0.002 0.020 + 200 (0.043) 0.002 0.020 + 202 (0.034) 0.001 0.009 + 176 (0.033) 0.001 0.009 + 185 (0.045) 0.002 0.026 + 167 (0.054) 0.002 0.043 + 158 (0.067) 0.003 0.076 + 155 (0.049) 0.002 0.032 + 152 (0.061) 0.003 0.060 + 179 (0.033) 0.001 0.009 + 145 (0.034) 0.001 0.009 + 149 (0.061) 0.003 0.060 + 161 (0.063) 0.003 0.065 + 136 (0.031) 0.872 0.003 + 101 (0.029) 0.044 0.003 + 139 (0.029) 0.044 0.003 + +Locus 5 : L5 +24 alleles +0.0% missing data + 182 (0.060) 0.090 0.059 + 188 (0.040) 0.002 0.036 + 185 (0.052) 0.002 0.080 + 194 (0.038) 0.002 0.031 + 209 (0.028) 0.001 0.008 + 191 (0.038) 0.002 0.031 + 160 (0.055) 0.265 0.043 + 200 (0.036) 0.002 0.025 + 173 (0.061) 0.090 0.065 + 176 (0.036) 0.002 0.025 + 169 (0.036) 0.002 0.025 + 131 (0.028) 0.001 0.008 + 166 (0.040) 0.002 0.036 + 154 (0.045) 0.002 0.053 + 144 (0.054) 0.002 0.097 + 157 (0.044) 0.002 0.047 + 203 (0.032) 0.001 0.014 + 147 (0.044) 0.002 0.053 + 134 (0.063) 0.003 0.146 + 141 (0.047) 0.002 0.064 + 206 (0.036) 0.002 0.025 + 151 (0.035) 0.001 0.020 + 137 (0.028) 0.001 0.008 + 179 (0.024) 0.520 0.002 + +Locus 6 : L6 +6 alleles +11.6% missing data + 177 (0.168) 0.166 0.167 + 165 (0.156) 0.152 0.150 + 171 (0.346) 0.358 0.426 + 175 (0.165) 0.160 0.161 + 183 (0.086) 0.086 0.051 + 179 (0.080) 0.078 0.045 + +Locus 7 : L7 +10 alleles +0.0% missing data + 187 (0.202) 0.009 0.288 + 191 (0.125) 0.005 0.141 + 183 (0.185) 0.008 0.254 + 195 (0.105) 0.004 0.102 + 199 (0.063) 0.003 0.033 + 180 (0.063) 0.003 0.033 + 203 (0.071) 0.003 0.045 + 206 (0.078) 0.003 0.056 + 214 (0.070) 0.003 0.044 + 138 (0.039) 0.959 0.004 + +Locus 8 : L8 +7 alleles +0.0% missing data + 151 (0.466) 0.020 0.632 + 148 (0.084) 0.003 0.051 + 145 (0.059) 0.960 0.010 + 157 (0.044) 0.002 0.010 + 155 (0.109) 0.005 0.086 + 135 (0.064) 0.003 0.028 + 141 (0.174) 0.007 0.184 + +Locus 9 : L9 +10 alleles +0.0% missing data + 138 (0.241) 0.010 0.389 + 140 (0.065) 0.003 0.039 + 147 (0.137) 0.964 0.098 + 142 (0.126) 0.005 0.152 + 145 (0.098) 0.004 0.096 + 136 (0.061) 0.003 0.033 + 134 (0.047) 0.002 0.015 + 132 (0.052) 0.002 0.021 + 153 (0.112) 0.005 0.124 + 149 (0.061) 0.003 0.033 + +Locus 10 : L10 +7 alleles +0.0% missing data + 313 (0.102) 0.004 0.080 + 317 (0.368) 0.016 0.493 + 321 (0.073) 0.003 0.039 + 319 (0.109) 0.445 0.047 + 325 (0.044) 0.002 0.010 + 306 (0.262) 0.011 0.327 + 324 (0.042) 0.519 0.004 + +Locus 11 : L11 +8 alleles +0.0% missing data + 250 (0.219) 0.009 0.312 + 247 (0.083) 0.003 0.062 + 242 (0.100) 0.004 0.090 + 251 (0.072) 0.003 0.045 + 245 (0.113) 0.005 0.113 + 257 (0.049) 0.002 0.016 + 243 (0.262) 0.969 0.266 + 253 (0.104) 0.004 0.096 + +Locus 12 : L12 +4 alleles +0.0% missing data + 204 (0.823) 0.950 0.929 + 180 (0.053) 0.002 0.016 + 218 (0.085) 0.004 0.051 + 210 (0.040) 0.044 0.004 + +Locus 13 : L13 +6 alleles +0.0% missing data + 260 (0.696) 0.857 0.884 + 263 (0.111) 0.092 0.059 + 257 (0.050) 0.002 0.016 + 269 (0.061) 0.003 0.028 + 275 (0.043) 0.002 0.010 + 246 (0.038) 0.044 0.004 + +Locus 14 : L14 +5 alleles +0.0% missing data + 157 (0.640) 0.985 0.723 + 146 (0.187) 0.008 0.206 + 153 (0.057) 0.002 0.022 + 155 (0.073) 0.003 0.039 + 163 (0.043) 0.002 0.010 + +Locus 15 : L15 +2 alleles +0.0% missing data + 243 (0.639) 0.943 0.636 + 238 (0.361) 0.057 0.364 + +Locus 16 : L16 +3 alleles +0.0% missing data + 173 (0.788) 0.991 0.845 + 165 (0.077) 0.003 0.040 + 169 (0.135) 0.006 0.115 + +Locus 17 : L17 +2 alleles +0.0% missing data + 171 (0.951) 0.041 0.995 + 168 (0.049) 0.959 0.005 + +Locus 18 : L18 +4 alleles +0.0% missing data + 286 (0.764) 0.032 0.898 + 287 (0.108) 0.005 0.070 + 283 (0.064) 0.003 0.022 + 290 (0.064) 0.960 0.010 + +Values of parameters used in structure: +DATAFILE=\project_data, OUTFILE=\Results_run_2, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=2, BURNIN=50000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/Admix_run_002_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,384 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + Code by J.K. Pritchard + Modified by Daniel Falush to + incorporate recombination breakpoints + Version 2.0 (July 2001) +---------------------------------------------------- + + + +Command line arguments: bin/structure.exe -m \mainparams -e \extraparams +Input File: \project_data + +Run parameters: + 95 individuals + 18 loci + 2 populations assumed + 50000 Burn-in period + 500000 Reps + + +-------------------------------------------- +Proportion of membership of each pre-defined + population in each of the 2 clusters + +Given Inferred Clusters Number of + Pop 1 2 Individuals + + 1: 0.006 0.994 6 + 2: 0.005 0.995 6 + 3: 0.004 0.996 6 + 4: 0.015 0.985 6 + 5: 0.013 0.987 6 + 6: 0.091 0.909 6 + 7: 0.007 0.993 6 + 8: 0.024 0.976 6 + 9: 0.638 0.362 6 + 10: 0.485 0.515 6 + 11: 0.995 0.005 6 + 12: 0.996 0.004 6 + 13: 0.996 0.004 6 + 14: 0.995 0.005 6 + 15: 0.004 0.996 6 + 16: 0.005 0.995 5 +-------------------------------------------- + +Allele-freq. divergence among pops (Kullback-Leibler distance), +computed using point estimates of P. + + 1 2 + 1 - 1.44 + 2 1.50 - +-------------------------------------------- +Estimated Ln Prob of Data = -3631.9 +Mean value of ln likelihood = -3562.2 +Variance of ln likelihood = 139.5 +Mean value of alpha = 0.0695 + +Mean value of Fst_1 = 0.2830 +Mean value of Fst_2 = 0.1203 + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters + 1 A01 (0) 1 : 0.005 0.995 + 2 A02 (0) 1 : 0.005 0.995 + 3 A03 (0) 1 : 0.009 0.991 + 4 A04 (0) 1 : 0.005 0.995 + 5 A05 (0) 1 : 0.006 0.994 + 6 A24 (0) 1 : 0.005 0.995 + 7 B466 (0) 2 : 0.005 0.995 + 8 B479 (0) 2 : 0.005 0.995 + 9 B480 (0) 2 : 0.005 0.995 + 10 B482 (0) 2 : 0.006 0.994 + 11 B484 (0) 2 : 0.004 0.996 + 12 B485 (0) 2 : 0.006 0.994 + 13 C02 (0) 3 : 0.004 0.996 + 14 C05 (0) 3 : 0.004 0.996 + 15 C14 (0) 3 : 0.004 0.996 + 16 C30 (0) 3 : 0.005 0.995 + 17 C31 (0) 3 : 0.004 0.996 + 18 C40 (0) 3 : 0.004 0.996 + 19 D08 (0) 4 : 0.004 0.996 + 20 D09 (0) 4 : 0.011 0.989 + 21 D13 (0) 4 : 0.007 0.993 + 22 D21 (0) 4 : 0.016 0.984 + 23 D25 (0) 4 : 0.014 0.986 + 24 D30 (0) 4 : 0.037 0.963 + 25 E01 (0) 5 : 0.017 0.983 + 26 E02 (0) 5 : 0.019 0.981 + 27 E03 (0) 5 : 0.006 0.994 + 28 E04 (0) 5 : 0.009 0.991 + 29 E05 (0) 5 : 0.006 0.994 + 30 E06 (0) 5 : 0.019 0.981 + 31 F03 (0) 6 : 0.009 0.991 + 32 F05 (0) 6 : 0.185 0.815 + 33 F08 (0) 6 : 0.095 0.905 + 34 F14 (0) 6 : 0.155 0.845 + 35 F25 (0) 6 : 0.023 0.977 + 36 F35 (0) 6 : 0.081 0.919 + 37 B360 (0) 7 : 0.006 0.994 + 38 B365 (0) 7 : 0.010 0.990 + 39 B367 (0) 7 : 0.005 0.995 + 40 B370 (0) 7 : 0.007 0.993 + 41 B371 (0) 7 : 0.008 0.992 + 42 B372 (0) 7 : 0.007 0.993 + 43 B341 (0) 8 : 0.008 0.992 + 44 B342 (0) 8 : 0.019 0.981 + 45 B343 (0) 8 : 0.014 0.986 + 46 B345 (0) 8 : 0.075 0.925 + 47 B346 (0) 8 : 0.009 0.991 + 48 B349 (0) 8 : 0.019 0.981 + 49 B121 (0) 9 : 0.439 0.561 + 50 B122 (0) 9 : 0.885 0.115 + 51 B125 (0) 9 : 0.452 0.548 + 52 B127 (0) 9 : 0.751 0.249 + 53 B128 (0) 9 : 0.651 0.349 + 54 B129 (0) 9 : 0.650 0.350 + 55 B306 (0) 10 : 0.407 0.593 + 56 B310 (0) 10 : 0.554 0.446 + 57 B312 (0) 10 : 0.542 0.458 + 58 B313 (0) 10 : 0.541 0.459 + 59 B317 (0) 10 : 0.427 0.573 + 60 B318 (0) 10 : 0.435 0.565 + 61 G19 (0) 11 : 0.996 0.004 + 62 G20 (0) 11 : 0.995 0.005 + 63 G21 (0) 11 : 0.996 0.004 + 64 G22 (0) 11 : 0.993 0.007 + 65 G23 (0) 11 : 0.995 0.005 + 66 G24 (0) 11 : 0.995 0.005 + 67 H01 (0) 12 : 0.995 0.005 + 68 H02 (0) 12 : 0.996 0.004 + 69 H03 (0) 12 : 0.996 0.004 + 70 H04 (0) 12 : 0.996 0.004 + 71 H05 (0) 12 : 0.996 0.004 + 72 H12 (0) 12 : 0.997 0.003 + 73 I20 (0) 13 : 0.996 0.004 + 74 I21 (0) 13 : 0.996 0.004 + 75 I23 (0) 13 : 0.994 0.006 + 76 I24 (0) 13 : 0.996 0.004 + 77 I25 (0) 13 : 0.996 0.004 + 78 I26 (0) 13 : 0.996 0.004 + 79 J02 (0) 14 : 0.996 0.004 + 80 J04 (0) 14 : 0.995 0.005 + 81 J05 (0) 14 : 0.995 0.005 + 82 J08 (0) 14 : 0.992 0.008 + 83 J09 (0) 14 : 0.996 0.004 + 84 J10 (0) 14 : 0.997 0.003 + 85 K20 (5) 15 : 0.004 0.996 + 86 K33 (5) 15 : 0.004 0.996 + 87 K34 (5) 15 : 0.004 0.996 + 88 K35 (5) 15 : 0.004 0.996 + 89 K53 (5) 15 : 0.004 0.996 + 90 K56 (5) 15 : 0.004 0.996 + 91 L04 (5) 16 : 0.004 0.996 + 92 L07 (5) 16 : 0.004 0.996 + 93 L14 (5) 16 : 0.007 0.993 + 94 L26 (5) 16 : 0.004 0.996 + 95 L27 (5) 16 : 0.004 0.996 + + +Estimated Allele Frequencies in each population +First column gives estimated ancestral frequencies + + +Locus 1 : L1 +7 alleles +0.0% missing data + 118 (0.436) 0.552 0.626 + 127 (0.098) 0.004 0.103 + 130 (0.102) 0.004 0.110 + 114 (0.077) 0.003 0.042 + 122 (0.123) 0.219 0.028 + 110 (0.069) 0.214 0.004 + 135 (0.094) 0.004 0.087 + +Locus 2 : L2 +15 alleles +0.0% missing data + 228 (0.071) 0.004 0.146 + 222 (0.114) 0.076 0.142 + 225 (0.082) 0.004 0.236 + 234 (0.048) 0.002 0.017 + 219 (0.118) 0.118 0.160 + 213 (0.112) 0.548 0.065 + 204 (0.042) 0.002 0.010 + 216 (0.073) 0.065 0.018 + 195 (0.047) 0.002 0.017 + 231 (0.046) 0.059 0.004 + 210 (0.048) 0.060 0.004 + 240 (0.042) 0.008 0.006 + 207 (0.044) 0.047 0.002 + 198 (0.073) 0.003 0.161 + 185 (0.042) 0.002 0.010 + +Locus 3 : L3 +3 alleles +0.0% missing data + 266 (0.766) 0.991 0.784 + 272 (0.090) 0.004 0.042 + 278 (0.144) 0.006 0.174 + +Locus 4 : L4 +19 alleles +0.0% missing data + 164 (0.100) 0.155 0.085 + 173 (0.091) 0.003 0.505 + 182 (0.061) 0.002 0.105 + 170 (0.061) 0.031 0.011 + 200 (0.048) 0.002 0.026 + 202 (0.040) 0.003 0.009 + 176 (0.041) 0.002 0.010 + 185 (0.050) 0.002 0.034 + 167 (0.046) 0.097 0.004 + 158 (0.051) 0.178 0.005 + 155 (0.045) 0.069 0.004 + 152 (0.045) 0.140 0.003 + 179 (0.040) 0.008 0.007 + 145 (0.040) 0.006 0.008 + 149 (0.045) 0.141 0.003 + 161 (0.045) 0.155 0.003 + 136 (0.068) 0.002 0.160 + 101 (0.040) 0.002 0.010 + 139 (0.041) 0.002 0.010 + +Locus 5 : L5 +24 alleles +0.0% missing data + 182 (0.041) 0.002 0.097 + 188 (0.038) 0.001 0.049 + 185 (0.041) 0.002 0.113 + 194 (0.037) 0.001 0.042 + 209 (0.030) 0.001 0.010 + 191 (0.038) 0.001 0.042 + 160 (0.061) 0.043 0.082 + 200 (0.036) 0.001 0.034 + 173 (0.042) 0.002 0.105 + 176 (0.037) 0.002 0.033 + 169 (0.043) 0.034 0.015 + 131 (0.030) 0.001 0.010 + 166 (0.037) 0.001 0.049 + 154 (0.056) 0.054 0.044 + 144 (0.046) 0.212 0.015 + 157 (0.050) 0.081 0.020 + 203 (0.035) 0.006 0.015 + 147 (0.042) 0.113 0.009 + 134 (0.065) 0.248 0.068 + 141 (0.058) 0.085 0.042 + 206 (0.034) 0.050 0.005 + 151 (0.031) 0.042 0.002 + 137 (0.030) 0.015 0.002 + 179 (0.041) 0.001 0.097 + +Locus 6 : L6 +6 alleles +11.6% missing data + 177 (0.234) 0.104 0.202 + 165 (0.202) 0.052 0.198 + 171 (0.337) 0.089 0.586 + 175 (0.082) 0.482 0.005 + 183 (0.073) 0.145 0.004 + 179 (0.072) 0.127 0.004 + +Locus 7 : L7 +10 alleles +0.0% missing data + 187 (0.145) 0.012 0.372 + 191 (0.106) 0.005 0.182 + 183 (0.160) 0.556 0.074 + 195 (0.094) 0.004 0.130 + 199 (0.095) 0.019 0.035 + 180 (0.091) 0.053 0.019 + 203 (0.081) 0.096 0.012 + 206 (0.069) 0.139 0.006 + 214 (0.058) 0.112 0.003 + 138 (0.101) 0.004 0.167 + +Locus 8 : L8 +7 alleles +0.0% missing data + 151 (0.437) 0.502 0.605 + 148 (0.121) 0.020 0.061 + 145 (0.122) 0.004 0.188 + 157 (0.056) 0.004 0.010 + 155 (0.105) 0.004 0.116 + 135 (0.075) 0.043 0.012 + 141 (0.084) 0.423 0.007 + +Locus 9 : L9 +10 alleles +0.0% missing data + 138 (0.172) 0.011 0.496 + 140 (0.076) 0.003 0.047 + 147 (0.150) 0.019 0.275 + 142 (0.155) 0.291 0.071 + 145 (0.124) 0.200 0.037 + 136 (0.072) 0.003 0.040 + 134 (0.060) 0.003 0.017 + 132 (0.066) 0.036 0.010 + 153 (0.067) 0.350 0.004 + 149 (0.059) 0.085 0.003 + +Locus 10 : L10 +7 alleles +0.0% missing data + 313 (0.122) 0.005 0.100 + 317 (0.357) 0.047 0.617 + 321 (0.098) 0.005 0.048 + 319 (0.146) 0.013 0.127 + 325 (0.064) 0.003 0.011 + 306 (0.096) 0.921 0.005 + 324 (0.118) 0.005 0.093 + +Locus 11 : L11 +8 alleles +0.0% missing data + 250 (0.164) 0.008 0.418 + 247 (0.090) 0.003 0.081 + 242 (0.100) 0.004 0.120 + 251 (0.092) 0.013 0.053 + 245 (0.162) 0.087 0.112 + 257 (0.063) 0.003 0.019 + 243 (0.249) 0.655 0.188 + 253 (0.080) 0.228 0.009 + +Locus 12 : L12 +4 alleles +0.0% missing data + 204 (0.795) 0.869 0.966 + 180 (0.070) 0.003 0.019 + 218 (0.073) 0.126 0.004 + 210 (0.061) 0.002 0.011 + +Locus 13 : L13 +6 alleles +0.0% missing data + 260 (0.654) 0.910 0.876 + 263 (0.100) 0.004 0.088 + 257 (0.066) 0.003 0.019 + 269 (0.064) 0.063 0.004 + 275 (0.058) 0.017 0.003 + 246 (0.058) 0.002 0.011 + +Locus 14 : L14 +5 alleles +0.0% missing data + 157 (0.592) 0.892 0.692 + 146 (0.170) 0.015 0.260 + 153 (0.073) 0.003 0.026 + 155 (0.107) 0.071 0.019 + 163 (0.058) 0.018 0.003 + +Locus 15 : L15 +2 alleles +0.0% missing data + 243 (0.690) 0.101 0.918 + 238 (0.310) 0.899 0.082 + +Locus 16 : L16 +3 alleles +0.0% missing data + 173 (0.737) 0.805 0.891 + 165 (0.090) 0.004 0.050 + 169 (0.173) 0.191 0.059 + +Locus 17 : L17 +2 alleles +0.0% missing data + 171 (0.850) 0.994 0.826 + 168 (0.150) 0.006 0.174 + +Locus 18 : L18 +4 alleles +0.0% missing data + 286 (0.676) 0.949 0.722 + 287 (0.108) 0.004 0.089 + 283 (0.076) 0.042 0.007 + 290 (0.140) 0.006 0.182 + +Values of parameters used in structure: +DATAFILE=\project_data, OUTFILE=\Results_run_3, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=2, BURNIN=50000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/Admix_run_004_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,386 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + Code by J.K. Pritchard + Modified by Daniel Falush to + incorporate recombination breakpoints + Version 2.0 (July 2001) +---------------------------------------------------- + + + +Command line arguments: bin/structure.exe -m \mainparams -e \extraparams +Input File: \project_data + +Run parameters: + 95 individuals + 18 loci + 3 populations assumed + 50000 Burn-in period + 500000 Reps + + +-------------------------------------------- +Proportion of membership of each pre-defined + population in each of the 3 clusters + +Given Inferred Clusters Number of + Pop 1 2 3 Individuals + + 1: 0.002 0.997 0.001 6 + 2: 0.002 0.997 0.002 6 + 3: 0.002 0.997 0.001 6 + 4: 0.003 0.996 0.001 6 + 5: 0.003 0.995 0.002 6 + 6: 0.016 0.981 0.003 6 + 7: 0.002 0.996 0.001 6 + 8: 0.004 0.994 0.002 6 + 9: 0.038 0.961 0.002 6 + 10: 0.082 0.913 0.005 6 + 11: 0.995 0.004 0.001 6 + 12: 0.997 0.002 0.001 6 + 13: 0.997 0.002 0.001 6 + 14: 0.997 0.002 0.001 6 + 15: 0.001 0.001 0.998 6 + 16: 0.002 0.001 0.997 5 +-------------------------------------------- + +Allele-freq. divergence among pops (Kullback-Leibler distance), +computed using point estimates of P. + + 1 2 3 + 1 - 1.29 2.61 + 2 1.55 - 2.34 + 3 3.44 2.90 - +-------------------------------------------- +Estimated Ln Prob of Data = -3020.8 +Mean value of ln likelihood = -2945.8 +Variance of ln likelihood = 150.0 +Mean value of alpha = 0.0269 + +Mean value of Fst_1 = 0.3266 +Mean value of Fst_2 = 0.1332 +Mean value of Fst_3 = 0.5223 + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters + 1 A01 (0) 1 : 0.002 0.997 0.001 + 2 A02 (0) 1 : 0.002 0.997 0.001 + 3 A03 (0) 1 : 0.002 0.997 0.001 + 4 A04 (0) 1 : 0.002 0.997 0.001 + 5 A05 (0) 1 : 0.002 0.996 0.001 + 6 A24 (0) 1 : 0.002 0.997 0.001 + 7 B466 (0) 2 : 0.002 0.997 0.001 + 8 B479 (0) 2 : 0.002 0.997 0.001 + 9 B480 (0) 2 : 0.002 0.997 0.001 + 10 B482 (0) 2 : 0.002 0.996 0.002 + 11 B484 (0) 2 : 0.002 0.996 0.002 + 12 B485 (0) 2 : 0.002 0.997 0.001 + 13 C02 (0) 3 : 0.002 0.997 0.001 + 14 C05 (0) 3 : 0.002 0.997 0.001 + 15 C14 (0) 3 : 0.001 0.997 0.001 + 16 C30 (0) 3 : 0.002 0.997 0.001 + 17 C31 (0) 3 : 0.002 0.997 0.001 + 18 C40 (0) 3 : 0.002 0.997 0.001 + 19 D08 (0) 4 : 0.001 0.997 0.001 + 20 D09 (0) 4 : 0.003 0.996 0.001 + 21 D13 (0) 4 : 0.002 0.996 0.002 + 22 D21 (0) 4 : 0.006 0.993 0.002 + 23 D25 (0) 4 : 0.003 0.996 0.001 + 24 D30 (0) 4 : 0.003 0.995 0.001 + 25 E01 (0) 5 : 0.004 0.994 0.002 + 26 E02 (0) 5 : 0.004 0.994 0.002 + 27 E03 (0) 5 : 0.003 0.996 0.001 + 28 E04 (0) 5 : 0.002 0.996 0.001 + 29 E05 (0) 5 : 0.002 0.996 0.001 + 30 E06 (0) 5 : 0.004 0.994 0.001 + 31 F03 (0) 6 : 0.003 0.985 0.012 + 32 F05 (0) 6 : 0.033 0.966 0.001 + 33 F08 (0) 6 : 0.015 0.982 0.002 + 34 F14 (0) 6 : 0.038 0.961 0.001 + 35 F25 (0) 6 : 0.005 0.994 0.001 + 36 F35 (0) 6 : 0.004 0.995 0.001 + 37 B360 (0) 7 : 0.002 0.997 0.001 + 38 B365 (0) 7 : 0.004 0.995 0.001 + 39 B367 (0) 7 : 0.002 0.997 0.001 + 40 B370 (0) 7 : 0.003 0.996 0.001 + 41 B371 (0) 7 : 0.003 0.996 0.001 + 42 B372 (0) 7 : 0.002 0.997 0.001 + 43 B341 (0) 8 : 0.008 0.985 0.007 + 44 B342 (0) 8 : 0.004 0.995 0.001 + 45 B343 (0) 8 : 0.002 0.996 0.001 + 46 B345 (0) 8 : 0.004 0.995 0.001 + 47 B346 (0) 8 : 0.002 0.997 0.001 + 48 B349 (0) 8 : 0.002 0.996 0.001 + 49 B121 (0) 9 : 0.007 0.991 0.002 + 50 B122 (0) 9 : 0.122 0.877 0.001 + 51 B125 (0) 9 : 0.005 0.993 0.002 + 52 B127 (0) 9 : 0.007 0.992 0.001 + 53 B128 (0) 9 : 0.026 0.973 0.002 + 54 B129 (0) 9 : 0.060 0.938 0.002 + 55 B306 (0) 10 : 0.011 0.974 0.015 + 56 B310 (0) 10 : 0.101 0.898 0.001 + 57 B312 (0) 10 : 0.176 0.822 0.002 + 58 B313 (0) 10 : 0.132 0.859 0.009 + 59 B317 (0) 10 : 0.053 0.945 0.001 + 60 B318 (0) 10 : 0.018 0.978 0.004 + 61 G19 (0) 11 : 0.997 0.002 0.001 + 62 G20 (0) 11 : 0.997 0.002 0.001 + 63 G21 (0) 11 : 0.997 0.002 0.001 + 64 G22 (0) 11 : 0.986 0.013 0.001 + 65 G23 (0) 11 : 0.996 0.003 0.001 + 66 G24 (0) 11 : 0.997 0.002 0.001 + 67 H01 (0) 12 : 0.997 0.002 0.001 + 68 H02 (0) 12 : 0.997 0.002 0.001 + 69 H03 (0) 12 : 0.997 0.002 0.001 + 70 H04 (0) 12 : 0.997 0.002 0.001 + 71 H05 (0) 12 : 0.997 0.002 0.001 + 72 H12 (0) 12 : 0.997 0.001 0.001 + 73 I20 (0) 13 : 0.997 0.002 0.001 + 74 I21 (0) 13 : 0.997 0.002 0.001 + 75 I23 (0) 13 : 0.993 0.004 0.002 + 76 I24 (0) 13 : 0.997 0.002 0.001 + 77 I25 (0) 13 : 0.997 0.002 0.001 + 78 I26 (0) 13 : 0.997 0.002 0.001 + 79 J02 (0) 14 : 0.997 0.002 0.001 + 80 J04 (0) 14 : 0.997 0.002 0.001 + 81 J05 (0) 14 : 0.997 0.002 0.001 + 82 J08 (0) 14 : 0.995 0.004 0.001 + 83 J09 (0) 14 : 0.997 0.002 0.001 + 84 J10 (0) 14 : 0.997 0.001 0.001 + 85 K20 (5) 15 : 0.001 0.001 0.998 + 86 K33 (5) 15 : 0.001 0.001 0.998 + 87 K34 (5) 15 : 0.001 0.001 0.998 + 88 K35 (5) 15 : 0.001 0.001 0.998 + 89 K53 (5) 15 : 0.001 0.001 0.998 + 90 K56 (5) 15 : 0.001 0.001 0.998 + 91 L04 (5) 16 : 0.001 0.001 0.998 + 92 L07 (5) 16 : 0.001 0.001 0.998 + 93 L14 (5) 16 : 0.005 0.002 0.993 + 94 L26 (5) 16 : 0.001 0.001 0.998 + 95 L27 (5) 16 : 0.001 0.001 0.998 + + +Estimated Allele Frequencies in each population +First column gives estimated ancestral frequencies + + +Locus 1 : L1 +7 alleles +0.0% missing data + 118 (0.408) 0.476 0.761 0.017 + 127 (0.105) 0.004 0.110 0.004 + 130 (0.114) 0.005 0.029 0.486 + 114 (0.084) 0.003 0.045 0.003 + 122 (0.142) 0.243 0.045 0.006 + 110 (0.084) 0.266 0.007 0.003 + 135 (0.064) 0.003 0.003 0.481 + +Locus 2 : L2 +15 alleles +0.0% missing data + 228 (0.070) 0.003 0.156 0.003 + 222 (0.102) 0.041 0.174 0.004 + 225 (0.077) 0.003 0.252 0.003 + 234 (0.050) 0.002 0.019 0.002 + 219 (0.111) 0.142 0.173 0.005 + 213 (0.113) 0.604 0.109 0.005 + 204 (0.046) 0.002 0.010 0.002 + 216 (0.075) 0.081 0.020 0.003 + 195 (0.051) 0.002 0.019 0.002 + 231 (0.055) 0.003 0.035 0.002 + 210 (0.071) 0.049 0.016 0.003 + 240 (0.046) 0.004 0.010 0.002 + 207 (0.048) 0.060 0.003 0.002 + 198 (0.045) 0.002 0.002 0.917 + 185 (0.042) 0.002 0.002 0.045 + +Locus 3 : L3 +3 alleles +0.0% missing data + 266 (0.818) 0.993 0.950 0.033 + 272 (0.103) 0.004 0.045 0.004 + 278 (0.078) 0.003 0.004 0.962 + +Locus 4 : L4 +19 alleles +0.0% missing data + 164 (0.086) 0.160 0.107 0.004 + 173 (0.074) 0.003 0.519 0.003 + 182 (0.056) 0.002 0.108 0.002 + 170 (0.058) 0.041 0.011 0.002 + 200 (0.047) 0.002 0.027 0.002 + 202 (0.041) 0.002 0.010 0.002 + 176 (0.041) 0.002 0.010 0.002 + 185 (0.047) 0.002 0.035 0.002 + 167 (0.069) 0.061 0.035 0.003 + 158 (0.080) 0.075 0.078 0.003 + 155 (0.066) 0.052 0.023 0.003 + 152 (0.053) 0.184 0.007 0.002 + 179 (0.041) 0.003 0.010 0.002 + 145 (0.040) 0.002 0.010 0.002 + 149 (0.044) 0.192 0.002 0.002 + 161 (0.044) 0.212 0.002 0.002 + 136 (0.039) 0.002 0.002 0.874 + 101 (0.038) 0.002 0.002 0.045 + 139 (0.037) 0.002 0.002 0.045 + +Locus 5 : L5 +24 alleles +0.0% missing data + 182 (0.050) 0.002 0.083 0.089 + 188 (0.038) 0.002 0.050 0.002 + 185 (0.041) 0.002 0.115 0.002 + 194 (0.037) 0.001 0.042 0.001 + 209 (0.031) 0.001 0.010 0.001 + 191 (0.036) 0.001 0.042 0.001 + 160 (0.062) 0.060 0.035 0.267 + 200 (0.036) 0.001 0.034 0.001 + 173 (0.050) 0.002 0.091 0.089 + 176 (0.036) 0.002 0.034 0.001 + 169 (0.037) 0.002 0.034 0.001 + 131 (0.032) 0.001 0.010 0.001 + 166 (0.038) 0.002 0.050 0.002 + 154 (0.052) 0.063 0.050 0.002 + 144 (0.053) 0.208 0.053 0.002 + 157 (0.049) 0.100 0.026 0.002 + 203 (0.033) 0.001 0.018 0.001 + 147 (0.052) 0.069 0.047 0.002 + 134 (0.058) 0.279 0.096 0.002 + 141 (0.052) 0.118 0.043 0.002 + 206 (0.036) 0.002 0.034 0.001 + 151 (0.032) 0.059 0.002 0.001 + 137 (0.030) 0.020 0.002 0.001 + 179 (0.029) 0.001 0.002 0.522 + +Locus 6 : L6 +6 alleles +11.6% missing data + 177 (0.259) 0.111 0.195 0.264 + 165 (0.219) 0.030 0.201 0.225 + 171 (0.262) 0.012 0.591 0.273 + 175 (0.092) 0.542 0.005 0.085 + 183 (0.084) 0.163 0.004 0.076 + 179 (0.084) 0.143 0.004 0.077 + +Locus 7 : L7 +10 alleles +0.0% missing data + 187 (0.127) 0.005 0.408 0.005 + 191 (0.105) 0.004 0.198 0.004 + 183 (0.178) 0.498 0.157 0.007 + 195 (0.095) 0.004 0.142 0.004 + 199 (0.100) 0.023 0.038 0.004 + 180 (0.096) 0.062 0.021 0.004 + 203 (0.095) 0.103 0.020 0.004 + 206 (0.084) 0.161 0.011 0.003 + 214 (0.064) 0.137 0.003 0.003 + 138 (0.058) 0.002 0.003 0.961 + +Locus 8 : L8 +7 alleles +0.0% missing data + 151 (0.366) 0.666 0.624 0.015 + 148 (0.120) 0.024 0.063 0.005 + 145 (0.085) 0.003 0.011 0.963 + 157 (0.062) 0.003 0.011 0.003 + 155 (0.102) 0.004 0.119 0.004 + 135 (0.078) 0.003 0.036 0.003 + 141 (0.187) 0.297 0.137 0.008 + +Locus 9 : L9 +10 alleles +0.0% missing data + 138 (0.146) 0.006 0.549 0.006 + 140 (0.078) 0.003 0.052 0.003 + 147 (0.151) 0.007 0.134 0.966 + 142 (0.146) 0.341 0.079 0.006 + 145 (0.138) 0.117 0.089 0.006 + 136 (0.075) 0.003 0.044 0.003 + 134 (0.065) 0.003 0.019 0.003 + 132 (0.070) 0.004 0.027 0.003 + 153 (0.069) 0.415 0.004 0.003 + 149 (0.063) 0.101 0.003 0.003 + +Locus 10 : L10 +7 alleles +0.0% missing data + 313 (0.126) 0.005 0.112 0.005 + 317 (0.261) 0.011 0.700 0.011 + 321 (0.103) 0.004 0.054 0.004 + 319 (0.163) 0.008 0.063 0.447 + 325 (0.071) 0.003 0.012 0.003 + 306 (0.202) 0.966 0.055 0.008 + 324 (0.073) 0.003 0.004 0.522 + +Locus 11 : L11 +8 alleles +0.0% missing data + 250 (0.165) 0.007 0.438 0.007 + 247 (0.100) 0.004 0.085 0.004 + 242 (0.111) 0.005 0.125 0.004 + 251 (0.094) 0.005 0.060 0.004 + 245 (0.173) 0.106 0.120 0.007 + 257 (0.072) 0.003 0.020 0.003 + 243 (0.171) 0.864 0.018 0.966 + 253 (0.115) 0.006 0.133 0.005 + +Locus 12 : L12 +4 alleles +0.0% missing data + 204 (0.791) 0.836 0.973 0.949 + 180 (0.074) 0.003 0.020 0.003 + 218 (0.075) 0.158 0.004 0.003 + 210 (0.060) 0.003 0.003 0.045 + +Locus 13 : L13 +6 alleles +0.0% missing data + 260 (0.615) 0.888 0.891 0.854 + 263 (0.131) 0.005 0.079 0.092 + 257 (0.069) 0.003 0.020 0.003 + 269 (0.067) 0.080 0.004 0.003 + 275 (0.061) 0.022 0.003 0.002 + 246 (0.057) 0.002 0.003 0.045 + +Locus 14 : L14 +5 alleles +0.0% missing data + 157 (0.607) 0.886 0.660 0.984 + 146 (0.143) 0.006 0.287 0.006 + 153 (0.076) 0.003 0.028 0.003 + 155 (0.110) 0.083 0.021 0.004 + 163 (0.063) 0.022 0.003 0.003 + +Locus 15 : L15 +2 alleles +0.0% missing data + 243 (0.625) 0.027 0.884 0.945 + 238 (0.375) 0.973 0.116 0.055 + +Locus 16 : L16 +3 alleles +0.0% missing data + 173 (0.728) 0.863 0.838 0.989 + 165 (0.091) 0.004 0.053 0.004 + 169 (0.181) 0.133 0.109 0.007 + +Locus 17 : L17 +2 alleles +0.0% missing data + 171 (0.919) 0.997 0.996 0.038 + 168 (0.081) 0.003 0.004 0.962 + +Locus 18 : L18 +4 alleles +0.0% missing data + 286 (0.673) 0.963 0.874 0.027 + 287 (0.119) 0.005 0.095 0.005 + 283 (0.109) 0.028 0.020 0.005 + 290 (0.099) 0.004 0.011 0.963 + +Values of parameters used in structure: +DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_6, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=3, BURNIN=50000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/Admix_run_005_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,386 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + Code by J.K. Pritchard + Modified by Daniel Falush to + incorporate recombination breakpoints + Version 2.0 (July 2001) +---------------------------------------------------- + + + +Command line arguments: bin/structure.exe -m \mainparams -e \extraparams +Input File: \project_data + +Run parameters: + 95 individuals + 18 loci + 3 populations assumed + 50000 Burn-in period + 500000 Reps + + +-------------------------------------------- +Proportion of membership of each pre-defined + population in each of the 3 clusters + +Given Inferred Clusters Number of + Pop 1 2 3 Individuals + + 1: 0.001 0.997 0.002 6 + 2: 0.002 0.997 0.002 6 + 3: 0.001 0.997 0.002 6 + 4: 0.001 0.996 0.003 6 + 5: 0.002 0.995 0.003 6 + 6: 0.003 0.981 0.016 6 + 7: 0.001 0.996 0.002 6 + 8: 0.002 0.994 0.004 6 + 9: 0.002 0.960 0.038 6 + 10: 0.005 0.913 0.081 6 + 11: 0.001 0.004 0.995 6 + 12: 0.001 0.002 0.997 6 + 13: 0.001 0.002 0.996 6 + 14: 0.001 0.002 0.997 6 + 15: 0.998 0.001 0.001 6 + 16: 0.997 0.001 0.002 5 +-------------------------------------------- + +Allele-freq. divergence among pops (Kullback-Leibler distance), +computed using point estimates of P. + + 1 2 3 + 1 - 2.90 3.44 + 2 2.33 - 1.55 + 3 2.61 1.29 - +-------------------------------------------- +Estimated Ln Prob of Data = -3020.8 +Mean value of ln likelihood = -2945.9 +Variance of ln likelihood = 149.7 +Mean value of alpha = 0.0269 + +Mean value of Fst_1 = 0.5216 +Mean value of Fst_2 = 0.1326 +Mean value of Fst_3 = 0.3273 + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters + 1 A01 (0) 1 : 0.001 0.997 0.002 + 2 A02 (0) 1 : 0.002 0.997 0.002 + 3 A03 (0) 1 : 0.001 0.997 0.002 + 4 A04 (0) 1 : 0.001 0.997 0.002 + 5 A05 (0) 1 : 0.001 0.996 0.002 + 6 A24 (0) 1 : 0.001 0.997 0.002 + 7 B466 (0) 2 : 0.001 0.997 0.002 + 8 B479 (0) 2 : 0.001 0.997 0.002 + 9 B480 (0) 2 : 0.001 0.997 0.002 + 10 B482 (0) 2 : 0.002 0.996 0.002 + 11 B484 (0) 2 : 0.002 0.996 0.002 + 12 B485 (0) 2 : 0.001 0.997 0.002 + 13 C02 (0) 3 : 0.001 0.997 0.001 + 14 C05 (0) 3 : 0.001 0.997 0.001 + 15 C14 (0) 3 : 0.002 0.997 0.001 + 16 C30 (0) 3 : 0.001 0.997 0.002 + 17 C31 (0) 3 : 0.001 0.997 0.002 + 18 C40 (0) 3 : 0.001 0.997 0.002 + 19 D08 (0) 4 : 0.001 0.997 0.001 + 20 D09 (0) 4 : 0.001 0.996 0.003 + 21 D13 (0) 4 : 0.002 0.996 0.002 + 22 D21 (0) 4 : 0.002 0.993 0.005 + 23 D25 (0) 4 : 0.001 0.996 0.003 + 24 D30 (0) 4 : 0.001 0.995 0.003 + 25 E01 (0) 5 : 0.002 0.994 0.004 + 26 E02 (0) 5 : 0.002 0.994 0.004 + 27 E03 (0) 5 : 0.002 0.996 0.002 + 28 E04 (0) 5 : 0.001 0.996 0.002 + 29 E05 (0) 5 : 0.002 0.996 0.002 + 30 E06 (0) 5 : 0.001 0.994 0.004 + 31 F03 (0) 6 : 0.012 0.985 0.003 + 32 F05 (0) 6 : 0.001 0.967 0.032 + 33 F08 (0) 6 : 0.002 0.982 0.015 + 34 F14 (0) 6 : 0.001 0.963 0.036 + 35 F25 (0) 6 : 0.001 0.994 0.005 + 36 F35 (0) 6 : 0.001 0.995 0.003 + 37 B360 (0) 7 : 0.001 0.997 0.002 + 38 B365 (0) 7 : 0.001 0.995 0.003 + 39 B367 (0) 7 : 0.001 0.997 0.002 + 40 B370 (0) 7 : 0.001 0.996 0.003 + 41 B371 (0) 7 : 0.001 0.996 0.002 + 42 B372 (0) 7 : 0.001 0.997 0.002 + 43 B341 (0) 8 : 0.008 0.984 0.008 + 44 B342 (0) 8 : 0.001 0.995 0.004 + 45 B343 (0) 8 : 0.001 0.996 0.002 + 46 B345 (0) 8 : 0.001 0.995 0.004 + 47 B346 (0) 8 : 0.001 0.997 0.002 + 48 B349 (0) 8 : 0.001 0.997 0.002 + 49 B121 (0) 9 : 0.002 0.991 0.007 + 50 B122 (0) 9 : 0.001 0.878 0.120 + 51 B125 (0) 9 : 0.002 0.993 0.005 + 52 B127 (0) 9 : 0.001 0.992 0.007 + 53 B128 (0) 9 : 0.002 0.972 0.026 + 54 B129 (0) 9 : 0.003 0.934 0.064 + 55 B306 (0) 10 : 0.015 0.974 0.010 + 56 B310 (0) 10 : 0.001 0.900 0.099 + 57 B312 (0) 10 : 0.002 0.823 0.175 + 58 B313 (0) 10 : 0.009 0.860 0.131 + 59 B317 (0) 10 : 0.001 0.943 0.055 + 60 B318 (0) 10 : 0.004 0.978 0.018 + 61 G19 (0) 11 : 0.001 0.002 0.997 + 62 G20 (0) 11 : 0.001 0.002 0.997 + 63 G21 (0) 11 : 0.001 0.002 0.997 + 64 G22 (0) 11 : 0.001 0.014 0.985 + 65 G23 (0) 11 : 0.001 0.003 0.996 + 66 G24 (0) 11 : 0.001 0.002 0.997 + 67 H01 (0) 12 : 0.001 0.002 0.997 + 68 H02 (0) 12 : 0.001 0.002 0.997 + 69 H03 (0) 12 : 0.001 0.002 0.997 + 70 H04 (0) 12 : 0.001 0.002 0.997 + 71 H05 (0) 12 : 0.001 0.002 0.997 + 72 H12 (0) 12 : 0.001 0.001 0.997 + 73 I20 (0) 13 : 0.001 0.002 0.997 + 74 I21 (0) 13 : 0.001 0.002 0.997 + 75 I23 (0) 13 : 0.002 0.004 0.993 + 76 I24 (0) 13 : 0.001 0.002 0.997 + 77 I25 (0) 13 : 0.001 0.002 0.997 + 78 I26 (0) 13 : 0.001 0.002 0.997 + 79 J02 (0) 14 : 0.001 0.002 0.997 + 80 J04 (0) 14 : 0.001 0.002 0.997 + 81 J05 (0) 14 : 0.001 0.002 0.997 + 82 J08 (0) 14 : 0.001 0.004 0.995 + 83 J09 (0) 14 : 0.001 0.002 0.997 + 84 J10 (0) 14 : 0.001 0.001 0.997 + 85 K20 (5) 15 : 0.998 0.001 0.001 + 86 K33 (5) 15 : 0.998 0.001 0.001 + 87 K34 (5) 15 : 0.998 0.001 0.001 + 88 K35 (5) 15 : 0.998 0.001 0.001 + 89 K53 (5) 15 : 0.998 0.001 0.001 + 90 K56 (5) 15 : 0.998 0.001 0.001 + 91 L04 (5) 16 : 0.998 0.001 0.001 + 92 L07 (5) 16 : 0.998 0.001 0.001 + 93 L14 (5) 16 : 0.993 0.002 0.005 + 94 L26 (5) 16 : 0.998 0.001 0.001 + 95 L27 (5) 16 : 0.998 0.001 0.001 + + +Estimated Allele Frequencies in each population +First column gives estimated ancestral frequencies + + +Locus 1 : L1 +7 alleles +0.0% missing data + 118 (0.406) 0.017 0.761 0.476 + 127 (0.106) 0.004 0.110 0.004 + 130 (0.114) 0.486 0.029 0.005 + 114 (0.084) 0.003 0.045 0.003 + 122 (0.141) 0.006 0.045 0.243 + 110 (0.085) 0.003 0.007 0.266 + 135 (0.064) 0.481 0.003 0.003 + +Locus 2 : L2 +15 alleles +0.0% missing data + 228 (0.071) 0.003 0.156 0.003 + 222 (0.101) 0.004 0.174 0.041 + 225 (0.077) 0.003 0.252 0.003 + 234 (0.050) 0.002 0.019 0.002 + 219 (0.112) 0.005 0.173 0.142 + 213 (0.112) 0.005 0.109 0.604 + 204 (0.047) 0.002 0.010 0.002 + 216 (0.074) 0.003 0.020 0.081 + 195 (0.051) 0.002 0.019 0.002 + 231 (0.056) 0.002 0.034 0.003 + 210 (0.069) 0.003 0.016 0.049 + 240 (0.046) 0.002 0.010 0.004 + 207 (0.047) 0.002 0.003 0.060 + 198 (0.045) 0.917 0.002 0.002 + 185 (0.042) 0.045 0.002 0.002 + +Locus 3 : L3 +3 alleles +0.0% missing data + 266 (0.819) 0.034 0.950 0.993 + 272 (0.103) 0.004 0.045 0.004 + 278 (0.078) 0.962 0.004 0.003 + +Locus 4 : L4 +19 alleles +0.0% missing data + 164 (0.088) 0.004 0.107 0.161 + 173 (0.076) 0.003 0.519 0.003 + 182 (0.056) 0.002 0.108 0.002 + 170 (0.056) 0.002 0.011 0.041 + 200 (0.047) 0.002 0.027 0.002 + 202 (0.041) 0.002 0.010 0.002 + 176 (0.041) 0.002 0.010 0.002 + 185 (0.049) 0.002 0.035 0.002 + 167 (0.069) 0.003 0.035 0.061 + 158 (0.079) 0.003 0.078 0.075 + 155 (0.063) 0.003 0.023 0.052 + 152 (0.052) 0.002 0.007 0.184 + 179 (0.042) 0.002 0.010 0.003 + 145 (0.041) 0.002 0.010 0.002 + 149 (0.044) 0.002 0.002 0.193 + 161 (0.045) 0.002 0.002 0.211 + 136 (0.038) 0.874 0.002 0.002 + 101 (0.037) 0.045 0.002 0.002 + 139 (0.038) 0.045 0.002 0.002 + +Locus 5 : L5 +24 alleles +0.0% missing data + 182 (0.051) 0.089 0.083 0.002 + 188 (0.038) 0.002 0.050 0.002 + 185 (0.040) 0.002 0.114 0.002 + 194 (0.037) 0.002 0.042 0.001 + 209 (0.031) 0.001 0.010 0.001 + 191 (0.037) 0.002 0.042 0.001 + 160 (0.064) 0.267 0.035 0.060 + 200 (0.035) 0.001 0.034 0.001 + 173 (0.051) 0.089 0.091 0.002 + 176 (0.036) 0.001 0.034 0.002 + 169 (0.035) 0.001 0.034 0.002 + 131 (0.031) 0.001 0.010 0.001 + 166 (0.037) 0.001 0.050 0.002 + 154 (0.052) 0.002 0.050 0.063 + 144 (0.054) 0.002 0.053 0.207 + 157 (0.050) 0.002 0.026 0.100 + 203 (0.034) 0.001 0.018 0.001 + 147 (0.051) 0.002 0.047 0.069 + 134 (0.057) 0.002 0.096 0.280 + 141 (0.052) 0.002 0.043 0.118 + 206 (0.035) 0.001 0.034 0.002 + 151 (0.032) 0.001 0.002 0.059 + 137 (0.030) 0.001 0.002 0.020 + 179 (0.029) 0.521 0.002 0.001 + +Locus 6 : L6 +6 alleles +11.6% missing data + 177 (0.259) 0.264 0.195 0.111 + 165 (0.218) 0.224 0.200 0.030 + 171 (0.264) 0.275 0.591 0.012 + 175 (0.092) 0.085 0.005 0.542 + 183 (0.084) 0.077 0.004 0.163 + 179 (0.082) 0.075 0.004 0.143 + +Locus 7 : L7 +10 alleles +0.0% missing data + 187 (0.129) 0.005 0.408 0.005 + 191 (0.103) 0.004 0.198 0.004 + 183 (0.178) 0.007 0.157 0.498 + 195 (0.095) 0.004 0.142 0.004 + 199 (0.099) 0.004 0.037 0.023 + 180 (0.095) 0.004 0.021 0.062 + 203 (0.096) 0.004 0.020 0.103 + 206 (0.084) 0.003 0.011 0.161 + 214 (0.063) 0.003 0.003 0.137 + 138 (0.057) 0.961 0.003 0.002 + +Locus 8 : L8 +7 alleles +0.0% missing data + 151 (0.366) 0.015 0.624 0.666 + 148 (0.120) 0.005 0.063 0.024 + 145 (0.084) 0.963 0.010 0.003 + 157 (0.061) 0.002 0.011 0.003 + 155 (0.102) 0.004 0.119 0.004 + 135 (0.078) 0.003 0.036 0.003 + 141 (0.188) 0.008 0.137 0.297 + +Locus 9 : L9 +10 alleles +0.0% missing data + 138 (0.147) 0.006 0.549 0.006 + 140 (0.077) 0.003 0.052 0.003 + 147 (0.151) 0.966 0.133 0.007 + 142 (0.144) 0.006 0.079 0.341 + 145 (0.140) 0.006 0.089 0.117 + 136 (0.075) 0.003 0.044 0.003 + 134 (0.064) 0.003 0.019 0.003 + 132 (0.070) 0.003 0.027 0.004 + 153 (0.069) 0.003 0.004 0.415 + 149 (0.063) 0.003 0.003 0.101 + +Locus 10 : L10 +7 alleles +0.0% missing data + 313 (0.127) 0.005 0.112 0.005 + 317 (0.263) 0.011 0.700 0.011 + 321 (0.103) 0.004 0.054 0.004 + 319 (0.163) 0.447 0.063 0.008 + 325 (0.071) 0.003 0.012 0.003 + 306 (0.199) 0.008 0.055 0.967 + 324 (0.073) 0.522 0.004 0.003 + +Locus 11 : L11 +8 alleles +0.0% missing data + 250 (0.166) 0.007 0.439 0.007 + 247 (0.101) 0.004 0.085 0.004 + 242 (0.111) 0.004 0.125 0.005 + 251 (0.092) 0.004 0.060 0.005 + 245 (0.174) 0.007 0.120 0.106 + 257 (0.071) 0.003 0.020 0.003 + 243 (0.170) 0.966 0.018 0.864 + 253 (0.115) 0.005 0.133 0.006 + +Locus 12 : L12 +4 alleles +0.0% missing data + 204 (0.789) 0.949 0.973 0.836 + 180 (0.074) 0.003 0.020 0.003 + 218 (0.075) 0.003 0.004 0.158 + 210 (0.062) 0.045 0.003 0.003 + +Locus 13 : L13 +6 alleles +0.0% missing data + 260 (0.621) 0.855 0.892 0.888 + 263 (0.129) 0.092 0.079 0.005 + 257 (0.067) 0.003 0.020 0.003 + 269 (0.065) 0.003 0.003 0.080 + 275 (0.060) 0.002 0.003 0.022 + 246 (0.057) 0.045 0.003 0.002 + +Locus 14 : L14 +5 alleles +0.0% missing data + 157 (0.608) 0.984 0.660 0.886 + 146 (0.144) 0.006 0.288 0.006 + 153 (0.077) 0.003 0.028 0.003 + 155 (0.109) 0.004 0.021 0.083 + 163 (0.063) 0.003 0.003 0.022 + +Locus 15 : L15 +2 alleles +0.0% missing data + 243 (0.627) 0.945 0.883 0.027 + 238 (0.373) 0.055 0.117 0.973 + +Locus 16 : L16 +3 alleles +0.0% missing data + 173 (0.730) 0.989 0.838 0.863 + 165 (0.092) 0.004 0.053 0.004 + 169 (0.179) 0.007 0.109 0.133 + +Locus 17 : L17 +2 alleles +0.0% missing data + 171 (0.919) 0.038 0.996 0.997 + 168 (0.081) 0.962 0.004 0.003 + +Locus 18 : L18 +4 alleles +0.0% missing data + 286 (0.672) 0.027 0.874 0.964 + 287 (0.120) 0.005 0.095 0.005 + 283 (0.110) 0.005 0.020 0.028 + 290 (0.099) 0.963 0.011 0.004 + +Values of parameters used in structure: +DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_54, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=3, BURNIN=50000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/Admix_run_007_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,388 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + Code by J.K. Pritchard + Modified by Daniel Falush to + incorporate recombination breakpoints + Version 2.0 (July 2001) +---------------------------------------------------- + + + +Command line arguments: bin/structure.exe -m \mainparams -e \extraparams +Input File: \project_data + +Run parameters: + 95 individuals + 18 loci + 4 populations assumed + 50000 Burn-in period + 500000 Reps + + +-------------------------------------------- +Proportion of membership of each pre-defined + population in each of the 4 clusters + +Given Inferred Clusters Number of + Pop 1 2 3 4 Individuals + + 1: 0.991 0.003 0.005 0.001 6 + 2: 0.990 0.002 0.006 0.002 6 + 3: 0.995 0.001 0.002 0.001 6 + 4: 0.968 0.003 0.027 0.002 6 + 5: 0.212 0.003 0.783 0.002 6 + 6: 0.104 0.015 0.878 0.003 6 + 7: 0.991 0.002 0.006 0.001 6 + 8: 0.022 0.002 0.974 0.002 6 + 9: 0.003 0.006 0.989 0.001 6 + 10: 0.036 0.021 0.940 0.004 6 + 11: 0.002 0.988 0.009 0.001 6 + 12: 0.002 0.995 0.002 0.001 6 + 13: 0.002 0.994 0.003 0.001 6 + 14: 0.002 0.995 0.002 0.001 6 + 15: 0.001 0.001 0.001 0.997 6 + 16: 0.001 0.002 0.002 0.995 5 +-------------------------------------------- + +Allele-freq. divergence among pops (Kullback-Leibler distance), +computed using point estimates of P. + + 1 2 3 4 + 1 - 1.82 0.54 2.44 + 2 1.91 - 1.05 2.63 + 3 0.75 1.36 - 2.31 + 4 3.37 3.50 2.55 - +-------------------------------------------- +Estimated Ln Prob of Data = -2773.7 +Mean value of ln likelihood = -2678.7 +Variance of ln likelihood = 190.1 +Mean value of alpha = 0.0270 + +Mean value of Fst_1 = 0.2745 +Mean value of Fst_2 = 0.3296 +Mean value of Fst_3 = 0.1303 +Mean value of Fst_4 = 0.5180 + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters + 1 A01 (0) 1 : 0.994 0.002 0.003 0.001 + 2 A02 (0) 1 : 0.995 0.001 0.003 0.001 + 3 A03 (0) 1 : 0.981 0.007 0.010 0.001 + 4 A04 (0) 1 : 0.995 0.002 0.002 0.001 + 5 A05 (0) 1 : 0.994 0.002 0.003 0.001 + 6 A24 (0) 1 : 0.989 0.002 0.008 0.002 + 7 B466 (0) 2 : 0.992 0.002 0.005 0.001 + 8 B479 (0) 2 : 0.995 0.001 0.003 0.001 + 9 B480 (0) 2 : 0.991 0.002 0.006 0.001 + 10 B482 (0) 2 : 0.984 0.003 0.010 0.003 + 11 B484 (0) 2 : 0.985 0.002 0.011 0.002 + 12 B485 (0) 2 : 0.993 0.002 0.004 0.001 + 13 C02 (0) 3 : 0.996 0.001 0.002 0.001 + 14 C05 (0) 3 : 0.995 0.001 0.002 0.001 + 15 C14 (0) 3 : 0.995 0.001 0.002 0.001 + 16 C30 (0) 3 : 0.995 0.002 0.002 0.001 + 17 C31 (0) 3 : 0.995 0.001 0.002 0.001 + 18 C40 (0) 3 : 0.995 0.001 0.003 0.001 + 19 D08 (0) 4 : 0.989 0.001 0.007 0.002 + 20 D09 (0) 4 : 0.990 0.002 0.006 0.001 + 21 D13 (0) 4 : 0.988 0.002 0.008 0.003 + 22 D21 (0) 4 : 0.975 0.007 0.016 0.002 + 23 D25 (0) 4 : 0.984 0.003 0.011 0.001 + 24 D30 (0) 4 : 0.881 0.004 0.114 0.001 + 25 E01 (0) 5 : 0.042 0.002 0.953 0.003 + 26 E02 (0) 5 : 0.009 0.002 0.988 0.002 + 27 E03 (0) 5 : 0.738 0.002 0.257 0.002 + 28 E04 (0) 5 : 0.332 0.002 0.664 0.002 + 29 E05 (0) 5 : 0.113 0.002 0.883 0.001 + 30 E06 (0) 5 : 0.038 0.005 0.956 0.001 + 31 F03 (0) 6 : 0.068 0.003 0.919 0.010 + 32 F05 (0) 6 : 0.040 0.011 0.948 0.001 + 33 F08 (0) 6 : 0.020 0.007 0.970 0.004 + 34 F14 (0) 6 : 0.471 0.065 0.463 0.001 + 35 F25 (0) 6 : 0.015 0.003 0.981 0.001 + 36 F35 (0) 6 : 0.010 0.002 0.987 0.001 + 37 B360 (0) 7 : 0.993 0.002 0.004 0.001 + 38 B365 (0) 7 : 0.993 0.002 0.003 0.001 + 39 B367 (0) 7 : 0.980 0.001 0.018 0.001 + 40 B370 (0) 7 : 0.994 0.002 0.003 0.001 + 41 B371 (0) 7 : 0.994 0.002 0.003 0.001 + 42 B372 (0) 7 : 0.994 0.002 0.003 0.001 + 43 B341 (0) 8 : 0.016 0.004 0.976 0.004 + 44 B342 (0) 8 : 0.065 0.002 0.932 0.001 + 45 B343 (0) 8 : 0.019 0.002 0.978 0.001 + 46 B345 (0) 8 : 0.011 0.002 0.985 0.001 + 47 B346 (0) 8 : 0.008 0.002 0.989 0.001 + 48 B349 (0) 8 : 0.012 0.002 0.985 0.001 + 49 B121 (0) 9 : 0.003 0.004 0.991 0.002 + 50 B122 (0) 9 : 0.002 0.010 0.987 0.001 + 51 B125 (0) 9 : 0.003 0.003 0.993 0.002 + 52 B127 (0) 9 : 0.003 0.003 0.993 0.001 + 53 B128 (0) 9 : 0.004 0.008 0.986 0.002 + 54 B129 (0) 9 : 0.003 0.010 0.985 0.002 + 55 B306 (0) 10 : 0.002 0.002 0.987 0.009 + 56 B310 (0) 10 : 0.002 0.023 0.973 0.001 + 57 B312 (0) 10 : 0.035 0.029 0.934 0.002 + 58 B313 (0) 10 : 0.003 0.017 0.973 0.007 + 59 B317 (0) 10 : 0.165 0.045 0.788 0.001 + 60 B318 (0) 10 : 0.006 0.007 0.985 0.002 + 61 G19 (0) 11 : 0.002 0.995 0.002 0.001 + 62 G20 (0) 11 : 0.002 0.994 0.003 0.001 + 63 G21 (0) 11 : 0.002 0.995 0.002 0.001 + 64 G22 (0) 11 : 0.003 0.959 0.037 0.001 + 65 G23 (0) 11 : 0.002 0.993 0.004 0.001 + 66 G24 (0) 11 : 0.002 0.994 0.003 0.001 + 67 H01 (0) 12 : 0.002 0.995 0.002 0.001 + 68 H02 (0) 12 : 0.001 0.995 0.003 0.001 + 69 H03 (0) 12 : 0.002 0.995 0.002 0.001 + 70 H04 (0) 12 : 0.002 0.995 0.002 0.001 + 71 H05 (0) 12 : 0.002 0.995 0.002 0.001 + 72 H12 (0) 12 : 0.001 0.996 0.002 0.001 + 73 I20 (0) 13 : 0.002 0.996 0.002 0.001 + 74 I21 (0) 13 : 0.002 0.996 0.002 0.001 + 75 I23 (0) 13 : 0.004 0.989 0.004 0.002 + 76 I24 (0) 13 : 0.002 0.995 0.002 0.001 + 77 I25 (0) 13 : 0.001 0.993 0.005 0.001 + 78 I26 (0) 13 : 0.002 0.996 0.002 0.001 + 79 J02 (0) 14 : 0.001 0.996 0.002 0.001 + 80 J04 (0) 14 : 0.002 0.995 0.002 0.001 + 81 J05 (0) 14 : 0.002 0.994 0.003 0.001 + 82 J08 (0) 14 : 0.005 0.991 0.003 0.001 + 83 J09 (0) 14 : 0.002 0.995 0.002 0.001 + 84 J10 (0) 14 : 0.001 0.996 0.001 0.001 + 85 K20 (5) 15 : 0.001 0.001 0.001 0.996 + 86 K33 (5) 15 : 0.001 0.001 0.001 0.997 + 87 K34 (5) 15 : 0.001 0.001 0.001 0.997 + 88 K35 (5) 15 : 0.001 0.001 0.001 0.996 + 89 K53 (5) 15 : 0.001 0.001 0.001 0.997 + 90 K56 (5) 15 : 0.001 0.001 0.001 0.997 + 91 L04 (5) 16 : 0.001 0.001 0.001 0.997 + 92 L07 (5) 16 : 0.001 0.001 0.001 0.997 + 93 L14 (5) 16 : 0.001 0.006 0.004 0.989 + 94 L26 (5) 16 : 0.001 0.001 0.001 0.996 + 95 L27 (5) 16 : 0.001 0.001 0.001 0.996 + + +Estimated Allele Frequencies in each population +First column gives estimated ancestral frequencies + + +Locus 1 : L1 +7 alleles +0.0% missing data + 118 (0.461) 0.704 0.478 0.807 0.019 + 127 (0.086) 0.186 0.004 0.022 0.004 + 130 (0.110) 0.034 0.005 0.027 0.487 + 114 (0.083) 0.065 0.003 0.023 0.003 + 122 (0.118) 0.005 0.244 0.093 0.005 + 110 (0.085) 0.004 0.265 0.022 0.003 + 135 (0.056) 0.002 0.002 0.006 0.479 + +Locus 2 : L2 +15 alleles +0.0% missing data + 228 (0.071) 0.245 0.003 0.049 0.003 + 222 (0.112) 0.079 0.036 0.278 0.005 + 225 (0.094) 0.286 0.004 0.203 0.004 + 234 (0.056) 0.017 0.002 0.022 0.002 + 219 (0.118) 0.224 0.146 0.112 0.005 + 213 (0.122) 0.118 0.610 0.111 0.005 + 204 (0.041) 0.016 0.002 0.005 0.002 + 216 (0.065) 0.003 0.083 0.039 0.003 + 195 (0.045) 0.002 0.002 0.037 0.002 + 231 (0.049) 0.002 0.002 0.070 0.002 + 210 (0.063) 0.003 0.043 0.039 0.003 + 240 (0.042) 0.002 0.002 0.021 0.002 + 207 (0.043) 0.002 0.061 0.005 0.002 + 198 (0.040) 0.002 0.002 0.004 0.917 + 185 (0.038) 0.002 0.002 0.004 0.044 + +Locus 3 : L3 +3 alleles +0.0% missing data + 266 (0.835) 0.932 0.993 0.968 0.035 + 272 (0.098) 0.066 0.004 0.025 0.004 + 278 (0.067) 0.003 0.003 0.007 0.961 + +Locus 4 : L4 +19 alleles +0.0% missing data + 164 (0.101) 0.127 0.165 0.087 0.004 + 173 (0.104) 0.572 0.004 0.428 0.004 + 182 (0.045) 0.196 0.002 0.005 0.002 + 170 (0.054) 0.016 0.043 0.006 0.002 + 200 (0.045) 0.002 0.002 0.053 0.002 + 202 (0.040) 0.002 0.002 0.020 0.002 + 176 (0.040) 0.002 0.002 0.020 0.002 + 185 (0.042) 0.062 0.002 0.005 0.002 + 167 (0.066) 0.003 0.062 0.072 0.003 + 158 (0.073) 0.003 0.063 0.169 0.003 + 155 (0.062) 0.003 0.045 0.053 0.003 + 152 (0.055) 0.002 0.183 0.020 0.002 + 179 (0.040) 0.002 0.002 0.020 0.002 + 145 (0.041) 0.002 0.002 0.021 0.002 + 149 (0.043) 0.002 0.199 0.005 0.002 + 161 (0.042) 0.002 0.219 0.005 0.002 + 136 (0.038) 0.002 0.002 0.004 0.874 + 101 (0.036) 0.001 0.002 0.004 0.044 + 139 (0.036) 0.001 0.002 0.004 0.044 + +Locus 5 : L5 +24 alleles +0.0% missing data + 182 (0.058) 0.099 0.002 0.063 0.090 + 188 (0.032) 0.092 0.001 0.004 0.001 + 185 (0.043) 0.185 0.002 0.033 0.002 + 194 (0.041) 0.060 0.002 0.022 0.002 + 209 (0.029) 0.016 0.001 0.003 0.001 + 191 (0.044) 0.048 0.002 0.035 0.002 + 160 (0.067) 0.026 0.062 0.045 0.268 + 200 (0.040) 0.047 0.002 0.020 0.002 + 173 (0.049) 0.155 0.002 0.018 0.089 + 176 (0.040) 0.049 0.002 0.018 0.002 + 169 (0.040) 0.012 0.002 0.057 0.002 + 131 (0.029) 0.001 0.001 0.019 0.001 + 166 (0.035) 0.001 0.001 0.100 0.001 + 154 (0.047) 0.002 0.061 0.101 0.002 + 144 (0.050) 0.002 0.206 0.112 0.002 + 157 (0.045) 0.002 0.101 0.053 0.002 + 203 (0.034) 0.004 0.002 0.032 0.001 + 147 (0.047) 0.002 0.060 0.103 0.002 + 134 (0.066) 0.113 0.283 0.078 0.003 + 141 (0.044) 0.077 0.120 0.005 0.002 + 206 (0.033) 0.001 0.001 0.068 0.001 + 151 (0.030) 0.001 0.060 0.003 0.001 + 137 (0.029) 0.001 0.021 0.003 0.001 + 179 (0.028) 0.001 0.001 0.003 0.520 + +Locus 6 : L6 +6 alleles +11.6% missing data + 177 (0.216) 0.300 0.109 0.081 0.225 + 165 (0.225) 0.229 0.028 0.174 0.231 + 171 (0.340) 0.463 0.014 0.721 0.343 + 175 (0.078) 0.003 0.543 0.008 0.072 + 183 (0.071) 0.003 0.163 0.008 0.065 + 179 (0.070) 0.003 0.143 0.008 0.064 + +Locus 7 : L7 +10 alleles +0.0% missing data + 187 (0.178) 0.360 0.007 0.444 0.007 + 191 (0.118) 0.292 0.005 0.092 0.005 + 183 (0.186) 0.022 0.486 0.321 0.008 + 195 (0.066) 0.257 0.003 0.009 0.003 + 199 (0.098) 0.051 0.023 0.025 0.004 + 180 (0.085) 0.004 0.063 0.041 0.004 + 203 (0.087) 0.004 0.103 0.041 0.004 + 206 (0.074) 0.005 0.167 0.016 0.003 + 214 (0.058) 0.002 0.140 0.006 0.002 + 138 (0.051) 0.002 0.002 0.006 0.961 + +Locus 8 : L8 +7 alleles +0.0% missing data + 151 (0.402) 0.745 0.693 0.462 0.017 + 148 (0.105) 0.099 0.024 0.022 0.004 + 145 (0.078) 0.004 0.003 0.021 0.962 + 157 (0.057) 0.003 0.002 0.022 0.002 + 155 (0.122) 0.141 0.005 0.093 0.005 + 135 (0.070) 0.003 0.003 0.073 0.003 + 141 (0.164) 0.007 0.269 0.306 0.007 + +Locus 9 : L9 +10 alleles +0.0% missing data + 138 (0.194) 0.769 0.008 0.295 0.008 + 140 (0.063) 0.092 0.003 0.007 0.003 + 147 (0.140) 0.006 0.006 0.270 0.965 + 142 (0.145) 0.113 0.346 0.043 0.006 + 145 (0.132) 0.006 0.107 0.189 0.005 + 136 (0.073) 0.003 0.003 0.088 0.003 + 134 (0.062) 0.003 0.003 0.039 0.003 + 132 (0.065) 0.003 0.003 0.055 0.003 + 153 (0.066) 0.003 0.420 0.007 0.003 + 149 (0.060) 0.002 0.102 0.007 0.002 + +Locus 10 : L10 +7 alleles +0.0% missing data + 313 (0.082) 0.196 0.003 0.011 0.003 + 317 (0.331) 0.707 0.014 0.659 0.014 + 321 (0.119) 0.035 0.005 0.077 0.005 + 319 (0.170) 0.035 0.007 0.099 0.446 + 325 (0.062) 0.017 0.003 0.007 0.003 + 306 (0.174) 0.007 0.966 0.140 0.007 + 324 (0.063) 0.003 0.003 0.007 0.522 + +Locus 11 : L11 +8 alleles +0.0% missing data + 250 (0.220) 0.486 0.009 0.379 0.009 + 247 (0.070) 0.153 0.003 0.008 0.003 + 242 (0.073) 0.227 0.003 0.009 0.003 + 251 (0.112) 0.040 0.005 0.086 0.005 + 245 (0.200) 0.080 0.108 0.168 0.008 + 257 (0.066) 0.003 0.003 0.039 0.003 + 243 (0.160) 0.007 0.865 0.045 0.965 + 253 (0.099) 0.004 0.004 0.267 0.004 + +Locus 12 : L12 +4 alleles +0.0% missing data + 204 (0.818) 0.963 0.833 0.979 0.950 + 180 (0.062) 0.032 0.003 0.007 0.003 + 218 (0.065) 0.003 0.162 0.007 0.003 + 210 (0.055) 0.002 0.002 0.006 0.045 + +Locus 13 : L13 +6 alleles +0.0% missing data + 260 (0.642) 0.932 0.886 0.843 0.856 + 263 (0.138) 0.029 0.006 0.133 0.093 + 257 (0.056) 0.032 0.002 0.006 0.002 + 269 (0.058) 0.002 0.082 0.006 0.002 + 275 (0.054) 0.002 0.022 0.006 0.002 + 246 (0.051) 0.002 0.002 0.006 0.045 + +Locus 14 : L14 +5 alleles +0.0% missing data + 157 (0.586) 0.947 0.884 0.366 0.983 + 146 (0.182) 0.042 0.008 0.532 0.007 + 153 (0.072) 0.003 0.003 0.055 0.003 + 155 (0.101) 0.005 0.084 0.041 0.004 + 163 (0.059) 0.002 0.022 0.006 0.002 + +Locus 15 : L15 +2 alleles +0.0% missing data + 243 (0.697) 0.985 0.029 0.774 0.950 + 238 (0.303) 0.015 0.971 0.226 0.050 + +Locus 16 : L16 +3 alleles +0.0% missing data + 173 (0.777) 0.901 0.873 0.766 0.991 + 165 (0.068) 0.093 0.003 0.008 0.003 + 169 (0.155) 0.006 0.124 0.227 0.006 + +Locus 17 : L17 +2 alleles +0.0% missing data + 171 (0.931) 0.997 0.997 0.992 0.039 + 168 (0.069) 0.003 0.003 0.008 0.961 + +Locus 18 : L18 +4 alleles +0.0% missing data + 286 (0.738) 0.824 0.970 0.926 0.030 + 287 (0.076) 0.169 0.003 0.008 0.003 + 283 (0.097) 0.004 0.023 0.043 0.004 + 290 (0.089) 0.004 0.004 0.023 0.962 + +Values of parameters used in structure: +DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_61, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=4, BURNIN=50000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/Admix_run_008_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,388 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + Code by J.K. Pritchard + Modified by Daniel Falush to + incorporate recombination breakpoints + Version 2.0 (July 2001) +---------------------------------------------------- + + + +Command line arguments: bin/structure.exe -m \mainparams -e \extraparams +Input File: \project_data + +Run parameters: + 95 individuals + 18 loci + 4 populations assumed + 50000 Burn-in period + 500000 Reps + + +-------------------------------------------- +Proportion of membership of each pre-defined + population in each of the 4 clusters + +Given Inferred Clusters Number of + Pop 1 2 3 4 Individuals + + 1: 0.003 0.005 0.991 0.001 6 + 2: 0.002 0.006 0.990 0.002 6 + 3: 0.001 0.002 0.995 0.001 6 + 4: 0.003 0.027 0.968 0.002 6 + 5: 0.003 0.784 0.211 0.002 6 + 6: 0.016 0.877 0.104 0.003 6 + 7: 0.002 0.006 0.991 0.001 6 + 8: 0.003 0.974 0.021 0.002 6 + 9: 0.006 0.989 0.003 0.002 6 + 10: 0.021 0.940 0.035 0.004 6 + 11: 0.988 0.009 0.002 0.001 6 + 12: 0.995 0.002 0.002 0.001 6 + 13: 0.994 0.003 0.002 0.001 6 + 14: 0.995 0.002 0.002 0.001 6 + 15: 0.001 0.001 0.001 0.997 6 + 16: 0.002 0.002 0.001 0.995 5 +-------------------------------------------- + +Allele-freq. divergence among pops (Kullback-Leibler distance), +computed using point estimates of P. + + 1 2 3 4 + 1 - 1.05 1.91 2.62 + 2 1.36 - 0.74 2.31 + 3 1.82 0.54 - 2.44 + 4 3.49 2.55 3.37 - +-------------------------------------------- +Estimated Ln Prob of Data = -2773.4 +Mean value of ln likelihood = -2678.8 +Variance of ln likelihood = 189.2 +Mean value of alpha = 0.0271 + +Mean value of Fst_1 = 0.3299 +Mean value of Fst_2 = 0.1302 +Mean value of Fst_3 = 0.2744 +Mean value of Fst_4 = 0.5177 + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters + 1 A01 (0) 1 : 0.002 0.003 0.994 0.001 + 2 A02 (0) 1 : 0.001 0.003 0.995 0.001 + 3 A03 (0) 1 : 0.008 0.010 0.981 0.001 + 4 A04 (0) 1 : 0.002 0.002 0.995 0.001 + 5 A05 (0) 1 : 0.002 0.003 0.994 0.001 + 6 A24 (0) 1 : 0.002 0.007 0.989 0.002 + 7 B466 (0) 2 : 0.002 0.005 0.993 0.001 + 8 B479 (0) 2 : 0.002 0.003 0.994 0.001 + 9 B480 (0) 2 : 0.002 0.006 0.991 0.001 + 10 B482 (0) 2 : 0.003 0.009 0.985 0.003 + 11 B484 (0) 2 : 0.002 0.011 0.985 0.003 + 12 B485 (0) 2 : 0.002 0.004 0.993 0.001 + 13 C02 (0) 3 : 0.001 0.002 0.995 0.001 + 14 C05 (0) 3 : 0.001 0.002 0.995 0.001 + 15 C14 (0) 3 : 0.001 0.002 0.995 0.001 + 16 C30 (0) 3 : 0.002 0.002 0.995 0.001 + 17 C31 (0) 3 : 0.001 0.002 0.995 0.001 + 18 C40 (0) 3 : 0.002 0.003 0.995 0.001 + 19 D08 (0) 4 : 0.001 0.007 0.990 0.002 + 20 D09 (0) 4 : 0.003 0.006 0.990 0.001 + 21 D13 (0) 4 : 0.002 0.008 0.988 0.002 + 22 D21 (0) 4 : 0.007 0.015 0.976 0.002 + 23 D25 (0) 4 : 0.003 0.012 0.983 0.001 + 24 D30 (0) 4 : 0.004 0.113 0.882 0.001 + 25 E01 (0) 5 : 0.003 0.953 0.041 0.003 + 26 E02 (0) 5 : 0.003 0.988 0.008 0.001 + 27 E03 (0) 5 : 0.003 0.261 0.735 0.002 + 28 E04 (0) 5 : 0.003 0.663 0.332 0.001 + 29 E05 (0) 5 : 0.002 0.884 0.113 0.001 + 30 E06 (0) 5 : 0.005 0.957 0.037 0.001 + 31 F03 (0) 6 : 0.003 0.921 0.066 0.010 + 32 F05 (0) 6 : 0.011 0.948 0.040 0.001 + 33 F08 (0) 6 : 0.006 0.970 0.020 0.004 + 34 F14 (0) 6 : 0.069 0.458 0.472 0.001 + 35 F25 (0) 6 : 0.003 0.981 0.015 0.001 + 36 F35 (0) 6 : 0.002 0.986 0.010 0.001 + 37 B360 (0) 7 : 0.002 0.004 0.993 0.001 + 38 B365 (0) 7 : 0.002 0.003 0.993 0.001 + 39 B367 (0) 7 : 0.001 0.018 0.980 0.001 + 40 B370 (0) 7 : 0.002 0.003 0.994 0.001 + 41 B371 (0) 7 : 0.002 0.003 0.994 0.001 + 42 B372 (0) 7 : 0.002 0.003 0.994 0.001 + 43 B341 (0) 8 : 0.004 0.975 0.017 0.004 + 44 B342 (0) 8 : 0.003 0.931 0.065 0.001 + 45 B343 (0) 8 : 0.002 0.980 0.016 0.001 + 46 B345 (0) 8 : 0.003 0.986 0.010 0.001 + 47 B346 (0) 8 : 0.002 0.989 0.008 0.001 + 48 B349 (0) 8 : 0.002 0.985 0.012 0.001 + 49 B121 (0) 9 : 0.004 0.992 0.003 0.002 + 50 B122 (0) 9 : 0.010 0.986 0.002 0.001 + 51 B125 (0) 9 : 0.003 0.993 0.002 0.002 + 52 B127 (0) 9 : 0.003 0.993 0.003 0.001 + 53 B128 (0) 9 : 0.009 0.986 0.004 0.002 + 54 B129 (0) 9 : 0.010 0.985 0.003 0.002 + 55 B306 (0) 10 : 0.002 0.987 0.002 0.009 + 56 B310 (0) 10 : 0.024 0.973 0.002 0.001 + 57 B312 (0) 10 : 0.030 0.935 0.033 0.002 + 58 B313 (0) 10 : 0.017 0.973 0.003 0.007 + 59 B317 (0) 10 : 0.047 0.788 0.164 0.001 + 60 B318 (0) 10 : 0.007 0.985 0.005 0.003 + 61 G19 (0) 11 : 0.995 0.002 0.002 0.001 + 62 G20 (0) 11 : 0.995 0.002 0.002 0.001 + 63 G21 (0) 11 : 0.995 0.002 0.002 0.001 + 64 G22 (0) 11 : 0.957 0.038 0.003 0.001 + 65 G23 (0) 11 : 0.993 0.004 0.002 0.001 + 66 G24 (0) 11 : 0.994 0.003 0.002 0.001 + 67 H01 (0) 12 : 0.995 0.002 0.002 0.001 + 68 H02 (0) 12 : 0.995 0.003 0.001 0.001 + 69 H03 (0) 12 : 0.995 0.002 0.002 0.001 + 70 H04 (0) 12 : 0.995 0.002 0.002 0.001 + 71 H05 (0) 12 : 0.995 0.002 0.001 0.001 + 72 H12 (0) 12 : 0.996 0.001 0.001 0.001 + 73 I20 (0) 13 : 0.996 0.002 0.002 0.001 + 74 I21 (0) 13 : 0.996 0.002 0.002 0.001 + 75 I23 (0) 13 : 0.990 0.004 0.004 0.002 + 76 I24 (0) 13 : 0.995 0.002 0.002 0.001 + 77 I25 (0) 13 : 0.993 0.005 0.001 0.001 + 78 I26 (0) 13 : 0.996 0.002 0.002 0.001 + 79 J02 (0) 14 : 0.996 0.002 0.001 0.001 + 80 J04 (0) 14 : 0.995 0.002 0.002 0.001 + 81 J05 (0) 14 : 0.994 0.003 0.002 0.001 + 82 J08 (0) 14 : 0.992 0.003 0.004 0.001 + 83 J09 (0) 14 : 0.995 0.002 0.002 0.001 + 84 J10 (0) 14 : 0.996 0.002 0.001 0.001 + 85 K20 (5) 15 : 0.001 0.001 0.001 0.996 + 86 K33 (5) 15 : 0.001 0.001 0.001 0.997 + 87 K34 (5) 15 : 0.001 0.001 0.001 0.997 + 88 K35 (5) 15 : 0.001 0.001 0.001 0.996 + 89 K53 (5) 15 : 0.001 0.001 0.001 0.997 + 90 K56 (5) 15 : 0.001 0.001 0.001 0.997 + 91 L04 (5) 16 : 0.001 0.001 0.001 0.997 + 92 L07 (5) 16 : 0.001 0.001 0.001 0.997 + 93 L14 (5) 16 : 0.006 0.004 0.001 0.989 + 94 L26 (5) 16 : 0.001 0.001 0.001 0.996 + 95 L27 (5) 16 : 0.001 0.001 0.001 0.996 + + +Estimated Allele Frequencies in each population +First column gives estimated ancestral frequencies + + +Locus 1 : L1 +7 alleles +0.0% missing data + 118 (0.461) 0.478 0.807 0.704 0.019 + 127 (0.087) 0.004 0.022 0.186 0.004 + 130 (0.110) 0.005 0.027 0.034 0.487 + 114 (0.083) 0.003 0.023 0.065 0.003 + 122 (0.117) 0.244 0.092 0.005 0.005 + 110 (0.085) 0.265 0.022 0.004 0.004 + 135 (0.056) 0.002 0.006 0.002 0.479 + +Locus 2 : L2 +15 alleles +0.0% missing data + 228 (0.072) 0.003 0.049 0.246 0.003 + 222 (0.114) 0.036 0.279 0.079 0.005 + 225 (0.094) 0.004 0.203 0.286 0.004 + 234 (0.056) 0.002 0.022 0.017 0.002 + 219 (0.117) 0.146 0.112 0.224 0.005 + 213 (0.122) 0.610 0.111 0.117 0.005 + 204 (0.041) 0.002 0.005 0.016 0.002 + 216 (0.064) 0.083 0.039 0.003 0.003 + 195 (0.044) 0.002 0.037 0.002 0.002 + 231 (0.049) 0.002 0.070 0.002 0.002 + 210 (0.063) 0.043 0.038 0.003 0.003 + 240 (0.041) 0.002 0.021 0.002 0.002 + 207 (0.042) 0.062 0.005 0.002 0.002 + 198 (0.040) 0.002 0.004 0.002 0.917 + 185 (0.038) 0.002 0.004 0.002 0.044 + +Locus 3 : L3 +3 alleles +0.0% missing data + 266 (0.835) 0.993 0.968 0.932 0.035 + 272 (0.098) 0.004 0.025 0.066 0.004 + 278 (0.067) 0.003 0.007 0.003 0.961 + +Locus 4 : L4 +19 alleles +0.0% missing data + 164 (0.100) 0.165 0.087 0.127 0.004 + 173 (0.103) 0.004 0.429 0.572 0.004 + 182 (0.044) 0.002 0.005 0.196 0.002 + 170 (0.054) 0.043 0.006 0.016 0.002 + 200 (0.044) 0.002 0.053 0.002 0.002 + 202 (0.041) 0.002 0.020 0.002 0.002 + 176 (0.040) 0.002 0.020 0.002 0.002 + 185 (0.042) 0.002 0.005 0.062 0.002 + 167 (0.064) 0.062 0.071 0.003 0.003 + 158 (0.075) 0.063 0.169 0.003 0.003 + 155 (0.062) 0.045 0.052 0.003 0.003 + 152 (0.055) 0.183 0.020 0.002 0.002 + 179 (0.039) 0.002 0.020 0.002 0.002 + 145 (0.040) 0.002 0.020 0.002 0.002 + 149 (0.042) 0.199 0.005 0.002 0.002 + 161 (0.042) 0.219 0.005 0.002 0.002 + 136 (0.038) 0.002 0.004 0.002 0.874 + 101 (0.037) 0.002 0.004 0.002 0.044 + 139 (0.036) 0.002 0.004 0.001 0.045 + +Locus 5 : L5 +24 alleles +0.0% missing data + 182 (0.058) 0.002 0.063 0.099 0.090 + 188 (0.031) 0.001 0.003 0.091 0.001 + 185 (0.044) 0.002 0.033 0.185 0.002 + 194 (0.041) 0.002 0.022 0.060 0.002 + 209 (0.030) 0.001 0.003 0.016 0.001 + 191 (0.043) 0.002 0.035 0.048 0.002 + 160 (0.068) 0.062 0.045 0.026 0.267 + 200 (0.040) 0.002 0.020 0.047 0.002 + 173 (0.050) 0.002 0.018 0.155 0.090 + 176 (0.040) 0.002 0.018 0.049 0.002 + 169 (0.041) 0.002 0.057 0.012 0.002 + 131 (0.030) 0.001 0.019 0.002 0.001 + 166 (0.035) 0.001 0.100 0.001 0.001 + 154 (0.047) 0.061 0.101 0.002 0.002 + 144 (0.050) 0.206 0.112 0.002 0.002 + 157 (0.045) 0.101 0.053 0.002 0.002 + 203 (0.034) 0.002 0.032 0.004 0.001 + 147 (0.046) 0.060 0.102 0.002 0.002 + 134 (0.066) 0.284 0.078 0.113 0.003 + 141 (0.044) 0.120 0.005 0.077 0.002 + 206 (0.033) 0.001 0.068 0.001 0.001 + 151 (0.029) 0.060 0.003 0.001 0.001 + 137 (0.029) 0.021 0.003 0.001 0.001 + 179 (0.028) 0.001 0.003 0.001 0.520 + +Locus 6 : L6 +6 alleles +11.6% missing data + 177 (0.214) 0.109 0.081 0.299 0.223 + 165 (0.226) 0.028 0.174 0.228 0.231 + 171 (0.342) 0.014 0.721 0.463 0.345 + 175 (0.078) 0.543 0.008 0.003 0.072 + 183 (0.071) 0.163 0.008 0.003 0.065 + 179 (0.070) 0.143 0.008 0.003 0.064 + +Locus 7 : L7 +10 alleles +0.0% missing data + 187 (0.181) 0.008 0.444 0.361 0.008 + 191 (0.116) 0.005 0.092 0.292 0.005 + 183 (0.185) 0.486 0.321 0.022 0.008 + 195 (0.066) 0.003 0.009 0.257 0.003 + 199 (0.098) 0.023 0.025 0.051 0.004 + 180 (0.085) 0.063 0.041 0.004 0.004 + 203 (0.087) 0.103 0.041 0.004 0.004 + 206 (0.071) 0.167 0.016 0.005 0.003 + 214 (0.058) 0.140 0.006 0.002 0.002 + 138 (0.053) 0.002 0.006 0.002 0.961 + +Locus 8 : L8 +7 alleles +0.0% missing data + 151 (0.398) 0.693 0.462 0.745 0.016 + 148 (0.107) 0.024 0.022 0.099 0.004 + 145 (0.079) 0.003 0.022 0.004 0.962 + 157 (0.057) 0.002 0.022 0.003 0.002 + 155 (0.123) 0.005 0.093 0.141 0.005 + 135 (0.071) 0.003 0.073 0.003 0.003 + 141 (0.166) 0.269 0.306 0.007 0.007 + +Locus 9 : L9 +10 alleles +0.0% missing data + 138 (0.192) 0.008 0.295 0.769 0.008 + 140 (0.063) 0.003 0.007 0.092 0.003 + 147 (0.141) 0.006 0.270 0.007 0.965 + 142 (0.146) 0.346 0.044 0.113 0.006 + 145 (0.131) 0.107 0.189 0.006 0.005 + 136 (0.072) 0.003 0.088 0.003 0.003 + 134 (0.062) 0.003 0.039 0.003 0.003 + 132 (0.066) 0.003 0.055 0.003 0.003 + 153 (0.065) 0.420 0.007 0.003 0.003 + 149 (0.060) 0.102 0.007 0.002 0.002 + +Locus 10 : L10 +7 alleles +0.0% missing data + 313 (0.081) 0.003 0.011 0.196 0.003 + 317 (0.331) 0.014 0.659 0.707 0.014 + 321 (0.118) 0.005 0.077 0.035 0.005 + 319 (0.169) 0.007 0.098 0.035 0.446 + 325 (0.063) 0.003 0.007 0.017 0.003 + 306 (0.175) 0.966 0.140 0.007 0.007 + 324 (0.063) 0.003 0.007 0.003 0.523 + +Locus 11 : L11 +8 alleles +0.0% missing data + 250 (0.222) 0.009 0.379 0.486 0.009 + 247 (0.069) 0.003 0.008 0.153 0.003 + 242 (0.073) 0.003 0.009 0.227 0.003 + 251 (0.113) 0.005 0.086 0.040 0.005 + 245 (0.198) 0.108 0.167 0.080 0.008 + 257 (0.066) 0.003 0.039 0.003 0.003 + 243 (0.162) 0.865 0.045 0.007 0.965 + 253 (0.098) 0.004 0.267 0.004 0.004 + +Locus 12 : L12 +4 alleles +0.0% missing data + 204 (0.819) 0.834 0.980 0.963 0.950 + 180 (0.061) 0.003 0.007 0.032 0.002 + 218 (0.065) 0.162 0.007 0.003 0.003 + 210 (0.054) 0.002 0.006 0.002 0.045 + +Locus 13 : L13 +6 alleles +0.0% missing data + 260 (0.639) 0.886 0.842 0.932 0.855 + 263 (0.140) 0.006 0.133 0.029 0.093 + 257 (0.057) 0.002 0.006 0.032 0.002 + 269 (0.059) 0.082 0.006 0.002 0.002 + 275 (0.054) 0.022 0.006 0.002 0.002 + 246 (0.051) 0.002 0.006 0.002 0.045 + +Locus 14 : L14 +5 alleles +0.0% missing data + 157 (0.590) 0.884 0.367 0.947 0.983 + 146 (0.179) 0.008 0.532 0.042 0.007 + 153 (0.071) 0.003 0.055 0.003 0.003 + 155 (0.101) 0.084 0.041 0.005 0.004 + 163 (0.058) 0.022 0.006 0.002 0.002 + +Locus 15 : L15 +2 alleles +0.0% missing data + 243 (0.697) 0.029 0.774 0.985 0.950 + 238 (0.303) 0.971 0.226 0.015 0.050 + +Locus 16 : L16 +3 alleles +0.0% missing data + 173 (0.778) 0.873 0.766 0.901 0.991 + 165 (0.068) 0.003 0.008 0.093 0.003 + 169 (0.154) 0.125 0.227 0.006 0.006 + +Locus 17 : L17 +2 alleles +0.0% missing data + 171 (0.931) 0.997 0.992 0.997 0.039 + 168 (0.069) 0.003 0.008 0.003 0.961 + +Locus 18 : L18 +4 alleles +0.0% missing data + 286 (0.737) 0.970 0.926 0.824 0.030 + 287 (0.076) 0.003 0.008 0.169 0.003 + 283 (0.097) 0.023 0.043 0.004 0.004 + 290 (0.090) 0.004 0.023 0.004 0.962 + +Values of parameters used in structure: +DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_66, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=4, BURNIN=50000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/K1ReRun_run_1_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,384 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard and Falush + Version 2.2 (March 2007) +---------------------------------------------------- + + + +Command line arguments: bin/structure.exe -m "/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/K1ReRun/mainparams" -e "/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/K1ReRun/extraparams" +Input File: \project_data + +Run parameters: + 95 individuals + 18 loci + 1 populations assumed + 50000 Burn-in period + 500000 Reps + + +-------------------------------------------- +Proportion of membership of each pre-defined + population in each of the 1 clusters + +Given Inferred Clusters Number of + Pop 1 Individuals + + 1: 1.000 6 + 2: 1.000 6 + 3: 1.000 6 + 4: 1.000 6 + 5: 1.000 6 + 6: 1.000 6 + 7: 1.000 6 + 8: 1.000 6 + 9: 1.000 6 + 10: 1.000 6 + 11: 1.000 6 + 12: 1.000 6 + 13: 1.000 6 + 14: 1.000 6 + 15: 1.000 6 + 16: 1.000 5 +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 + 1 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : -122.5714 + +-------------------------------------------- +Estimated Ln Prob of Data = -4329.9 +Mean value of ln likelihood = -4300.3 +Variance of ln likelihood = 59.2 + +Mean value of Fst_1 = 0.0012 + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters + 1 99-70-01 (0) 1 : 1.000 + 2 99-70-02 (0) 1 : 1.000 + 3 99-70-03 (0) 1 : 1.000 + 4 99-70-04 (0) 1 : 1.000 + 5 99-70-05 (0) 1 : 1.000 + 6 99-70-24 (0) 1 : 1.000 + 7 En_466 (0) 2 : 1.000 + 8 En_479 (0) 2 : 1.000 + 9 En_480 (0) 2 : 1.000 + 10 En_482 (0) 2 : 1.000 + 11 En_484 (0) 2 : 1.000 + 12 En_485 (0) 2 : 1.000 + 13 99-69-02 (0) 3 : 1.000 + 14 99-69-05 (0) 3 : 1.000 + 15 99-69-14 (0) 3 : 1.000 + 16 99-69-30 (0) 3 : 1.000 + 17 99-69-31 (0) 3 : 1.000 + 18 99-69-40 (0) 3 : 1.000 + 19 99-72-08 (0) 4 : 1.000 + 20 99-72-09 (0) 4 : 1.000 + 21 99-72-13 (0) 4 : 1.000 + 22 99-72-21 (0) 4 : 1.000 + 23 99-72-25 (0) 4 : 1.000 + 24 99-72-30 (0) 4 : 1.000 + 25 99-78-01 (0) 5 : 1.000 + 26 99-78-02 (0) 5 : 1.000 + 27 99-78-03 (0) 5 : 1.000 + 28 99-78-04 (0) 5 : 1.000 + 29 99-78-05 (0) 5 : 1.000 + 30 99-78-06 (0) 5 : 1.000 + 31 99-83-03 (0) 6 : 1.000 + 32 99-83-05 (0) 6 : 1.000 + 33 99-83-08 (0) 6 : 1.000 + 34 99-83-14 (0) 6 : 1.000 + 35 99-83-25 (0) 6 : 1.000 + 36 99-83-35 (0) 6 : 1.000 + 37 En_360 (0) 7 : 1.000 + 38 En_365 (0) 7 : 1.000 + 39 En_367 (0) 7 : 1.000 + 40 En_370 (0) 7 : 1.000 + 41 En_371 (0) 7 : 1.000 + 42 En_372 (0) 7 : 1.000 + 43 En_341 (0) 8 : 1.000 + 44 En_342 (0) 8 : 1.000 + 45 En_343 (0) 8 : 1.000 + 46 En_345 (0) 8 : 1.000 + 47 En_346 (0) 8 : 1.000 + 48 En_349 (0) 8 : 1.000 + 49 En_121 (0) 9 : 1.000 + 50 En_122 (0) 9 : 1.000 + 51 En_125 (0) 9 : 1.000 + 52 En_127 (0) 9 : 1.000 + 53 En_128 (0) 9 : 1.000 + 54 En_129 (0) 9 : 1.000 + 55 En_306 (0) 10 : 1.000 + 56 En_310 (0) 10 : 1.000 + 57 En_312 (0) 10 : 1.000 + 58 En_313 (0) 10 : 1.000 + 59 En_317 (0) 10 : 1.000 + 60 En_318 (0) 10 : 1.000 + 61 99-45-19 (0) 11 : 1.000 + 62 99-45-20 (0) 11 : 1.000 + 63 99-45-21 (0) 11 : 1.000 + 64 99-45-22 (0) 11 : 1.000 + 65 99-45-23 (0) 11 : 1.000 + 66 99-45-24 (0) 11 : 1.000 + 67 98-123-01 (0) 12 : 1.000 + 68 98-123-02 (0) 12 : 1.000 + 69 98-123-03 (0) 12 : 1.000 + 70 98-123-04 (0) 12 : 1.000 + 71 98-123-05 (0) 12 : 1.000 + 72 98-123-12 (0) 12 : 1.000 + 73 99-93-20 (0) 13 : 1.000 + 74 99-93-21 (0) 13 : 1.000 + 75 99-93-23 (0) 13 : 1.000 + 76 99-93-24 (0) 13 : 1.000 + 77 99-93-25 (0) 13 : 1.000 + 78 99-93-26 (0) 13 : 1.000 + 79 99-21-02 (0) 14 : 1.000 + 80 99-21-04 (0) 14 : 1.000 + 81 99-21-05 (0) 14 : 1.000 + 82 99-21-08 (0) 14 : 1.000 + 83 99-21-09 (0) 14 : 1.000 + 84 99-21-10 (0) 14 : 1.000 + 85 01-58-20 (5) 15 : 1.000 + 86 01-58-33 (5) 15 : 1.000 + 87 01-58-34 (5) 15 : 1.000 + 88 01-58-35 (5) 15 : 1.000 + 89 01-58-53 (5) 15 : 1.000 + 90 01-58-56 (5) 15 : 1.000 + 91 98-116-04 (5) 16 : 1.000 + 92 98-116-07 (5) 16 : 1.000 + 93 98-116-14 (5) 16 : 1.000 + 94 98-116-26 (5) 16 : 1.000 + 95 98-116-27 (5) 16 : 1.000 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : TAGA40 +7 alleles +0.0% missing data + 118 (0.590) 0.594 + 127 (0.072) 0.071 + 130 (0.077) 0.076 + 114 (0.031) 0.030 + 122 (0.092) 0.091 + 110 (0.077) 0.076 + 135 (0.062) 0.061 + +Locus 2 : B113 +15 alleles +0.0% missing data + 228 (0.097) 0.098 + 222 (0.116) 0.117 + 225 (0.154) 0.156 + 234 (0.015) 0.015 + 219 (0.140) 0.142 + 213 (0.217) 0.220 + 204 (0.011) 0.010 + 216 (0.035) 0.034 + 195 (0.016) 0.015 + 231 (0.025) 0.024 + 210 (0.025) 0.024 + 240 (0.011) 0.010 + 207 (0.020) 0.020 + 198 (0.106) 0.107 + 185 (0.011) 0.010 + +Locus 3 : B117 +3 alleles +0.0% missing data + 266 (0.848) 0.850 + 272 (0.032) 0.031 + 278 (0.120) 0.119 + +Locus 4 : ATG16.1 +19 alleles +0.0% missing data + 164 (0.104) 0.105 + 173 (0.305) 0.311 + 182 (0.067) 0.067 + 170 (0.020) 0.019 + 200 (0.020) 0.019 + 202 (0.010) 0.009 + 176 (0.010) 0.009 + 185 (0.025) 0.024 + 167 (0.039) 0.038 + 158 (0.067) 0.067 + 155 (0.029) 0.029 + 152 (0.052) 0.052 + 179 (0.011) 0.010 + 145 (0.011) 0.010 + 149 (0.053) 0.053 + 161 (0.057) 0.057 + 136 (0.100) 0.101 + 101 (0.010) 0.009 + 139 (0.010) 0.009 + +Locus 5 : ATG17 +24 alleles +0.0% missing data + 182 (0.060) 0.061 + 188 (0.033) 0.033 + 185 (0.069) 0.070 + 194 (0.028) 0.028 + 209 (0.010) 0.009 + 191 (0.029) 0.028 + 160 (0.065) 0.065 + 200 (0.024) 0.024 + 173 (0.065) 0.065 + 176 (0.024) 0.023 + 169 (0.024) 0.023 + 131 (0.010) 0.009 + 166 (0.033) 0.033 + 154 (0.046) 0.047 + 144 (0.083) 0.084 + 157 (0.042) 0.042 + 203 (0.015) 0.014 + 147 (0.046) 0.047 + 134 (0.124) 0.126 + 141 (0.056) 0.056 + 206 (0.024) 0.023 + 151 (0.019) 0.019 + 137 (0.010) 0.009 + 179 (0.060) 0.061 + +Locus 6 : ENE2 +6 alleles +11.6% missing data + 177 (0.166) 0.166 + 165 (0.149) 0.149 + 171 (0.424) 0.426 + 175 (0.161) 0.161 + 183 (0.053) 0.052 + 179 (0.047) 0.046 + +Locus 7 : CATG2 +10 alleles +0.0% missing data + 187 (0.254) 0.255 + 191 (0.124) 0.125 + 183 (0.223) 0.225 + 195 (0.090) 0.090 + 199 (0.031) 0.030 + 180 (0.031) 0.030 + 203 (0.041) 0.040 + 206 (0.050) 0.050 + 214 (0.041) 0.040 + 138 (0.115) 0.115 + +Locus 8 : ATG13 +7 alleles +0.0% missing data + 151 (0.556) 0.559 + 148 (0.046) 0.046 + 145 (0.121) 0.121 + 157 (0.011) 0.010 + 155 (0.077) 0.076 + 135 (0.026) 0.025 + 141 (0.162) 0.162 + +Locus 9 : TAGA11 +10 alleles +0.0% missing data + 138 (0.342) 0.345 + 140 (0.036) 0.035 + 147 (0.194) 0.195 + 142 (0.135) 0.135 + 145 (0.085) 0.085 + 136 (0.031) 0.030 + 134 (0.016) 0.015 + 132 (0.021) 0.020 + 153 (0.110) 0.110 + 149 (0.031) 0.030 + +Locus 10 : A018 +7 alleles +0.0% missing data + 313 (0.072) 0.071 + 317 (0.434) 0.436 + 321 (0.037) 0.036 + 319 (0.092) 0.092 + 325 (0.011) 0.010 + 306 (0.288) 0.289 + 324 (0.067) 0.066 + +Locus 11 : A019 +8 alleles +0.0% missing data + 250 (0.276) 0.278 + 247 (0.056) 0.056 + 242 (0.081) 0.081 + 251 (0.041) 0.040 + 245 (0.101) 0.101 + 257 (0.016) 0.015 + 243 (0.341) 0.343 + 253 (0.087) 0.086 + +Locus 12 : ATG26 +4 alleles +0.0% missing data + 204 (0.925) 0.928 + 180 (0.017) 0.015 + 218 (0.047) 0.046 + 210 (0.011) 0.010 + +Locus 13 : C111 +6 alleles +0.0% missing data + 260 (0.873) 0.878 + 263 (0.062) 0.061 + 257 (0.016) 0.015 + 269 (0.026) 0.025 + 275 (0.011) 0.010 + 246 (0.011) 0.010 + +Locus 14 : ENE3 +5 alleles +0.0% missing data + 157 (0.745) 0.749 + 146 (0.185) 0.185 + 153 (0.022) 0.021 + 155 (0.037) 0.036 + 163 (0.011) 0.010 + +Locus 15 : ENE4 +2 alleles +0.0% missing data + 243 (0.672) 0.672 + 238 (0.328) 0.328 + +Locus 16 : CATG14 +3 alleles +0.0% missing data + 173 (0.858) 0.860 + 165 (0.037) 0.036 + 169 (0.105) 0.104 + +Locus 17 : ATG18 +2 alleles +0.0% missing data + 171 (0.880) 0.880 + 168 (0.120) 0.120 + +Locus 18 : C114 +4 alleles +0.0% missing data + 286 (0.791) 0.794 + 287 (0.063) 0.062 + 283 (0.022) 0.021 + 290 (0.125) 0.124 + +Values of parameters used in structure: +DATAFILE=/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/project_data, OUTFILE=/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/K1ReRun/Results/K1ReRun_run_1, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=1, BURNIN=50000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, SEED=1213373734, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/K1ReRun_run_2_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,384 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard and Falush + Version 2.2 (March 2007) +---------------------------------------------------- + + + +Command line arguments: bin/structure.exe -m "/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/K1ReRun/mainparams" -e "/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/K1ReRun/extraparams" +Input File: \project_data + +Run parameters: + 95 individuals + 18 loci + 1 populations assumed + 50000 Burn-in period + 500000 Reps + + +-------------------------------------------- +Proportion of membership of each pre-defined + population in each of the 1 clusters + +Given Inferred Clusters Number of + Pop 1 Individuals + + 1: 1.000 6 + 2: 1.000 6 + 3: 1.000 6 + 4: 1.000 6 + 5: 1.000 6 + 6: 1.000 6 + 7: 1.000 6 + 8: 1.000 6 + 9: 1.000 6 + 10: 1.000 6 + 11: 1.000 6 + 12: 1.000 6 + 13: 1.000 6 + 14: 1.000 6 + 15: 1.000 6 + 16: 1.000 5 +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 + 1 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : -122.5537 + +-------------------------------------------- +Estimated Ln Prob of Data = -4330.0 +Mean value of ln likelihood = -4300.2 +Variance of ln likelihood = 59.7 + +Mean value of Fst_1 = 0.0009 + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters + 1 99-70-01 (0) 1 : 1.000 + 2 99-70-02 (0) 1 : 1.000 + 3 99-70-03 (0) 1 : 1.000 + 4 99-70-04 (0) 1 : 1.000 + 5 99-70-05 (0) 1 : 1.000 + 6 99-70-24 (0) 1 : 1.000 + 7 En_466 (0) 2 : 1.000 + 8 En_479 (0) 2 : 1.000 + 9 En_480 (0) 2 : 1.000 + 10 En_482 (0) 2 : 1.000 + 11 En_484 (0) 2 : 1.000 + 12 En_485 (0) 2 : 1.000 + 13 99-69-02 (0) 3 : 1.000 + 14 99-69-05 (0) 3 : 1.000 + 15 99-69-14 (0) 3 : 1.000 + 16 99-69-30 (0) 3 : 1.000 + 17 99-69-31 (0) 3 : 1.000 + 18 99-69-40 (0) 3 : 1.000 + 19 99-72-08 (0) 4 : 1.000 + 20 99-72-09 (0) 4 : 1.000 + 21 99-72-13 (0) 4 : 1.000 + 22 99-72-21 (0) 4 : 1.000 + 23 99-72-25 (0) 4 : 1.000 + 24 99-72-30 (0) 4 : 1.000 + 25 99-78-01 (0) 5 : 1.000 + 26 99-78-02 (0) 5 : 1.000 + 27 99-78-03 (0) 5 : 1.000 + 28 99-78-04 (0) 5 : 1.000 + 29 99-78-05 (0) 5 : 1.000 + 30 99-78-06 (0) 5 : 1.000 + 31 99-83-03 (0) 6 : 1.000 + 32 99-83-05 (0) 6 : 1.000 + 33 99-83-08 (0) 6 : 1.000 + 34 99-83-14 (0) 6 : 1.000 + 35 99-83-25 (0) 6 : 1.000 + 36 99-83-35 (0) 6 : 1.000 + 37 En_360 (0) 7 : 1.000 + 38 En_365 (0) 7 : 1.000 + 39 En_367 (0) 7 : 1.000 + 40 En_370 (0) 7 : 1.000 + 41 En_371 (0) 7 : 1.000 + 42 En_372 (0) 7 : 1.000 + 43 En_341 (0) 8 : 1.000 + 44 En_342 (0) 8 : 1.000 + 45 En_343 (0) 8 : 1.000 + 46 En_345 (0) 8 : 1.000 + 47 En_346 (0) 8 : 1.000 + 48 En_349 (0) 8 : 1.000 + 49 En_121 (0) 9 : 1.000 + 50 En_122 (0) 9 : 1.000 + 51 En_125 (0) 9 : 1.000 + 52 En_127 (0) 9 : 1.000 + 53 En_128 (0) 9 : 1.000 + 54 En_129 (0) 9 : 1.000 + 55 En_306 (0) 10 : 1.000 + 56 En_310 (0) 10 : 1.000 + 57 En_312 (0) 10 : 1.000 + 58 En_313 (0) 10 : 1.000 + 59 En_317 (0) 10 : 1.000 + 60 En_318 (0) 10 : 1.000 + 61 99-45-19 (0) 11 : 1.000 + 62 99-45-20 (0) 11 : 1.000 + 63 99-45-21 (0) 11 : 1.000 + 64 99-45-22 (0) 11 : 1.000 + 65 99-45-23 (0) 11 : 1.000 + 66 99-45-24 (0) 11 : 1.000 + 67 98-123-01 (0) 12 : 1.000 + 68 98-123-02 (0) 12 : 1.000 + 69 98-123-03 (0) 12 : 1.000 + 70 98-123-04 (0) 12 : 1.000 + 71 98-123-05 (0) 12 : 1.000 + 72 98-123-12 (0) 12 : 1.000 + 73 99-93-20 (0) 13 : 1.000 + 74 99-93-21 (0) 13 : 1.000 + 75 99-93-23 (0) 13 : 1.000 + 76 99-93-24 (0) 13 : 1.000 + 77 99-93-25 (0) 13 : 1.000 + 78 99-93-26 (0) 13 : 1.000 + 79 99-21-02 (0) 14 : 1.000 + 80 99-21-04 (0) 14 : 1.000 + 81 99-21-05 (0) 14 : 1.000 + 82 99-21-08 (0) 14 : 1.000 + 83 99-21-09 (0) 14 : 1.000 + 84 99-21-10 (0) 14 : 1.000 + 85 01-58-20 (5) 15 : 1.000 + 86 01-58-33 (5) 15 : 1.000 + 87 01-58-34 (5) 15 : 1.000 + 88 01-58-35 (5) 15 : 1.000 + 89 01-58-53 (5) 15 : 1.000 + 90 01-58-56 (5) 15 : 1.000 + 91 98-116-04 (5) 16 : 1.000 + 92 98-116-07 (5) 16 : 1.000 + 93 98-116-14 (5) 16 : 1.000 + 94 98-116-26 (5) 16 : 1.000 + 95 98-116-27 (5) 16 : 1.000 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : TAGA40 +7 alleles +0.0% missing data + 118 (0.591) 0.594 + 127 (0.072) 0.071 + 130 (0.077) 0.077 + 114 (0.031) 0.030 + 122 (0.092) 0.091 + 110 (0.076) 0.076 + 135 (0.061) 0.061 + +Locus 2 : B113 +15 alleles +0.0% missing data + 228 (0.097) 0.097 + 222 (0.117) 0.117 + 225 (0.155) 0.156 + 234 (0.015) 0.015 + 219 (0.141) 0.142 + 213 (0.217) 0.219 + 204 (0.011) 0.010 + 216 (0.035) 0.034 + 195 (0.015) 0.015 + 231 (0.025) 0.024 + 210 (0.025) 0.024 + 240 (0.010) 0.010 + 207 (0.020) 0.019 + 198 (0.107) 0.107 + 185 (0.010) 0.010 + +Locus 3 : B117 +3 alleles +0.0% missing data + 266 (0.848) 0.849 + 272 (0.032) 0.031 + 278 (0.120) 0.120 + +Locus 4 : ATG16.1 +19 alleles +0.0% missing data + 164 (0.104) 0.105 + 173 (0.307) 0.311 + 182 (0.067) 0.067 + 170 (0.020) 0.019 + 200 (0.020) 0.019 + 202 (0.010) 0.010 + 176 (0.010) 0.010 + 185 (0.024) 0.024 + 167 (0.039) 0.038 + 158 (0.067) 0.067 + 155 (0.029) 0.029 + 152 (0.053) 0.053 + 179 (0.010) 0.010 + 145 (0.010) 0.010 + 149 (0.053) 0.053 + 161 (0.057) 0.057 + 136 (0.100) 0.100 + 101 (0.010) 0.010 + 139 (0.010) 0.009 + +Locus 5 : ATG17 +24 alleles +0.0% missing data + 182 (0.060) 0.061 + 188 (0.033) 0.033 + 185 (0.070) 0.070 + 194 (0.028) 0.028 + 209 (0.010) 0.009 + 191 (0.028) 0.028 + 160 (0.065) 0.065 + 200 (0.024) 0.023 + 173 (0.065) 0.065 + 176 (0.024) 0.023 + 169 (0.024) 0.023 + 131 (0.010) 0.009 + 166 (0.033) 0.033 + 154 (0.047) 0.047 + 144 (0.083) 0.084 + 157 (0.042) 0.042 + 203 (0.015) 0.014 + 147 (0.047) 0.047 + 134 (0.125) 0.126 + 141 (0.056) 0.056 + 206 (0.024) 0.024 + 151 (0.019) 0.019 + 137 (0.010) 0.009 + 179 (0.060) 0.061 + +Locus 6 : ENE2 +6 alleles +11.6% missing data + 177 (0.166) 0.166 + 165 (0.150) 0.150 + 171 (0.424) 0.425 + 175 (0.161) 0.161 + 183 (0.052) 0.052 + 179 (0.047) 0.046 + +Locus 7 : CATG2 +10 alleles +0.0% missing data + 187 (0.253) 0.255 + 191 (0.125) 0.125 + 183 (0.223) 0.225 + 195 (0.090) 0.090 + 199 (0.030) 0.030 + 180 (0.031) 0.030 + 203 (0.041) 0.040 + 206 (0.050) 0.050 + 214 (0.041) 0.040 + 138 (0.115) 0.115 + +Locus 8 : ATG13 +7 alleles +0.0% missing data + 151 (0.556) 0.558 + 148 (0.046) 0.046 + 145 (0.122) 0.122 + 157 (0.011) 0.010 + 155 (0.077) 0.076 + 135 (0.026) 0.026 + 141 (0.162) 0.162 + +Locus 9 : TAGA11 +10 alleles +0.0% missing data + 138 (0.343) 0.346 + 140 (0.035) 0.035 + 147 (0.194) 0.195 + 142 (0.135) 0.135 + 145 (0.085) 0.085 + 136 (0.030) 0.030 + 134 (0.016) 0.015 + 132 (0.021) 0.020 + 153 (0.110) 0.110 + 149 (0.031) 0.030 + +Locus 10 : A018 +7 alleles +0.0% missing data + 313 (0.071) 0.071 + 317 (0.435) 0.437 + 321 (0.036) 0.036 + 319 (0.092) 0.091 + 325 (0.011) 0.010 + 306 (0.289) 0.290 + 324 (0.066) 0.066 + +Locus 11 : A019 +8 alleles +0.0% missing data + 250 (0.276) 0.277 + 247 (0.056) 0.056 + 242 (0.081) 0.081 + 251 (0.041) 0.040 + 245 (0.102) 0.101 + 257 (0.016) 0.015 + 243 (0.342) 0.343 + 253 (0.086) 0.086 + +Locus 12 : ATG26 +4 alleles +0.0% missing data + 204 (0.926) 0.928 + 180 (0.016) 0.015 + 218 (0.047) 0.046 + 210 (0.011) 0.010 + +Locus 13 : C111 +6 alleles +0.0% missing data + 260 (0.873) 0.877 + 263 (0.062) 0.061 + 257 (0.016) 0.015 + 269 (0.026) 0.026 + 275 (0.011) 0.010 + 246 (0.011) 0.010 + +Locus 14 : ENE3 +5 alleles +0.0% missing data + 157 (0.747) 0.749 + 146 (0.185) 0.185 + 153 (0.021) 0.020 + 155 (0.037) 0.036 + 163 (0.011) 0.010 + +Locus 15 : ENE4 +2 alleles +0.0% missing data + 243 (0.672) 0.672 + 238 (0.328) 0.328 + +Locus 16 : CATG14 +3 alleles +0.0% missing data + 173 (0.859) 0.860 + 165 (0.037) 0.036 + 169 (0.104) 0.104 + +Locus 17 : ATG18 +2 alleles +0.0% missing data + 171 (0.880) 0.880 + 168 (0.120) 0.120 + +Locus 18 : C114 +4 alleles +0.0% missing data + 286 (0.792) 0.794 + 287 (0.062) 0.061 + 283 (0.022) 0.021 + 290 (0.124) 0.124 + +Values of parameters used in structure: +DATAFILE=/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/project_data, OUTFILE=/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/K1ReRun/Results/K1ReRun_run_2, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=1, BURNIN=50000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, SEED=1213374129, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary.txt Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,41 @@ +# This document produced by structureHarvester core version vA.2 July 2014 +# http://www.structureharvester.com/ +# https://github.com/dentearl/structureHarvester/ +# http://taylor0.biology.ucla.edu/structureHarvester +# http://users.soe.ucsc.edu/~dearl/software/structureHarvester +# Written by Dent Earl, dearl (a) soe ucsc edu. +# CITATION: +# Earl, Dent A. and vonHoldt, Bridgett M. (2012) +# STRUCTURE HARVESTER: a website and program for visualizing +# STRUCTURE output and implementing the Evanno method. +# Conservation Genetics Resources 4(2) 359-361. DOI: 10.1007/s12686-011-9548-7 +# Core version: vA.2 July 2014 +# File generated at 2017-Dec-06 15:21:48 CET +# + +########## +# K Reps mean est. LnP(Data) stdev est. LnP(Data) +1 2 -4329.950000 0.070711 +2 2 -3639.200000 10.323759 +3 2 -3020.800000 0.000000 +4 2 -2773.550000 0.212132 + +########## +# File name Run # K Est. Ln prob. of data Mean value of Ln likelihood Variance of Ln likelihood +K1ReRun_run_2_f 2 1 -4330.0 -4300.2 59.7 +K1ReRun_run_1_f 1 1 -4329.9 -4300.3 59.2 +Admix_run_002_f 002 2 -3631.9 -3562.2 139.5 +Admix_run_001_f 001 2 -3646.5 -3597.1 98.8 +Admix_run_004_f 004 3 -3020.8 -2945.8 150.0 +Admix_run_005_f 005 3 -3020.8 -2945.9 149.7 +Admix_run_007_f 007 4 -2773.7 -2678.7 190.1 +Admix_run_008_f 008 4 -2773.4 -2678.8 189.2 + +Software written by Dent Earl while at EEB Dept, UCLA, BME Dept UCSC +dearl (a) soe ucsc edu +CITATION: +Earl, Dent A. and vonHoldt, Bridgett M. (2012) +STRUCTURE HARVESTER: a website and program for visualizing +STRUCTURE output and implementing the Evanno method. +# Conservation Genetics Resources 4(2) 359-361. DOI: 10.1007/s12686-011-9548-7 +Core version: vA.2 July 2014 \ No newline at end of file