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   "cells": [
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## IPython Notebook for downloading and analyzing data from preprint: \"Indication of family-specific DNA methylation patterns in developing oysters\"\n",
      "[http://dx.doi.org/10.1101/012831](http://dx.doi.org/10.1101/012831)\n",
      "\n",
      "---\n",
      "To execute the IPython Notebook in its entirety you will need:   \n",
      "\n",
      "* IPython - [install instructions](http://ipython.org/install.html)    \n",
      "* BSMAP - [install instructions](https://code.google.com/p/bsmap/)   \n",
      "* bedtools - [install instructions](https://github.com/arq5x/bedtools2/releases/tag/v2.22.0)    \n",
      "* R - [install instructions](http://www.r-project.org/)  \n",
      "* rpy2 (interface to R from Python) - [install instructions](http://rpy.sourceforge.net/)   \n",
      "\n",
      "\n",
      "---"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "The analysis was originally done on the Mac OSX operating system. \n",
      "\n",
      "The intent is to download the github repository locally and run so accompaning scripts, etc. are available.\n",
      "Detailed Instructions are provided in [GitHub Repo Readme](https://github.com/che625/olson-ms-nb).\n",
      "Please note Data files that you will download and will produce are large (>20Gb).\n",
      "\n",
      "\n",
      "The notebook is divided into 5 sections \n",
      "\n",
      "* [Downloading data](#Downloading-Files) \n",
      "\n",
      "* [Read aligning: BSMAP](#Running-BSMAP) \n",
      "\n",
      "* [Global differences: methylkit](#Global-Differences:-methylkit)  \n",
      "\n",
      "* [Differentially methylated loci: methylkit](#Differentially-methylated-loci)  \n",
      "\n",
      "* [Genomic location of DMLs: bedtools](#Genomic-location-of-DMLs)   \n",
      "\n",
      "\n",
      "Please post any comments and questions in [issues](https://github.com/che625/olson-ms-nb/issues).\n",
      "\n",
      "---"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Before getting started, set the location of BSMAP on your computer and hit shift-enter"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "bsmaploc=\"/Users/Shared/Apps/bsmap-2.74/\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Downloading Data"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#to confirm you current directory run the command and you should see a wd directory\n",
      "!ls\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\u001b[31mBiGo_dev.ipynb\u001b[m\u001b[m \u001b[31mREADME.md\u001b[m\u001b[m      \u001b[30m\u001b[43mscripts\u001b[m\u001b[m        \u001b[30m\u001b[43mwd\u001b[m\u001b[m\r\n"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd wd"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/Volumes/web/cnidarian/olson-ms-nb-master_12_1714/wd\n"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#This command downloads a archived file including six BS-seq libraries (4.3 Gb)\n",
      "\n",
      "#!wget http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_HTSdata/BiGo_lar_fastq_mcf.tgz\n",
      "!curl -O http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_HTSdata/BiGo_lar_fastq_mcf.tgz    \n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
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       "text": [
        "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\r\n",
        "                                 Dload  Upload   Total   Spent    Left  Speed\r\n",
        "\r",
        "  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0"
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      },
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       "stream": "stdout",
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        "\r",
        "  0 4221M    0 11.0M    0     0  40.8M      0  0:01:43 --:--:--  0:01:43 44.4M"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "\r",
        "  1 4221M    1 50.0M    0     0  39.5M      0  0:01:46  0:00:01  0:01:45 40.2M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "  2 4221M    2 84.7M    0   "
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  0  36.7M      0  0:01:54  0:00:02  0:01:52 37.1M"
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       "stream": "stdout",
       "text": [
        "\r",
        "  2 4221M    2  104M    0     0  31.8M      0  0:02:12  0:00:03  0:02:09 32.1M"
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      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "  2 4221M    2  122M    0     0  28.6M      0  0:02:27  0:00:04  0:02:23 28.7M"
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       "stream": "stdout",
       "text": [
        "\r",
        "  3 4221M    3  154M    0     0  29.1M      0  0:02:24  0:00:05  0:02:19 28.4M"
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        "\r",
        "  4 4221M    4  170M    0     0  27.0M      0  0:02:36  0:00:06  0:02:30 23.9M"
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        "\r",
        "  5 4221M    5  231M    0     0  27.9M      0  0:02:30  0:00:08  0:02:22 25.4M"
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        "\r",
        "  5 4221M    5  247M    0     0  26.1M      0  0:02:41  0:00:09  0:02:32 24.1M"
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        "\r",
        "  6 4221M    6  275M    0     0  26.7M      0  0:02:37  0:00:10  0:02:27 24.3M"
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        "  7 4221M    7  305M    0     0  27.0M      0  0:02:36  0:00:11  0:02:25 27.0M"
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        "\r",
        "  7 4221M    7  325M    0     0  26.5M      0  0:02:38  0:00:12  0:02:26 24.9M"
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        "\r",
        "  8 4221M    8  359M    0     0  27.0M      0  0:02:35  0:00:13  0:02:22 25.5M"
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        "\r",
        "  9 4221M    9  387M    0     0  27.1M      0  0:02:35  0:00:14  0:02:21 29.0M"
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        "\r",
        "  9 4221M    9  410M    0     0  26.8M      0  0:02:37  0:00:15  0:02:22 27.0M"
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        "\r",
        " 10 4221M   10  442M    0     0  27.1M      0  0:02:35  0:00:16  0:02:19 27.3M"
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        "\r",
        " 10 4221M   10  462M    0     0  26.7M      0  0:02:37  0:00:17  0:02:20 27.2M"
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        " 11 4221M   11  492M    0     0  26.9M      0  0:02:36  0:00:18  0:02:18 26.7M"
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        "\r",
        " 12 4221M   12  547M    0     0  27.0M      0  0:02:36  0:00:20  0:02:16 27.4M"
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        " 15 4221M   15  673M    0     0  26.6M      0  0:02:38  0:00:25  0:02:13 24.9M"
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        "\r",
        " 16 4221M   16  690M    0     0  26.2M      0  0:02:40  0:00:26  0:02:14 22.2M"
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        " 17 4221M   17  730M    0     0  26.7M      0  0:02:37  0:00:27  0:02:10 24.7M"
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        " 18 4221M   18  772M    0     0  26.3M      0  0:02:40  0:00:29  0:02:11 23.3M"
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        " 20 4221M   20  882M    0     0  26.5M      0  0:02:39  0:00:33  0:02:06 26.6M"
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        " 26 4221M   26 1112M    0     0  26.3M      0  0:02:40  0:00:42  0:01:58 25.4M"
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        " 26 4221M   26 1133M    0     0  26.2M      0  0:02:41  0:00:43  0:01:58 22.4M"
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        " 27 4221M   27 1168M    0     0  26.3M      0  0:02:39  0:00:44  0:01:55 25.2M"
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        " 28 4221M   28 1192M    0     0  26.3M      0  0:02:40  0:00:45  0:01:55 26.1M"
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        " 28 4221M   28 1210M    0     0  26.1M      0  0:02:41  0:00:46  0:01:55 24.1M"
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      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 93 4221M   93 3929M    0     0  25.4M      0  0:02:45  0:02:34  0:00:11 24.9M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 93 4221M   93 3964M    0     0  25.5M      0  0:02:45  0:02:35  0:00:10 25.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 94 4221M   94 3982M    0     0  25.4M      0  0:02:45  0:02:36  0:00:09 25.2M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 94 4221M   94 4002M    0     0  25.4M      0  0:02:45  0:02:37  0:00:08 24.4M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 95 4221M   95 4039M    0     0  25.5M      0  0:02:45  0:02:38  0:00:07 26.8M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 96 4221M   96 4059M    0     0  25.4M      0  0:02:45  0:02:39  0:00:06 26.1M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 96 4221M   96 4082M    0     0  25.4M      0  0:02:45  0:02:40  0:00:05 23.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 97 4221M   97 4115M    0     0  25.5M      0  0:02:45  0:02:41  0:00:04 27.3M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 97 4221M   97 4133M    0     0  25.4M      0  0:02:45  0:02:42  0:00:03 26.5M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 98 4221M   98 4165M    0     0  25.5M      0  0:02:45  0:02:43  0:00:02 25.2M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 99 4221M   99 4196M    0     0  25.5M      0  0:02:45  0:02:44  0:00:01 27.3M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 99 4221M   99 4214M    0     0  25.5M      0  0:02:45  0:02:45 --:--:-- 26.3M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "100 4221M  100 4221M    0     0  25.5M      0  0:02:45  0:02:45 --:--:-- 25.6M\r\n"
       ]
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#uncompress files\n",
      "!tar -zxvf BiGo_lar_fastq_mcf.tgz"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "x mcf_M1_R1.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_M1_R2.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_M3_R1.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_M3_R2.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_T1D3_R1.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_T1D3_R2.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_T1D5_R1.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_T1D5_R2.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_T3D3_R1.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_T3D3_R2.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_T3D5_R1.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "x mcf_T3D5_R2.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n"
       ]
      }
     ],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#remove BiGo_lar_fastq_mcf.tgz\n",
      "#!rm BiGo_lar_fastq_mcf.tgz "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Downloading the oyster genome \n",
      "#!wget http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa\n",
      "!curl -O http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa    \n",
      "    "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\r\n",
        "                                 Dload  Upload   Total   Spent    Left  Speed\r\n",
        "\r",
        "  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "  4  541M    4 25.0M    0     0  42.5M      0  0:00:12 --:--:--  0:00:12 42.6M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 12  541M   12 66.0M    0     0  40.8M      0  0:00:13  0:00:01  0:00:12 40.8M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 15  541M   15 86.5M    0     0  32.5M      0  0:00:16  0:00:02  0:00:14 32.5M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 17  541M   17 95.0M    0     0  26.4M      0  0:00:20  0:00:03  0:00:17 26.4M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 20  541M   20  108M    0     0  23.5M      0  0:00:23  0:00:04  0:00:19 23.5M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 27  541M   27  147M    0     0  26.2M      0  0:00:20  0:00:05  0:00:15 24.3M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 31  541M   31  170M    0     0  25.4M      0  0:00:21  0:00:06  0:00:15 20.5M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 34  541M   34  189M    0     0  24.8M      0  0:00:21  0:00:07  0:00:14 20.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 41  541M   41  222M    0     0  25.8M      0  0:00:20  0:00:08  0:00:12 25.3M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 44  541M   44  240M    0     0  24.9M      0  0:00:21  0:00:09  0:00:12 26.2M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 48  541M   48  265M    0     0  25.0M      0  0:00:21  0:00:10  0:00:11 23.5M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 55  541M   55  301M    0     0  25.9M      0  0:00:20  0:00:11  0:00:09 26.5M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 60  541M   60  325M    0     0  25.8M      0  0:00:20  0:00:12  0:00:08 27.1M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 65  541M   65  355M    0     0  26.1M      0  0:00:20  0:00:13  0:00:07 26.6M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 70  541M   70  379M    0     0  25.9M      0  0:00:20  0:00:14  0:00:06 27.8M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 74  541M   74  404M    0     0  25.9M      0  0:00:20  0:00:15  0:00:05 27.8M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 81  541M   81  440M    0     0  26.5M      0  0:00:20  0:00:16  0:00:04 27.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 84  541M   84  458M    0     0  26.0M      0  0:00:20  0:00:17  0:00:03 26.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 88  541M   88  481M    0     0  25.8M      0  0:00:20  0:00:18  0:00:02 25.1M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 95  541M   95  514M    0     0  26.2M      0  0:00:20  0:00:19  0:00:01 27.0M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 99  541M   99  536M    0     0  26.0M      0  0:00:20  0:00:20 --:--:-- 26.3M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "100  541M  100  541M    0     0  26.0M      0  0:00:20  0:00:20 --:--:-- 24.0M\r\n"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Running BSMAP"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#bsmap will need to be downloaded if not already installed from https://code.google.com/p/bsmap/\n",
      "#another option in running bsmap on iPlant (iplantcollaborative.org)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for i in (\"M1\",\"T1D3\",\"T1D5\", \"M3\", \"T3D3\", \"T3D5\"):\n",
      "    !{bsmaploc}bsmap \\\n",
      "-a mcf_{i}_R1.fastq \\\n",
      "-b mcf_{i}_R2.fastq \\\n",
      "-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \\\n",
      "-o bsmap_out_{i}.sam \\\n",
      "-p 4"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "BSMAP v2.74\r\n",
        "Start at:  Wed Dec 17 10:01:09 2014\r\n",
        "\r\n",
        "Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " \t(format: FASTA)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Load in 7658 db seqs, total size 557717710 bp. 12 secs passed\r\n",
        "total_kmers: 43046721\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Create seed table. 36 secs passed\r\n",
        "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n",
        "kmer cut-off ratio: "
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "5e-07\r\n",
        "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n",
        "quality cutoff: 0\tbase quality char: '!'\r\n",
        "min fragment size:28\tmax fragemt size:500\r\n",
        "start from read #1\tend at read #4294967295\r\n",
        "additional alignment: T in reads => C in reference\r\n",
        "mapping strand (read_1): ++,-+\r\n",
        "mapping strand (read_2): +-,--\r\n",
        "Pair-end alignment(4 threads)\r\n",
        "Input read file #1: mcf_M1_R1.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " \t(format: FASTQ)\r\n",
        "Input read file #2: mcf_M1_R2.fastq \t(format: FASTQ)\r\n",
        "Output file: bsmap_out_M1.sam\t (format: SAM)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t50000 read pairs finished. 59 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t100000 read pairs finished. 60 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t150000 read pairs finished. 60 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t200000 read pairs finished. 61 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t250000 read pairs finished. 82 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t300000 read pairs finished. 83 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t350000 read pairs finished. 84 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t400000 read pairs finished. 84 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t450000 read pairs finished. 105 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t500000 read pairs finished. 106 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t550000 read pairs finished. 107 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t600000 read pairs finished. 107 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t650000 read pairs finished. 129 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t700000 read pairs finished. 130 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t750000 read pairs finished. 131 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t800000 read pairs finished. 131 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t850000 read pairs finished. 153 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t900000 read pairs finished. 154 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t950000 read pairs finished. 155 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1000000 read pairs finished. 155 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1050000 read pairs finished. 175 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1100000 read pairs finished. 177 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1150000 read pairs finished. 178 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1200000 read pairs finished. 179 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1250000 read pairs finished. 198 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1300000 read pairs finished. 201 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1350000 read pairs finished. 201 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1400000 read pairs finished. 202 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1450000 read pairs finished. 221 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1500000 read pairs finished. 223 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1550000 read pairs finished. 224 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1600000 read pairs finished. 225 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1650000 read pairs finished. 244 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1700000 read pairs finished. 247 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1750000 read pairs finished. 248 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1800000 read pairs finished. 249 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1850000 read pairs finished. 267 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1900000 read pairs finished. 270 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1950000 read pairs finished. 272 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2000000 read pairs finished. 273 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2050000 read pairs finished. 291 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2100000 read pairs finished. 292 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2150000 read pairs finished. 295 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2200000 read pairs finished. 296 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2250000 read pairs finished. 315 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2300000 read pairs finished. 316 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2350000 read pairs finished. 318 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2400000 read pairs finished. 319 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2450000 read pairs finished. 338 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2500000 read pairs finished. 339 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2550000 read pairs finished. 341 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2600000 read pairs finished. 342 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2650000 read pairs finished. 362 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2700000 read pairs finished. 363 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2750000 read pairs finished. 365 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2800000 read pairs finished. 366 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2850000 read pairs finished. 385 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2900000 read pairs finished. 387 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2950000 read pairs finished. 388 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3000000 read pairs finished. 389 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3050000 read pairs finished. 408 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3100000 read pairs finished. 410 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3150000 read pairs finished. 411 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3200000 read pairs finished. 412 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3250000 read pairs finished. 430 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3300000 read pairs finished. 432 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3350000 read pairs finished. 434 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3400000 read pairs finished. 434 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3450000 read pairs finished. 453 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3500000 read pairs finished. 455 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3550000 read pairs finished. 458 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3600000 read pairs finished. 459 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3650000 read pairs finished. 477 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3700000 read pairs finished. 479 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3750000 read pairs finished. 481 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3800000 read pairs finished. 483 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3850000 read pairs finished. 501 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "2: \t3900000 read pairs finished. 502 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3950000 read pairs finished. 505 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4000000 read pairs finished. 506 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4050000 read pairs finished. 524 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4100000 read pairs finished. 525 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4150000 read pairs finished. 528 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4200000 read pairs finished. 529 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4250000 read pairs finished. 546 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4300000 read pairs finished. 548 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4350000 read pairs finished. 550 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4400000 read pairs finished. 553 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4450000 read pairs finished. 570 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4500000 read pairs finished. 572 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4550000 read pairs finished. 574 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4600000 read pairs finished. 577 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4650000 read pairs finished. 593 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4700000 read pairs finished. 595 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4750000 read pairs finished. 597 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4800000 read pairs finished. 599 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4850000 read pairs finished. 618 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4900000 read pairs finished. 619 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4950000 read pairs finished. 620 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5000000 read pairs finished. 622 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5050000 read pairs finished. 641 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5100000 read pairs finished. 642 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5150000 read pairs finished. 643 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5200000 read pairs finished. 645 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5250000 read pairs finished. 664 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5300000 read pairs finished. 666 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5350000 read pairs finished. 667 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5400000 read pairs finished. 669 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5450000 read pairs finished. 688 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5500000 read pairs finished. 689 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5550000 read pairs finished. 690 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5600000 read pairs finished. 693 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5650000 read pairs finished. 711 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5700000 read pairs finished. 713 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5750000 read pairs finished. 714 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5800000 read pairs finished. 715 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5850000 read pairs finished. 735 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5900000 read pairs finished. 736 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "1: \t5950000 read pairs finished. 737 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6000000 read pairs finished. 738 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6050000 read pairs finished. 757 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6100000 read pairs finished. 760 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6150000 read pairs finished. 760 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6200000 read pairs finished. 761 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6250000 read pairs finished. 782 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6350000 read pairs finished. 784 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6300000 read pairs finished. 785 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6400000 read pairs finished. 785 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6450000 read pairs finished. 806 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6500000 read pairs finished. 808 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6550000 read pairs finished. 808 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6600000 read pairs finished. 809 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6650000 read pairs finished. 829 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6700000 read pairs finished. 832 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6750000 read pairs finished. 833 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6800000 read pairs finished. 833 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6850000 read pairs finished. 852 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6900000 read pairs finished. 856 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6950000 read pairs finished. 856 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7000000 read pairs finished. 857 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7050000 read pairs finished. 875 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7100000 read pairs finished. 878 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7150000 read pairs finished. 879 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7200000 read pairs finished. 880 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7250000 read pairs finished. 894 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7300000 read pairs finished. 896 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7350000 read pairs finished. 898 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7400000 read pairs finished. 900 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7450000 read pairs finished. 917 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7500000 read pairs finished. 920 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7550000 read pairs finished. 921 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7600000 read pairs finished. 923 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7650000 read pairs finished. 940 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7700000 read pairs finished. 943 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7750000 read pairs finished. 944 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7800000 read pairs finished. 946 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7850000 read pairs finished. 963 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7900000 read pairs finished. 965 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7950000 read pairs finished. 967 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t8000000 read pairs finished. 969 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t8023643 read pairs finished. 971 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Total number of aligned reads: \r\n",
        "pairs:       3982551 (50%)\r\n",
        "single a:    1489442 (19%)\r\n",
        "single b:    1430646 (18%)\r\n",
        "Done.\r\n",
        "Finished at Wed Dec 17 10:17:20 2014\r\n",
        "Total time consumed:  971 secs\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "BSMAP v2.74\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Start at:  Wed Dec 17 10:17:21 2014\r\n",
        "\r\n",
        "Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \t(format: FASTA)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Load in 7658 db seqs, total size 557717710 bp. 20 secs passed\r\n",
        "total_kmers: 43046721\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Create seed table. 42 secs passed\r\n",
        "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n",
        "kmer cut-off ratio: 5e-07\r\n",
        "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n",
        "quality cutoff: 0\tbase quality char: '!'\r\n",
        "min fragment size:28\tmax fragemt size:500\r\n",
        "start from read #1\tend at read #4294967295\r\n",
        "additional alignment: T in reads => C in reference\r\n",
        "mapping strand (read_1): ++,-+\r\n",
        "mapping strand (read_2): +-,--\r\n",
        "Pair-end alignment(4 threads)\r\n",
        "Input read file #1: mcf_T1D3_R1.fastq \t(format: FASTQ)\r\n",
        "Input read file #2: mcf_T1D3_R2.fastq \t(format: FASTQ)\r\n",
        "Output file: bsmap_out_T1D3.sam\t (format: SAM)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t50000 read pairs finished. 62 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t100000 read pairs finished. 63 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t150000 read pairs finished. 64 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t200000 read pairs finished. 64 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t250000 read pairs finished. 83 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t300000 read pairs finished. 83 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t350000 read pairs finished. 84 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t400000 read pairs finished. 85 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t450000 read pairs finished. 103 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t500000 read pairs finished. 104 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t550000 read pairs finished. 105 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t600000 read pairs finished. 105 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t650000 read pairs finished. 124 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t700000 read pairs finished. 126 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t750000 read pairs finished. 127 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t800000 read pairs finished. 128 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t850000 read pairs finished. 144 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t900000 read pairs finished. 147 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t950000 read pairs finished. 148 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1000000 read pairs finished. 149 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1050000 read pairs finished. 165 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1100000 read pairs finished. 168 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1150000 read pairs finished. 169 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1200000 read pairs finished. 170 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1250000 read pairs finished. 186 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1300000 read pairs finished. 189 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1350000 read pairs finished. 190 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1400000 read pairs finished. 191 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1450000 read pairs finished. 207 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1500000 read pairs finished. 211 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1550000 read pairs finished. 212 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1600000 read pairs finished. 213 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1650000 read pairs finished. 229 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1700000 read pairs finished. 232 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1750000 read pairs finished. 233 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1800000 read pairs finished. 234 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1850000 read pairs finished. 249 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1900000 read pairs finished. 253 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1950000 read pairs finished. 254 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2000000 read pairs finished. 255 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2050000 read pairs finished. 271 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2100000 read pairs finished. 274 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2150000 read pairs finished. 274 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2200000 read pairs finished. 275 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2250000 read pairs finished. 291 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2300000 read pairs finished. 295 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2350000 read pairs finished. 296 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2400000 read pairs finished. 296 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2450000 read pairs finished. 311 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2500000 read pairs finished. 317 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2550000 read pairs finished. 317 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2600000 read pairs finished. 317 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2650000 read pairs finished. 331 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2700000 read pairs finished. 338 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2750000 read pairs finished. 338 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2800000 read pairs finished. 339 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2850000 read pairs finished. 352 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2900000 read pairs finished. 358 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2950000 read pairs finished. 360 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3000000 read pairs finished. 361 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3050000 read pairs finished. 373 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3100000 read pairs finished. 379 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3150000 read pairs finished. 381 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3200000 read pairs finished. 382 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3250000 read pairs finished. 394 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3300000 read pairs finished. 400 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3350000 read pairs finished. 402 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3400000 read pairs finished. 403 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3450000 read pairs finished. 415 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3500000 read pairs finished. 422 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3550000 read pairs finished. 423 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3600000 read pairs finished. 425 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3650000 read pairs finished. 436 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3700000 read pairs finished. 442 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3750000 read pairs finished. 444 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3800000 read pairs finished. 445 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3850000 read pairs finished. 456 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3900000 read pairs finished. 463 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3950000 read pairs finished. 464 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4000000 read pairs finished. 467 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4050000 read pairs finished. 479 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4100000 read pairs finished. 485 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4150000 read pairs finished. 486 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4200000 read pairs finished. 488 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4250000 read pairs finished. 500 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4300000 read pairs finished. 506 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4350000 read pairs finished. 507 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4400000 read pairs finished. 509 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4450000 read pairs finished. 521 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4500000 read pairs finished. 528 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4550000 read pairs finished. 529 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4600000 read pairs finished. 531 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4650000 read pairs finished. 541 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4700000 read pairs finished. 548 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4750000 read pairs finished. 549 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4800000 read pairs finished. 551 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4850000 read pairs finished. 561 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5016400 read pairs finished. 568 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4900000 read pairs finished. 569 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4950000 read pairs finished. 569 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5000000 read pairs finished. 571 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Total number of aligned reads: \r\n",
        "pairs:       2717832 (54%)\r\n",
        "single a:    1117376 (22%)\r\n",
        "single b:    1178713 (23%)\r\n",
        "Done.\r\n",
        "Finished at Wed Dec 17 10:26:52 2014\r\n",
        "Total time consumed:  571 secs\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "BSMAP v2.74\r\n",
        "Start at:  Wed Dec 17 10:26:53 2014\r\n",
        "\r\n",
        "Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \t(format: FASTA)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Load in 7658 db seqs, total size 557717710 bp. 11 secs passed\r\n",
        "total_kmers: 43046721\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Create seed table. 35 secs passed\r\n",
        "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n",
        "kmer cut-off ratio: 5e-07\r\n",
        "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n",
        "quality cutoff: 0\tbase quality char: '!'\r\n",
        "min fragment size:28\tmax fragemt size:500\r\n",
        "start from read #1\tend at read #4294967295\r\n",
        "additional alignment: T in reads => C in reference\r\n",
        "mapping strand (read_1): ++,-+\r\n",
        "mapping strand (read_2): +-,--\r\n",
        "Pair-end alignment(4 threads)\r\n",
        "Input read file #1: mcf_T1D5_R1.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " \t(format: FASTQ)\r\n",
        "Input read file #2: mcf_T1D5_R2.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " \t(format: FASTQ)\r\n",
        "Output file: bsmap_out_T1D5.sam\t (format: SAM)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t50000 read pairs finished. 59 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t100000 read pairs finished. 60 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #2: \t150000 read pairs finished. 60 secs passed\r\n"
       ]
      },
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       "text": [
        "Thread #3: \t200000 read pairs finished. 60 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #0: \t250000 read pairs finished. 82 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #1: \t300000 read pairs finished. 83 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #2: \t350000 read pairs finished. 84 secs passed\r\n"
       ]
      },
      {
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       "text": [
        "Thread #3: \t400000 read pairs finished. 85 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #0: \t450000 read pairs finished. 106 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t500000 read pairs finished. 107 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #2: \t550000 read pairs finished. 108 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #3: \t600000 read pairs finished. 108 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #0: \t650000 read pairs finished. 130 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #1: \t700000 read pairs finished. 132 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #2: \t750000 read pairs finished. 132 secs passed\r\n"
       ]
      },
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       "text": [
        "Thread #3: \t800000 read pairs finished. 133 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #0: \t850000 read pairs finished. 154 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t900000 read pairs finished. 155 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #2: \t950000 read pairs finished. 156 secs passed\r\n"
       ]
      },
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       "text": [
        "Thread #3: \t1000000 read pairs finished. 157 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #0: \t1050000 read pairs finished. 178 secs passed\r\n"
       ]
      },
      {
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       "text": [
        "Thread #1: \t1100000 read pairs finished. 179 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #2: \t1150000 read pairs finished. 180 secs passed\r\n"
       ]
      },
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       "text": [
        "Thread #3: \t1200000 read pairs finished. 181 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #0: \t1250000 read pairs finished. 202 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #1: \t1300000 read pairs finished. 203 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1350000 read pairs finished. 204 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1400000 read pairs finished. 205 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1450000 read pairs finished. 225 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1500000 read pairs finished. 226 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1550000 read pairs finished. 228 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1600000 read pairs finished. 229 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1650000 read pairs finished. 249 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1700000 read pairs finished. 250 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1750000 read pairs finished. 252 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1800000 read pairs finished. 253 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1850000 read pairs finished. 273 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1900000 read pairs finished. 274 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1950000 read pairs finished. 276 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2000000 read pairs finished. 277 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2050000 read pairs finished. 297 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2100000 read pairs finished. 298 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2150000 read pairs finished. 299 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2200000 read pairs finished. 300 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2250000 read pairs finished. 321 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2300000 read pairs finished. 322 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2350000 read pairs finished. 323 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2400000 read pairs finished. 325 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2450000 read pairs finished. 345 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2500000 read pairs finished. 346 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2550000 read pairs finished. 347 secs passed\r\n"
       ]
      },
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       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2600000 read pairs finished. 348 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2650000 read pairs finished. 369 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2700000 read pairs finished. 370 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2750000 read pairs finished. 371 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2800000 read pairs finished. 372 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2850000 read pairs finished. 393 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2900000 read pairs finished. 394 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2950000 read pairs finished. 394 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3000000 read pairs finished. 396 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3050000 read pairs finished. 417 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3100000 read pairs finished. 418 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3150000 read pairs finished. 419 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3200000 read pairs finished. 419 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3250000 read pairs finished. 440 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3300000 read pairs finished. 441 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3350000 read pairs finished. 442 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3400000 read pairs finished. 443 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3450000 read pairs finished. 463 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3500000 read pairs finished. 464 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3550000 read pairs finished. 466 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3600000 read pairs finished. 467 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3650000 read pairs finished. 488 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3700000 read pairs finished. 489 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3750000 read pairs finished. 490 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3800000 read pairs finished. 491 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3850000 read pairs finished. 512 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3900000 read pairs finished. 514 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3950000 read pairs finished. 514 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4000000 read pairs finished. 518 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4050000 read pairs finished. 538 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4100000 read pairs finished. 539 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4150000 read pairs finished. 540 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4200000 read pairs finished. 544 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4250000 read pairs finished. 563 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4300000 read pairs finished. 565 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4350000 read pairs finished. 566 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4400000 read pairs finished. 569 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4450000 read pairs finished. 589 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4500000 read pairs finished. 592 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4550000 read pairs finished. 592 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4600000 read pairs finished. 593 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4650000 read pairs finished. 613 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4700000 read pairs finished. 616 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4750000 read pairs finished. 617 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4800000 read pairs finished. 618 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4850000 read pairs finished. 638 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4900000 read pairs finished. 641 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4950000 read pairs finished. 642 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5000000 read pairs finished. 643 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5050000 read pairs finished. 663 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5100000 read pairs finished. 666 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5150000 read pairs finished. 667 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5200000 read pairs finished. 668 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5250000 read pairs finished. 687 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5300000 read pairs finished. 693 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5400000 read pairs finished. 695 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5350000 read pairs finished. 695 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5450000 read pairs finished. 712 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5500000 read pairs finished. 718 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5550000 read pairs finished. 720 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5600000 read pairs finished. 721 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5650000 read pairs finished. 738 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5700000 read pairs finished. 743 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5750000 read pairs finished. 746 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5800000 read pairs finished. 747 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5850000 read pairs finished. 763 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5900000 read pairs finished. 768 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5950000 read pairs finished. 771 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6000000 read pairs finished. 772 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6179274 read pairs finished. 786 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6050000 read pairs finished. 787 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6100000 read pairs finished. 791 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6150000 read pairs finished. 792 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Total number of aligned reads: \r\n",
        "pairs:       2725017 (44%)\r\n",
        "single a:    1704213 (28%)\r\n",
        "single b:    1415455 (23%)\r\n",
        "Done.\r\n",
        "Finished at Wed Dec 17 10:40:06 2014\r\n",
        "Total time consumed:  793 secs\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "BSMAP v2.74\r\n",
        "Start at:  Wed Dec 17 10:40:07 2014\r\n",
        "\r\n",
        "Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " \t(format: FASTA)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Load in 7658 db seqs, total size 557717710 bp. 19 secs passed\r\n",
        "total_kmers: 43046721\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Create seed table. 42 secs passed\r\n",
        "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n",
        "kmer cut-off ratio: 5e-07\r\n",
        "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n",
        "quality cutoff: 0\tbase quality char: '!'\r\n",
        "min fragment size:28\tmax fragemt size:500\r\n",
        "start from read #1\tend at read #4294967295\r\n",
        "additional alignment: T in reads => C in reference\r\n",
        "mapping strand (read_1): ++,-+\r\n",
        "mapping strand (read_2): +-,--\r\n",
        "Pair-end alignment(4 threads)\r\n",
        "Input read file #1: mcf_M3_R1.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " \t(format: FASTQ)\r\n",
        "Input read file #2: mcf_M3_R2.fastq \t(format: FASTQ)\r\n",
        "Output file: bsmap_out_M3.sam\t (format: SAM)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t50000 read pairs finished. 63 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t100000 read pairs finished. 64 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t150000 read pairs finished. 64 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t200000 read pairs finished. 65 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t250000 read pairs finished. 85 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t300000 read pairs finished. 86 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t350000 read pairs finished. 86 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t400000 read pairs finished. 87 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t450000 read pairs finished. 106 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t500000 read pairs finished. 108 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t550000 read pairs finished. 108 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t600000 read pairs finished. 109 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t650000 read pairs finished. 128 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t700000 read pairs finished. 129 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t750000 read pairs finished. 130 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t800000 read pairs finished. 132 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t850000 read pairs finished. 150 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t900000 read pairs finished. 151 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t950000 read pairs finished. 152 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1000000 read pairs finished. 154 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1050000 read pairs finished. 171 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1100000 read pairs finished. 173 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1150000 read pairs finished. 173 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1200000 read pairs finished. 175 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1250000 read pairs finished. 193 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1300000 read pairs finished. 194 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1350000 read pairs finished. 196 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1400000 read pairs finished. 197 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1450000 read pairs finished. 215 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1500000 read pairs finished. 216 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1550000 read pairs finished. 218 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1600000 read pairs finished. 219 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1650000 read pairs finished. 237 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1700000 read pairs finished. 238 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1750000 read pairs finished. 239 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1800000 read pairs finished. 241 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1850000 read pairs finished. 258 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1900000 read pairs finished. 260 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1950000 read pairs finished. 261 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2000000 read pairs finished. 262 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2050000 read pairs finished. 280 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2100000 read pairs finished. 282 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2150000 read pairs finished. 283 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2200000 read pairs finished. 284 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2250000 read pairs finished. 302 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2300000 read pairs finished. 303 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2350000 read pairs finished. 305 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2400000 read pairs finished. 307 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2450000 read pairs finished. 323 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2500000 read pairs finished. 326 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2550000 read pairs finished. 328 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2600000 read pairs finished. 329 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2650000 read pairs finished. 345 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2700000 read pairs finished. 347 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2750000 read pairs finished. 350 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2800000 read pairs finished. 351 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2850000 read pairs finished. 367 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2900000 read pairs finished. 369 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2950000 read pairs finished. 372 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3000000 read pairs finished. 373 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3050000 read pairs finished. 389 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3100000 read pairs finished. 391 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3150000 read pairs finished. 393 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3200000 read pairs finished. 394 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3250000 read pairs finished. 411 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3300000 read pairs finished. 412 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3350000 read pairs finished. 414 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "2: \t3400000 read pairs finished. 418 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3500000 read pairs finished. 435 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3450000 read pairs finished. 436 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3550000 read pairs finished. 437 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3600000 read pairs finished. 439 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3650000 read pairs finished. 458 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3700000 read pairs finished. 460 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3750000 read pairs finished. 460 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3800000 read pairs finished. 461 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3850000 read pairs finished. 480 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3900000 read pairs finished. 482 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3950000 read pairs finished. 483 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4000000 read pairs finished. 483 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4050000 read pairs finished. 502 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4100000 read pairs finished. 504 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4150000 read pairs finished. 504 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4200000 read pairs finished. 505 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4250000 read pairs finished. 525 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4300000 read pairs finished. 526 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4350000 read pairs finished. 527 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4400000 read pairs finished. 528 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4450000 read pairs finished. 547 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4500000 read pairs finished. 549 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4550000 read pairs finished. 550 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4600000 read pairs finished. 551 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4650000 read pairs finished. 569 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4700000 read pairs finished. 570 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4750000 read pairs finished. 572 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4800000 read pairs finished. 573 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4850000 read pairs finished. 590 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4900000 read pairs finished. 592 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4950000 read pairs finished. 594 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5000000 read pairs finished. 595 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5050000 read pairs finished. 611 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5100000 read pairs finished. 613 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5150000 read pairs finished. 617 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5200000 read pairs finished. 618 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5250000 read pairs finished. 634 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5300000 read pairs finished. 636 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5350000 read pairs finished. 639 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5400000 read pairs finished. 640 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5450000 read pairs finished. 656 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5500000 read pairs finished. 658 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5550000 read pairs finished. 662 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5600000 read pairs finished. 663 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5650000 read pairs finished. 678 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5700000 read pairs finished. 680 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5750000 read pairs finished. 684 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5800000 read pairs finished. 685 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5850000 read pairs finished. 699 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5900000 read pairs finished. 701 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5950000 read pairs finished. 706 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6000000 read pairs finished. 707 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6050000 read pairs finished. 721 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6100000 read pairs finished. 725 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6200000 read pairs finished. 729 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6150000 read pairs finished. 730 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6250000 read pairs finished. 743 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6300000 read pairs finished. 747 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6350000 read pairs finished. 752 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6400000 read pairs finished. 752 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6450000 read pairs finished. 765 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6500000 read pairs finished. 769 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6550000 read pairs finished. 773 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6600000 read pairs finished. 775 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6650000 read pairs finished. 787 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6700000 read pairs finished. 791 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6750000 read pairs finished. 795 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6800000 read pairs finished. 796 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6850000 read pairs finished. 809 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6900000 read pairs finished. 813 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6950000 read pairs finished. 817 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7000000 read pairs finished. 819 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7050000 read pairs finished. 831 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7100000 read pairs finished. 836 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7150000 read pairs finished. 839 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7200000 read pairs finished. 842 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7250000 read pairs finished. 853 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7300000 read pairs finished. 858 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7350000 read pairs finished. 862 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7400000 read pairs finished. 864 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7450000 read pairs finished. 875 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7500000 read pairs finished. 880 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7550000 read pairs finished. 883 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7600000 read pairs finished. 886 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7650000 read pairs finished. 897 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7700000 read pairs finished. 903 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7750000 read pairs finished. 905 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7800000 read pairs finished. 907 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7867124 read pairs finished. 909 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7850000 read pairs finished. 914 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Total number of aligned reads: \r\n",
        "pairs:       4545285 (58%)\r\n",
        "single a:    1331429 (17%)\r\n",
        "single b:    1233410 (16%)\r\n",
        "Done.\r\n",
        "Finished at Wed Dec 17 10:55:21 2014\r\n",
        "Total time consumed:  914 secs\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "BSMAP v2.74\r\n",
        "Start at:  Wed Dec 17 10:55:23 2014\r\n",
        "\r\n",
        "Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " \t(format: FASTA)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Load in 7658 db seqs, total size 557717710 bp. 18 secs passed\r\n",
        "total_kmers: 43046721\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Create seed table. 40 secs passed\r\n",
        "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n",
        "kmer cut-off ratio: 5e-07\r\n",
        "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n",
        "quality cutoff: 0\tbase quality char: '!'\r\n",
        "min fragment size:28\tmax fragemt size:500\r\n",
        "start from read #1\tend at read #4294967295\r\n",
        "additional alignment: T in reads => C in reference\r\n",
        "mapping strand (read_1): ++,-+\r\n",
        "mapping strand (read_2): +-,--\r\n",
        "Pair-end alignment(4 threads)\r\n",
        "Input read file #1: mcf_T3D3_R1.fastq \t(format: FASTQ)\r\n",
        "Input read file #2: mcf_T3D3_R2.fastq"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " \t(format: FASTQ)\r\n",
        "Output file: bsmap_out_T3D3.sam\t (format: SAM)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t50000 read pairs finished. 62 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t100000 read pairs finished. 63 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t150000 read pairs finished. 63 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t200000 read pairs finished. 64 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t250000 read pairs finished. 84 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t300000 read pairs finished. 85 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t350000 read pairs finished. 86 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t400000 read pairs finished. 86 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t450000 read pairs finished. 107 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t500000 read pairs finished. 108 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t550000 read pairs finished. 108 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t600000 read pairs finished. 109 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t650000 read pairs finished. 130 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t700000 read pairs finished. 131 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t750000 read pairs finished. 132 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t800000 read pairs finished. 132 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t850000 read pairs finished. 152 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t900000 read pairs finished. 153 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t950000 read pairs finished. 154 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1000000 read pairs finished. 155 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1050000 read pairs finished. 174 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1100000 read pairs finished. 176 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1150000 read pairs finished. 177 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1200000 read pairs finished. 177 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1250000 read pairs finished. 197 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1300000 read pairs finished. 199 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1350000 read pairs finished. 200 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1400000 read pairs finished. 201 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1450000 read pairs finished. 218 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1500000 read pairs finished. 224 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1550000 read pairs finished. 224 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1600000 read pairs finished. 225 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "1: \t1650000 read pairs finished. 241 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1700000 read pairs finished. 246 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1750000 read pairs finished. 247 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1800000 read pairs finished. 248 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1850000 read pairs finished. 263 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1900000 read pairs finished. 269 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1950000 read pairs finished. 270 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2000000 read pairs finished. 271 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2050000 read pairs finished. 285 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2100000 read pairs finished. 291 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2150000 read pairs finished. 292 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2200000 read pairs finished. 293 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2250000 read pairs finished. 307 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2300000 read pairs finished. 313 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2350000 read pairs finished. 314 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2400000 read pairs finished. 316 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2450000 read pairs finished. 332 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2500000 read pairs finished. 338 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2550000 read pairs finished. 339 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2600000 read pairs finished. 340 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2650000 read pairs finished. 354 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2700000 read pairs finished. 362 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2750000 read pairs finished. 363 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2800000 read pairs finished. 363 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2850000 read pairs finished. 376 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2900000 read pairs finished. 384 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2950000 read pairs finished. 385 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3000000 read pairs finished. 386 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3050000 read pairs finished. 398 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3100000 read pairs finished. 407 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3150000 read pairs finished. 408 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3200000 read pairs finished. 409 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3250000 read pairs finished. 420 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3300000 read pairs finished. 430 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3350000 read pairs finished. 431 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3400000 read pairs finished. 431 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3450000 read pairs finished. 443 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3500000 read pairs finished. 452 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3550000 read pairs finished. 454 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3600000 read pairs finished. 454 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3650000 read pairs finished. 465 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3700000 read pairs finished. 475 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3750000 read pairs finished. 476 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t3800000 read pairs finished. 477 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t3850000 read pairs finished. 488 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t3900000 read pairs finished. 497 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t3950000 read pairs finished. 498 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4000000 read pairs finished. 499 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4050000 read pairs finished. 510 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4100000 read pairs finished. 519 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4150000 read pairs finished. 520 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4200000 read pairs finished. 521 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4250000 read pairs finished. 533 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4300000 read pairs finished. 542 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4350000 read pairs finished. 543 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4400000 read pairs finished. 544 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4450000 read pairs finished. 556 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4500000 read pairs finished. 565 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4550000 read pairs finished. 566 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4600000 read pairs finished. 567 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4650000 read pairs finished. 578 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4700000 read pairs finished. 588 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4750000 read pairs finished. 589 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t4800000 read pairs finished. 590 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4850000 read pairs finished. 600 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4900000 read pairs finished. 610 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t4950000 read pairs finished. 611 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5000000 read pairs finished. 613 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5050000 read pairs finished. 622 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5100000 read pairs finished. 632 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5150000 read pairs finished. 634 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5200000 read pairs finished. 635 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5250000 read pairs finished. 647 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5300000 read pairs finished. 656 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5400000 read pairs finished. 658 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5350000 read pairs finished. 659 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5450000 read pairs finished. 670 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5500000 read pairs finished. 679 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5550000 read pairs finished. 681 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5600000 read pairs finished. 682 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5650000 read pairs finished. 693 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5700000 read pairs finished. 701 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5750000 read pairs finished. 704 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5800000 read pairs finished. 705 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5850000 read pairs finished. 715 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5900000 read pairs finished. 724 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5950000 read pairs finished. 727 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6000000 read pairs finished. 728 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6050000 read pairs finished. 737 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6100000 read pairs finished. 746 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6150000 read pairs finished. 750 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6200000 read pairs finished. 751 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6250000 read pairs finished. 760 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6300000 read pairs finished. 768 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6350000 read pairs finished. 773 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6400000 read pairs finished. 774 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6450000 read pairs finished. 783 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6500000 read pairs finished. 791 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6550000 read pairs finished. 796 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6600000 read pairs finished. 796 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6650000 read pairs finished. 805 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6700000 read pairs finished. 813 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6750000 read pairs finished. 818 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6800000 read pairs finished. 819 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6850000 read pairs finished. 827 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6900000 read pairs finished. 835 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6950000 read pairs finished. 840 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7000000 read pairs finished. 841 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7109789 read pairs finished. 844 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7050000 read pairs finished. 848 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7100000 read pairs finished. 852 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Total number of aligned reads: \r\n",
        "pairs:       4047152 ("
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "57%)\r\n",
        "single a:    1332491 (19%)\r\n",
        "single b:    1205102 (17%)\r\n",
        "Done.\r\n",
        "Finished at Wed Dec 17 11:09:35 2014\r\n",
        "Total time consumed:  852 secs\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "BSMAP v2.74\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Start at:  Wed Dec 17 11:09:37 2014\r\n",
        "\r\n",
        "Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \t(format: FASTA)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Load in 7658 db seqs, total size 557717710 bp. 19 secs passed\r\n",
        "total_kmers: 43046721\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Create seed table. 43 secs passed\r\n",
        "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n",
        "kmer cut-off ratio: 5e-07\r\n",
        "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n",
        "quality cutoff: 0\tbase quality char: '!'\r\n",
        "min fragment size:28\tmax fragemt size:500\r\n",
        "start from read #1\tend at read #4294967295\r\n",
        "additional alignment: T in reads => C in reference\r\n",
        "mapping strand (read_1): ++,-+\r\n",
        "mapping strand (read_2): +-,--\r\n",
        "Pair-end alignment(4 threads)\r\n",
        "Input read file #1: mcf_T3D5_R1.fastq \t(format: FASTQ)\r\n",
        "Input read file #2: mcf_T3D5_R2.fastq \t(format: FASTQ)\r\n",
        "Output file: bsmap_out_T3D5.sam\t (format: SAM)\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t50000 read pairs finished. 65 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t100000 read pairs finished. 65 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t150000 read pairs finished. 66 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t200000 read pairs finished. 66 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t250000 read pairs finished. 86 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t300000 read pairs finished. 87 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t350000 read pairs finished. 88 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t400000 read pairs finished. 89 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t450000 read pairs finished. 108 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t500000 read pairs finished. 109 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t550000 read pairs finished. 111 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t600000 read pairs finished. 111 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t650000 read pairs finished. 130 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t700000 read pairs finished. 131 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t750000 read pairs finished. 133 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t800000 read pairs finished. 134 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t850000 read pairs finished. 152 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t900000 read pairs finished. 153 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t950000 read pairs finished. 157 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1000000 read pairs finished. 158 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1050000 read pairs finished. 175 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1100000 read pairs finished. 176 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1150000 read pairs finished. 179 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1200000 read pairs finished. 180 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1250000 read pairs finished. 197 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1300000 read pairs finished. 199 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1350000 read pairs finished. 202 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1400000 read pairs finished. 203 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1450000 read pairs finished. 221 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1500000 read pairs finished. 222 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1550000 read pairs finished. 225 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1600000 read pairs finished. 226 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1650000 read pairs finished. 244 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1700000 read pairs finished. 245 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1750000 read pairs finished. 247 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t1800000 read pairs finished. 248 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t1850000 read pairs finished. 266 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t1900000 read pairs finished. 267 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t1950000 read pairs finished. 270 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2000000 read pairs finished. 271 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t2050000 read pairs finished. 289 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t2100000 read pairs finished. 290 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t2150000 read pairs finished. 292 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t2200000 read pairs finished. 293 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #1: \t2250000 read pairs finished. 311 secs passed\r\n"
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        "Thread #3: \t2300000 read pairs finished. 312 secs passed\r\n"
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        "Thread #0: \t2350000 read pairs finished. 314 secs passed\r\n"
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        "Thread #2: \t2400000 read pairs finished. 316 secs passed\r\n"
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        "Thread #1: \t2450000 read pairs finished. 334 secs passed\r\n"
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       "text": [
        "Thread #3: \t2500000 read pairs finished. 335 secs passed\r\n"
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       "text": [
        "Thread #0: \t2550000 read pairs finished. 337 secs passed\r\n"
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      },
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       "text": [
        "Thread #2: \t2600000 read pairs finished. 338 secs passed\r\n"
       ]
      },
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       "text": [
        "Thread #1: \t2650000 read pairs finished. 356 secs passed\r\n"
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        "Thread #3: \t2700000 read pairs finished. 357 secs passed\r\n"
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       "text": [
        "Thread #0: \t2750000 read pairs finished. 359 secs passed\r\n"
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       "text": [
        "Thread #2: \t2800000 read pairs finished. 361 secs passed\r\n"
       ]
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       "text": [
        "Thread #1: \t2850000 read pairs finished. 379 secs passed\r\n"
       ]
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        "Thread #3: \t2900000 read pairs finished. 381 secs passed\r\n"
       ]
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        "Thread #0: \t2950000 read pairs finished. 382 secs passed\r\n"
       ]
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       "text": [
        "Thread #2: \t3000000 read pairs finished. 384 secs passed\r\n"
       ]
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       "text": [
        "Thread #1: \t3050000 read pairs finished. 402 secs passed\r\n"
       ]
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       "text": [
        "Thread #3: \t3100000 read pairs finished. 403 secs passed\r\n"
       ]
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        "Thread #0: \t3150000 read pairs finished. 405 secs passed\r\n"
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       "text": [
        "Thread #2: \t3200000 read pairs finished. 407 secs passed\r\n"
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        "Thread #1: \t3250000 read pairs finished. 424 secs passed\r\n"
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        "Thread #1: \t3450000 read pairs finished. 447 secs passed\r\n"
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        "Thread #3: \t3500000 read pairs finished. 448 secs passed\r\n"
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        "Thread #2: \t3600000 read pairs finished. 454 secs passed\r\n"
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        "Thread #1: \t3650000 read pairs finished. 470 secs passed\r\n"
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        "Thread #3: \t3700000 read pairs finished. 471 secs passed\r\n"
       ]
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       "text": [
        "Thread #0: \t3750000 read pairs finished. 473 secs passed\r\n"
       ]
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       "text": [
        "Thread #2: \t3800000 read pairs finished. 477 secs passed\r\n"
       ]
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       "text": [
        "Thread #1: \t3850000 read pairs finished. 493 secs passed\r\n"
       ]
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        "Thread #3: \t3900000 read pairs finished. 493 secs passed\r\n"
       ]
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        "Thread #0: \t3950000 read pairs finished. 495 secs passed\r\n"
       ]
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       "text": [
        "Thread #2: \t4000000 read pairs finished. 500 secs passed\r\n"
       ]
      },
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       "text": [
        "Thread #1: \t4050000 read pairs finished. 515 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #3: \t4100000 read pairs finished. 516 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #0: \t4150000 read pairs finished. 517 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t4200000 read pairs finished. 521 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #1: \t4250000 read pairs finished. 538 secs passed\r\n"
       ]
      },
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       "text": [
        "Thread #3: \t4300000 read pairs finished. 540 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #0: \t4350000 read pairs finished. 541 secs passed\r\n"
       ]
      },
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       "text": [
        "Thread #2: \t4400000 read pairs finished. 544 secs passed\r\n"
       ]
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       "text": [
        "Thread #1: \t4450000 read pairs finished. 561 secs passed\r\n"
       ]
      },
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       "text": [
        "Thread #3: \t4500000 read pairs finished. 563 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #0: \t4550000 read pairs finished. 563 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #2: \t4600000 read pairs finished. 566 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t4650000 read pairs finished. 584 secs passed\r\n"
       ]
      },
      {
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       "text": [
        "Thread #3: \t4700000 read pairs finished. 585 secs passed\r\n"
       ]
      },
      {
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       "text": [
        "Thread #0: \t4750000 read pairs finished. 586 secs passed\r\n"
       ]
      },
      {
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       "text": [
        "Thread #2: \t4800000 read pairs finished. 588 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #1: \t4850000 read pairs finished. 606 secs passed\r\n"
       ]
      },
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       "text": [
        "Thread #3: \t4900000 read pairs finished. 607 secs passed\r\n"
       ]
      },
      {
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       "text": [
        "Thread #0: \t4950000 read pairs finished. 609 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5000000 read pairs finished. 611 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5050000 read pairs finished. 628 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5100000 read pairs finished. 629 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5150000 read pairs finished. 632 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5200000 read pairs finished. 634 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #1: \t5250000 read pairs finished. 650 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #3: \t5300000 read pairs finished. 651 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5350000 read pairs finished. 654 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5400000 read pairs finished. 657 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5450000 read pairs finished. 672 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5500000 read pairs finished. 673 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5550000 read pairs finished. 676 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5600000 read pairs finished. 679 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5650000 read pairs finished. 695 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5700000 read pairs finished. 697 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t5750000 read pairs finished. 701 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t5800000 read pairs finished. 703 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t5850000 read pairs finished. 718 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t5900000 read pairs finished. 720 secs passed\r\n"
       ]
      },
      {
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       "stream": "stdout",
       "text": [
        "Thread #0: \t5950000 read pairs finished. 723 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #2: \t6000000 read pairs finished. 726 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
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       "text": [
        "Thread #1: \t6050000 read pairs finished. 740 secs passed\r\n"
       ]
      },
      {
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       "text": [
        "Thread #3: \t6100000 read pairs finished. 743 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6150000 read pairs finished. 746 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6200000 read pairs finished. 748 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6250000 read pairs finished. 762 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6300000 read pairs finished. 766 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6350000 read pairs finished. 769 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6400000 read pairs finished. 772 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6450000 read pairs finished. 785 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6500000 read pairs finished. 789 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6550000 read pairs finished. 792 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6600000 read pairs finished. 795 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6650000 read pairs finished. 807 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6700000 read pairs finished. 811 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6750000 read pairs finished. 815 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t6800000 read pairs finished. 818 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t6850000 read pairs finished. 829 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t6900000 read pairs finished. 833 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t6950000 read pairs finished. 837 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #2: \t7000000 read pairs finished. 840 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #0: \t7125800 read pairs finished. 847 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #1: \t7050000 read pairs finished. 849 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Thread #3: \t7100000 read pairs finished. 851 secs passed\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Total number of aligned reads: \r\n",
        "pairs:       4092568 (57%)\r\n",
        "single a:    1250715 (18%)\r\n",
        "single b:    1133306 (16%)\r\n",
        "Done.\r\n",
        "Finished at Wed Dec 17 11:23:48 2014\r\n",
        "Total time consumed:  851 secs\r\n"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 9
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "_methratio_"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "methratio is a python script that accompanies BSMAP that determines methylation level on CpG loci"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for i in (\"M1\",\"T1D3\",\"T1D5\", \"M3\", \"T3D3\", \"T3D5\"):\n",
      "    !python {bsmaploc}methratio.py \\\n",
      "-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \\\n",
      "-u -z -g \\\n",
      "-o methratio_out_{i}.txt \\\n",
      "-s {bsmaploc}samtools \\\n",
      "bsmap_out_{i}.sam \\\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:23:58 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:24:47 2014: reading bsmap_out_M1.sam ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[samopen] SAM header is present: 7658 sequences.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\t@ Wed Dec 17 11:31:21 2014: read 10000000 lines\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:32:02 2014: combining CpG methylation from both strands ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:32:28 2014: writing methratio_out_M1.txt ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:44:36 2014: done.\r\n",
        "total 8716467 valid mappings, 48671764 covered cytosines, average coverage: 1.78 fold.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:44:45 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:45:34 2014: reading bsmap_out_T1D3.sam ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[samopen] SAM header is present: 7658 sequences.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[sam_read1] reference '40311' is recognized as '*'.\r\n",
        "Parse error at line 4984809: invalid CIGAR operation\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:48:02 2014: combining CpG methylation from both strands ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:48:31 2014: writing methratio_out_T1D3.txt ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:54:10 2014: done.\r\n",
        "total 3738314 valid mappings, 18812679 covered cytosines, average coverage: 1.23 fold.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:54:15 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 11:55:05 2014: reading bsmap_out_T1D5.sam ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[samopen] SAM header is present: 7658 sequences.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:00:44 2014: combining CpG methylation from both strands ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:01:15 2014: writing methratio_out_T1D5.txt ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:12:40 2014: done.\r\n",
        "total 6974208 valid mappings, 45446465 covered cytosines, average coverage: 1.54 fold.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:12:44 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:13:34 2014: reading bsmap_out_M3.sam ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[samopen] SAM header is present: 7658 sequences.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\t@ Wed Dec 17 12:20:17 2014: read 10000000 lines\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:21:23 2014: combining CpG methylation from both strands ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:21:53 2014: writing methratio_out_M3.txt ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:35:02 2014: done.\r\n",
        "total 9773223 valid mappings, 53389886 covered cytosines, average coverage: 1.78 fold.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:35:16 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:36:05 2014: reading bsmap_out_T3D3.sam ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[samopen] SAM header is present: 7658 sequences.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\t@ Wed Dec 17 12:42:54 2014: read 10000000 lines\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:43:19 2014: combining CpG methylation from both strands ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:43:50 2014: writing methratio_out_T3D3.txt ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:56:50 2014: done.\r\n",
        "total 8847902 valid mappings, 52255860 covered cytosines, average coverage: 1.65 fold.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:57:00 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 12:57:49 2014: reading bsmap_out_T3D5.sam ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[samopen] SAM header is present: 7658 sequences.\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\t@ Wed Dec 17 13:04:27 2014: read 10000000 lines\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 13:04:49 2014: combining CpG methylation from both strands ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 13:05:20 2014: writing methratio_out_T3D5.txt ...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "@ Wed Dec 17 13:18:12 2014: done.\r\n",
        "total 8808414 valid mappings, 51732152 covered cytosines, average coverage: 1.69 fold.\r\n"
       ]
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Global Differences: methylkit"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "**Converting methratio files for methylkit**"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#first methratio files are converted to filter for CG context, 3x coverage (mr3x.awk), and reformatting (mr_gg.awk.sh).\n",
      "#due to issue passing variable to awk, simple scripts were used (included in repository)\n",
      "for i in (\"M1\",\"T1D3\",\"T1D5\", \"M3\", \"T3D3\", \"T3D5\"):\n",
      "    !echo {i}\n",
      "    !grep \"[A-Z][A-Z]CG[A-Z]\" <methratio_out_{i}.txt> methratio_out_{i}CG.txt\n",
      "    !awk -f ../scripts/mr3x.awk methratio_out_{i}CG.txt > mr3x.{i}.txt\n",
      "    !awk -f ../scripts/mr_gg.awk.sh mr3x.{i}.txt > mkfmt_{i}.txt\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "M1\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "T1D3\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "T1D5\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "M3\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "T3D3\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "T3D5\r\n"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "**Running R > methylkit**"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%pylab inline"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Populating the interactive namespace from numpy and matplotlib\n"
       ]
      }
     ],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%load_ext rpy2.ipython\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 13
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "#UNCOMMENT IF YOU NEED TO INSTALL PACKAGES\n",
      "# dependencies\n",
      "#install.packages( c(\"data.table\",\"devtools\"))\n",
      "#source(\"http://bioconductor.org/biocLite.R\")\n",
      "#biocLite(c(\"GenomicRanges\",\"IRanges\"))\n",
      "\n",
      "# install the development version from github\n",
      "#library(devtools)\n",
      "#install_github(\"al2na/methylKit\",build_vignettes=FALSE)\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "display_data",
       "text": [
        "NULL\n"
       ]
      }
     ],
     "prompt_number": 14
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%R library(methylKit)\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 15,
       "text": [
        "array(['methylKit', 'tools', 'stats', 'graphics', 'grDevices', 'utils',\n",
        "       'datasets', 'methods', 'base'], \n",
        "      dtype='|S9')"
       ]
      }
     ],
     "prompt_number": 15
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R file.list <- list \n",
      "('mkfmt_M1.txt',\n",
      " 'mkfmt_T1D3.txt',\n",
      " 'mkfmt_T1D5.txt',\n",
      " 'mkfmt_M3.txt',\n",
      " 'mkfmt_T3D3.txt',\n",
      " 'mkfmt_T3D5.txt'\n",
      ")\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 16
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "myobj=read(file.list,sample.id=list(\"1_sperm\",\"1_72hpf\",\"1_120hpf\",\"3_sperm\",\"3_72hpf\",\"3_120hpf\"),assembly=\"v9\",treatment=c(0,0,0,1,1,1))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 17
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "meth<-unite(myobj)\n",
      "#getCorrelation(meth,plot=T)\n",
      "hc<- clusterSamples(meth, dist=\"correlation\", method=\"ward\", plot=T)\n",
      "#PCA<-PCASamples(meth)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "display_data",
       "text": [
        "The \"ward\" method has been renamed to \"ward.D\"; note new \"ward.D2\"\n"
       ]
      },
      {
       "metadata": {},
       "output_type": "display_data",
       "png": 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hARIgARIgAT8SsCIKOhZYtIwxRphCAiRAAiRAAn4iYL0Bhut44sSJfmJOXUiA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\nQmCC\n"
      }
     ],
     "prompt_number": 18
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Differentially methylated loci"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Determining differentially methylated loci using methylkit\n"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "#Family-specific DMLs\n",
      "#note that file.list was defined in prior section\n",
      "DMLobj=read(file.list,sample.id=list(\"M1\",\"T1D3\",\"T1D5\",\"M3\",\"T3D3\",\"T3D5\"),assembly=\"v9\",treatment=c(1,1,1,0,0,0), context=\"CpG\")\n",
      "lin<-unite(DMLobj)\n",
      "lin.pooled <- pool(lin, sample.ids <- c(\"lin_1\", \"lin_3\"))\n",
      "lin_DML.fisher <- calculateDiffMeth(lin.pooled)\n",
      "select(lin_DML.fisher, 1)\n",
      "lin_DML_p <- getData(lin_DML.fisher)\n",
      "lin_DML_filt <- lin_DML_p[lin_DML_p$pvalue < 0.01 & lin_DML_p$meth.diff > 25,]\n",
      "write.csv(lin_DML_filt,file=\"lin_DML_filt\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc -l lin_DML_filt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     113 lin_DML_filt\r\n"
       ]
      }
     ],
     "prompt_number": 20
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "####Differentially methylated loci during development. \n",
      "This is done by doing three pairwise comparisons"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R file.list <- list \n",
      "('mkfmt_M1.txt',\n",
      " 'mkfmt_T1D3.txt',\n",
      " 'mkfmt_M3.txt',\n",
      " 'mkfmt_T3D3.txt'\n",
      ")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 21
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R \n",
      "#Developmentally different DMLs (Males v Day3)\n",
      "DMLobj=read(file.list,sample.id=list(\"M1\",\"T1D3\",\"M3\",\"T3D3\"), assembly=\"v9\",treatment=c(1,0,1,0), context=\"CpG\")\n",
      "DevelMvD3<-unite(DMLobj)\n",
      "DevelMvD3.pooled <- pool(DevelMvD3, sample.ids <- c(\"Males\", \"Day3\"))\n",
      "DevelMvD3_DML.fisher <- calculateDiffMeth(DevelMvD3.pooled)\n",
      "select(DevelMvD3_DML.fisher, 1)\n",
      "DevelMvD3_DML_p <- getData(DevelMvD3_DML.fisher)\n",
      "DevelMvD3_DML_filt <- DevelMvD3_DML_p[DevelMvD3_DML_p$pvalue < 0.01 & DevelMvD3_DML_p$meth.diff > 25,]\n",
      "write.csv(DevelMvD3_DML_filt,file=\"DevelMvD3_DML_filt\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 22
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc -l DevelMvD3_DML_filt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "      18 DevelMvD3_DML_filt\r\n"
       ]
      }
     ],
     "prompt_number": 23
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R file.list <- list \n",
      "('mkfmt_M1.txt',\n",
      " 'mkfmt_T1D5.txt',\n",
      " 'mkfmt_M3.txt',\n",
      " 'mkfmt_T3D5.txt'\n",
      ")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 24
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R \n",
      "#Developmentally different DMLs (Males v Day5)\n",
      "DMLobj=read(file.list,sample.id=list(\"M1\",\"T1D5\",\"M3\",\"T3D5\"), assembly=\"v9\",treatment=c(1,0,1,0), context=\"CpG\")\n",
      "DevelMvD5<-unite(DMLobj)\n",
      "DevelMvD5.pooled <- pool(DevelMvD5, sample.ids <- c(\"Males\", \"Day5\"))\n",
      "DevelMvD5_DML.fisher <- calculateDiffMeth(DevelMvD5.pooled)\n",
      "select(DevelMvD5_DML.fisher, 1)\n",
      "DevelMvD5_DML_p <- getData(DevelMvD5_DML.fisher)\n",
      "DevelMvD5_DML_filt <- DevelMvD5_DML_p[DevelMvD5_DML_p$pvalue < 0.01 & DevelMvD5_DML_p$meth.diff > 25,]\n",
      "write.csv(DevelMvD5_DML_filt,file=\"DevelMvD5_DML_filt\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 25
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc -l DevelMvD5_DML_filt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "      86 DevelMvD5_DML_filt\r\n"
       ]
      }
     ],
     "prompt_number": 26
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R file.list <- list \n",
      "('mkfmt_T1D3.txt',\n",
      " 'mkfmt_T1D5.txt',\n",
      " 'mkfmt_T3D3.txt',\n",
      " 'mkfmt_T3D5.txt'\n",
      ")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 27
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R \n",
      "#Developmentally different DMLs (Day3 v Day5)\n",
      "DMLobj=read(file.list,sample.id=list(\"T1D3\",\"T1D5\",\"T3D3\",\"T3D5\"), assembly=\"v9\",treatment=c(1,0,1,0), context=\"CpG\")\n",
      "DevelD3vD5<-unite(DMLobj)\n",
      "DevelD3vD5.pooled <- pool(DevelD3vD5, sample.ids <- c(\"Day3\", \"Day5\"))\n",
      "DevelD3vD5_DML.fisher <- calculateDiffMeth(DevelD3vD5.pooled)\n",
      "select(DevelD3vD5_DML.fisher, 1)\n",
      "DevelD3vD5_DML_p <- getData(DevelD3vD5_DML.fisher)\n",
      "DevelD3vD5_DML_filt <- DevelD3vD5_DML_p[DevelD3vD5_DML_p$pvalue < 0.01 & DevelD3vD5_DML_p$meth.diff > 25,]\n",
      "write.csv(DevelD3vD5_DML_filt,file=\"DevelD3vD5_DML_filt\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 28
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc -l DevelD3vD5_DML_filt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "      22 DevelD3vD5_DML_filt\r\n"
       ]
      }
     ],
     "prompt_number": 29
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#removing column titles\n",
      "!tail -n +2 DevelMvD5_DML_filt > DevelMvD5_DML\n",
      "!tail -n +2 DevelD3vD5_DML_filt > DevelD3vD5_DML "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 30
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Concatenate all developmetnally different DMLs to one file\n",
      "!cat DevelMvD3_DML_filt DevelMvD5_DML DevelD3vD5_DML > Devel_DML_filt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 31
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc -l Devel_DML_filt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     124 Devel_DML_filt\r\n"
       ]
      }
     ],
     "prompt_number": 32
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "###Creating DML BED files"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!tail -n +2 lin_DML_filt | awk -F, '{print $2, $3, $4, \"DML_lin\" }' | tr -d '\"' | tr ' ' \"\\t\"  > lineage_dml.bed"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 33
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc -l lineage_dml.bed"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     112 lineage_dml.bed\r\n"
       ]
      }
     ],
     "prompt_number": 34
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!tail -n +2 Devel_DML_filt | awk -F, '{print $2, $3, $4, \"DML_dev\" }' | tr -d '\"' | tr ' ' \"\\t\"  > dev_dml.bed"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 35
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc -l dev_dml.bed"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "     123 dev_dml.bed\r\n"
       ]
      }
     ],
     "prompt_number": 36
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Genomic location of DMLs"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#In order to find location of DMLs oyster genome tracks will be downloaded\n",
      "#and intersectbed (bedtools suite) run\n",
      "#Note track with all CG's is large (~977mb)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 37
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd genome_tracks\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/Volumes/web/cnidarian/olson-ms-nb-master_12_1714/wd/genome_tracks\n"
       ]
      }
     ],
     "prompt_number": 38
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for i in (\"exon\",\"intron\",\"TE\",\"gene\",\"1k5p_gene_promoter\",\"CG\"):\n",
      "    !curl -O http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_{i}.gff \n",
      "\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\r\n",
        "                                 Dload  Upload   Total   Spent    Left  Speed\r\n",
        "\r",
        "  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "  0 11.7M    0  4122    0     0   8189      0  0:25:09 --:--:--  0:25:09 24831"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "100 11.7M  100 11.7M    0     0  12.7M      0 --:--:-- --:--:-- --:--:-- 20.0M\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\r\n",
        "                                 Dload  Upload   Total   Spent    Left  Speed\r\n",
        "\r",
        "  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 87 12.0M   87 10.5M    0     0  50.4M      0 --:--:-- --:--:-- --:--:-- 50.6M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "100 12.0M  100 12.0M    0     0  48.4M      0 --:--:-- --:--:-- --:--:-- 48.6M\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\r\n",
        "                                 Dload  Upload   Total   Spent    Left  Speed\r\n",
        "\r",
        "  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "100 6325k  100 6325k    0     0  56.7M      0 --:--:-- --:--:-- --:--:-- 57.7M\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\r\n",
        "                                 Dload  Upload   Total   Spent    Left  Speed\r\n",
        "\r",
        "  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "100 1777k  100 1777k    0     0  22.3M      0 --:--:-- --:--:-- --:--:-- 39.4M\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\r\n",
        "                                 Dload  Upload   Total   Spent    Left  Speed\r\n",
        "\r",
        "  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "100 1848k  100 1848k    0     0  22.0M      0 --:--:-- --:--:-- --:--:-- 22.5M\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\r\n",
        "                                 Dload  Upload   Total   Spent    Left  Speed\r\n",
        "\r",
        "  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "  4  932M    4 43.0M    0     0  43.4M      0  0:00:21 --:--:--  0:00:21 43.4M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "  6  932M    6 61.0M    0     0  30.4M      0  0:00:30  0:00:02  0:00:28 30.4M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "  8  932M    8 81.0M    0     0  27.1M      0  0:00:34  0:00:02  0:00:32 27.1M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 10  932M   10  100M    0     0  24.9M      0  0:00:37  0:00:04  0:00:33 24.9M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 15  932M   15  140M    0     0  28.0M      0  0:00:33  0:00:04  0:00:29 28.0M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 15  932M   15  148M    0     0  24.1M      0  0:00:38  0:00:06  0:00:32 20.4M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 17  932M   17  167M    0     0  23.9M      0  0:00:38  0:00:06  0:00:32 21.3M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 22  932M   22  206M    0     0  25.8M      0  0:00:36  0:00:07  0:00:29 25.1M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 24  932M   24  223M    0     0  24.9M      0  0:00:37  0:00:08  0:00:29 24.8M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 26  932M   26  246M    0     0  24.7"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "M      0  0:00:37  0:00:09  0:00:28 21.3M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 29  932M   29  276M    0     0  25.1M      0  0:00:37  0:00:10  0:00:27 26.4M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 32  932M   32  302M    0     0  25.1M      0  0:00:37  0:00:12  0:00:25 26.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 34  932M   34  325M    0     0  25.0M      0  0:00:37  0:00:12  0:00:25 23.8M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 38  932M   38  360M    0     0  25.7M      0  0:00:36  0:00:14  0:00:22 27.1M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 40  932M   40  374M    0     0  24.9M      0  0:00:37  0:00:15  0:00:22 25.3M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 41  932M   41  386M    0     0  24.0M      0  0:00:38  0:00:16  0:00:22 21.5M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 44  932M   44  418M    0     0  24.6M      0  0:00:37  0:00:16  0:00:21 23.4M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 47  932M   47  441M    0     0  24.5M      0  0:00:37  0:00:18  0:00:19 23.0M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 49  932M   49  459M    0     0  24.2M      0  0:00:38  0:00:18  0:00:20 20.0M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 53  932M   53  495M    0     0  24.7M      0  0:00:37  0:00:19  0:00:18 24.3M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 54  932M   54  510M    0     0  24.1M      0  0:00:38  0:00:21  0:00:17 24.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 56  932M   56  529M    0     0  23.8M      0  0:00:39  0:00:22  0:00:17 21.2M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 59  932M   59  551M    0     0  24.0M      0  0:00:38  0:00:22  0:00:16 22.1M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 62  932M   62  583M    0     0  24.3M      0  0:00:38  0:00:23  0:00:15 24.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 64  932M   64  600M    0     0  24.0M      0  0:00:38  0:00:25  0:00:13 20.9M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 66  932M   66  620M    0     0  23.8M      0  0:00:39  0:00:25  0:00:14 22.5M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 69  932M   69  643M    0     0  23.8M      0  0:00:39  0:00:26  0:00:13 23.8M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 70  932M   70  658M    0     0  23.3M      0  0:00:39  0:00:28  0:00:11 20.6M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 71  932M   71  669M    0     0  23.1M      0  0:00:40  0:00:28  0:00:12 17.2M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 73  932M   73  680M    0     0  22.6M      0  0:00:41  0:00:30  0:00:11 15.9M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 76  932M   76  713M    0     0  23.0M      0  0:00:40  0:00:31  0:00:09 18.5M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 79  932M   79  740M    0     0  23.0M      0  0:00:40  0:00:32  0:00:08 18.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 81  932M   81  755M    0     0  22.9M      0  0:00:40  0:00:32  0:00:08 20.0M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 84  932M   84  783M    0     0  23.0M      0  0:0"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "0:40  0:00:33  0:00:07 22.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 86  932M   86  806M    0     0  23.0M      0  0:00:40  0:00:35  0:00:05 25.1M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 88  932M   88  828M    0     0  23.0M      0  0:00:40  0:00:36  0:00:04 22.9M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 91  932M   91  850M    0     0  23.0M      0  0:00:40  0:00:36  0:00:04 22.8M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 94  932M   94  877M    0     0  23.1M      0  0:00:40  0:00:37  0:00:03 24.4M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 95  932M   95  891M    0     0  22.8M      0  0:00:40  0:00:38  0:00:02 21.6M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        " 98  932M   98  914M    0     0  22.8M      0  0:00:40  0:00:39  0:00:01 21.7M"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "100  932M  100  932M    0     0  23.0M      0  0:00:40  0:00:40 --:--:-- 23.0M\r\n"
       ]
      }
     ],
     "prompt_number": 39
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd .."
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/Volumes/web/cnidarian/olson-ms-nb-master_12_1714/wd\n"
       ]
      }
     ],
     "prompt_number": 40
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for i in (\"exon\",\"intron\",\"TE\",\"1k5p_gene_promoter\"):\n",
      "    !intersectbed \\\n",
      "    -u \\\n",
      "    -a lineage_dml.bed \\\n",
      "    -b ./genome_tracks/Cgigas_v9_{i}.gff \\\n",
      "    > {i}_intersect_DML_lin_u.txt\n",
      "    !wc -l {i}_intersect_DML_lin_u.txt > lin{i}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 41
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Concatenate counts of genomic regions into one table for lineage-specific DMLs\n",
      "!cat linintron linexon lin1k5p_gene_promoter linTE > lintable"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 42
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk 'FNR==NR{sum+=$1;next}; {print $0,sum}' lintable{,} > lin_total"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 43
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $2, $1, $3, (($1/$3)*100)}' lin_total > lineage_DMLs"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 44
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for i in (\"exon\",\"intron\",\"TE\",\"1k5p_gene_promoter\"):\n",
      "    !intersectbed \\\n",
      "    -u \\\n",
      "    -a dev_dml.bed \\\n",
      "    -b ./genome_tracks/Cgigas_v9_{i}.gff \\\n",
      "    > {i}_intersect_DML_dev_u.txt\n",
      "    !wc -l {i}_intersect_DML_dev_u.txt > dev{i}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 45
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Concatenate counts of genomic regions into one table for developmentally different DMLs\n",
      "!cat devintron devexon dev1k5p_gene_promoter devTE  > devtable"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 46
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk 'FNR==NR{sum+=$1;next}; {print $0,sum}' devtable{,} > dev_total"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 47
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $2, $1, $3, (($1/$3)*100)}' dev_total > developmental_DMLs"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 48
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for i in (\"exon\",\"intron\",\"TE\",\"gene\",\"1k5p_gene_promoter\"):\n",
      "    !intersectbed \\\n",
      "    -u \\\n",
      "    -a ./genome_tracks/Cgigas_v9_CG.gff \\\n",
      "    -b ./genome_tracks/Cgigas_v9_{i}.gff \\\n",
      "    > {i}_intersect_CG_u.txt\n",
      "    !wc -l {i}_intersect_CG_u.txt > CG{i}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 49
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Concatenate counts of genomic regions into one table for all CGs in oyster genome\n",
      "!cat CGintron CGexon CG1k5p_gene_promoter CGTE > CGtable"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 50
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk 'FNR==NR{sum+=$1;next}; {print $0,sum}' CGtable{,} > CG_total"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 51
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $2, $1, $3, (($1/$3)*100)}' CG_total > all_CGs"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 52
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!paste -d\" \" lineage_DMLs developmental_DMLs all_CGs > StackedBars"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 53
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $4, $8, $12}' StackedBars | tr ' ' \"\\t\" > StackedBars_DMLs"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 54
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Stacked Bar Plot of DMLs versus all CGs"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R \n",
      "DMLs<-as.matrix(read.table('StackedBars_DMLs', header=F))\n",
      "colnames(DMLs)<-c(\"Lin DMLs\",\"Devel DMLs\", \"All CpGs\")\n",
      "par(mar=c(5.1, 4.1, 4.1, 8.1), xpd=T)\n",
      "par(xpd=T, mar=par()$mar+c(0,0,0,5))\n",
      "barplot(as.matrix(DMLs), col=c(\"#BCCCC1\", \"#8DAB96\", \"#4A7958\", \"#2F583B\"), ylab=\"Proportion of CpG within a genomic region (%)\")\n",
      "legend(\"topright\",inset=c(-0.63,-0), legend=c(\"Transposable Element\", \"Promoter Region\", \"Exon\", \"Intron\"), pch=c(19,19,19), col=c(\"#2F583B\",\"#4A7958\",\"#8DAB96\",\"#BCCCC1\"))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "display_data",
       "png": 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VLlzY5s+f79paFXy//vprt1z/aFq8bt26WcOGDV3J76233nIBSCU9zcymkqMmoWjQoIG9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\nN7rPTJ+bHjJIb2cslfLVvvvnP/85fGucejbLWR2v1CFL6dN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      }
     ],
     "prompt_number": 55
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Statistical Analysis (Chi-squared test)"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Formatting family-specific DML files for stats\n",
      "!wc -l lineage_dml.bed > lineage_countstotal"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 56
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wc -l ./genome_tracks/Cgigas_v9_CG.gff > CG_countstotal"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 57
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!cat linTE lineage_countstotal > Lineage_TEs"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 58
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $1}' Lineage_TEs > Lineage_TEs_counts"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 59
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!cat CGTE CG_countstotal > CG_TEs"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 60
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $1}' CG_TEs > CG_TEs_counts"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 61
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!paste Lineage_TEs_counts CG_TEs_counts > LinTEs_combined"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 62
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $1, $2}' LinTEs_combined > Lineage_TEs_stats"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 63
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "#Stats for TEs: family-specific\n",
      "LinStats<- read.table('Lineage_TEs_stats')\n",
      "chisq.test(LinStats)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "display_data",
       "text": [
        "\n",
        "\tPearson's Chi-squared test with Yates' continuity correction\n",
        "\n",
        "data:  LinStats\n",
        "X-squared = 12.9119, df = 1, p-value = 0.0003265\n",
        "\n"
       ]
      }
     ],
     "prompt_number": 64
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#formatting developmental DML files for stats\n",
      "!wc -l dev_dml.bed > dev_countstotal"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 65
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!cat devTE dev_countstotal > Dev_TEs"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 66
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $1}' Dev_TEs > Dev_TEs_counts"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 67
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!paste Dev_TEs_counts CG_TEs_counts > DevTEs_combined"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 68
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print $1, $2}' DevTEs_combined > Dev_TEs_stats"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 69
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "#Stats for TEs: developmentally different\n",
      "DevStats<-read.table('Dev_TEs_stats')\n",
      "chisq.test(DevStats)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "display_data",
       "text": [
        "\n",
        "\tPearson's Chi-squared test with Yates' continuity correction\n",
        "\n",
        "data:  DevStats\n",
        "X-squared = 8.3265, df = 1, p-value = 0.003907\n",
        "\n"
       ]
      }
     ],
     "prompt_number": 70
    }
   ],
   "metadata": {}
  }
 ]
}