{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Bash - Commands used for running the analyses in the Workshop" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Exploring the Genotype Data" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "genotypes.geno genotypes.ind genotypes.snp outgroupf3stats.params.txt\n" ] } ], "source": [ "SDIR=~/share;\n", "cd $SDIR/genotype_data;\n", "ls" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Exploring the files. Here are the first 20 individuals:" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " Yuk_009 M Yukagir\n", " Yuk_025 F Yukagir\n", " Yuk_022 F Yukagir\n", " Yuk_020 F Yukagir\n", " MC_40 M Chukchi\n", " Yuk_024 F Yukagir\n", " Yuk_023 F Yukagir\n", " MC_16 M Chukchi\n", " MC_15 F Chukchi\n", " MC_18 M Chukchi\n", " Yuk_004 M Yukagir\n", " MC_08 F Chukchi\n", " Nov_005 M Nganasan\n", " MC_25 F Chukchi\n", " Yuk_019 F Yukagir\n", " Yuk_011 M Yukagir\n", " Sesk_47 M Chukchi1\n", " MC_17 M Chukchi\n", " Yuk_021 M Yukagir\n", " MC_06 F Chukchi\n" ] } ], "source": [ "head -20 genotypes.ind" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "And here the first 20 SNP rows:" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 1_752566 1 0.020130 752566 G A\n", " 1_842013 1 0.022518 842013 T G\n", " 1_891021 1 0.024116 891021 G A\n", " 1_903426 1 0.024457 903426 C T\n", " 1_949654 1 0.025727 949654 A G\n", " 1_1018704 1 0.026288 1018704 A G\n", " 1_1045331 1 0.026665 1045331 G A\n", " 1_1048955 1 0.026674 1048955 A G\n", " 1_1061166 1 0.026711 1061166 T C\n", " 1_1108637 1 0.028311 1108637 G A\n", " 1_1120431 1 0.028916 1120431 G A\n", " 1_1156131 1 0.029335 1156131 T C\n", " 1_1157547 1 0.029356 1157547 T C\n", " 1_1158277 1 0.029367 1158277 G A\n", " 1_1161780 1 0.029391 1161780 C T\n", " 1_1170587 1 0.029450 1170587 C T\n", " 1_1205155 1 0.029735 1205155 A C\n", " 1_1211292 1 0.029785 1211292 C T\n", " 1_1235792 1 0.030045 1235792 C T\n", " 1_1254255 1 0.030111 1254255 G A\n" ] } ], "source": [ "head -20 genotypes.snp" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "And here are the first 20 genotypes of the first 100 individuals:" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0101101211102210102021200100010200000011001000200001010110001100001111101001110200110111212110000011\n", "2012121012210011122100111202201222121102222121121012202221211212202201101201220222122012011112122022\n", "1100112001110021001001111000011200000111100001110001110100002100110111120000102200110112011020001001\n", "0000112210222121221121100202221222122112112211202122222221022222111221102200112222122211012121022011\n", "0000000000000000000000000000100000000000000000100010000000000000000000000000000100000011201120010000\n", "1012100221102201101121110120110000010012002010200100010011100100011011101110120200010100000002010111\n", "2222222222222222222222222222222222222222222222222222222222222222222222222222222222121222222222122222\n", "2211222002212022102001212222212212222210122212121222112222221112122111222222122021221122222222222222\n", "2211222002212022102001212202012212212210122212121122112221221112121111222122112021211121011121222211\n", "2222222222102222202222222222222222222222222211222212122222122122222222222222222122221212212212222222\n", "2212222212122222222222222222221222222222222220221122222222122221212222221222222202222210012292222222\n", "1101100001000001001000000222010021200001202110101111110122100021211110001221120002110000202110121222\n", "1221121221222211221222222121221222212222222222222222222211121221212122221202101222212222021012222222\n", "1221121221222211221222222121221222212222222222222222222211121221212122221202101222212222021012222222\n", "1221121221222211221222222121221222212222222222222222222211121221212122221202101222212222021012222222\n", "2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222021012222222\n", "2222222222222222222222222222222222222222222222222222222222222222222222222222222222121211000001222222\n", "1011111102100111001100200122221022211211222021212200120222112121221120012221222102020101000001222212\n", "2222222222222222222222222222222222222222222222222222222222222222222222222222222222222211000112222222\n", "2122121212102221202222222222222221122212222192222211122222222112222222222122222122221222222222122222\n" ] } ], "source": [ "head -20 genotypes.geno | cut -c1-100" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Counting how many individuals and SNPs there are:" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1351 genotypes.ind\n", "593124 genotypes.snp\n" ] } ], "source": [ "wc -l genotypes.ind\n", "wc -l genotypes.snp" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "And now we check that the first row of the `*.geno` file indeed contains the same number of columns:" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1352\n" ] } ], "source": [ "head -1 genotypes.geno | wc -c" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "which is one more, including the newline character at the end of the line. Now counting the number of rows in the `*.geno`-file (this takes a few seconds, as the file is >2Gb):" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "593124 genotypes.geno\n" ] } ], "source": [ "wc -l genotypes.geno" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Great, the number of rows and columns agrees with the numbers indicated in the `*.ind` and `*.snp` file!\n", "Now we're counting how many different populations there are. Let's first see the first 10 populations in the sorted list, alongside the number of individuals in each group:" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 9 Abkhasian\n", " 16 Adygei\n", " 6 Albanian\n", " 7 Aleut\n", " 4 Aleut_Tlingit\n", " 7 Altaian\n", " 10 Ami\n", " 10 Armenian\n", " 9 Atayal\n", " 10 Balkar\n", " 29 Basque\n", " 25 BedouinA\n", " 19 BedouinB\n", " 10 Belarusian\n", " 6 BolshoyOleniOstrov\n", " 9 Borneo\n", " 10 Bulgarian\n", " 8 Cambodian\n", " 2 Canary_Islander\n", " 2 ChalmnyVarre\n" ] } ], "source": [ "awk '{print $3}' genotypes.ind | sort | uniq -c | head -20" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "As you can see, there are a number of populations with only one sample. Those are typically ancient individuals which are considered individually in most analyses. Let's filter those out and count only populations with at least two individuals and count them:" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "114\n" ] } ], "source": [ "awk '{print $3}' genotypes.ind | sort | uniq -c | awk '$1>1' | wc -l" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "OK, so there are 114 populations in this dataset." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Running `smartPCA`" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We first have to create a parameter file with the input and output data." ] }, { "cell_type": "code", "execution_count": 73, "metadata": { "collapsed": true }, "outputs": [], "source": [ "WDIR=~/work/share/solutions\n", "mkdir -p $WDIR\n", "cd $WDIR\n", "cat < pca.WestEurasia.params.txt\n", "genotypename: $SDIR/genotype_data/genotypes.geno\n", "snpname: $SDIR/genotype_data/genotypes.snp\n", "indivname: $SDIR/genotype_data/genotypes.ind\n", "evecoutname: $WDIR/pca.WestEurasia.evec\n", "evaloutname: $WDIR/pca.WestEurasia.eval\n", "poplistname: $SDIR/WestEurasia.poplist.txt\n", "lsqproject: YES\n", "numoutevec: 4\n", "numthreads: 1\n", "EOF" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's see whether it worked:" ] }, { "cell_type": "code", "execution_count": 74, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "genotypename: /home/training/share/genotype_data/genotypes.geno\n", "snpname: /home/training/share/genotype_data/genotypes.snp\n", "indivname: /home/training/share/genotype_data/genotypes.ind\n", "evecoutname: /home/training/work/share/solutions/pca.WestEurasia.evec\n", "evaloutname: /home/training/work/share/solutions/pca.WestEurasia.eval\n", "poplistname: /home/training/share/WestEurasia.poplist.txt\n", "lsqproject: YES\n", "numoutevec: 4\n" ] } ], "source": [ "cat pca.WestEurasia.params.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Good, now we can run `smartPCA`:" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "scrolled": true }, "outputs": [], "source": [ "time smartpca -p pca.WestEurasia.params.txt > pca.WestEurasia.log.txt" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "This has run for 15 minutes. Now we'll run the AllEurasia one:" ] }, { "cell_type": "code", "execution_count": 75, "metadata": { "collapsed": true }, "outputs": [], "source": [ "WDIR=~/work/share/solutions\n", "mkdir -p $WDIR\n", "cd $WDIR\n", "cat < pca.AllEurasia.params.txt\n", "genotypename: $SDIR/genotype_data/genotypes.geno\n", "snpname: $SDIR/genotype_data/genotypes.snp\n", "indivname: $SDIR/genotype_data/genotypes.ind\n", "evecoutname: $WDIR/pca.AllEurasia.evec\n", "evaloutname: $WDIR/pca.AllEurasia.eval\n", "poplistname: $SDIR/AllEurasia.poplist.txt\n", "lsqproject: YES\n", "numoutevec: 4\n", "numthreads: 1\n", "EOF" ] }, { "cell_type": "code", "execution_count": 76, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "genotypename: /home/training/share/genotype_data/genotypes.geno\n", "snpname: /home/training/share/genotype_data/genotypes.snp\n", "indivname: /home/training/share/genotype_data/genotypes.ind\n", "evecoutname: /home/training/work/share/solutions/pca.AllEurasia.evec\n", "evaloutname: /home/training/work/share/solutions/pca.AllEurasia.eval\n", "poplistname: /home/training/share/AllEurasia.poplist.txt\n", "lsqproject: YES\n", "numoutevec: 4\n" ] } ], "source": [ "cat pca.AllEurasia.params.txt" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "time smartpca -p pca.AllEurasia.params.txt" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "## Running Admixture F3" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Preparing the population file:" ] }, { "cell_type": "code", "execution_count": 39, "metadata": { "collapsed": true }, "outputs": [], "source": [ "WDIR=~/work/share/solutions\n", "mkdir -p $WDIR\n", "cd $WDIR\n", "cat < $WDIR/f3.poplist.txt\n", "Nganasan French Finnish \n", "Nganasan Icelandic Finnish \n", "Nganasan Lithuanian Finnish \n", "Nganasan Norwegian Finnish \n", "BolshoyOleniOstrov French Finnish \n", "BolshoyOleniOstrov Icelandic Finnish \n", "BolshoyOleniOstrov Lithuanian Finnish \n", "BolshoyOleniOstrov Norwegian Finnish\n", "EOF" ] }, { "cell_type": "code", "execution_count": 41, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Nganasan French Finnish \n", "Nganasan Icelandic Finnish \n", "Nganasan Lithuanian Finnish \n", "Nganasan Norwegian Finnish \n", "BolshoyOleniOstrov French Finnish \n", "BolshoyOleniOstrov Icelandic Finnish \n", "BolshoyOleniOstrov Lithuanian Finnish \n", "BolshoyOleniOstrov Norwegian Finnish\n" ] } ], "source": [ "cat $WDIR/f3.poplist.txt" ] }, { "cell_type": "code", "execution_count": 42, "metadata": { "collapsed": true }, "outputs": [], "source": [ "WDIR=~/work/share/solutions\n", "mkdir -p $WDIR\n", "cd $WDIR\n", "cat < f3stats.params.txt\n", "genotypename: $SDIR/genotype_data/genotypes.smaller.geno\n", "snpname: $SDIR/genotype_data/genotypes.smaller.snp\n", "indivname: $SDIR/genotype_data/genotypes.smaller.ind\n", "popfilename: $WDIR/f3.poplist.txt\n", "inbreed: YES\n", "EOF" ] }, { "cell_type": "code", "execution_count": 43, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "genotypename: /home/training/work/share/genotype_data/genotypes.smaller.geno\n", "snpname: /home/training/work/share/genotype_data/genotypes.smaller.snp\n", "indivname: /home/training/work/share/genotype_data/genotypes.smaller.ind\n", "popfilename: /home/training/work/share/solutions/f3.poplist.txt\n", "inbreed: YES\n" ] } ], "source": [ "cat f3stats.params.txt" ] }, { "cell_type": "code", "execution_count": 44, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "qp3Pop: parameter file: f3stats.params.txt\n", "### THE INPUT PARAMETERS\n", "##PARAMETER NAME: VALUE\n", "genotypename: /home/training/work/share/genotype_data/genotypes.smaller.geno\n", "snpname: /home/training/work/share/genotype_data/genotypes.smaller.snp\n", "indivname: /home/training/work/share/genotype_data/genotypes.smaller.ind\n", "popfilename: /home/training/work/share/solutions/f3.poplist.txt\n", "inbreed: YES\n", "## qp3Pop version: 435\n", "inbreed set\n", "nplist: 8\n", "number of blocks for block jackknife: 711\n", "snps: 593124\n", " Source 1 Source 2 Target f_3 std. err Z SNPs\n", " result: Nganasan French Finnish -0.004539 0.000510 -8.894 442567\n", " result: Nganasan Icelandic Finnish -0.005297 0.000563 -9.404 427954\n", " result: Nganasan Lithuanian Finnish -0.005062 0.000590 -8.574 426231\n", " result: Nganasan Norwegian Finnish -0.004744 0.000569 -8.332 428161\n", " result: BolshoyOleniOstrov French Finnish -0.002814 0.000444 -6.341 402958\n", " result: BolshoyOleniOstrov Icelandic Finnish -0.002590 0.000486 -5.323 386418\n", " result: BolshoyOleniOstrov Lithuanian Finnish -0.001523 0.000536 -2.840 384134\n", " result: BolshoyOleniOstrov Norwegian Finnish -0.001553 0.000502 -3.092 386203\n", "##end of qp3Pop: 190.789 seconds cpu 327.410 Mbytes in use\n", "\n", "real\t3m10.903s\n", "user\t3m10.156s\n", "sys\t0m0.664s\n" ] } ], "source": [ "time qp3Pop -p f3stats.params.txt" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "## Running D stats" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": true }, "outputs": [], "source": [ "WDIR=~/work/share/solutions\n", "cat < $WDIR/dstat.poplist.txt\n", "Mbuti Nganasan French Finnish \n", "Mbuti Nganasan Icelandic Finnish \n", "Mbuti Nganasan Lithuanian Finnish \n", "Mbuti Nganasan Norwegian Finnish \n", "Mbuti BolshoyOleniOstrov French Finnish \n", "Mbuti BolshoyOleniOstrov Icelandic Finnish \n", "Mbuti BolshoyOleniOstrov Lithuanian Finnish \n", "Mbuti BolshoyOleniOstrov Norwegian Finnish\n", "EOF" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Mbuti Nganasan French Finnish \n", "Mbuti Nganasan Icelandic Finnish \n", "Mbuti Nganasan Lithuanian Finnish \n", "Mbuti Nganasan Norwegian Finnish \n", "Mbuti BolshoyOleniOstrov French Finnish \n", "Mbuti BolshoyOleniOstrov Icelandic Finnish \n", "Mbuti BolshoyOleniOstrov Lithuanian Finnish \n", "Mbuti BolshoyOleniOstrov Norwegian Finnish\n" ] } ], "source": [ "cat $WDIR/dstat.poplist.txt" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": true }, "outputs": [], "source": [ "cat < $WDIR/dstats.params.txt\n", "genotypename: $SDIR/genotype_data/genotypes.geno\n", "snpname: $SDIR/genotype_data/genotypes.snp\n", "indivname: $SDIR/genotype_data/genotypes.ind\n", "popfilename: $WDIR/dstat.poplist.txt\n", "f4mode: YES\n", "EOF" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "genotypename: /home/training/share/genotype_data/genotypes.geno\n", "snpname: /home/training/share/genotype_data/genotypes.snp\n", "indivname: /home/training/share/genotype_data/genotypes.ind\n", "popfilename: /home/training/work/share/solutions/dstat.poplist.txt\n", "f4mode: YES\n" ] } ], "source": [ "cat $WDIR/dstats.params.txt" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "qpDstat: parameter file: /home/training/work/share/solutions/dstats.params.txt\n", "### THE INPUT PARAMETERS\n", "##PARAMETER NAME: VALUE\n", "genotypename: /home/training/share/genotype_data/genotypes.geno\n", "snpname: /home/training/share/genotype_data/genotypes.snp\n", "indivname: /home/training/share/genotype_data/genotypes.ind\n", "popfilename: /home/training/work/share/solutions/dstat.poplist.txt\n", "f4mode: YES\n", "## qpDstat version: 755\n", "number of quadruples 8\n", " 0 Mbuti 10\n", " 1 Nganasan 11\n", " 2 BolshoyOleniOstrov 6\n", " 3 French 32\n", " 4 Icelandic 12\n", " 5 Lithuanian 10\n", " 6 Norwegian 11\n", " 7 Finnish 8\n", "jackknife block size: 0.050\n", "snps: 593124 indivs: 100\n", "number of blocks for jackknife: 711\n", "nrows, ncols: 100 593124\n", "result: Mbuti Nganasan French Finnish 0.002363 19.016 29254 27852 593124 \n", "result: Mbuti Nganasan Icelandic Finnish 0.001721 11.926 28915 27894 593124 \n", "result: Mbuti Nganasan Lithuanian Finnish 0.001368 9.664 28745 27933 593124 \n", "result: Mbuti Nganasan Norwegian Finnish 0.001685 11.663 28933 27934 593124 \n", "result: Mbuti BolshoyOleniOstrov French Finnish 0.001962 16.737 27249 26175 547486 \n", "result: Mbuti BolshoyOleniOstrov Icelandic Finnish 0.001084 7.776 26876 26282 547486 \n", "result: Mbuti BolshoyOleniOstrov Lithuanian Finnish 0.000554 3.942 26683 26380 547486 \n", "result: Mbuti BolshoyOleniOstrov Norwegian Finnish 0.000952 6.707 26873 26351 547486 \n", "##end of qpDstat: 172.851 seconds cpu 731.099 Mbytes in use\n", "\n", "real\t2m52.891s\n", "user\t2m52.136s\n", "sys\t0m0.744s\n" ] } ], "source": [ "time qpDstat -p $WDIR/dstats.params.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Outgroup F3 stats" ] }, { "cell_type": "code", "execution_count": 27, "metadata": {}, "outputs": [], "source": [ "cat < $WDIR/outgroupf3stats.params.txt\n", "genotypename: $SDIR/genotype_data/genotypes.geno\n", "snpname: $SDIR/genotype_data/genotypes.snp\n", "indivname: $SDIR/genotype_data/genotypes.ind\n", "popfilename: $WDIR/outgroupF3pops_Han.txt\n", "EOF" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "genotypename: /home/training/share/genotype_data/genotypes.geno\n", "snpname: /home/training/share/genotype_data/genotypes.snp\n", "indivname: /home/training/share/genotype_data/genotypes.ind\n", "popfilename: /home/training/work/share/solutions/outgroupF3pops_Han.txt\n" ] } ], "source": [ "cat $WDIR/outgroupf3stats.params.txt" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "qp3Pop: parameter file: /home/training/work/share/solutions/outgroupf3stats.params.txt\n", "### THE INPUT PARAMETERS\n", "##PARAMETER NAME: VALUE\n", "genotypename: /home/training/share/genotype_data/genotypes.geno\n", "snpname: /home/training/share/genotype_data/genotypes.snp\n", "indivname: /home/training/share/genotype_data/genotypes.ind\n", "popfilename: /home/training/work/share/solutions/outgroupF3pops_Han.txt\n", "## qp3Pop version: 435\n", "nplist: 32\n", "number of blocks for block jackknife: 711\n", "snps: 593124\n", " Source 1 Source 2 Target f_3 std. err Z SNPs\n", " result: Han Chuvash Mbuti 0.233652 0.002072 112.782 502678\n", " result: Han Albanian Mbuti 0.215629 0.002029 106.291 501734\n", " result: Han Armenian Mbuti 0.213724 0.001963 108.882 504370\n", " result: Han Bulgarian Mbuti 0.216193 0.001979 109.266 504310\n", " result: Han Czech Mbuti 0.218060 0.002002 108.939 504089\n", " result: Han Druze Mbuti 0.209551 0.001919 109.205 510853\n", " result: Han English Mbuti 0.216959 0.001973 109.954 504161\n", " result: Han Estonian Mbuti 0.220730 0.002019 109.332 503503\n", " result: Han Finnish Mbuti 0.223447 0.002044 109.345 502217\n", " result: Han French Mbuti 0.216623 0.001969 110.012 509613\n", " result: Han Georgian Mbuti 0.214295 0.001935 110.721 503598\n", " result: Han Greek Mbuti 0.215203 0.001984 108.465 507475\n", " result: Han Hungarian Mbuti 0.217894 0.001999 109.004 507409\n", " result: Han Icelandic Mbuti 0.218683 0.002015 108.553 504655\n", " result: Han Italian_North Mbuti 0.215332 0.001978 108.854 507589\n", " result: Han Italian_South Mbuti 0.211787 0.002271 93.265 492400\n", " result: Han Lithuanian Mbuti 0.219615 0.002032 108.098 503681\n", " result: Han Maltese Mbuti 0.210359 0.001956 107.542 503985\n", " result: Han Mordovian Mbuti 0.223469 0.002008 111.296 503441\n", " result: Han Norwegian Mbuti 0.218873 0.002023 108.197 504621\n", " result: Han Orcadian Mbuti 0.217773 0.002014 108.115 504993\n", " result: Han Russian Mbuti 0.223993 0.001995 112.274 506525\n", " result: Han Sardinian Mbuti 0.213230 0.001980 107.711 508413\n", " result: Han Scottish Mbuti 0.218489 0.002039 107.145 499784\n", " result: Han Sicilian Mbuti 0.212272 0.001975 107.486 505477\n", " result: Han Spanish_North Mbuti 0.215885 0.002029 106.383 500853\n", " result: Han Spanish Mbuti 0.213869 0.001975 108.297 513648\n", " result: Han Ukrainian Mbuti 0.218716 0.002007 108.950 503981\n", " result: Han Levanluhta Mbuti 0.236252 0.002383 99.123 263049\n", " result: Han BolshoyOleniOstrov Mbuti 0.247814 0.002177 113.849 457102\n", " result: Han ChalmnyVarre Mbuti 0.233499 0.002304 101.345 366220\n", " result: Han Saami.DG Mbuti 0.236198 0.002274 103.852 489038\n", "##end of qp3Pop: 296.879 seconds cpu 327.410 Mbytes in use\n", "\n", "real\t4m56.909s\n", "user\t4m56.140s\n", "sys\t0m0.756s\n" ] } ], "source": [ "time qp3Pop -p $WDIR/outgroupf3stats.params.txt" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": true }, "outputs": [], "source": [ "cat < $WDIR/outgroupf3stats.params.txt\n", "genotypename: $SDIR/genotype_data/genotypes.geno\n", "snpname: $SDIR/genotype_data/genotypes.snp\n", "indivname: $SDIR/genotype_data/genotypes.ind\n", "popfilename: $WDIR/outgroupF3pops_MA1.txt\n", "EOF" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "genotypename: /home/training/share/genotype_data/genotypes.geno\n", "snpname: /home/training/share/genotype_data/genotypes.snp\n", "indivname: /home/training/share/genotype_data/genotypes.ind\n", "popfilename: /home/training/work/share/solutions/outgroupF3pops_MA1.txt\n" ] } ], "source": [ "cat $WDIR/outgroupf3stats.params.txt" ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "qp3Pop: parameter file: /home/training/work/share/solutions/outgroupf3stats.params.txt\n", "### THE INPUT PARAMETERS\n", "##PARAMETER NAME: VALUE\n", "genotypename: /home/training/share/genotype_data/genotypes.geno\n", "snpname: /home/training/share/genotype_data/genotypes.snp\n", "indivname: /home/training/share/genotype_data/genotypes.ind\n", "popfilename: /home/training/work/share/solutions/outgroupF3pops_MA1.txt\n", "## qp3Pop version: 435\n", "nplist: 32\n", "number of blocks for block jackknife: 711\n", "snps: 593124\n", " Source 1 Source 2 Target f_3 std. err Z SNPs\n", " result: MA1_HG.SG Chuvash Mbuti 0.243818 0.002349 103.781 350484\n", " result: MA1_HG.SG Albanian Mbuti 0.236494 0.002296 103.008 344332\n", " result: MA1_HG.SG Armenian Mbuti 0.231399 0.002264 102.229 349612\n", " result: MA1_HG.SG Bulgarian Mbuti 0.237498 0.002281 104.103 349800\n", " result: MA1_HG.SG Czech Mbuti 0.243224 0.002328 104.457 349553\n", " result: MA1_HG.SG Druze Mbuti 0.226740 0.002197 103.193 359004\n", " result: MA1_HG.SG English Mbuti 0.243135 0.002317 104.941 349321\n", " result: MA1_HG.SG Estonian Mbuti 0.247065 0.002362 104.619 348861\n", " result: MA1_HG.SG Finnish Mbuti 0.245684 0.002379 103.266 347208\n", " result: MA1_HG.SG French Mbuti 0.240235 0.002269 105.886 357842\n", " result: MA1_HG.SG Georgian Mbuti 0.232645 0.002253 103.243 349082\n", " result: MA1_HG.SG Greek Mbuti 0.236566 0.002280 103.757 355261\n", " result: MA1_HG.SG Hungarian Mbuti 0.241720 0.002313 104.483 355340\n", " result: MA1_HG.SG Icelandic Mbuti 0.244488 0.002386 102.481 350287\n", " result: MA1_HG.SG Italian_North Mbuti 0.236407 0.002273 104.002 354999\n", " result: MA1_HG.SG Italian_South Mbuti 0.230839 0.002767 83.427 321217\n", " result: MA1_HG.SG Lithuanian Mbuti 0.246864 0.002403 102.718 348656\n", " result: MA1_HG.SG Maltese Mbuti 0.230200 0.002259 101.903 347725\n", " result: MA1_HG.SG Mordovian Mbuti 0.245284 0.002346 104.571 350058\n", " result: MA1_HG.SG Norwegian Mbuti 0.243930 0.002301 106.031 350182\n", " result: MA1_HG.SG Orcadian Mbuti 0.243614 0.002320 105.008 351053\n", " result: MA1_HG.SG Russian Mbuti 0.245212 0.002298 106.698 355953\n", " result: MA1_HG.SG Sardinian Mbuti 0.231967 0.002264 102.449 355548\n", " result: MA1_HG.SG Scottish Mbuti 0.244598 0.002434 100.512 339441\n", " result: MA1_HG.SG Sicilian Mbuti 0.231141 0.002260 102.297 351028\n", " result: MA1_HG.SG Spanish_North Mbuti 0.238479 0.002426 98.319 341661\n", " result: MA1_HG.SG Spanish Mbuti 0.235386 0.002257 104.293 361951\n", " result: MA1_HG.SG Ukrainian Mbuti 0.243551 0.002345 103.881 348948\n", " result: MA1_HG.SG Levanluhta Mbuti 0.247704 0.003055 81.090 172055\n", " result: MA1_HG.SG BolshoyOleniOstrov Mbuti 0.256041 0.002624 97.561 305851\n", " result: MA1_HG.SG ChalmnyVarre Mbuti 0.249619 0.002862 87.212 239594\n", " result: MA1_HG.SG Saami.DG Mbuti 0.251530 0.002622 95.922 326072\n", "##end of qp3Pop: 219.087 seconds cpu 327.410 Mbytes in use\n", "\n", "real\t3m39.156s\n", "user\t3m38.432s\n", "sys\t0m0.672s\n" ] } ], "source": [ "time qp3Pop -p $WDIR/outgroupf3stats.params.txt" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Bash", "language": "bash", "name": "bash" }, "language_info": { "codemirror_mode": "shell", "file_extension": ".sh", "mimetype": "text/x-sh", "name": "bash" } }, "nbformat": 4, "nbformat_minor": 2 }