notebooks/Download PanCan12 data.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Download PanCan12 data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In this notebook, we download various data files required for the analyses performed in the other notebooks.\n",
    "\n",
    "> **Attention**\n",
    ">\n",
    "> Downloading the TCGA data requires the [firehose_get](https://confluence.broadinstitute.org/display/GDAC/Download) utility, which we assume has been installed and added to the executable `PATH`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import sys\n",
    "sys.path.append(\"../lib\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import nbsupport.tcga\n",
    "import nbsupport.util"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "firehoseDate = \"2014_07_15\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "DATA_DIR = \"../data\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "!mkdir {DATA_DIR}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/data/s.canisius/notebooks/discover/data\n"
     ]
    }
   ],
   "source": [
    "%cd {DATA_DIR}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "!mkdir downloads\n",
    "!mkdir entrez\n",
    "!mkdir tcga"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/data/s.canisius/notebooks/discover/data/downloads\n"
     ]
    }
   ],
   "source": [
    "%cd downloads"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## PanCan12 alteration data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Validating run selection against Broad Institute website ...\n",
      "You've asked to download archives for the following tasks\n",
      "\n",
      "     copynumber_gistic MutSigNozzleReport2CV\n",
      "\n",
      "run against the disease cohorts\n",
      "\n",
      "      COAD LUSC READ GBM LAML HNSC BLCA UCEC LUAD OV BRCA KIRC\n",
      "\n",
      "from the analyses__2014_07_15 Firehose run. \n",
      "Attempting to retrieve data for Broad GDAC run analyses__2014_07_15 ...\n",
      "--2016-02-24 11:50:39--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/COAD/\n",
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      "--2016-02-24 11:50:45--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/COAD/20140715/gdac.broadinstitute.org_COAD-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/COAD/20140715/gdac.broadinstitute.org_COAD-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
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      "--2016-02-24 11:51:12--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/COAD/20140715/gdac.broadinstitute.org_COAD-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
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      "--2016-02-24 11:51:12--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/COAD/20140715/gdac.broadinstitute.org_COAD-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
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      "--2016-02-24 11:52:54--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/COAD/20140715/gdac.broadinstitute.org_COAD-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
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      " 55296K ........ ........ ........ ........ ........ ........ 53% 1.91M 40s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 56% 2.19M 37s\n",
      " 61440K ........ ........ ........ ........ ........ ........ 59% 2.29M 34s\n",
      " 64512K ........ ........ ........ ........ ........ ........ 62% 2.35M 31s\n",
      " 67584K ........ ........ ........ ........ ........ ........ 64% 2.36M 28s\n",
      " 70656K ........ ........ ........ ........ ........ ........ 67% 2.36M 25s\n",
      " 73728K ........ ........ ........ ........ ........ ........ 70% 2.05M 23s\n",
      " 76800K ........ ........ ........ ........ ........ ........ 73% 2.20M 20s\n",
      " 79872K ........ ........ ........ ........ ........ ........ 76% 2.52M 18s\n",
      " 82944K ........ ........ ........ ........ ........ ........ 79% 1.96M 15s\n",
      " 86016K ........ ........ ........ ........ ........ ........ 81% 2.16M 13s\n",
      " 89088K ........ ........ ........ ........ ........ ........ 84% 2.52M 11s\n",
      " 92160K ........ ........ ........ ........ ........ ........ 87% 2.53M 9s\n",
      " 95232K ........ ........ ........ ........ ........ ........ 90% 2.53M 7s\n",
      " 98304K ........ ........ ........ ........ ........ ........ 93% 2.36M 5s\n",
      "101376K ........ ........ ........ ........ ........ ........ 95% 2.73M 3s\n",
      "104448K ........ ........ ........ ........ ........ ........ 98% 2.74M 1s\n",
      "107520K ........ ........ .....                              100% 2.44M=67s\n",
      "--2016-02-24 11:54:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.2M=0s\n",
      "--2016-02-24 11:54:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  574M=0s\n",
      "--2016-02-24 11:54:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 22.2M=0s\n",
      "--2016-02-24 11:54:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 18% 1.83M 7s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 36% 2.67M 5s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 55% 2.73M 3s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 73% 2.69M 2s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 91% 2.65M 1s\n",
      " 15360K ........ ........ .....                              100% 1.95M=6.8s\n",
      "--2016-02-24 11:55:04--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.8M=0s\n",
      "--2016-02-24 11:55:04--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  407M=0s\n",
      "--2016-02-24 11:55:05--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 34.2M=0s\n",
      "--2016-02-24 11:55:05--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  987M=0s\n",
      "--2016-02-24 11:55:05--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUSC/20140715/gdac.broadinstitute.org_LUSC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 34.1M=0s\n",
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      "Downloaded: 26 files, 153M in 1m 48s (1.41 MB/s)\n",
      "--2016-02-24 11:55:05--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/\n",
      "     0K                                                      100%  158M=0s\n",
      "2016-02-24 11:55:06 ERROR 404: Not Found.\n",
      "--2016-02-24 11:55:06--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/?C=N;O=D\n",
      "     0K                                                      100%  110M=0s\n",
      "--2016-02-24 11:55:06--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/?C=M;O=A\n",
      "     0K                                                      100%  282M=0s\n",
      "--2016-02-24 11:55:06--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/?C=S;O=A\n",
      "     0K                                                      100%  273M=0s\n",
      "--2016-02-24 11:55:06--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/?C=D;O=A\n",
      "     0K                                                      100%  163M=0s\n",
      "--2016-02-24 11:55:06--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/\n",
      "     0K .                                                      496K=0.2s\n",
      "--2016-02-24 11:55:08--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/?C=N;O=A\n",
      "     0K                                                      100%  233M=0s\n",
      "--2016-02-24 11:55:08--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/?C=M;O=D\n",
      "     0K                                                      100%  167M=0s\n",
      "--2016-02-24 11:55:08--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/?C=S;O=D\n",
      "     0K                                                      100%  287M=0s\n",
      "--2016-02-24 11:55:08--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/?C=D;O=D\n",
      "     0K                                                      100%  284M=0s\n",
      "--2016-02-24 11:55:09--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/?C=N;O=D\n",
      "     0K .                                                      497K=0.2s\n",
      "--2016-02-24 11:55:09--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/?C=M;O=A\n",
      "     0K .                                                      498K=0.2s\n",
      "--2016-02-24 11:55:09--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/?C=S;O=A\n",
      "     0K .                                                      497K=0.2s\n",
      "--2016-02-24 11:55:10--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/?C=D;O=A\n",
      "     0K .                                                      498K=0.2s\n",
      "--2016-02-24 11:55:10--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 13% 1.90M 10s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 27% 2.74M 7s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 41% 2.74M 5s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 55% 2.65M 4s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 68% 2.54M 3s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 82% 2.73M 1s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 96% 2.74M 0s\n",
      " 21504K ........ ...                                         100% 2.73M=8.6s\n",
      "--2016-02-24 11:55:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.3M=0s\n",
      "--2016-02-24 11:55:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  4% 1.92M 36s\n",
      "  3072K ........ ........ ........ ........ ........ ........  8% 2.71M 29s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 12% 2.74M 26s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 16% 2.72M 24s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 20% 2.64M 23s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 25% 2.53M 21s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 29% 1.56M 22s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 33% 1.65M 22s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 37% 1.73M 21s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 41% 1.84M 20s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 46% 2.05M 18s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 50% 2.49M 17s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 54% 2.72M 15s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 58% 2.62M 14s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 62% 2.74M 12s\n",
      " 46080K ........ ........ ........ ........ ........ ........ 66% 2.70M 11s\n",
      " 49152K ........ ........ ........ ........ ........ ........ 71% 2.33M 9s\n",
      " 52224K ........ ........ ........ ........ ........ ........ 75% 2.04M 8s\n",
      " 55296K ........ ........ ........ ........ ........ ........ 79% 1.94M 7s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 83% 1.68M 5s\n",
      " 61440K ........ ........ ........ ........ ........ ........ 87% 1.87M 4s\n",
      " 64512K ........ ........ ........ ........ ........ ........ 92% 2.01M 3s\n",
      " 67584K ........ ........ ........ ........ ........ ........ 96% 1.83M 1s\n",
      " 70656K ........ ........ ........ ........ ........ ...     100% 2.10M=34s\n",
      "--2016-02-24 11:55:53--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 19.1M=0s\n",
      "--2016-02-24 11:55:53--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  358M=0s\n",
      "--2016-02-24 11:55:53--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.3M=0s\n",
      "--2016-02-24 11:55:54--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ......           100% 1.58M=1.5s\n",
      "--2016-02-24 11:55:55--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 30.0M=0s\n",
      "--2016-02-24 11:55:56--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  199M=0s\n",
      "--2016-02-24 11:55:56--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.0M=0s\n",
      "--2016-02-24 11:55:56--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  410M=0s\n",
      "--2016-02-24 11:55:56--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/READ/20140715/gdac.broadinstitute.org_READ-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.8M=0s\n",
      "FINISHED --2016-02-24 11:55:56--\n",
      "Total wall clock time: 51s\n",
      "Downloaded: 26 files, 96M in 45s (2.16 MB/s)\n",
      "--2016-02-24 11:55:56--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/\n",
      "     0K                                                      100%  111M=0s\n",
      "2016-02-24 11:55:57 ERROR 404: Not Found.\n",
      "--2016-02-24 11:55:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/?C=N;O=D\n",
      "     0K                                                      100%  107M=0s\n",
      "--2016-02-24 11:55:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/?C=M;O=A\n",
      "     0K                                                      100%  165M=0s\n",
      "--2016-02-24 11:55:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/?C=S;O=A\n",
      "     0K                                                      100%  156M=0s\n",
      "--2016-02-24 11:55:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/?C=D;O=A\n",
      "     0K                                                      100%  165M=0s\n",
      "--2016-02-24 11:55:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/\n",
      "     0K .                                                      483K=0.2s\n",
      "--2016-02-24 11:56:00--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/?C=N;O=A\n",
      "     0K                                                      100%  221M=0s\n",
      "--2016-02-24 11:56:00--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/?C=M;O=D\n",
      "     0K                                                      100%  172M=0s\n",
      "--2016-02-24 11:56:00--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/?C=S;O=D\n",
      "     0K                                                      100%  167M=0s\n",
      "--2016-02-24 11:56:00--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/?C=D;O=D\n",
      "     0K                                                      100%  170M=0s\n",
      "--2016-02-24 11:56:01--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/?C=N;O=D\n",
      "     0K .                                                      483K=0.2s\n",
      "--2016-02-24 11:56:01--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/?C=M;O=A\n",
      "     0K .                                                      186K=0.5s\n",
      "--2016-02-24 11:56:02--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/?C=S;O=A\n",
      "     0K .                                                      242K=0.4s\n",
      "--2016-02-24 11:56:02--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/?C=D;O=A\n",
      "     0K .                                                      242K=0.4s\n",
      "--2016-02-24 11:56:03--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 10%  720K 38s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 20% 2.35M 22s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 30% 2.19M 16s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 40% 2.53M 12s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 50% 2.74M 9s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 60% 2.74M 7s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 71% 2.74M 5s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 81% 2.53M 3s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 91% 2.74M 1s\n",
      " 27648K ........ ........ ........ ........ ........ .       100% 2.77M=15s\n",
      "--2016-02-24 11:56:18--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.5M=0s\n",
      "--2016-02-24 11:56:18--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  2% 1.61M 76s\n",
      "  3072K ........ ........ ........ ........ ........ ........  4% 2.31M 63s\n",
      "  6144K ........ ........ ........ ........ ........ ........  7% 2.73M 55s\n",
      "  9216K ........ ........ ........ ........ ........ ........  9% 2.73M 51s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 11% 2.06M 51s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 14% 2.01M 50s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 16% 1.80M 50s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 19% 1.94M 49s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 21% 1.93M 48s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 23% 1.81M 47s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 26% 1.24M 48s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 28% 1.50M 48s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 30% 1.64M 47s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 33% 1.53M 46s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 35% 1.57M 45s\n",
      " 46080K ........ ........ ........ ........ ........ ........ 38% 1.80M 43s\n",
      " 49152K ........ ........ ........ ........ ........ ........ 40% 1.46M 42s\n",
      " 52224K ........ ........ ........ ........ ........ ........ 42% 1.63M 41s\n",
      " 55296K ........ ........ ........ ........ ........ ........ 45% 1.74M 39s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 47% 1.83M 37s\n",
      " 61440K ........ ........ ........ ........ ........ ........ 49% 1.83M 36s\n",
      " 64512K ........ ........ ........ ........ ........ ........ 52% 2.19M 34s\n",
      " 67584K ........ ........ ........ ........ ........ ........ 54% 2.45M 32s\n",
      " 70656K ........ ........ ........ ........ ........ ........ 57% 2.85M 29s\n",
      " 73728K ........ ........ ........ ........ ........ ........ 59% 1.63M 28s\n",
      " 76800K ........ ........ ........ ........ ........ ........ 61% 1.65M 26s\n",
      " 79872K ........ ........ ........ ........ ........ ........ 64% 1.74M 25s\n",
      " 82944K ........ ........ ........ ........ ........ ........ 66% 1.93M 23s\n",
      " 86016K ........ ........ ........ ........ ........ ........ 68% 1.95M 21s\n",
      " 89088K ........ ........ ........ ........ ........ ........ 71% 2.35M 20s\n",
      " 92160K ........ ........ ........ ........ ........ ........ 73% 2.74M 18s\n",
      " 95232K ........ ........ ........ ........ ........ ........ 76% 2.74M 16s\n",
      " 98304K ........ ........ ........ ........ ........ ........ 78% 2.09M 14s\n",
      "101376K ........ ........ ........ ........ ........ ........ 80% 1.74M 13s\n",
      "104448K ........ ........ ........ ........ ........ ........ 83% 1.83M 11s\n",
      "107520K ........ ........ ........ ........ ........ ........ 85% 1.93M 10s\n",
      "110592K ........ ........ ........ ........ ........ ........ 87% 1.95M 8s\n",
      "113664K ........ ........ ........ ........ ........ ........ 90% 2.17M 6s\n",
      "116736K ........ ........ ........ ........ ........ ........ 92% 2.35M 5s\n",
      "119808K ........ ........ ........ ........ ........ ........ 95% 2.74M 3s\n",
      "122880K ........ ........ ........ ........ ........ ........ 97% 2.74M 2s\n",
      "125952K ........ ........ ........ ........ ........ ........ 99% 2.74M 0s\n",
      "129024K ...                                                  100% 2.36M=65s\n",
      "--2016-02-24 11:57:23--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 19.8M=0s\n",
      "--2016-02-24 11:57:23--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  810M=0s\n",
      "--2016-02-24 11:57:24--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 34.9M=0s\n",
      "--2016-02-24 11:57:24--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 41% 1.30M 3s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 82% 1.74M 1s\n",
      "  6144K ........ ........ .....                              100% 1.81M=4.8s\n",
      "--2016-02-24 11:57:29--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.8M=0s\n",
      "--2016-02-24 11:57:29--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  460M=0s\n",
      "--2016-02-24 11:57:29--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 31.9M=0s\n",
      "--2016-02-24 11:57:29--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100% 1.09G=0s\n",
      "--2016-02-24 11:57:30--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/GBM/20140715/gdac.broadinstitute.org_GBM-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.4M=0s\n",
      "FINISHED --2016-02-24 11:57:30--\n",
      "Total wall clock time: 1m 33s\n",
      "Downloaded: 26 files, 164M in 1m 26s (1.90 MB/s)\n",
      "--2016-02-24 11:57:30--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/\n",
      "     0K                                                      100%  162M=0s\n",
      "2016-02-24 11:57:30 ERROR 404: Not Found.\n",
      "--2016-02-24 11:57:30--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/?C=N;O=D\n",
      "     0K                                                      100%  111M=0s\n",
      "--2016-02-24 11:57:30--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/?C=M;O=A\n",
      "     0K                                                      100%  172M=0s\n",
      "--2016-02-24 11:57:30--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/?C=S;O=A\n",
      "     0K                                                      100%  167M=0s\n",
      "--2016-02-24 11:57:31--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/?C=D;O=A\n",
      "     0K                                                      100%  168M=0s\n",
      "--2016-02-24 11:57:31--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/\n",
      "     0K                                                        348K=0.2s\n",
      "--2016-02-24 11:57:32--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/?C=N;O=A\n",
      "     0K                                                      100%  111M=0s\n",
      "--2016-02-24 11:57:33--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/?C=M;O=D\n",
      "     0K                                                      100%  172M=0s\n",
      "--2016-02-24 11:57:33--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/?C=S;O=D\n",
      "     0K                                                      100%  172M=0s\n",
      "--2016-02-24 11:57:33--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/?C=D;O=D\n",
      "     0K                                                      100%  171M=0s\n",
      "--2016-02-24 11:57:33--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/?C=N;O=D\n",
      "     0K                                                        347K=0.2s\n",
      "--2016-02-24 11:57:34--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/?C=M;O=A\n",
      "     0K                                                        348K=0.2s\n",
      "--2016-02-24 11:57:34--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/?C=S;O=A\n",
      "     0K                                                        342K=0.2s\n",
      "--2016-02-24 11:57:34--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/?C=D;O=A\n",
      "     0K                                                        348K=0.2s\n",
      "--2016-02-24 11:57:35--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 14% 1.57M 11s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 28% 2.74M 7s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 42% 2.70M 5s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 57% 2.74M 4s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 71% 2.68M 3s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 85% 2.01M 1s\n",
      " 18432K ........ ........ ........ ........ ........ ......  100% 2.48M=9.0s\n",
      "--2016-02-24 11:57:44--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.1M=0s\n",
      "--2016-02-24 11:57:44--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  4% 1.93M 31s\n",
      "  3072K ........ ........ ........ ........ ........ ........  9% 2.73M 25s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 14% 2.55M 23s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 19% 2.74M 21s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 23% 2.74M 19s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 28% 2.73M 18s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 33% 2.75M 16s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 38% 2.74M 15s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 43% 2.50M 14s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 47% 1.78M 13s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 52% 1.04M 14s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 57% 1.22M 13s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 62% 1.37M 12s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 67% 1.57M 11s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 71% 2.06M 9s\n",
      " 46080K ........ ........ ........ ........ ........ ........ 76% 2.74M 7s\n",
      " 49152K ........ ........ ........ ........ ........ ........ 81% 2.74M 6s\n",
      " 52224K ........ ........ ........ ........ ........ ........ 86% 2.55M 4s\n",
      " 55296K ........ ........ ........ ........ ........ ........ 91% 2.46M 3s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 95% 2.20M 1s\n",
      " 61440K ........ ........ ........ ........ ........ .       100% 2.57M=30s\n",
      "--2016-02-24 11:58:14--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.0M=0s\n",
      "--2016-02-24 11:58:15--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  515M=0s\n",
      "--2016-02-24 11:58:15--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.9M=0s\n",
      "--2016-02-24 11:58:15--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........                           100% 1.02M=1.5s\n",
      "--2016-02-24 11:58:17--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.2M=0s\n",
      "--2016-02-24 11:58:17--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  321M=0s\n",
      "--2016-02-24 11:58:17--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.8M=0s\n",
      "--2016-02-24 11:58:17--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  478M=0s\n",
      "--2016-02-24 11:58:18--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LAML/20140715/gdac.broadinstitute.org_LAML-TB.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.3M=0s\n",
      "FINISHED --2016-02-24 11:58:18--\n",
      "Total wall clock time: 48s\n",
      "Downloaded: 26 files, 85M in 41s (2.06 MB/s)\n",
      "--2016-02-24 11:58:18--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/\n",
      "     0K                                                      100%  160M=0s\n",
      "2016-02-24 11:58:18 ERROR 404: Not Found.\n",
      "--2016-02-24 11:58:18--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/?C=N;O=D\n",
      "     0K                                                      100%  109M=0s\n",
      "--2016-02-24 11:58:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/?C=M;O=A\n",
      "     0K                                                      100%  165M=0s\n",
      "--2016-02-24 11:58:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/?C=S;O=A\n",
      "     0K                                                      100%  164M=0s\n",
      "--2016-02-24 11:58:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/?C=D;O=A\n",
      "     0K                                                      100%  163M=0s\n",
      "--2016-02-24 11:58:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/\n",
      "     0K .                                                      466K=0.2s\n",
      "--2016-02-24 11:58:21--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/?C=N;O=A\n",
      "     0K                                                      100%  155M=0s\n",
      "--2016-02-24 11:58:21--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/?C=M;O=D\n",
      "     0K                                                      100%  168M=0s\n",
      "--2016-02-24 11:58:21--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/?C=S;O=D\n",
      "     0K                                                      100%  168M=0s\n",
      "--2016-02-24 11:58:21--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/?C=D;O=D\n",
      "     0K                                                      100%  171M=0s\n",
      "--2016-02-24 11:58:22--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/?C=N;O=D\n",
      "     0K .                                                      418K=0.2s\n",
      "--2016-02-24 11:58:22--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/?C=M;O=A\n",
      "     0K .                                                      418K=0.2s\n",
      "--2016-02-24 11:58:22--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/?C=S;O=A\n",
      "     0K .                                                      417K=0.2s\n",
      "--2016-02-24 11:58:23--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/?C=D;O=A\n",
      "     0K .                                                      417K=0.2s\n",
      "--2016-02-24 11:58:23--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 10% 1.37M 19s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 21% 2.73M 12s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 31% 2.74M 10s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 42% 2.55M 8s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 52% 2.73M 6s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 63% 2.74M 5s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 73% 2.32M 3s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 84% 2.52M 2s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 94% 2.72M 1s\n",
      " 27648K ........ ........ ........                           100% 2.17M=12s\n",
      "--2016-02-24 11:58:35--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.0M=0s\n",
      "--2016-02-24 11:58:36--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  2% 1.73M 59s\n",
      "  3072K ........ ........ ........ ........ ........ ........  5% 2.35M 50s\n",
      "  6144K ........ ........ ........ ........ ........ ........  8% 1.90M 49s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 11% 1.17M 56s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 14% 1.15M 59s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 17% 1.30M 59s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 19% 1.14M 59s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 22% 1.31M 58s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 25% 1.37M 56s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 28% 1.57M 53s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 31% 2.05M 49s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 34% 1.98M 46s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 37% 2.35M 43s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 39% 2.53M 40s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 42% 2.49M 37s\n",
      " 46080K ........ ........ ........ ........ ........ ........ 45% 2.53M 34s\n",
      " 49152K ........ ........ ........ ........ ........ ........ 48% 2.53M 32s\n",
      " 52224K ........ ........ ........ ........ ........ ........ 51% 2.58M 30s\n",
      " 55296K ........ ........ ........ ........ ........ ........ 54% 2.71M 27s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 57% 2.71M 25s\n",
      " 61440K ........ ........ ........ ........ ........ ........ 59% 2.74M 23s\n",
      " 64512K ........ ........ ........ ........ ........ ........ 62% 2.70M 21s\n",
      " 67584K ........ ........ ........ ........ ........ ........ 65% 2.70M 19s\n",
      " 70656K ........ ........ ........ ........ ........ ........ 68% 2.72M 17s\n",
      " 73728K ........ ........ ........ ........ ........ ........ 71% 2.74M 16s\n",
      " 76800K ........ ........ ........ ........ ........ ........ 74% 2.62M 14s\n",
      " 79872K ........ ........ ........ ........ ........ ........ 77% 2.31M 12s\n",
      " 82944K ........ ........ ........ ........ ........ ........ 79% 1.79M 11s\n",
      " 86016K ........ ........ ........ ........ ........ ........ 82% 1.83M 9s\n",
      " 89088K ........ ........ ........ ........ ........ ........ 85% 1.93M 8s\n",
      " 92160K ........ ........ ........ ........ ........ ........ 88% 1.94M 6s\n",
      " 95232K ........ ........ ........ ........ ........ ........ 91% 2.06M 5s\n",
      " 98304K ........ ........ ........ ........ ........ ........ 94% 2.35M 3s\n",
      "101376K ........ ........ ........ ........ ........ ........ 96% 2.73M 2s\n",
      "104448K ........ ........ ........ ........ ........ ........ 99% 2.53M 0s\n",
      "107520K ..                                                   100%  864K=53s\n",
      "--2016-02-24 11:59:29--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 19.5M=0s\n",
      "--2016-02-24 11:59:29--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  521M=0s\n",
      "--2016-02-24 11:59:29--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 32.8M=0s\n",
      "--2016-02-24 11:59:30--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 18% 1.85M 7s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 37% 2.55M 5s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 56% 2.72M 3s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 75% 2.67M 2s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 93% 2.74M 0s\n",
      " 15360K ........ .......                                     100% 2.68M=6.5s\n",
      "--2016-02-24 11:59:36--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.7M=0s\n",
      "--2016-02-24 11:59:36--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  439M=0s\n",
      "--2016-02-24 11:59:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.3M=0s\n",
      "--2016-02-24 11:59:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  981M=0s\n",
      "--2016-02-24 11:59:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/HNSC/20140715/gdac.broadinstitute.org_HNSC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.4M=0s\n",
      "FINISHED --2016-02-24 11:59:37--\n",
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      "--2016-02-24 11:59:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/\n",
      "     0K                                                      100%  162M=0s\n",
      "2016-02-24 11:59:38 ERROR 404: Not Found.\n",
      "--2016-02-24 11:59:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/?C=N;O=D\n",
      "     0K                                                      100%  111M=0s\n",
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      "--2016-02-24 11:59:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/?C=S;O=A\n",
      "     0K                                                      100%  201M=0s\n",
      "--2016-02-24 11:59:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/?C=D;O=A\n",
      "     0K                                                      100%  197M=0s\n",
      "--2016-02-24 11:59:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/\n",
      "     0K .                                                      416K=0.2s\n",
      "--2016-02-24 11:59:40--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/?C=N;O=A\n",
      "     0K                                                      100%  209M=0s\n",
      "--2016-02-24 11:59:40--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/?C=M;O=D\n",
      "     0K                                                      100%  210M=0s\n",
      "--2016-02-24 11:59:40--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/?C=S;O=D\n",
      "     0K                                                      100%  197M=0s\n",
      "--2016-02-24 11:59:40--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/?C=D;O=D\n",
      "     0K                                                      100%  195M=0s\n",
      "--2016-02-24 11:59:40--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/?C=N;O=D\n",
      "     0K .                                                      418K=0.2s\n",
      "--2016-02-24 11:59:41--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/?C=M;O=A\n",
      "     0K .                                                      418K=0.2s\n",
      "--2016-02-24 11:59:41--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/?C=S;O=A\n",
      "     0K .                                                      417K=0.2s\n",
      "--2016-02-24 11:59:42--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/?C=D;O=A\n",
      "     0K .                                                      417K=0.2s\n",
      "--2016-02-24 11:59:42--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 12% 1.93M 11s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 24% 2.54M 8s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 37% 2.74M 6s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 49% 2.74M 5s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 61% 2.49M 4s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 74% 2.34M 3s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 86% 2.54M 1s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 99% 2.74M 0s\n",
      " 24576K ...                                                  100% 2.47M=9.8s\n",
      "--2016-02-24 11:59:52--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 33.5M=0s\n",
      "--2016-02-24 11:59:52--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  3% 1.93M 45s\n",
      "  3072K ........ ........ ........ ........ ........ ........  6% 2.60M 38s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 10% 2.74M 34s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 13% 2.74M 32s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 16% 2.74M 30s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 20% 2.55M 28s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 23% 2.74M 27s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 26% 2.69M 25s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 30% 2.31M 25s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 33% 2.53M 23s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 36% 2.73M 22s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 40% 2.74M 21s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 43% 2.74M 20s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 47% 2.52M 18s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 50% 2.71M 17s\n",
      " 46080K ........ ........ ........ ........ ........ ........ 53% 2.69M 16s\n",
      " 49152K ........ ........ ........ ........ ........ ........ 57% 2.05M 15s\n",
      " 52224K ........ ........ ........ ........ ........ ........ 60% 2.20M 14s\n",
      " 55296K ........ ........ ........ ........ ........ ........ 63% 2.35M 13s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 67% 2.31M 12s\n",
      " 61440K ........ ........ ........ ........ ........ ........ 70% 2.34M 11s\n",
      " 64512K ........ ........ ........ ........ ........ ........ 73% 2.53M 9s\n",
      " 67584K ........ ........ ........ ........ ........ ........ 77% 2.74M 8s\n",
      " 70656K ........ ........ ........ ........ ........ ........ 80% 2.54M 7s\n",
      " 73728K ........ ........ ........ ........ ........ ........ 84% 2.71M 6s\n",
      " 76800K ........ ........ ........ ........ ........ ........ 87% 2.51M 4s\n",
      " 79872K ........ ........ ........ ........ ........ ........ 90% 2.19M 3s\n",
      " 82944K ........ ........ ........ ........ ........ ........ 94% 2.52M 2s\n",
      " 86016K ........ ........ ........ ........ ........ ........ 97% 2.72M 1s\n",
      " 89088K ........ ........ ........ ........ ...              100% 2.60M=36s\n",
      "--2016-02-24 12:00:28--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 19.6M=0s\n",
      "--2016-02-24 12:00:28--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  526M=0s\n",
      "--2016-02-24 12:00:28--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.9M=0s\n",
      "--2016-02-24 12:00:29--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 25% 1.92M 5s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 50% 2.72M 3s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 75% 2.51M 1s\n",
      "  9216K ........ ........ ........ ........ ........ .....   100% 1.52M=5.7s\n",
      "--2016-02-24 12:00:35--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.9M=0s\n",
      "--2016-02-24 12:00:35--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  291M=0s\n",
      "--2016-02-24 12:00:35--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.5M=0s\n",
      "--2016-02-24 12:00:35--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  760M=0s\n",
      "--2016-02-24 12:00:36--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BLCA/20140715/gdac.broadinstitute.org_BLCA-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.2M=0s\n",
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      "--2016-02-24 12:00:36--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/\n",
      "     0K                                                      100%  166M=0s\n",
      "2016-02-24 12:00:36 ERROR 404: Not Found.\n",
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      "     0K                                                      100%  111M=0s\n",
      "--2016-02-24 12:00:36--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/?C=M;O=A\n",
      "     0K                                                      100%  167M=0s\n",
      "--2016-02-24 12:00:36--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/?C=S;O=A\n",
      "     0K                                                      100%  165M=0s\n",
      "--2016-02-24 12:00:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/?C=D;O=A\n",
      "     0K                                                      100%  165M=0s\n",
      "--2016-02-24 12:00:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/\n",
      "     0K .                                                      498K=0.2s\n",
      "--2016-02-24 12:00:39--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/?C=N;O=A\n",
      "     0K                                                      100%  221M=0s\n",
      "--2016-02-24 12:00:39--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/?C=M;O=D\n",
      "     0K                                                      100%  171M=0s\n",
      "--2016-02-24 12:00:39--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/?C=S;O=D\n",
      "     0K                                                      100%  170M=0s\n",
      "--2016-02-24 12:00:39--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/?C=D;O=D\n",
      "     0K                                                      100%  168M=0s\n",
      "--2016-02-24 12:00:40--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/?C=N;O=D\n",
      "     0K .                                                      333K=0.3s\n",
      "--2016-02-24 12:00:40--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/?C=M;O=A\n",
      "     0K .                                                      493K=0.2s\n",
      "--2016-02-24 12:00:40--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/?C=S;O=A\n",
      "     0K .                                                      497K=0.2s\n",
      "--2016-02-24 12:00:41--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/?C=D;O=A\n",
      "     0K .                                                      497K=0.2s\n",
      "--2016-02-24 12:00:41--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 10% 1.64M 16s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 20% 2.73M 11s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 30% 2.73M 9s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 40% 2.74M 7s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 51% 2.73M 6s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 61% 2.74M 5s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 71% 2.57M 3s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 81% 2.71M 2s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 91% 2.70M 1s\n",
      " 27648K ........ ........ ........ ........ .....            100% 2.85M=12s\n",
      "--2016-02-24 12:00:53--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.6M=0s\n",
      "--2016-02-24 12:00:53--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  3% 1.65M 50s\n",
      "  3072K ........ ........ ........ ........ ........ ........  7% 2.74M 38s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 10% 2.74M 34s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 14% 2.74M 31s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 17% 2.74M 29s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 21% 2.54M 27s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 24% 2.71M 26s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 28% 2.74M 24s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 31% 2.74M 23s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 35% 2.73M 22s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 38% 2.67M 20s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 42% 2.74M 19s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 45% 2.74M 18s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 49% 2.56M 17s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 52% 2.74M 15s\n",
      " 46080K ........ ........ ........ ........ ........ ........ 56% 2.74M 14s\n",
      " 49152K ........ ........ ........ ........ ........ ........ 60% 2.74M 13s\n",
      " 52224K ........ ........ ........ ........ ........ ........ 63% 2.72M 12s\n",
      " 55296K ........ ........ ........ ........ ........ ........ 67% 2.74M 11s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 70% 2.74M 10s\n",
      " 61440K ........ ........ ........ ........ ........ ........ 74% 2.74M 8s\n",
      " 64512K ........ ........ ........ ........ ........ ........ 77% 2.56M 7s\n",
      " 67584K ........ ........ ........ ........ ........ ........ 81% 2.72M 6s\n",
      " 70656K ........ ........ ........ ........ ........ ........ 84% 2.69M 5s\n",
      " 73728K ........ ........ ........ ........ ........ ........ 88% 2.69M 4s\n",
      " 76800K ........ ........ ........ ........ ........ ........ 91% 2.72M 3s\n",
      " 79872K ........ ........ ........ ........ ........ ........ 95% 2.74M 2s\n",
      " 82944K ........ ........ ........ ........ ........ ........ 98% 2.74M 0s\n",
      " 86016K ........ .......                                     100% 2.69M=32s\n",
      "--2016-02-24 12:01:25--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 19.3M=0s\n",
      "--2016-02-24 12:01:26--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  526M=0s\n",
      "--2016-02-24 12:01:26--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.3M=0s\n",
      "--2016-02-24 12:01:26--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 14% 1.71M 11s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 28% 2.04M 8s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 42% 2.60M 6s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 56% 2.04M 5s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 70% 2.20M 3s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 84% 2.35M 2s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 98% 2.19M 0s\n",
      " 21504K ....                                                 100% 3.07M=10s\n",
      "--2016-02-24 12:01:36--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 22.2M=0s\n",
      "--2016-02-24 12:01:36--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  307M=0s\n",
      "--2016-02-24 12:01:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 22.0M=0s\n",
      "--2016-02-24 12:01:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  431M=0s\n",
      "--2016-02-24 12:01:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/UCEC/20140715/gdac.broadinstitute.org_UCEC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 22.3M=0s\n",
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      "Downloaded: 26 files, 136M in 55s (2.49 MB/s)\n",
      "--2016-02-24 12:01:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/\n",
      "     0K                                                      100%  165M=0s\n",
      "2016-02-24 12:01:38 ERROR 404: Not Found.\n",
      "--2016-02-24 12:01:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/?C=N;O=D\n",
      "     0K                                                      100%  110M=0s\n",
      "--2016-02-24 12:01:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/?C=M;O=A\n",
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      "--2016-02-24 12:01:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/?C=S;O=A\n",
      "     0K                                                      100%  163M=0s\n",
      "--2016-02-24 12:01:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/?C=D;O=A\n",
      "     0K                                                      100%  168M=0s\n",
      "--2016-02-24 12:01:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/\n",
      "     0K .                                                      333K=0.3s\n",
      "--2016-02-24 12:01:40--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/?C=N;O=A\n",
      "     0K                                                      100%  129M=0s\n",
      "--2016-02-24 12:01:40--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/?C=M;O=D\n",
      "     0K                                                      100%  166M=0s\n",
      "--2016-02-24 12:01:41--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/?C=S;O=D\n",
      "     0K                                                      100%  166M=0s\n",
      "--2016-02-24 12:01:41--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/?C=D;O=D\n",
      "     0K                                                      100%  169M=0s\n",
      "--2016-02-24 12:01:41--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/?C=N;O=D\n",
      "     0K .                                                      498K=0.2s\n",
      "--2016-02-24 12:01:41--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/?C=M;O=A\n",
      "     0K .                                                      498K=0.2s\n",
      "--2016-02-24 12:01:42--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/?C=S;O=A\n",
      "     0K .                                                      496K=0.2s\n",
      "--2016-02-24 12:01:42--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/?C=D;O=A\n",
      "     0K .                                                      334K=0.3s\n",
      "--2016-02-24 12:01:43--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 10% 1.70M 15s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 20% 2.35M 12s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 30% 2.53M 9s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 41% 2.54M 8s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 51% 2.54M 6s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 61% 2.73M 5s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 72% 2.74M 3s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 82% 2.74M 2s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 92% 2.55M 1s\n",
      " 27648K ........ ........ ........ ........ .                100% 2.87M=12s\n",
      "--2016-02-24 12:01:55--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.6M=0s\n",
      "--2016-02-24 12:01:55--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  3% 1.61M 58s\n",
      "  3072K ........ ........ ........ ........ ........ ........  6% 2.31M 47s\n",
      "  6144K ........ ........ ........ ........ ........ ........  9% 2.53M 42s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 12% 2.74M 38s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 15% 2.74M 35s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 18% 2.73M 33s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 21% 2.74M 31s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 25% 2.74M 29s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 28% 2.56M 28s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 31% 2.75M 26s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 34% 2.74M 25s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 37% 2.72M 24s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 40% 2.74M 22s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 43% 2.72M 21s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 47% 2.72M 20s\n",
      " 46080K ........ ........ ........ ........ ........ ........ 50% 2.60M 19s\n",
      " 49152K ........ ........ ........ ........ ........ ........ 53% 2.74M 17s\n",
      " 52224K ........ ........ ........ ........ ........ ........ 56% 2.70M 16s\n",
      " 55296K ........ ........ ........ ........ ........ ........ 59% 2.74M 15s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 62% 2.54M 14s\n",
      " 61440K ........ ........ ........ ........ ........ ........ 65% 2.62M 13s\n",
      " 64512K ........ ........ ........ ........ ........ ........ 68% 2.74M 11s\n",
      " 67584K ........ ........ ........ ........ ........ ........ 72% 2.73M 10s\n",
      " 70656K ........ ........ ........ ........ ........ ........ 75% 2.71M 9s\n",
      " 73728K ........ ........ ........ ........ ........ ........ 78% 2.66M 8s\n",
      " 76800K ........ ........ ........ ........ ........ ........ 81% 2.66M 7s\n",
      " 79872K ........ ........ ........ ........ ........ ........ 84% 2.70M 6s\n",
      " 82944K ........ ........ ........ ........ ........ ........ 87% 2.56M 4s\n",
      " 86016K ........ ........ ........ ........ ........ ........ 90% 2.71M 3s\n",
      " 89088K ........ ........ ........ ........ ........ ........ 94% 2.71M 2s\n",
      " 92160K ........ ........ ........ ........ ........ ........ 97% 2.72M 1s\n",
      " 95232K ........ ........ ........ ........ ........ ..      100% 2.65M=37s\n",
      "--2016-02-24 12:02:32--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 14.5M=0s\n",
      "--2016-02-24 12:02:32--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  509M=0s\n",
      "--2016-02-24 12:02:32--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.9M=0s\n",
      "--2016-02-24 12:02:32--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 25% 2.04M 4s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 51% 2.73M 2s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 77% 2.54M 1s\n",
      "  9216K ........ ........ ........ ........ ........ ..      100% 2.91M=4.7s\n",
      "--2016-02-24 12:02:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.9M=0s\n",
      "--2016-02-24 12:02:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  464M=0s\n",
      "--2016-02-24 12:02:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 31.6M=0s\n",
      "--2016-02-24 12:02:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  450M=0s\n",
      "--2016-02-24 12:02:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/LUAD/20140715/gdac.broadinstitute.org_LUAD-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
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      "--2016-02-24 12:02:38--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/\n",
      "     0K                                                      100%  156M=0s\n",
      "2016-02-24 12:02:38 ERROR 404: Not Found.\n",
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      "     0K                                                      100%  108M=0s\n",
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      "--2016-02-24 12:02:39--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/?C=D;O=A\n",
      "     0K                                                      100%  163M=0s\n",
      "--2016-02-24 12:02:39--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/\n",
      "     0K .                                                      505K=0.2s\n",
      "--2016-02-24 12:02:41--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/?C=N;O=A\n",
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      "--2016-02-24 12:02:41--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/?C=M;O=D\n",
      "     0K                                                      100%  167M=0s\n",
      "--2016-02-24 12:02:42--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/?C=S;O=D\n",
      "     0K                                                      100%  170M=0s\n",
      "--2016-02-24 12:02:42--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/?C=D;O=D\n",
      "     0K                                                      100%  167M=0s\n",
      "--2016-02-24 12:02:42--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/?C=N;O=D\n",
      "     0K .                                                      502K=0.2s\n",
      "--2016-02-24 12:02:42--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/?C=M;O=A\n",
      "     0K .                                                      503K=0.2s\n",
      "--2016-02-24 12:02:43--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/?C=S;O=A\n",
      "     0K .                                                      503K=0.2s\n",
      "--2016-02-24 12:02:43--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/?C=D;O=A\n",
      "     0K .                                                      337K=0.3s\n",
      "--2016-02-24 12:02:44--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  8% 1.93M 17s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 16% 2.31M 14s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 25% 2.27M 12s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 33% 1.84M 11s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 42% 2.18M 10s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 50% 2.19M 8s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 59% 2.03M 7s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 67% 2.32M 5s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 75% 2.52M 4s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 84% 2.59M 3s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 92% 2.70M 1s\n",
      " 33792K ........ ........ ........ ........ ........         100% 2.69M=16s\n",
      "--2016-02-24 12:03:00--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.2M=0s\n",
      "--2016-02-24 12:03:00--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  2% 1.83M 71s\n",
      "  3072K ........ ........ ........ ........ ........ ........  4% 2.52M 60s\n",
      "  6144K ........ ........ ........ ........ ........ ........  6% 2.34M 56s\n",
      "  9216K ........ ........ ........ ........ ........ ........  9% 2.53M 53s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 11% 2.74M 50s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 13% 2.43M 48s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 15% 2.19M 48s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 18% 2.20M 47s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 20% 1.92M 46s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 22% 2.05M 46s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 24% 2.20M 44s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 27% 2.34M 43s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 29% 2.12M 42s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 31% 2.35M 40s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 34% 2.52M 39s\n",
      " 46080K ........ ........ ........ ........ ........ ........ 36% 2.73M 37s\n",
      " 49152K ........ ........ ........ ........ ........ ........ 38% 2.35M 35s\n",
      " 52224K ........ ........ ........ ........ ........ ........ 40% 2.34M 34s\n",
      " 55296K ........ ........ ........ ........ ........ ........ 43% 2.53M 33s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 45% 2.74M 31s\n",
      " 61440K ........ ........ ........ ........ ........ ........ 47% 2.74M 30s\n",
      " 64512K ........ ........ ........ ........ ........ ........ 49% 2.70M 28s\n",
      " 67584K ........ ........ ........ ........ ........ ........ 52% 2.59M 27s\n",
      " 70656K ........ ........ ........ ........ ........ ........ 54% 2.32M 26s\n",
      " 73728K ........ ........ ........ ........ ........ ........ 56% 2.65M 24s\n",
      " 76800K ........ ........ ........ ........ ........ ........ 59% 2.69M 23s\n",
      " 79872K ........ ........ ........ ........ ........ ........ 61% 2.74M 21s\n",
      " 82944K ........ ........ ........ ........ ........ ........ 63% 2.73M 20s\n",
      " 86016K ........ ........ ........ ........ ........ ........ 65% 2.70M 19s\n",
      " 89088K ........ ........ ........ ........ ........ ........ 68% 2.74M 17s\n",
      " 92160K ........ ........ ........ ........ ........ ........ 70% 2.57M 16s\n",
      " 95232K ........ ........ ........ ........ ........ ........ 72% 2.71M 15s\n",
      " 98304K ........ ........ ........ ........ ........ ........ 74% 2.73M 14s\n",
      "101376K ........ ........ ........ ........ ........ ........ 77% 2.73M 12s\n",
      "104448K ........ ........ ........ ........ ........ ........ 79% 2.74M 11s\n",
      "107520K ........ ........ ........ ........ ........ ........ 81% 2.73M 10s\n",
      "110592K ........ ........ ........ ........ ........ ........ 83% 2.74M 9s\n",
      "113664K ........ ........ ........ ........ ........ ........ 86% 2.73M 7s\n",
      "116736K ........ ........ ........ ........ ........ ........ 88% 2.55M 6s\n",
      "119808K ........ ........ ........ ........ ........ ........ 90% 2.74M 5s\n",
      "122880K ........ ........ ........ ........ ........ ........ 93% 2.74M 4s\n",
      "125952K ........ ........ ........ ........ ........ ........ 95% 2.73M 2s\n",
      "129024K ........ ........ ........ ........ ........ ........ 97% 2.74M 1s\n",
      "132096K ........ ........ ........ ........ ........ ........ 99% 2.68M 0s\n",
      "135168K ...                                                  100% 2.33M=53s\n",
      "--2016-02-24 12:03:53--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 19.6M=0s\n",
      "--2016-02-24 12:03:53--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  518M=0s\n",
      "--2016-02-24 12:03:53--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.4M=0s\n",
      "--2016-02-24 12:03:54--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ..      100% 1.76M=1.5s\n",
      "--2016-02-24 12:03:55--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.9M=0s\n",
      "--2016-02-24 12:03:55--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  291M=0s\n",
      "--2016-02-24 12:03:56--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.5M=0s\n",
      "--2016-02-24 12:03:56--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  593M=0s\n",
      "--2016-02-24 12:03:56--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/OV/20140715/gdac.broadinstitute.org_OV-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.8M=0s\n",
      "FINISHED --2016-02-24 12:03:56--\n",
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      "--2016-02-24 12:03:56--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/\n",
      "     0K                                                      100%  162M=0s\n",
      "2016-02-24 12:03:57 ERROR 404: Not Found.\n",
      "--2016-02-24 12:03:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/?C=N;O=D\n",
      "     0K                                                      100%  113M=0s\n",
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      "--2016-02-24 12:03:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/?C=S;O=A\n",
      "     0K                                                      100%  167M=0s\n",
      "--2016-02-24 12:03:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/?C=D;O=A\n",
      "     0K                                                      100%  163M=0s\n",
      "--2016-02-24 12:03:57--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/\n",
      "     0K .                                                      444K=0.2s\n",
      "--2016-02-24 12:03:59--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/?C=N;O=A\n",
      "     0K                                                      100%  158M=0s\n",
      "--2016-02-24 12:03:59--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/?C=M;O=D\n",
      "     0K                                                      100%  168M=0s\n",
      "--2016-02-24 12:03:59--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/?C=S;O=D\n",
      "     0K                                                      100%  170M=0s\n",
      "--2016-02-24 12:03:59--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/?C=D;O=D\n",
      "     0K                                                      100%  171M=0s\n",
      "--2016-02-24 12:04:00--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/?C=N;O=D\n",
      "     0K .                                                      462K=0.2s\n",
      "--2016-02-24 12:04:00--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/?C=M;O=A\n",
      "     0K .                                                      463K=0.2s\n",
      "--2016-02-24 12:04:00--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/?C=S;O=A\n",
      "     0K .                                                      463K=0.2s\n",
      "--2016-02-24 12:04:01--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/?C=D;O=A\n",
      "     0K .                                                      462K=0.2s\n",
      "--2016-02-24 12:04:01--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  6% 1.92M 23s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 12% 2.74M 18s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 19% 2.74M 16s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 25% 2.74M 14s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 32% 2.74M 12s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 38% 2.55M 11s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 45% 2.74M 10s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 51% 2.74M 9s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 58% 2.74M 7s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 64% 2.73M 6s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 71% 2.63M 5s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 77% 2.74M 4s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 84% 2.66M 3s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 90% 2.74M 2s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 97% 2.35M 1s\n",
      " 46080K ........ ........ ......                             100% 2.18M=18s\n",
      "--2016-02-24 12:04:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.2M=0s\n",
      "--2016-02-24 12:04:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  2% 1.92M 61s\n",
      "  3072K ........ ........ ........ ........ ........ ........  4% 2.64M 51s\n",
      "  6144K ........ ........ ........ ........ ........ ........  7% 2.68M 47s\n",
      "  9216K ........ ........ ........ ........ ........ ........  9% 2.71M 45s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 12% 2.20M 44s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 14% 2.53M 43s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 17% 2.72M 41s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 19% 2.69M 39s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 22% 2.65M 38s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 24% 2.52M 36s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 27% 2.70M 35s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 29% 2.65M 34s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 32% 2.72M 32s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 34% 2.71M 31s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 37% 2.23M 30s\n",
      " 46080K ........ ........ ........ ........ ........ ........ 39% 2.19M 29s\n",
      " 49152K ........ ........ ........ ........ ........ ........ 42% 2.04M 28s\n",
      " 52224K ........ ........ ........ ........ ........ ........ 44% 1.82M 28s\n",
      " 55296K ........ ........ ........ ........ ........ ........ 47% 1.73M 27s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 49% 1.83M 26s\n",
      " 61440K ........ ........ ........ ........ ........ ........ 52% 1.55M 25s\n",
      " 64512K ........ ........ ........ ........ ........ ........ 54% 1.82M 24s\n",
      " 67584K ........ ........ ........ ........ ........ ........ 57% 1.83M 23s\n",
      " 70656K ........ ........ ........ ........ ........ ........ 59% 1.77M 22s\n",
      " 73728K ........ ........ ........ ........ ........ ........ 62% 1.92M 21s\n",
      " 76800K ........ ........ ........ ........ ........ ........ 64% 2.16M 19s\n",
      " 79872K ........ ........ ........ ........ ........ ........ 67% 2.53M 18s\n",
      " 82944K ........ ........ ........ ........ ........ ........ 69% 2.71M 17s\n",
      " 86016K ........ ........ ........ ........ ........ ........ 72% 2.74M 15s\n",
      " 89088K ........ ........ ........ ........ ........ ........ 74% 2.69M 14s\n",
      " 92160K ........ ........ ........ ........ ........ ........ 77% 2.74M 12s\n",
      " 95232K ........ ........ ........ ........ ........ ........ 79% 2.62M 11s\n",
      " 98304K ........ ........ ........ ........ ........ ........ 82% 2.73M 9s\n",
      "101376K ........ ........ ........ ........ ........ ........ 84% 2.61M 8s\n",
      "104448K ........ ........ ........ ........ ........ ........ 87% 2.74M 7s\n",
      "107520K ........ ........ ........ ........ ........ ........ 89% 2.71M 5s\n",
      "110592K ........ ........ ........ ........ ........ ........ 92% 2.74M 4s\n",
      "113664K ........ ........ ........ ........ ........ ........ 94% 2.35M 3s\n",
      "116736K ........ ........ ........ ........ ........ ........ 96% 2.26M 2s\n",
      "119808K ........ ........ ........ ........ ........ ........ 99% 2.54M 0s\n",
      "122880K ........ ..                                          100% 3.32M=52s\n",
      "--2016-02-24 12:05:11--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.3M=0s\n",
      "--2016-02-24 12:05:12--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  283M=0s\n",
      "--2016-02-24 12:05:12--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 26.5M=0s\n",
      "--2016-02-24 12:05:12--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 18% 1.94M 7s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 37% 2.74M 4s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 56% 2.74M 3s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 75% 2.60M 2s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 94% 2.71M 0s\n",
      " 15360K ........ .....                                       100% 2.36M=6.4s\n",
      "--2016-02-24 12:05:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.2M=0s\n",
      "--2016-02-24 12:05:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  303M=0s\n",
      "--2016-02-24 12:05:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.1M=0s\n",
      "--2016-02-24 12:05:19--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  463M=0s\n",
      "--2016-02-24 12:05:20--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/BRCA/20140715/gdac.broadinstitute.org_BRCA-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.8M=0s\n",
      "FINISHED --2016-02-24 12:05:20--\n",
      "Total wall clock time: 1m 23s\n",
      "Downloaded: 26 files, 183M in 1m 17s (2.38 MB/s)\n",
      "--2016-02-24 12:05:20--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/\n",
      "     0K                                                      100%  110M=0s\n",
      "2016-02-24 12:05:20 ERROR 404: Not Found.\n",
      "--2016-02-24 12:05:20--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/?C=N;O=D\n",
      "     0K                                                      100%  115M=0s\n",
      "--2016-02-24 12:05:20--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/?C=M;O=A\n",
      "     0K                                                      100%  168M=0s\n",
      "--2016-02-24 12:05:20--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/?C=S;O=A\n",
      "     0K                                                      100%  165M=0s\n",
      "--2016-02-24 12:05:21--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/?C=D;O=A\n",
      "     0K                                                      100%  171M=0s\n",
      "--2016-02-24 12:05:21--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/\n",
      "     0K .                                                      487K=0.2s\n",
      "--2016-02-24 12:05:23--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/?C=N;O=A\n",
      "     0K                                                      100%  232M=0s\n",
      "--2016-02-24 12:05:23--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/?C=M;O=D\n",
      "     0K                                                      100%  173M=0s\n",
      "--2016-02-24 12:05:23--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/?C=S;O=D\n",
      "     0K                                                      100%  261M=0s\n",
      "--2016-02-24 12:05:24--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/?C=D;O=D\n",
      "     0K                                                      100%  256M=0s\n",
      "--2016-02-24 12:05:24--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/?C=N;O=D\n",
      "     0K .                                                      487K=0.2s\n",
      "--2016-02-24 12:05:24--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/?C=M;O=A\n",
      "     0K .                                                      485K=0.2s\n",
      "--2016-02-24 12:05:24--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/?C=S;O=A\n",
      "     0K .                                                      486K=0.2s\n",
      "--2016-02-24 12:05:25--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/?C=D;O=A\n",
      "     0K .                                                      478K=0.2s\n",
      "--2016-02-24 12:05:25--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 11% 1.93M 12s\n",
      "  3072K ........ ........ ........ ........ ........ ........ 22% 2.74M 9s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 34% 2.55M 7s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 45% 2.74M 6s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 56% 2.74M 5s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 68% 2.74M 3s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 79% 1.93M 2s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 91% 1.83M 1s\n",
      " 24576K ........ ........ ........ ........ .....            100% 1.83M=12s\n",
      "--2016-02-24 12:05:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.Level_4.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.2M=0s\n",
      "--2016-02-24 12:05:37--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........  3% 1.73M 42s\n",
      "  3072K ........ ........ ........ ........ ........ ........  7% 2.74M 33s\n",
      "  6144K ........ ........ ........ ........ ........ ........ 11% 2.73M 29s\n",
      "  9216K ........ ........ ........ ........ ........ ........ 15% 2.52M 27s\n",
      " 12288K ........ ........ ........ ........ ........ ........ 19% 2.20M 26s\n",
      " 15360K ........ ........ ........ ........ ........ ........ 23% 2.73M 24s\n",
      " 18432K ........ ........ ........ ........ ........ ........ 27% 1.91M 24s\n",
      " 21504K ........ ........ ........ ........ ........ ........ 31% 2.34M 23s\n",
      " 24576K ........ ........ ........ ........ ........ ........ 35% 2.16M 21s\n",
      " 27648K ........ ........ ........ ........ ........ ........ 39% 2.34M 20s\n",
      " 30720K ........ ........ ........ ........ ........ ........ 43% 2.03M 19s\n",
      " 33792K ........ ........ ........ ........ ........ ........ 47% 2.06M 18s\n",
      " 36864K ........ ........ ........ ........ ........ ........ 51% 2.33M 16s\n",
      " 39936K ........ ........ ........ ........ ........ ........ 55% 2.35M 15s\n",
      " 43008K ........ ........ ........ ........ ........ ........ 59% 2.35M 14s\n",
      " 46080K ........ ........ ........ ........ ........ ........ 63% 2.52M 12s\n",
      " 49152K ........ ........ ........ ........ ........ ........ 67% 2.37M 11s\n",
      " 52224K ........ ........ ........ ........ ........ ........ 71% 2.73M 10s\n",
      " 55296K ........ ........ ........ ........ ........ ........ 75% 2.65M 8s\n",
      " 58368K ........ ........ ........ ........ ........ ........ 79% 2.51M 7s\n",
      " 61440K ........ ........ ........ ........ ........ ........ 82% 2.69M 6s\n",
      " 64512K ........ ........ ........ ........ ........ ........ 86% 2.73M 4s\n",
      " 67584K ........ ........ ........ ........ ........ ........ 90% 2.66M 3s\n",
      " 70656K ........ ........ ........ ........ ........ ........ 94% 2.45M 2s\n",
      " 73728K ........ ........ ........ ........ ........ ........ 98% 2.74M 0s\n",
      " 76800K ........ .......                                     100% 2.59M=32s\n",
      "--2016-02-24 12:06:09--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.aux.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 20.2M=0s\n",
      "--2016-02-24 12:06:10--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz’\n",
      "     0K                                                      100%  533M=0s\n",
      "--2016-02-24 12:06:10--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.CopyNumber_Gistic2.mage-tab.2014071500.0.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.5M=0s\n",
      "--2016-02-24 12:06:10--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz’\n",
      "     0K ........ ........ ........ ........ ........ ........ 65% 1.35M 1s\n",
      "  3072K ........ ........ ........ .                         100% 2.47M=2.9s\n",
      "--2016-02-24 12:06:13--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.Level_4.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.7M=0s\n",
      "--2016-02-24 12:06:13--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  302M=0s\n",
      "--2016-02-24 12:06:13--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.aux.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.5M=0s\n",
      "--2016-02-24 12:06:14--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz’\n",
      "     0K                                                      100%  435M=0s\n",
      "--2016-02-24 12:06:14--  http://gdac.broadinstitute.org/runs/analyses__2014_07_15/data/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5\n",
      "Saving to: ‘analyses__2014_07_15/KIRC/20140715/gdac.broadinstitute.org_KIRC-TP.MutSigNozzleReport2CV.mage-tab.2014071500.1.0.tar.gz.md5’\n",
      "     0K                                                      100% 21.8M=0s\n",
      "FINISHED --2016-02-24 12:06:14--\n",
      "Total wall clock time: 54s\n",
      "Downloaded: 26 files, 107M in 47s (2.28 MB/s)\n",
      "\n",
      "\n",
      "Now performing post-processing on retrieved files ...\n"
     ]
    }
   ],
   "source": [
    "!firehose_get -b -only copynumber_gistic MutSigNozzleReport2CV analyses {firehoseDate} {\" \".join(nbsupport.tcga.PANCAN12_STUDIES)}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import shutil\n",
    "import tarfile\n",
    "import tempfile\n",
    "\n",
    "from contextlib import closing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "for study in nbsupport.tcga.PANCAN12_STUDIES:\n",
    "    filePrefix = \"analyses__{date}/{study}/{date2}/gdac.broadinstitute.org_{study}-{tumourType}\".format(\n",
    "        date=firehoseDate, date2=firehoseDate.replace(\"_\", \"\"), study=study, tumourType=\"TB\" if study == \"LAML\" else \"TP\")\n",
    "    \n",
    "    gisticResults = \"{prefix}.CopyNumber_Gistic2.Level_4.{date2}00.0.0.tar.gz\".format(\n",
    "        prefix=filePrefix, date2=firehoseDate.replace(\"_\", \"\"))\n",
    "    with tarfile.open(gisticResults, \"r|gz\") as archive:\n",
    "        for entry in archive:\n",
    "            if entry.name.endswith(\"all_thresholded.by_genes.txt\"):\n",
    "                with closing(archive.extractfile(entry)) as stream, tempfile.TemporaryFile() as out:\n",
    "                    shutil.copyfileobj(stream, out)\n",
    "                    out.seek(0)\n",
    "                    cn = nbsupport.tcga.read_copynumber_data(out)\n",
    "                    cn.to_hdf(\"../tcga/tcga-pancan12.h5\", \"/data/{}/cn\".format(study), complevel=9, complib=\"bzip2\")\n",
    "    \n",
    "    mutsigResults = \"{prefix}.MutSigNozzleReport2CV.Level_4.{date2}00.1.0.tar.gz\".format(\n",
    "        prefix=filePrefix, date2=firehoseDate.replace(\"_\", \"\"))\n",
    "    with tarfile.open(mutsigResults, \"r|gz\") as archive:\n",
    "        for entry in archive:\n",
    "            if entry.name.endswith(\".final_analysis_set.maf\"):\n",
    "                with closing(archive.extractfile(entry)) as stream, tempfile.TemporaryFile() as out:\n",
    "                    shutil.copyfileobj(stream, out)\n",
    "                    out.seek(0)\n",
    "                    mut = nbsupport.tcga.read_mutation_data(out)\n",
    "                    mut.to_hdf(\"../tcga/tcga-pancan12.h5\", \"/data/{}/mut\".format(study), complevel=9, complib=\"bzip2\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "filePrefix = \"analyses__{date}/BRCA/{date2}/gdac.broadinstitute.org_BRCA-TP\".format(\n",
    "        date=firehoseDate, date2=firehoseDate.replace(\"_\", \"\"))\n",
    "\n",
    "gisticResults = \"{prefix}.CopyNumber_Gistic2.Level_4.{date2}00.0.0.tar.gz\".format(\n",
    "        prefix=filePrefix, date2=firehoseDate.replace(\"_\", \"\"))\n",
    "\n",
    "with tarfile.open(gisticResults, \"r|gz\") as archive:\n",
    "    for entry in archive:\n",
    "        if entry.name.endswith(\"amp_genes.conf_99.txt\"):\n",
    "            with closing(archive.extractfile(entry)) as stream, open(\"../tcga/amp_genes.conf_99.BRCA.txt\", \"w\") as out:\n",
    "                shutil.copyfileobj(stream, out)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## High-confidence mutational drivers list"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "A list of high-confidence mutational drivers has been published in the following paper.\n",
    "\n",
    "> Tamborero, D. *et al*. Comprehensive identification of mutational cancer\n",
    "driver genes across 12 tumor types. *Sci Rep* **3**, 2650 (2013), [doi:10.1038/srep02650](http://doi.org/10.1038/srep02650)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import urllib\n",
    "import zipfile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "url = \"http://www.nature.com/article-assets/npg/srep/2013/131002/srep02650/extref/srep02650-s2.zip\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "filename, response = urllib.urlretrieve(url, \"srep02650-s2.zip\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "nbsupport.util.check_digest(filename, \"5a56134a26ff9e83b40e8cd1e7043e5e\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "with zipfile.ZipFile(filename) as zip:\n",
    "    with zip.open(\"srep02650-s3.csv\") as stream, open(\"../tcga/mutational-drivers.csv\", \"w\") as out:\n",
    "        shutil.copyfileobj(stream, out)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Cancer gene list"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The [Bushman lab](http://www.bushmanlab.org) maintains a list of genes implicated in cancer."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "url = \"http://www.bushmanlab.org/assets/doc/allonco_20130923.tsv\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "filename, respose = urllib.urlretrieve(url, \"../tcga/cancer-genes.tsv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "nbsupport.util.check_digest(filename, \"72832c847db96c7fb019fa97050fb9a4\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Entrez gene annotation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "url = \"ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/mapview/seq_gene.md.gz\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "filename, respose = urllib.urlretrieve(url, \"../entrez/seq_gene.md.gz\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "nbsupport.util.check_digest(filename, \"6fa4691b852dd9bb603c2a2f64718317\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Manual downloads"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The following downloads are protected by passwords, and so they cannot be downloaded automatically."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Recurrent copy number alterations"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Download the following two files from synapse, and add them to the `data/tcga` directory."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "* [amp_genes.conf_95.pancan12.txt](https://www.synapse.org/#!Synapse:syn2204280)\n",
    "* [del_genes.conf_95.pancan12.txt](https://www.synapse.org/#!Synapse:syn2204295)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "nbsupport.util.check_digest(\"../tcga/amp_genes.conf_95.pancan12.txt\", \"0f23349056bc5d451c2bf8358e99dab8\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "nbsupport.util.check_digest(\"../tcga/del_genes.conf_95.pancan12.txt\", \"80b3e9027ba6ca0e6b56eedde6bb019f\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### MSigDb pathways"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Download the following file from MSigDb and add it to the `data/msigdb` directory."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "* [c2.cp.v5.0.symbols.gmt](http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/5.1/c2.cp.v5.1.symbols.gmt)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "nbsupport.util.check_digest(\"../msigdb/c2.cp.v5.0.symbols.gmt\", \"9790879a470eda3c6c431a91f3b652f8\")"
   ]
  }
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