analyses/20191220_DMRfind_5xmerg.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#copy all .tab files over to ostrich\n",
    "#did this from mox \n",
    "#(base) [strigg@mox2 20191220]$ scp -r merged_tab/ strigg@ostrich.fish.washington.edu:/Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/20191220_DMRfind_5xmerg\n",
    "#Password:\n",
    "#EPI-182_S17_L003_5x.tab                                                                                     100%   75MB  40.1MB/s   00:01    \n",
    "#EPI-43_S40_L005_10x.tab                                                                                     100% 6244KB  17.2MB/s   00:00    \n",
    "#EPI-167_S10_L002_5x.tab                                                                                     100%   46MB  54.3MB/s   00:00    \n",
    "#EPI-152_S3_L002_5x.tab                                                                                      100%   57MB  45.6MB/s   00:01    \n",
    "#EPI-220_S32_L004_10x.tab                                                                                    100% 3108KB  11.9MB/s   00:00    \n",
    "#EPI-221_S33_L004_5x.tab                                                                                     100%   20MB  30.1MB/s   00:00    \n",
    "#EPI-229_S36_L004_10x.tab                                                                                    100% 5712KB  12.5MB/s   00:00    \n",
    "#EPI-227_S35_L004_10x.tab                                                                                    100% 2817KB  13.5MB/s   00:00    \n",
    "#EPI-209_S29_L004_10x.tab                                                                                    100%   14MB  21.3MB/s   00:00    \n",
    "#EPI-128_S34_L005_5x.tab                                                                                     100%   76MB  49.7MB/s   00:01    \n",
    "#EPI-206_S27_L004_5x.tab                                                                                     100%   35MB  57.6MB/s   00:00    \n",
    "#EPI-184_S18_L003_5x.tab                                                                                     100%   32MB  42.5MB/s   00:00    \n",
    "#EPI-42_S39_L005_10x.tab                                                                                     100%   14MB  35.6MB/s   00:00    \n",
    "#EPI-199_S24_L003_5x.tab                                                                                     100%   18MB  28.1MB/s   00:00    \n",
    "#EPI-43_S40_L005_5x.tab                                                                                      100%   35MB  31.1MB/s   00:01    \n",
    "#EPI-220_S32_L004_5x.tab                                                                                     100%   17MB  37.3MB/s   00:00    \n",
    "#EPI-41_S38_L005_10x.tab                                                                                     100% 6459KB  22.9MB/s   00:00    \n",
    "#EPI-214_S30_L004_10x.tab                                                                                    100%   11MB  23.4MB/s   00:00    \n",
    "#EPI-151_S2_L002_5x.tab                                                                                      100%   44MB  40.7MB/s   00:01    \n",
    "#EPI-143_S37_L005_5x.tab                                                                                     100%   56MB  33.9MB/s   00:01    \n",
    "#EPI-113_S30_L005_5x.tab                                                                                     100%   78MB  49.0MB/s   00:01    \n",
    "#EPI-229_S36_L004_5x.tab                                                                                     100%   30MB  29.2MB/s   00:01    \n",
    "#EPI-161_S8_L002_5x.tab                                                                                      100%   28MB  31.7MB/s   00:00    \n",
    "#EPI-226_S34_L004_5x.tab                                                                                     100%   13MB  24.7MB/s   00:00    \n",
    "#EPI-111_S29_L005_5x.tab                                                                                     100%   83MB  62.0MB/s   00:01    \n",
    "#EPI-103_S27_L005_5x.tab                                                                                     100%   56MB  43.0MB/s   00:01    \n",
    "#EPI-44_S41_L005_10x.tab                                                                                     100% 2795KB   8.0MB/s   00:00    \n",
    "#EPI-208_S28_L004_10x.tab                                                                                    100% 9646KB  21.0MB/s   00:00    \n",
    "#EPI-168_S11_L002_5x.tab                                                                                     100%   36MB  34.4MB/s   00:01    \n",
    "#EPI-170_S13_L002_5x.tab                                                                                     100%   42MB  37.6MB/s   00:01    \n",
    "#EPI-162_S9_L002_5x.tab                                                                                      100%   28MB  25.6MB/s   00:01    \n",
    "#EPI-153_S4_L002_5x.tab                                                                                      100%   36MB  36.1MB/s   00:01    \n",
    "#EPI-230_S37_L004_10x.tab                                                                                    100% 7313KB  19.5MB/s   00:00    \n",
    "#EPI-44_S41_L005_5x.tab                                                                                      100%   17MB  19.8MB/s   00:00    \n",
    "#EPI-104_S28_L005_5x.tab                                                                                     100%   92MB  37.0MB/s   00:02    \n",
    "#EPI-154_S5_L002_5x.tab                                                                                      100%   38MB  34.3MB/s   00:01    \n",
    "#EPI-226_S34_L004_10x.tab                                                                                    100% 2389KB  12.1MB/s   00:00    \n",
    "#EPI-221_S33_L004_10x.tab                                                                                    100% 3512KB  13.5MB/s   00:00    \n",
    "#EPI-181_S16_L003_5x.tab                                                                                     100%   57MB  32.6MB/s   00:01    \n",
    "#EPI-185_S19_L003_5x.tab                                                                                     100% 6835KB  20.2MB/s   00:00    \n",
    "#EPI-42_S39_L005_5x.tab                                                                                      100%   57MB  46.1MB/s   00:01    \n",
    "#EPI-169_S12_L002_5x.tab                                                                                     100%   32MB  21.4MB/s   00:01    \n",
    "#EPI-127_S33_L005_5x.tab                                                                                     100%   65MB  42.3MB/s   00:01    \n",
    "#EPI-215_S31_L004_10x.tab                                                                                    100% 7183KB  17.3MB/s   00:00    \n",
    "#EPI-215_S31_L004_5x.tab                                                                                     100%   35MB  32.7MB/s   00:01    \n",
    "#EPI-119_S31_L005_5x.tab                                                                                     100%   91MB  46.4MB/s   00:01    \n",
    "#EPI-200_S25_L003_5x.tab                                                                                     100%   42MB  37.2MB/s   00:01    \n",
    "#EPI-209_S29_L004_5x.tab                                                                                     100%   59MB  38.7MB/s   00:01    \n",
    "#EPI-135_S35_L005_5x.tab                                                                                     100%   82MB  44.5MB/s   00:01    \n",
    "#EPI-230_S37_L004_5x.tab                                                                                     100%   38MB  36.7MB/s   00:01    \n",
    "#EPI-160_S7_L002_5x.tab                                                                                      100%   54MB  49.6MB/s   00:01    \n",
    "#EPI-187_S20_L003_5x.tab                                                                                     100%   45MB  34.8MB/s   00:01    \n",
    "#EPI-159_S6_L002_5x.tab                                                                                      100%   20MB  18.2MB/s   00:01    \n",
    "#EPI-188_S21_L003_5x.tab                                                                                     100%   27MB  25.9MB/s   00:01    \n",
    "#EPI-214_S30_L004_5x.tab                                                                                     100%   57MB  43.8MB/s   00:01    \n",
    "#EPI-194_S23_L003_5x.tab                                                                                     100%   68MB  45.7MB/s   00:01    \n",
    "#EPI-176_S15_L003_5x.tab                                                                                     100%   72MB  59.6MB/s   00:01    \n",
    "#EPI-227_S35_L004_5x.tab                                                                                     100%   16MB  22.3MB/s   00:00    \n",
    "#EPI-120_S32_L005_5x.tab                                                                                     100%   76MB  40.9MB/s   00:01    \n",
    "#EPI-205_S26_L004_5x.tab                                                                                     100%   18MB  18.4MB/s   00:01    \n",
    "#EPI-175_S14_L003_5x.tab                                                                                     100%   51MB  33.2MB/s   00:01    \n",
    "#EPI-145_S38_L005_5x.tab                                                                                     100%   75MB  31.0MB/s   00:02    \n",
    "#EPI-193_S22_L003_5x.tab                                                                                     100%   46MB  42.1MB/s   00:01    \n",
    "#EPI-41_S38_L005_5x.tab                                                                                      100%   34MB  29.0MB/s   00:01    \n",
    "#EPI-136_S36_L005_5x.tab                                                                                     100%   79MB  46.6MB/s   00:01    \n",
    "#EPI-208_S28_L004_5x.tab                                                                                     100%   48MB  30.9MB/s   00:01"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#change into 20191220 directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/strigg/Documents/GitHub/Shelly_Pgenerosa/analyses/20191220_DMRfind_5xmerg\n"
     ]
    }
   ],
   "source": [
    "cd ~/Documents/GitHub/Shelly_Pgenerosa/analyses/20191220_DMRfind_5xmerg/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# convert 5x.tab files to allc format"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "for f in merged_tab/*_5x.tab\n",
    "do\n",
    "awk -F\"\\t\" '{print $1\"\\t\"$3-1\"\\t\"\"+\"\"\\t\"\"CGA\"\"\\t\"$5\"\\t\"$6\"\\t\"1}' ${f} \\\n",
    "> $(basename ${f} _5x.tab)_5xmerg_allc.tsv\n",
    "done"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#preview files\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Scaffold_01\t209\t+\tCGA\t0\t5\t1\r\n",
      "Scaffold_01\t213\t+\tCGA\t0\t5\t1\r\n",
      "Scaffold_01\t221\t+\tCGA\t0\t6\t1\r\n",
      "Scaffold_01\t238\t+\tCGA\t0\t8\t1\r\n",
      "Scaffold_01\t565\t+\tCGA\t0\t6\t1\r\n",
      "Scaffold_01\t577\t+\tCGA\t0\t6\t1\r\n",
      "Scaffold_01\t583\t+\tCGA\t0\t5\t1\r\n",
      "Scaffold_01\t2509\t+\tCGA\t0\t7\t1\r\n",
      "Scaffold_01\t2554\t+\tCGA\t0\t6\t1\r\n",
      "Scaffold_01\t3002\t+\tCGA\t0\t5\t1\r\n"
     ]
    }
   ],
   "source": [
    "!head EPI-103_S27_L005_5xmerg_allc.tsv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#move _5xmerg_allc.tsv files to gannet"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "!mkdir /Volumes/web/metacarcinus/Pgenerosa/analyses/20191220"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "cp *_5xmerg_allc.tsv /Volumes/web/metacarcinus/Pgenerosa/analyses/20191220"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 3789030\r\n",
      "-rwx------  1 strigg  staff    42M Dec 20 20:42 \u001b[31mEPI-103_S27_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    70M Dec 20 20:42 \u001b[31mEPI-104_S28_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    63M Dec 20 20:42 \u001b[31mEPI-111_S29_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    59M Dec 20 20:42 \u001b[31mEPI-113_S30_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    69M Dec 20 20:42 \u001b[31mEPI-119_S31_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    58M Dec 20 20:42 \u001b[31mEPI-120_S32_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    50M Dec 20 20:42 \u001b[31mEPI-127_S33_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    57M Dec 20 20:42 \u001b[31mEPI-128_S34_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    62M Dec 20 20:42 \u001b[31mEPI-135_S35_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    60M Dec 20 20:42 \u001b[31mEPI-136_S36_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    42M Dec 20 20:42 \u001b[31mEPI-143_S37_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    57M Dec 20 20:42 \u001b[31mEPI-145_S38_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    33M Dec 20 20:42 \u001b[31mEPI-151_S2_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    43M Dec 20 20:42 \u001b[31mEPI-152_S3_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    27M Dec 20 20:42 \u001b[31mEPI-153_S4_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    29M Dec 20 20:42 \u001b[31mEPI-154_S5_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    15M Dec 20 20:42 \u001b[31mEPI-159_S6_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    41M Dec 20 20:42 \u001b[31mEPI-160_S7_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    21M Dec 20 20:42 \u001b[31mEPI-161_S8_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    21M Dec 20 20:42 \u001b[31mEPI-162_S9_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    35M Dec 20 20:42 \u001b[31mEPI-167_S10_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    27M Dec 20 20:42 \u001b[31mEPI-168_S11_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    24M Dec 20 20:42 \u001b[31mEPI-169_S12_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    32M Dec 20 20:42 \u001b[31mEPI-170_S13_L002_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    39M Dec 20 20:42 \u001b[31mEPI-175_S14_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    54M Dec 20 20:42 \u001b[31mEPI-176_S15_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    44M Dec 20 20:42 \u001b[31mEPI-181_S16_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    57M Dec 20 20:42 \u001b[31mEPI-182_S17_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    24M Dec 20 20:42 \u001b[31mEPI-184_S18_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff   5.1M Dec 20 20:42 \u001b[31mEPI-185_S19_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    34M Dec 20 20:42 \u001b[31mEPI-187_S20_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    21M Dec 20 20:42 \u001b[31mEPI-188_S21_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    35M Dec 20 20:42 \u001b[31mEPI-193_S22_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    51M Dec 20 20:42 \u001b[31mEPI-194_S23_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    13M Dec 20 20:42 \u001b[31mEPI-199_S24_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    32M Dec 20 20:42 \u001b[31mEPI-200_S25_L003_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    14M Dec 20 20:42 \u001b[31mEPI-205_S26_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    26M Dec 20 20:42 \u001b[31mEPI-206_S27_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    37M Dec 20 20:42 \u001b[31mEPI-208_S28_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    45M Dec 20 20:42 \u001b[31mEPI-209_S29_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    43M Dec 20 20:42 \u001b[31mEPI-214_S30_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    27M Dec 20 20:42 \u001b[31mEPI-215_S31_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    13M Dec 20 20:42 \u001b[31mEPI-220_S32_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    15M Dec 20 20:42 \u001b[31mEPI-221_S33_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff   9.9M Dec 20 20:42 \u001b[31mEPI-226_S34_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    12M Dec 20 20:42 \u001b[31mEPI-227_S35_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    23M Dec 20 20:42 \u001b[31mEPI-229_S36_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    29M Dec 20 20:42 \u001b[31mEPI-230_S37_L004_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    26M Dec 20 20:42 \u001b[31mEPI-41_S38_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    43M Dec 20 20:42 \u001b[31mEPI-42_S39_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    26M Dec 20 20:42 \u001b[31mEPI-43_S40_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n",
      "-rwx------  1 strigg  staff    13M Dec 20 20:42 \u001b[31mEPI-44_S41_L005_5xmerg_allc.tsv\u001b[m\u001b[m\r\n"
     ]
    }
   ],
   "source": [
    "!ls -lh /Volumes/web/metacarcinus/Pgenerosa/analyses/20191220"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#run methylpy test since I updated the software\n",
    "\n",
    "\n",
    "#(base) ostrich:20191220_DMRfind_5xmerg strigg$ pip install --upgrade methylpy\n",
    "#Collecting methylpy\n",
    "#  Downloading https://files.pythonhosted.org/packages/9a/a3/722c388a618b2f791e96753a3314e5b97d55107058f4d05bb05a6cc738ff/methylpy-1.4.1.tar.gz (110kB)\n",
    "#     |████████████████████████████████| 112kB 14.0MB/s \n",
    "#Requirement already satisfied, skipping upgrade: numpy>=1.6.1 in /Users/strigg/anaconda3/lib/python3.6/site-packages (from methylpy) (1.16.4)\n",
    "#Requirement already satisfied, skipping upgrade: scipy>=0.10.0 in /Users/strigg/anaconda3/lib/python3.6/site-packages (from methylpy) (1.3.0)\n",
    "#Collecting pysam>=0.5.3 (from methylpy)\n",
    "#  Downloading https://files.pythonhosted.org/packages/15/e7/2dab8bb0ac739555e69586f1492f0ff6bc4a1f8312992a83001d3deb77ac/pysam-0.15.3.tar.gz (3.2MB)\n",
    "#     |████████████████████████████████| 3.2MB 24.8MB/s \n",
    "#Building wheels for collected packages: methylpy, pysam\n",
    "#  Building wheel for methylpy (setup.py) ... done\n",
    "#  Stored in directory: /Users/strigg/Library/Caches/pip/wheels/66/15/aa/47b8e87d74b6510f9575ab7fdeb2817de6abd15553b0208424\n",
    "#  Building wheel for pysam (setup.py) ... done\n",
    "#  Stored in directory: /Users/strigg/Library/Caches/pip/wheels/85/ab/84/86ca6dda37a6fc85687b67be7345b735cd82f6584bea56f327\n",
    "#Successfully built methylpy pysam\n",
    "#Installing collected packages: pysam, methylpy\n",
    "#  Found existing installation: methylpy 1.3.8\n",
    "#    Uninstalling methylpy-1.3.8:\n",
    "#      Successfully uninstalled methylpy-1.3.8\n",
    "#Successfully installed methylpy-1.4.1 pysam-0.15.3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#tested methylpy after installing updates\n",
    "#DMRfind failed\n",
    "#had to recompile run_rms_tests.out\n",
    "#see https://github.com/yupenghe/methylpy#optional-step---compile-rmscpp\n",
    "#ran run_test.py and everything passed!\n",
    "# (base) ostrich:methylpy_test strigg$ python run_test.py \n",
    "# Tests start\n",
    "# Fri Dec 20 18:31:04 2019\n",
    "\n",
    "# Test importing methylpy module.\n",
    "# - importing call_mc_se: pass\n",
    "# - importing call_mc_pe: pass\n",
    "# - importing DMRfind: pass\n",
    "# - importing parser: pass\n",
    "# Check methylpy executable:pass\n",
    "\n",
    "# methylpy is successfully installed!\n",
    "\n",
    "# Check whether dependencies are available in PATH\n",
    "# - find bowtie: failed\n",
    "# - find bowtie2: found version 2.3.4.3\n",
    "# - find minimap2: found version 2.12-r827\n",
    "# - find samtools: found version 1.9\n",
    "# - find cutadapt: found version 2.4\n",
    "# - find java: found version 2018-09-25\n",
    "# Only bowtie2 is available. Skip tests for bowtie related code\n",
    "\n",
    "# Test DMRfind: pass\n",
    "# Test reidentify-DMR: pass\n",
    "\n",
    "# Test build-reference with bowtie2: pass\n",
    "# Test build-reference with minimap2: pass\n",
    "\n",
    "# Test single-end-pipeline with bowtie2: pass\n",
    "# Test single-end-pipeline with minimap2: pass\n",
    "\n",
    "# Test paired-end-pipeline with bowtie2: pass\n",
    "# Test paired-end-pipeline with minimap2: pass\n",
    "\n",
    "# Test quality filter for BAM file of single-end data: pass\n",
    "\n",
    "# Test call-methylation-state for single-end data: pass\n",
    "# Test call-methylation-state for paired-end data: pass\n",
    "\n",
    "# Test merge-allc: pass\n",
    "\n",
    "# Test filter-allc: pass\n",
    "\n",
    "# All tests are done!\n",
    "# Fri Dec 20 18:33:41 2019\n",
    "# The tests took 156.55 seconds!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#now run DMRfind on new allc files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#perform DMR find"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Filtering allc files using 8 node(s).\n",
      "Fri Dec 20 18:36:45 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_01\n",
      "Fri Dec 20 18:37:39 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_01\n",
      "Fri Dec 20 18:37:45 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_02\n",
      "Fri Dec 20 18:37:45 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_02\n",
      "Fri Dec 20 18:37:51 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_03\n",
      "Fri Dec 20 18:37:51 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_03\n",
      "Fri Dec 20 18:37:56 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_04\n",
      "Fri Dec 20 18:37:56 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_04\n",
      "Fri Dec 20 18:38:01 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_05\n",
      "Fri Dec 20 18:38:01 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_05\n",
      "Fri Dec 20 18:38:06 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_06\n",
      "Fri Dec 20 18:38:06 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_06\n",
      "Fri Dec 20 18:38:11 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_07\n",
      "Fri Dec 20 18:38:11 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_07\n",
      "Fri Dec 20 18:38:15 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_08\n",
      "Fri Dec 20 18:38:15 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_08\n",
      "Fri Dec 20 18:38:19 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_09\n",
      "Fri Dec 20 18:38:19 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_09\n",
      "Fri Dec 20 18:38:23 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_10\n",
      "Fri Dec 20 18:38:23 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_10\n",
      "Fri Dec 20 18:38:27 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_11\n",
      "Fri Dec 20 18:38:27 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_11\n",
      "Fri Dec 20 18:38:31 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_12\n",
      "Fri Dec 20 18:38:31 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_12\n",
      "Fri Dec 20 18:38:35 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_13\n",
      "Fri Dec 20 18:38:35 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_13\n",
      "Fri Dec 20 18:38:41 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_14\n",
      "Fri Dec 20 18:38:41 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_14\n",
      "Fri Dec 20 18:38:47 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_15\n",
      "Fri Dec 20 18:38:47 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_15\n",
      "Fri Dec 20 18:38:53 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_16\n",
      "Fri Dec 20 18:38:53 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_16\n",
      "Fri Dec 20 18:38:57 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_17\n",
      "Fri Dec 20 18:38:57 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_17\n",
      "Fri Dec 20 18:39:01 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_18\n",
      "Fri Dec 20 18:39:01 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_18\n",
      "Fri Dec 20 18:39:05 2019\n",
      "\n",
      "Merging sorted amb_AllTimes_DMR250bp_MCmax25_cov5x_rms_results.tsv files.\n",
      "Fri Dec 20 18:47:59 2019\n",
      "\n",
      "Begin FDR Correction\n",
      "Fri Dec 20 18:48:00 2019\n",
      "\n",
      "m0 estimate for iteration 0: 9730\n",
      "Histogram FDR correction did not converge. Using the smallest p-value 0.0003333333333333333 as cutoff.\n",
      "\n",
      "Calculating Residual Cutoff\n",
      "Fri Dec 20 18:48:00 2019\n",
      "\n",
      "Filtering allc files using 8 node(s).\n",
      "Fri Dec 20 18:48:01 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_01\n",
      "Fri Dec 20 18:49:00 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_01\n",
      "Fri Dec 20 18:49:07 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_02\n",
      "Fri Dec 20 18:49:07 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_02\n",
      "Fri Dec 20 18:49:13 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_03\n",
      "Fri Dec 20 18:49:13 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_03\n",
      "Fri Dec 20 18:49:18 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_04\n",
      "Fri Dec 20 18:49:18 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_04\n",
      "Fri Dec 20 18:49:23 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_05\n",
      "Fri Dec 20 18:49:23 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_05\n",
      "Fri Dec 20 18:49:28 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_06\n",
      "Fri Dec 20 18:49:28 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_06\n",
      "Fri Dec 20 18:49:34 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_07\n",
      "Fri Dec 20 18:49:34 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_07\n",
      "Fri Dec 20 18:49:38 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_08\n",
      "Fri Dec 20 18:49:38 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_08\n",
      "Fri Dec 20 18:49:43 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_09\n",
      "Fri Dec 20 18:49:43 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_09\n",
      "Fri Dec 20 18:49:46 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_10\n",
      "Fri Dec 20 18:49:46 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_10\n",
      "Fri Dec 20 18:49:51 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_11\n",
      "Fri Dec 20 18:49:51 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_11\n",
      "Fri Dec 20 18:49:55 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_12\n",
      "Fri Dec 20 18:49:55 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_12\n",
      "Fri Dec 20 18:50:02 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_13\n",
      "Fri Dec 20 18:50:02 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_13\n",
      "Fri Dec 20 18:50:05 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_14\n",
      "Fri Dec 20 18:50:05 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_14\n",
      "Fri Dec 20 18:50:10 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_15\n",
      "Fri Dec 20 18:50:10 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_15\n",
      "Fri Dec 20 18:50:14 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_16\n",
      "Fri Dec 20 18:50:14 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_16\n",
      "Fri Dec 20 18:50:16 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_17\n",
      "Fri Dec 20 18:50:16 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_17\n",
      "Fri Dec 20 18:50:20 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_18\n",
      "Fri Dec 20 18:50:20 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_18\n",
      "Fri Dec 20 18:50:23 2019\n",
      "\n",
      "Merging sorted day10_AllpH_DMR250bp_MCmax25_cov5x_rms_results.tsv files.\n",
      "Fri Dec 20 18:52:38 2019\n",
      "\n",
      "Begin FDR Correction\n",
      "Fri Dec 20 18:52:39 2019\n",
      "\n",
      "m0 estimate for iteration 0: 11884\n",
      "Histogram FDR correction did not converge. Using the smallest p-value 0.0003333333333333333 as cutoff.\n",
      "\n",
      "Calculating Residual Cutoff\n",
      "Fri Dec 20 18:52:39 2019\n",
      "\n",
      "Filtering allc files using 8 node(s).\n",
      "Fri Dec 20 18:52:41 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_01\n",
      "Fri Dec 20 18:53:09 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_01\n",
      "Fri Dec 20 18:53:12 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_02\n",
      "Fri Dec 20 18:53:12 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_02\n",
      "Fri Dec 20 18:53:15 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_03\n",
      "Fri Dec 20 18:53:15 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_03\n",
      "Fri Dec 20 18:53:18 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_04\n",
      "Fri Dec 20 18:53:18 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_04\n",
      "Fri Dec 20 18:53:21 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_05\n",
      "Fri Dec 20 18:53:21 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_05\n",
      "Fri Dec 20 18:53:24 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_06\n",
      "Fri Dec 20 18:53:24 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_06\n",
      "Fri Dec 20 18:53:27 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_07\n",
      "Fri Dec 20 18:53:27 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_07\n",
      "Fri Dec 20 18:53:29 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_08\n",
      "Fri Dec 20 18:53:29 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_08\n",
      "Fri Dec 20 18:53:32 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_09\n",
      "Fri Dec 20 18:53:32 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_09\n",
      "Fri Dec 20 18:53:34 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_10\n",
      "Fri Dec 20 18:53:34 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_10\n",
      "Fri Dec 20 18:53:36 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_11\n",
      "Fri Dec 20 18:53:36 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_11\n",
      "Fri Dec 20 18:53:39 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_12\n",
      "Fri Dec 20 18:53:39 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_12\n",
      "Fri Dec 20 18:53:43 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_13\n",
      "Fri Dec 20 18:53:43 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_13\n",
      "Fri Dec 20 18:53:45 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_14\n",
      "Fri Dec 20 18:53:45 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_14\n",
      "Fri Dec 20 18:53:48 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_15\n",
      "Fri Dec 20 18:53:48 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_15\n",
      "Fri Dec 20 18:53:50 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_16\n",
      "Fri Dec 20 18:53:50 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_16\n",
      "Fri Dec 20 18:53:51 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_17\n",
      "Fri Dec 20 18:53:51 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_17\n",
      "Fri Dec 20 18:53:54 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_18\n",
      "Fri Dec 20 18:53:54 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_18\n",
      "Fri Dec 20 18:53:56 2019\n",
      "\n",
      "Merging sorted day135_AllpH_DMR250bp_MCmax25_cov5x_rms_results.tsv files.\n",
      "Fri Dec 20 19:03:27 2019\n",
      "\n",
      "Begin FDR Correction\n",
      "Fri Dec 20 19:03:28 2019\n",
      "\n",
      "m0 estimate for iteration 0: 6489\n",
      "Histogram FDR correction did not converge. Using the smallest p-value 0.0003333333333333333 as cutoff.\n",
      "\n",
      "Calculating Residual Cutoff\n",
      "Fri Dec 20 19:03:28 2019\n",
      "\n",
      "Filtering allc files using 8 node(s).\n",
      "Fri Dec 20 19:03:29 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_01\n",
      "Fri Dec 20 19:04:21 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_01\n",
      "Fri Dec 20 19:04:27 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_02\n",
      "Fri Dec 20 19:04:27 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_02\n",
      "Fri Dec 20 19:04:32 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_03\n",
      "Fri Dec 20 19:04:32 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_03\n",
      "Fri Dec 20 19:04:37 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_04\n",
      "Fri Dec 20 19:04:37 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_04\n",
      "Fri Dec 20 19:04:42 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_05\n",
      "Fri Dec 20 19:04:42 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_05\n",
      "Fri Dec 20 19:04:46 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_06\n",
      "Fri Dec 20 19:04:46 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_06\n",
      "Fri Dec 20 19:04:51 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_07\n",
      "Fri Dec 20 19:04:51 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_07\n",
      "Fri Dec 20 19:04:54 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_08\n",
      "Fri Dec 20 19:04:54 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_08\n",
      "Fri Dec 20 19:04:59 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_09\n",
      "Fri Dec 20 19:04:59 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_09\n",
      "Fri Dec 20 19:05:03 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_10\n",
      "Fri Dec 20 19:05:03 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_10\n",
      "Fri Dec 20 19:05:07 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_11\n",
      "Fri Dec 20 19:05:07 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_11\n",
      "Fri Dec 20 19:05:11 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_12\n",
      "Fri Dec 20 19:05:11 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_12\n",
      "Fri Dec 20 19:05:16 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_13\n",
      "Fri Dec 20 19:05:16 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_13\n",
      "Fri Dec 20 19:05:21 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_14\n",
      "Fri Dec 20 19:05:21 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_14\n",
      "Fri Dec 20 19:05:26 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_15\n",
      "Fri Dec 20 19:05:26 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_15\n",
      "Fri Dec 20 19:05:32 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_16\n",
      "Fri Dec 20 19:05:32 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_16\n",
      "Fri Dec 20 19:05:36 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_17\n",
      "Fri Dec 20 19:05:36 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_17\n",
      "Fri Dec 20 19:05:41 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_18\n",
      "Fri Dec 20 19:05:41 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_18\n",
      "Fri Dec 20 19:05:45 2019\n",
      "\n",
      "Merging sorted day145_AllpH_DMR250bp_MCmax25_cov5x_rms_results.tsv files.\n",
      "Fri Dec 20 19:18:18 2019\n",
      "\n",
      "Begin FDR Correction\n",
      "Fri Dec 20 19:18:20 2019\n",
      "\n",
      "m0 estimate for iteration 0: 9079\n",
      "Histogram FDR correction did not converge. Using the smallest p-value 0.0003333333333333333 as cutoff.\n",
      "\n",
      "Calculating Residual Cutoff\n",
      "Fri Dec 20 19:18:20 2019\n",
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "Traceback (most recent call last):\n",
      "  File \"/Users/strigg/anaconda3/bin/methylpy\", line 5, in <module>\n",
      "    parse_args()\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/parser.py\", line 71, in parse_args\n",
      "    seed=args.seed)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 274, in DMRfind\n",
      "    convergence_diff=convergence_diff)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 319, in merge_DMS_to_DMR\n",
      "    input_rms_file)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 482, in get_resid_cutoff\n",
      "    residuals.append(float(resid))\n",
      "ValueError: could not convert string to float: '-Scaffold_01'\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "Traceback (most recent call last):\n",
      "  File \"/Users/strigg/anaconda3/bin/methylpy\", line 5, in <module>\n",
      "    parse_args()\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/parser.py\", line 71, in parse_args\n",
      "    seed=args.seed)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 274, in DMRfind\n",
      "    convergence_diff=convergence_diff)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 319, in merge_DMS_to_DMR\n",
      "    input_rms_file)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 482, in get_resid_cutoff\n",
      "    residuals.append(float(resid))\n",
      "ValueError: could not convert string to float: '-Scaffold_01'\n",
      "bash: line 55: fg: no job control\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "Traceback (most recent call last):\n",
      "  File \"/Users/strigg/anaconda3/bin/methylpy\", line 5, in <module>\n",
      "    parse_args()\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/parser.py\", line 71, in parse_args\n",
      "    seed=args.seed)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 274, in DMRfind\n",
      "    convergence_diff=convergence_diff)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 319, in merge_DMS_to_DMR\n",
      "    input_rms_file)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 482, in get_resid_cutoff\n",
      "    residuals.append(float(resid))\n",
      "ValueError: could not convert string to float: 'CGA'\n",
      "bash: line 80: fg: no job control\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "Traceback (most recent call last):\n",
      "  File \"/Users/strigg/anaconda3/bin/methylpy\", line 5, in <module>\n",
      "    parse_args()\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/parser.py\", line 71, in parse_args\n",
      "    seed=args.seed)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 274, in DMRfind\n",
      "    convergence_diff=convergence_diff)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 319, in merge_DMS_to_DMR\n",
      "    input_rms_file)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 482, in get_resid_cutoff\n",
      "    residuals.append(float(resid))\n",
      "ValueError: could not convert string to float: '-Scaffold_02'\n"
     ]
    },
    {
     "ename": "CalledProcessError",
     "evalue": "Command 'b'methylpy DMRfind \\\\\\n--allc-files EPI-41_S38_L005_5xmerg_allc.tsv \\\\\\nEPI-42_S39_L005_5xmerg_allc.tsv \\\\\\nEPI-43_S40_L005_5xmerg_allc.tsv \\\\\\nEPI-44_S41_L005_5xmerg_allc.tsv \\\\\\nEPI-119_S31_L005_5xmerg_allc.tsv \\\\\\nEPI-120_S32_L005_5xmerg_allc.tsv \\\\\\nEPI-135_S35_L005_5xmerg_allc.tsv \\\\\\nEPI-136_S36_L005_5xmerg_allc.tsv \\\\\\nEPI-151_S2_L002_5xmerg_allc.tsv \\\\\\nEPI-152_S3_L002_5xmerg_allc.tsv \\\\\\nEPI-153_S4_L002_5xmerg_allc.tsv \\\\\\nEPI-154_S5_L002_5xmerg_allc.tsv \\\\\\nEPI-181_S16_L003_5xmerg_allc.tsv \\\\\\nEPI-182_S17_L003_5xmerg_allc.tsv \\\\\\nEPI-184_S18_L003_5xmerg_allc.tsv \\\\\\nEPI-185_S19_L003_5xmerg_allc.tsv \\\\\\n--samples EPI-41 EPI-42 EPI-43 EPI-44 EPI-119 EPI-120 EPI-135 EPI-136 EPI-151 EPI-152 EPI-153 EPI-154 EPI-181 EPI-182 EPI-184 EPI-185 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix amb_AllTimes_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3 \\n\\n\\n\\n# For table S2, compare pH treatments at Day 10\\nmethylpy DMRfind \\\\\\n--allc-files EPI-103_S27_L005_5xmerg_allc.tsv \\\\\\nEPI-104_S28_L005_5xmerg_allc.tsv \\\\\\nEPI-111_S29_L005_5xmerg_allc.tsv \\\\\\nEPI-113_S30_L005_5xmerg_allc.tsv \\\\\\nEPI-119_S31_L005_5xmerg_allc.tsv \\\\\\nEPI-120_S32_L005_5xmerg_allc.tsv \\\\\\nEPI-135_S35_L005_5xmerg_allc.tsv \\\\\\nEPI-136_S36_L005_5xmerg_allc.tsv \\\\\\nEPI-127_S33_L005_5xmerg_allc.tsv \\\\\\nEPI-128_S34_L005_5xmerg_allc.tsv \\\\\\nEPI-143_S37_L005_5xmerg_allc.tsv \\\\\\nEPI-145_S38_L005_5xmerg_allc.tsv \\\\\\n--samples EPI-103 EPI-104 EPI-111 EPI-113 EPI-119 EPI-120 EPI-135 EPI-136 EPI-127 EPI-128 EPI-143 EPI-145 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day10_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 1 1 2 2 2 2 0 0 1 1 \\n\\n\\n\\n# For table S3, compare pH treatments at Day 135\\n%%bash\\n\\nmethylpy DMRfind \\\\\\n--allc-files EPI-151_S2_L002_5xmerg_allc.tsv \\\\\\nEPI-152_S3_L002_5xmerg_allc.tsv \\\\\\nEPI-153_S4_L002_5xmerg_allc.tsv \\\\\\nEPI-154_S5_L002_5xmerg_allc.tsv \\\\\\nEPI-159_S6_L002_5xmerg_allc.tsv \\\\\\nEPI-160_S7_L002_5xmerg_allc.tsv \\\\\\nEPI-161_S8_L002_5xmerg_allc.tsv \\\\\\nEPI-162_S9_L002_5xmerg_allc.tsv \\\\\\nEPI-167_S10_L002_5xmerg_allc.tsv \\\\\\nEPI-168_S11_L002_5xmerg_allc.tsv \\\\\\nEPI-169_S12_L002_5xmerg_allc.tsv \\\\\\nEPI-170_S13_L002_5xmerg_allc.tsv \\\\\\n--samples EPI-151 EPI-152 EPI-153 EPI-154 EPI-159 EPI-160 EPI-161 EPI-162 EPI-167 EPI-168 EPI-169 EPI-170 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day135_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 0 0 1 1 1 1 2 2 2 2 \\n\\n# For table S4, compare pH treatments at Day 145\\n%%bash\\n\\nmethylpy DMRfind \\\\\\n--allc-files EPI-175_S14_L003_5xmerg_allc.tsv \\\\\\nEPI-176_S15_L003_5xmerg_allc.tsv \\\\\\nEPI-181_S16_L003_5xmerg_allc.tsv \\\\\\nEPI-182_S17_L003_5xmerg_allc.tsv \\\\\\nEPI-184_S18_L003_5xmerg_allc.tsv \\\\\\nEPI-185_S19_L003_5xmerg_allc.tsv \\\\\\nEPI-187_S20_L003_5xmerg_allc.tsv \\\\\\nEPI-188_S21_L003_5xmerg_allc.tsv \\\\\\nEPI-193_S22_L003_5xmerg_allc.tsv \\\\\\nEPI-194_S23_L003_5xmerg_allc.tsv \\\\\\nEPI-199_S24_L003_5xmerg_allc.tsv \\\\\\nEPI-200_S25_L003_5xmerg_allc.tsv \\\\\\nEPI-205_S26_L004_5xmerg_allc.tsv \\\\\\nEPI-206_S27_L004_5xmerg_allc.tsv \\\\\\nEPI-208_S28_L004_5xmerg_allc.tsv \\\\\\nEPI-209_S29_L004_5xmerg_allc.tsv \\\\\\nEPI-214_S30_L004_5xmerg_allc.tsv \\\\\\nEPI-215_S31_L004_5xmerg_allc.tsv \\\\\\nEPI-220_S32_L004_5xmerg_allc.tsv \\\\\\nEPI-221_S33_L004_5xmerg_allc.tsv \\\\\\nEPI-226_S34_L004_5xmerg_allc.tsv \\\\\\nEPI-227_S35_L004_5xmerg_allc.tsv \\\\\\nEPI-229_S36_L004_5xmerg_allc.tsv \\\\\\nEPI-230_S37_L004_5xmerg_allc.tsv \\\\\\n--samples EPI-175 EPI-176 EPI-181 EPI-182 EPI-184 EPI-185 EPI-187 EPI-188 EPI-193 EPI-194 EPI-199 EPI-200 EPI-205 EPI-206 EPI-208 EPI-209 EPI-214 EPI-215 EPI-220 EPI-221 EPI-226 EPI-227 EPI-229 EPI-230 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day145_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 1 1 1 1 2 2 0 0 2 2 3 3 4 4 5 5 5 5 3 3 4 4 \\n'' returned non-zero exit status 1.",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mCalledProcessError\u001b[0m                        Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-22-4c685ce22a37>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_cell_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'bash'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'methylpy DMRfind \\\\\\n--allc-files EPI-41_S38_L005_5xmerg_allc.tsv \\\\\\nEPI-42_S39_L005_5xmerg_allc.tsv \\\\\\nEPI-43_S40_L005_5xmerg_allc.tsv \\\\\\nEPI-44_S41_L005_5xmerg_allc.tsv \\\\\\nEPI-119_S31_L005_5xmerg_allc.tsv \\\\\\nEPI-120_S32_L005_5xmerg_allc.tsv \\\\\\nEPI-135_S35_L005_5xmerg_allc.tsv \\\\\\nEPI-136_S36_L005_5xmerg_allc.tsv \\\\\\nEPI-151_S2_L002_5xmerg_allc.tsv \\\\\\nEPI-152_S3_L002_5xmerg_allc.tsv \\\\\\nEPI-153_S4_L002_5xmerg_allc.tsv \\\\\\nEPI-154_S5_L002_5xmerg_allc.tsv \\\\\\nEPI-181_S16_L003_5xmerg_allc.tsv \\\\\\nEPI-182_S17_L003_5xmerg_allc.tsv \\\\\\nEPI-184_S18_L003_5xmerg_allc.tsv \\\\\\nEPI-185_S19_L003_5xmerg_allc.tsv \\\\\\n--samples EPI-41 EPI-42 EPI-43 EPI-44 EPI-119 EPI-120 EPI-135 EPI-136 EPI-151 EPI-152 EPI-153 EPI-154 EPI-181 EPI-182 EPI-184 EPI-185 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix amb_AllTimes_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3 \\n\\n\\n\\n# For table S2, compare pH treatments at Day 10\\nmethylpy DMRfind \\\\\\n--allc-files EPI-103_S27_L005_5xmerg_allc.tsv \\\\\\nEPI-104_S28_L005_5xmerg_allc.tsv \\\\\\nEPI-111_S29_L005_5xmerg_allc.tsv \\\\\\nEPI-113_S30_L005_5xmerg_allc.tsv \\\\\\nEPI-119_S31_L005_5xmerg_allc.tsv \\\\\\nEPI-120_S32_L005_5xmerg_allc.tsv \\\\\\nEPI-135_S35_L005_5xmerg_allc.tsv \\\\\\nEPI-136_S36_L005_5xmerg_allc.tsv \\\\\\nEPI-127_S33_L005_5xmerg_allc.tsv \\\\\\nEPI-128_S34_L005_5xmerg_allc.tsv \\\\\\nEPI-143_S37_L005_5xmerg_allc.tsv \\\\\\nEPI-145_S38_L005_5xmerg_allc.tsv \\\\\\n--samples EPI-103 EPI-104 EPI-111 EPI-113 EPI-119 EPI-120 EPI-135 EPI-136 EPI-127 EPI-128 EPI-143 EPI-145 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day10_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 1 1 2 2 2 2 0 0 1 1 \\n\\n\\n\\n# For table S3, compare pH treatments at Day 135\\n%%bash\\n\\nmethylpy DMRfind \\\\\\n--allc-files EPI-151_S2_L002_5xmerg_allc.tsv \\\\\\nEPI-152_S3_L002_5xmerg_allc.tsv \\\\\\nEPI-153_S4_L002_5xmerg_allc.tsv \\\\\\nEPI-154_S5_L002_5xmerg_allc.tsv \\\\\\nEPI-159_S6_L002_5xmerg_allc.tsv \\\\\\nEPI-160_S7_L002_5xmerg_allc.tsv \\\\\\nEPI-161_S8_L002_5xmerg_allc.tsv \\\\\\nEPI-162_S9_L002_5xmerg_allc.tsv \\\\\\nEPI-167_S10_L002_5xmerg_allc.tsv \\\\\\nEPI-168_S11_L002_5xmerg_allc.tsv \\\\\\nEPI-169_S12_L002_5xmerg_allc.tsv \\\\\\nEPI-170_S13_L002_5xmerg_allc.tsv \\\\\\n--samples EPI-151 EPI-152 EPI-153 EPI-154 EPI-159 EPI-160 EPI-161 EPI-162 EPI-167 EPI-168 EPI-169 EPI-170 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day135_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 0 0 1 1 1 1 2 2 2 2 \\n\\n# For table S4, compare pH treatments at Day 145\\n%%bash\\n\\nmethylpy DMRfind \\\\\\n--allc-files EPI-175_S14_L003_5xmerg_allc.tsv \\\\\\nEPI-176_S15_L003_5xmerg_allc.tsv \\\\\\nEPI-181_S16_L003_5xmerg_allc.tsv \\\\\\nEPI-182_S17_L003_5xmerg_allc.tsv \\\\\\nEPI-184_S18_L003_5xmerg_allc.tsv \\\\\\nEPI-185_S19_L003_5xmerg_allc.tsv \\\\\\nEPI-187_S20_L003_5xmerg_allc.tsv \\\\\\nEPI-188_S21_L003_5xmerg_allc.tsv \\\\\\nEPI-193_S22_L003_5xmerg_allc.tsv \\\\\\nEPI-194_S23_L003_5xmerg_allc.tsv \\\\\\nEPI-199_S24_L003_5xmerg_allc.tsv \\\\\\nEPI-200_S25_L003_5xmerg_allc.tsv \\\\\\nEPI-205_S26_L004_5xmerg_allc.tsv \\\\\\nEPI-206_S27_L004_5xmerg_allc.tsv \\\\\\nEPI-208_S28_L004_5xmerg_allc.tsv \\\\\\nEPI-209_S29_L004_5xmerg_allc.tsv \\\\\\nEPI-214_S30_L004_5xmerg_allc.tsv \\\\\\nEPI-215_S31_L004_5xmerg_allc.tsv \\\\\\nEPI-220_S32_L004_5xmerg_allc.tsv \\\\\\nEPI-221_S33_L004_5xmerg_allc.tsv \\\\\\nEPI-226_S34_L004_5xmerg_allc.tsv \\\\\\nEPI-227_S35_L004_5xmerg_allc.tsv \\\\\\nEPI-229_S36_L004_5xmerg_allc.tsv \\\\\\nEPI-230_S37_L004_5xmerg_allc.tsv \\\\\\n--samples EPI-175 EPI-176 EPI-181 EPI-182 EPI-184 EPI-185 EPI-187 EPI-188 EPI-193 EPI-194 EPI-199 EPI-200 EPI-205 EPI-206 EPI-208 EPI-209 EPI-214 EPI-215 EPI-220 EPI-221 EPI-226 EPI-227 EPI-229 EPI-230 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day145_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 1 1 1 1 2 2 0 0 2 2 3 3 4 4 5 5 5 5 3 3 4 4 \\n'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py\u001b[0m in \u001b[0;36mrun_cell_magic\u001b[0;34m(self, magic_name, line, cell)\u001b[0m\n\u001b[1;32m   2356\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2357\u001b[0m                 \u001b[0margs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2358\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2359\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2360\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/anaconda3/lib/python3.6/site-packages/IPython/core/magics/script.py\u001b[0m in \u001b[0;36mnamed_script_magic\u001b[0;34m(line, cell)\u001b[0m\n\u001b[1;32m    140\u001b[0m             \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    141\u001b[0m                 \u001b[0mline\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mscript\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 142\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshebang\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mline\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    143\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    144\u001b[0m         \u001b[0;31m# write a basic docstring:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m</Users/strigg/anaconda3/lib/python3.6/site-packages/decorator.py:decorator-gen-110>\u001b[0m in \u001b[0;36mshebang\u001b[0;34m(self, line, cell)\u001b[0m\n",
      "\u001b[0;32m~/anaconda3/lib/python3.6/site-packages/IPython/core/magic.py\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m    185\u001b[0m     \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    186\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 187\u001b[0;31m         \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    188\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    189\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/anaconda3/lib/python3.6/site-packages/IPython/core/magics/script.py\u001b[0m in \u001b[0;36mshebang\u001b[0;34m(self, line, cell)\u001b[0m\n\u001b[1;32m    243\u001b[0m             \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstderr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mflush\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    244\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraise_error\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreturncode\u001b[0m\u001b[0;34m!=\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 245\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mCalledProcessError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreturncode\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mout\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstderr\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0merr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    246\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    247\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_run_script\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mto_close\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mCalledProcessError\u001b[0m: Command 'b'methylpy DMRfind \\\\\\n--allc-files EPI-41_S38_L005_5xmerg_allc.tsv \\\\\\nEPI-42_S39_L005_5xmerg_allc.tsv \\\\\\nEPI-43_S40_L005_5xmerg_allc.tsv \\\\\\nEPI-44_S41_L005_5xmerg_allc.tsv \\\\\\nEPI-119_S31_L005_5xmerg_allc.tsv \\\\\\nEPI-120_S32_L005_5xmerg_allc.tsv \\\\\\nEPI-135_S35_L005_5xmerg_allc.tsv \\\\\\nEPI-136_S36_L005_5xmerg_allc.tsv \\\\\\nEPI-151_S2_L002_5xmerg_allc.tsv \\\\\\nEPI-152_S3_L002_5xmerg_allc.tsv \\\\\\nEPI-153_S4_L002_5xmerg_allc.tsv \\\\\\nEPI-154_S5_L002_5xmerg_allc.tsv \\\\\\nEPI-181_S16_L003_5xmerg_allc.tsv \\\\\\nEPI-182_S17_L003_5xmerg_allc.tsv \\\\\\nEPI-184_S18_L003_5xmerg_allc.tsv \\\\\\nEPI-185_S19_L003_5xmerg_allc.tsv \\\\\\n--samples EPI-41 EPI-42 EPI-43 EPI-44 EPI-119 EPI-120 EPI-135 EPI-136 EPI-151 EPI-152 EPI-153 EPI-154 EPI-181 EPI-182 EPI-184 EPI-185 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix amb_AllTimes_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3 \\n\\n\\n\\n# For table S2, compare pH treatments at Day 10\\nmethylpy DMRfind \\\\\\n--allc-files EPI-103_S27_L005_5xmerg_allc.tsv \\\\\\nEPI-104_S28_L005_5xmerg_allc.tsv \\\\\\nEPI-111_S29_L005_5xmerg_allc.tsv \\\\\\nEPI-113_S30_L005_5xmerg_allc.tsv \\\\\\nEPI-119_S31_L005_5xmerg_allc.tsv \\\\\\nEPI-120_S32_L005_5xmerg_allc.tsv \\\\\\nEPI-135_S35_L005_5xmerg_allc.tsv \\\\\\nEPI-136_S36_L005_5xmerg_allc.tsv \\\\\\nEPI-127_S33_L005_5xmerg_allc.tsv \\\\\\nEPI-128_S34_L005_5xmerg_allc.tsv \\\\\\nEPI-143_S37_L005_5xmerg_allc.tsv \\\\\\nEPI-145_S38_L005_5xmerg_allc.tsv \\\\\\n--samples EPI-103 EPI-104 EPI-111 EPI-113 EPI-119 EPI-120 EPI-135 EPI-136 EPI-127 EPI-128 EPI-143 EPI-145 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day10_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 1 1 2 2 2 2 0 0 1 1 \\n\\n\\n\\n# For table S3, compare pH treatments at Day 135\\n%%bash\\n\\nmethylpy DMRfind \\\\\\n--allc-files EPI-151_S2_L002_5xmerg_allc.tsv \\\\\\nEPI-152_S3_L002_5xmerg_allc.tsv \\\\\\nEPI-153_S4_L002_5xmerg_allc.tsv \\\\\\nEPI-154_S5_L002_5xmerg_allc.tsv \\\\\\nEPI-159_S6_L002_5xmerg_allc.tsv \\\\\\nEPI-160_S7_L002_5xmerg_allc.tsv \\\\\\nEPI-161_S8_L002_5xmerg_allc.tsv \\\\\\nEPI-162_S9_L002_5xmerg_allc.tsv \\\\\\nEPI-167_S10_L002_5xmerg_allc.tsv \\\\\\nEPI-168_S11_L002_5xmerg_allc.tsv \\\\\\nEPI-169_S12_L002_5xmerg_allc.tsv \\\\\\nEPI-170_S13_L002_5xmerg_allc.tsv \\\\\\n--samples EPI-151 EPI-152 EPI-153 EPI-154 EPI-159 EPI-160 EPI-161 EPI-162 EPI-167 EPI-168 EPI-169 EPI-170 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day135_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 0 0 1 1 1 1 2 2 2 2 \\n\\n# For table S4, compare pH treatments at Day 145\\n%%bash\\n\\nmethylpy DMRfind \\\\\\n--allc-files EPI-175_S14_L003_5xmerg_allc.tsv \\\\\\nEPI-176_S15_L003_5xmerg_allc.tsv \\\\\\nEPI-181_S16_L003_5xmerg_allc.tsv \\\\\\nEPI-182_S17_L003_5xmerg_allc.tsv \\\\\\nEPI-184_S18_L003_5xmerg_allc.tsv \\\\\\nEPI-185_S19_L003_5xmerg_allc.tsv \\\\\\nEPI-187_S20_L003_5xmerg_allc.tsv \\\\\\nEPI-188_S21_L003_5xmerg_allc.tsv \\\\\\nEPI-193_S22_L003_5xmerg_allc.tsv \\\\\\nEPI-194_S23_L003_5xmerg_allc.tsv \\\\\\nEPI-199_S24_L003_5xmerg_allc.tsv \\\\\\nEPI-200_S25_L003_5xmerg_allc.tsv \\\\\\nEPI-205_S26_L004_5xmerg_allc.tsv \\\\\\nEPI-206_S27_L004_5xmerg_allc.tsv \\\\\\nEPI-208_S28_L004_5xmerg_allc.tsv \\\\\\nEPI-209_S29_L004_5xmerg_allc.tsv \\\\\\nEPI-214_S30_L004_5xmerg_allc.tsv \\\\\\nEPI-215_S31_L004_5xmerg_allc.tsv \\\\\\nEPI-220_S32_L004_5xmerg_allc.tsv \\\\\\nEPI-221_S33_L004_5xmerg_allc.tsv \\\\\\nEPI-226_S34_L004_5xmerg_allc.tsv \\\\\\nEPI-227_S35_L004_5xmerg_allc.tsv \\\\\\nEPI-229_S36_L004_5xmerg_allc.tsv \\\\\\nEPI-230_S37_L004_5xmerg_allc.tsv \\\\\\n--samples EPI-175 EPI-176 EPI-181 EPI-182 EPI-184 EPI-185 EPI-187 EPI-188 EPI-193 EPI-194 EPI-199 EPI-200 EPI-205 EPI-206 EPI-208 EPI-209 EPI-214 EPI-215 EPI-220 EPI-221 EPI-226 EPI-227 EPI-229 EPI-230 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day145_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 1 1 1 1 2 2 0 0 2 2 3 3 4 4 5 5 5 5 3 3 4 4 \\n'' returned non-zero exit status 1."
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "methylpy DMRfind \\\n",
    "--allc-files EPI-41_S38_L005_5xmerg_allc.tsv \\\n",
    "EPI-42_S39_L005_5xmerg_allc.tsv \\\n",
    "EPI-43_S40_L005_5xmerg_allc.tsv \\\n",
    "EPI-44_S41_L005_5xmerg_allc.tsv \\\n",
    "EPI-119_S31_L005_5xmerg_allc.tsv \\\n",
    "EPI-120_S32_L005_5xmerg_allc.tsv \\\n",
    "EPI-135_S35_L005_5xmerg_allc.tsv \\\n",
    "EPI-136_S36_L005_5xmerg_allc.tsv \\\n",
    "EPI-151_S2_L002_5xmerg_allc.tsv \\\n",
    "EPI-152_S3_L002_5xmerg_allc.tsv \\\n",
    "EPI-153_S4_L002_5xmerg_allc.tsv \\\n",
    "EPI-154_S5_L002_5xmerg_allc.tsv \\\n",
    "EPI-181_S16_L003_5xmerg_allc.tsv \\\n",
    "EPI-182_S17_L003_5xmerg_allc.tsv \\\n",
    "EPI-184_S18_L003_5xmerg_allc.tsv \\\n",
    "EPI-185_S19_L003_5xmerg_allc.tsv \\\n",
    "--samples EPI-41 EPI-42 EPI-43 EPI-44 EPI-119 EPI-120 EPI-135 EPI-136 EPI-151 EPI-152 EPI-153 EPI-154 EPI-181 EPI-182 EPI-184 EPI-185 \\\n",
    "--mc-type \"CGN\" \\\n",
    "--num-procs 8 \\\n",
    "--output-prefix amb_AllTimes_DMR250bp_MCmax25_cov5x \\\n",
    "--mc-max-dist 25 \\\n",
    "--dmr-max-dist 250 \\\n",
    "--min-num-dms 3 \\\n",
    "--sample-category 0 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3 \n",
    "\n",
    "\n",
    "\n",
    "# For table S2, compare pH treatments at Day 10\n",
    "methylpy DMRfind \\\n",
    "--allc-files EPI-103_S27_L005_5xmerg_allc.tsv \\\n",
    "EPI-104_S28_L005_5xmerg_allc.tsv \\\n",
    "EPI-111_S29_L005_5xmerg_allc.tsv \\\n",
    "EPI-113_S30_L005_5xmerg_allc.tsv \\\n",
    "EPI-119_S31_L005_5xmerg_allc.tsv \\\n",
    "EPI-120_S32_L005_5xmerg_allc.tsv \\\n",
    "EPI-135_S35_L005_5xmerg_allc.tsv \\\n",
    "EPI-136_S36_L005_5xmerg_allc.tsv \\\n",
    "EPI-127_S33_L005_5xmerg_allc.tsv \\\n",
    "EPI-128_S34_L005_5xmerg_allc.tsv \\\n",
    "EPI-143_S37_L005_5xmerg_allc.tsv \\\n",
    "EPI-145_S38_L005_5xmerg_allc.tsv \\\n",
    "--samples EPI-103 EPI-104 EPI-111 EPI-113 EPI-119 EPI-120 EPI-135 EPI-136 EPI-127 EPI-128 EPI-143 EPI-145 \\\n",
    "--mc-type \"CGN\" \\\n",
    "--num-procs 8 \\\n",
    "--output-prefix day10_AllpH_DMR250bp_MCmax25_cov5x \\\n",
    "--mc-max-dist 25 \\\n",
    "--dmr-max-dist 250 \\\n",
    "--min-num-dms 3 \\\n",
    "--sample-category 0 0 1 1 2 2 2 2 0 0 1 1 \n",
    "\n",
    "\n",
    "\n",
    "# For table S3, compare pH treatments at Day 135\n",
    "%%bash\n",
    "\n",
    "methylpy DMRfind \\\n",
    "--allc-files EPI-151_S2_L002_5xmerg_allc.tsv \\\n",
    "EPI-152_S3_L002_5xmerg_allc.tsv \\\n",
    "EPI-153_S4_L002_5xmerg_allc.tsv \\\n",
    "EPI-154_S5_L002_5xmerg_allc.tsv \\\n",
    "EPI-159_S6_L002_5xmerg_allc.tsv \\\n",
    "EPI-160_S7_L002_5xmerg_allc.tsv \\\n",
    "EPI-161_S8_L002_5xmerg_allc.tsv \\\n",
    "EPI-162_S9_L002_5xmerg_allc.tsv \\\n",
    "EPI-167_S10_L002_5xmerg_allc.tsv \\\n",
    "EPI-168_S11_L002_5xmerg_allc.tsv \\\n",
    "EPI-169_S12_L002_5xmerg_allc.tsv \\\n",
    "EPI-170_S13_L002_5xmerg_allc.tsv \\\n",
    "--samples EPI-151 EPI-152 EPI-153 EPI-154 EPI-159 EPI-160 EPI-161 EPI-162 EPI-167 EPI-168 EPI-169 EPI-170 \\\n",
    "--mc-type \"CGN\" \\\n",
    "--num-procs 8 \\\n",
    "--output-prefix day135_AllpH_DMR250bp_MCmax25_cov5x \\\n",
    "--mc-max-dist 25 \\\n",
    "--dmr-max-dist 250 \\\n",
    "--min-num-dms 3 \\\n",
    "--sample-category 0 0 0 0 1 1 1 1 2 2 2 2 \n",
    "\n",
    "# For table S4, compare pH treatments at Day 145\n",
    "%%bash\n",
    "\n",
    "methylpy DMRfind \\\n",
    "--allc-files EPI-175_S14_L003_5xmerg_allc.tsv \\\n",
    "EPI-176_S15_L003_5xmerg_allc.tsv \\\n",
    "EPI-181_S16_L003_5xmerg_allc.tsv \\\n",
    "EPI-182_S17_L003_5xmerg_allc.tsv \\\n",
    "EPI-184_S18_L003_5xmerg_allc.tsv \\\n",
    "EPI-185_S19_L003_5xmerg_allc.tsv \\\n",
    "EPI-187_S20_L003_5xmerg_allc.tsv \\\n",
    "EPI-188_S21_L003_5xmerg_allc.tsv \\\n",
    "EPI-193_S22_L003_5xmerg_allc.tsv \\\n",
    "EPI-194_S23_L003_5xmerg_allc.tsv \\\n",
    "EPI-199_S24_L003_5xmerg_allc.tsv \\\n",
    "EPI-200_S25_L003_5xmerg_allc.tsv \\\n",
    "EPI-205_S26_L004_5xmerg_allc.tsv \\\n",
    "EPI-206_S27_L004_5xmerg_allc.tsv \\\n",
    "EPI-208_S28_L004_5xmerg_allc.tsv \\\n",
    "EPI-209_S29_L004_5xmerg_allc.tsv \\\n",
    "EPI-214_S30_L004_5xmerg_allc.tsv \\\n",
    "EPI-215_S31_L004_5xmerg_allc.tsv \\\n",
    "EPI-220_S32_L004_5xmerg_allc.tsv \\\n",
    "EPI-221_S33_L004_5xmerg_allc.tsv \\\n",
    "EPI-226_S34_L004_5xmerg_allc.tsv \\\n",
    "EPI-227_S35_L004_5xmerg_allc.tsv \\\n",
    "EPI-229_S36_L004_5xmerg_allc.tsv \\\n",
    "EPI-230_S37_L004_5xmerg_allc.tsv \\\n",
    "--samples EPI-175 EPI-176 EPI-181 EPI-182 EPI-184 EPI-185 EPI-187 EPI-188 EPI-193 EPI-194 EPI-199 EPI-200 EPI-205 EPI-206 EPI-208 EPI-209 EPI-214 EPI-215 EPI-220 EPI-221 EPI-226 EPI-227 EPI-229 EPI-230 \\\n",
    "--mc-type \"CGN\" \\\n",
    "--num-procs 8 \\\n",
    "--output-prefix day145_AllpH_DMR250bp_MCmax25_cov5x \\\n",
    "--mc-max-dist 25 \\\n",
    "--dmr-max-dist 250 \\\n",
    "--min-num-dms 3 \\\n",
    "--sample-category 0 0 1 1 1 1 2 2 0 0 2 2 3 3 4 4 5 5 5 5 3 3 4 4 "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "#chr\tstart\tend\tnumber_of_dms\thypermethylated_samples\thypomethylated_samples\tmethylation_level_EPI-103\tmethylation_level_EPI-104\tmethylation_level_EPI-111\tmethylation_level_EPI-113\tmethylation_level_EPI-119\tmethylation_level_EPI-120\tmethylation_level_EPI-135\tmethylation_level_EPI-136\tmethylation_level_EPI-127\tmethylation_level_EPI-128\tmethylation_level_EPI-143\tmethylation_level_EPI-145\r\n"
     ]
    }
   ],
   "source": [
    "!head day10_AllpH_DMR250bp_MCmax25_cov5x_rms_results_collapsed.tsv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Filtering allc files using 8 node(s).\n",
      "Fri Dec 20 16:36:48 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_01\n",
      "Fri Dec 20 16:36:59 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_01\n",
      "Fri Dec 20 16:37:05 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_02\n",
      "Fri Dec 20 16:37:05 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_02\n",
      "Fri Dec 20 16:37:11 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_03\n",
      "Fri Dec 20 16:37:11 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_03\n",
      "Fri Dec 20 16:37:15 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_04\n",
      "Fri Dec 20 16:37:15 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_04\n",
      "Fri Dec 20 16:37:20 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_05\n",
      "Fri Dec 20 16:37:20 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_05\n",
      "Fri Dec 20 16:37:24 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_06\n",
      "Fri Dec 20 16:37:24 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_06\n",
      "Fri Dec 20 16:37:28 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_07\n",
      "Fri Dec 20 16:37:28 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_07\n",
      "Fri Dec 20 16:37:31 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_08\n",
      "Fri Dec 20 16:37:31 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_08\n",
      "Fri Dec 20 16:37:36 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_09\n",
      "Fri Dec 20 16:37:36 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_09\n",
      "Fri Dec 20 16:37:38 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_10\n",
      "Fri Dec 20 16:37:38 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_10\n",
      "Fri Dec 20 16:37:42 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_11\n",
      "Fri Dec 20 16:37:42 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_11\n",
      "Fri Dec 20 16:37:45 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_12\n",
      "Fri Dec 20 16:37:45 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_12\n",
      "Fri Dec 20 16:37:49 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_13\n",
      "Fri Dec 20 16:37:49 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_13\n",
      "Fri Dec 20 16:37:52 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_14\n",
      "Fri Dec 20 16:37:52 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_14\n",
      "Fri Dec 20 16:37:56 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_15\n",
      "Fri Dec 20 16:37:56 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_15\n",
      "Fri Dec 20 16:37:59 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_16\n",
      "Fri Dec 20 16:37:59 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_16\n",
      "Fri Dec 20 16:38:02 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_17\n",
      "Fri Dec 20 16:38:02 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_17\n",
      "Fri Dec 20 16:38:04 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_18\n",
      "Fri Dec 20 16:38:04 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_18\n",
      "Fri Dec 20 16:38:06 2019\n",
      "\n",
      "Merging sorted day10_AllpH_DMR250bp_MCmax25_cov5x_rms_results.tsv files.\n",
      "Fri Dec 20 16:38:07 2019\n",
      "\n",
      "Begin FDR Correction\n",
      "Fri Dec 20 16:38:07 2019\n",
      "\n",
      "m0 estimate for iteration 0: 0\n",
      "Histogram FDR correction did not converge. Using the smallest p-value 0.0003333333333333333 as cutoff.\n",
      "\n",
      "Calculating Residual Cutoff\n",
      "Fri Dec 20 16:38:07 2019\n",
      "\n",
      "There are no null residuals to calculate resid_cutoff. Using 2 as the cutoff.\n",
      "Begin Defining Windows\n",
      "Fri Dec 20 16:38:07 2019\n",
      "\n",
      "Adding Methylation Levels\n",
      "Fri Dec 20 16:38:07 2019\n",
      "\n",
      "Done\n",
      "Fri Dec 20 16:38:07 2019\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# no results still"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#updated gsl\n",
    "# (base) ostrich:20191220_DMRfind_5xmerg strigg$ conda install -c conda-forge gsl \n",
    "# Collecting package metadata (current_repodata.json): done\n",
    "# Solving environment: \\ \n",
    "# The environment is inconsistent, please check the package plan carefully\n",
    "# The following packages are causing the inconsistency:\n",
    "\n",
    "#   - defaults/osx-64::blaze==0.11.3=py36_0\n",
    "#   - defaults/osx-64::numba==0.45.0=py36h6440ff4_0\n",
    "# done\n",
    "\n",
    "# ## Package Plan ##\n",
    "\n",
    "#   environment location: /Users/strigg/anaconda3\n",
    "\n",
    "#   added / updated specs:\n",
    "#     - gsl\n",
    "\n",
    "\n",
    "# The following packages will be downloaded:\n",
    "\n",
    "#     package                    |            build\n",
    "#     ---------------------------|-----------------\n",
    "#     ca-certificates-2019.11.28 |       hecc5488_0         145 KB  conda-forge\n",
    "#     certifi-2019.11.28         |           py36_0         148 KB  conda-forge\n",
    "#     conda-4.8.0                |           py36_1         3.0 MB  conda-forge\n",
    "#     gsl-2.6                    |       ha2d443c_0         3.0 MB  conda-forge\n",
    "#     libblas-3.8.0              |           14_mkl          10 KB  conda-forge\n",
    "#     libcblas-3.8.0             |           14_mkl          10 KB  conda-forge\n",
    "#     openssl-1.1.1d             |       h0b31af3_0         1.9 MB  conda-forge\n",
    "#     tbb-2018.0.5               |       h2d50403_0         150 KB  conda-forge\n",
    "#     ------------------------------------------------------------\n",
    "#                                            Total:         8.3 MB\n",
    "\n",
    "# The following NEW packages will be INSTALLED:\n",
    "\n",
    "#   gsl                conda-forge/osx-64::gsl-2.6-ha2d443c_0\n",
    "#   libblas            conda-forge/osx-64::libblas-3.8.0-14_mkl\n",
    "#   libcblas           conda-forge/osx-64::libcblas-3.8.0-14_mkl\n",
    "#   tbb                conda-forge/osx-64::tbb-2018.0.5-h2d50403_0\n",
    "\n",
    "# The following packages will be UPDATED:\n",
    "\n",
    "#   ca-certificates                      2019.6.16-hecc5488_0 --> 2019.11.28-hecc5488_0\n",
    "#   certifi                                  2019.6.16-py36_1 --> 2019.11.28-py36_0\n",
    "#   conda                                       4.7.11-py36_0 --> 4.8.0-py36_1\n",
    "#   openssl                                 1.1.1c-h01d97ff_0 --> 1.1.1d-h0b31af3_0\n",
    "\n",
    "\n",
    "# Proceed ([y]/n)? y\n",
    "\n",
    "\n",
    "# Downloading and Extracting Packages\n",
    "# libblas-3.8.0        | 10 KB     | ########################################################################################################################################################################################## | 100% \n",
    "# conda-4.8.0          | 3.0 MB    | ########################################################################################################################################################################################## | 100% \n",
    "# openssl-1.1.1d       | 1.9 MB    | ########################################################################################################################################################################################## | 100% \n",
    "# gsl-2.6              | 3.0 MB    | ########################################################################################################################################################################################## | 100% \n",
    "# certifi-2019.11.28   | 148 KB    | ########################################################################################################################################################################################## | 100% \n",
    "# tbb-2018.0.5         | 150 KB    | ########################################################################################################################################################################################## | 100% \n",
    "# libcblas-3.8.0       | 10 KB     | ########################################################################################################################################################################################## | 100% \n",
    "# ca-certificates-2019 | 145 KB    | ########################################################################################################################################################################################## | 100% \n",
    "# Preparing transaction: done\n",
    "# Verifying transaction: done\n",
    "# Executing transaction: done\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#test on just day10"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Filtering allc files using 8 node(s).\n",
      "Fri Dec 20 20:02:47 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_01\n",
      "Fri Dec 20 20:03:45 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_01\n",
      "Fri Dec 20 20:03:51 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_02\n",
      "Fri Dec 20 20:03:51 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_02\n",
      "Fri Dec 20 20:03:57 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_03\n",
      "Fri Dec 20 20:03:57 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_03\n",
      "Fri Dec 20 20:04:02 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_04\n",
      "Fri Dec 20 20:04:02 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_04\n",
      "Fri Dec 20 20:04:08 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_05\n",
      "Fri Dec 20 20:04:08 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_05\n",
      "Fri Dec 20 20:04:12 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_06\n",
      "Fri Dec 20 20:04:12 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_06\n",
      "Fri Dec 20 20:04:18 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_07\n",
      "Fri Dec 20 20:04:18 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_07\n",
      "Fri Dec 20 20:04:22 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_08\n",
      "Fri Dec 20 20:04:22 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_08\n",
      "Fri Dec 20 20:04:28 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_09\n",
      "Fri Dec 20 20:04:28 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_09\n",
      "Fri Dec 20 20:04:31 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_10\n",
      "Fri Dec 20 20:04:31 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_10\n",
      "Fri Dec 20 20:04:36 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_11\n",
      "Fri Dec 20 20:04:36 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_11\n",
      "Fri Dec 20 20:04:40 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_12\n",
      "Fri Dec 20 20:04:40 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_12\n",
      "Fri Dec 20 20:04:47 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_13\n",
      "Fri Dec 20 20:04:47 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_13\n",
      "Fri Dec 20 20:04:50 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_14\n",
      "Fri Dec 20 20:04:50 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_14\n",
      "Fri Dec 20 20:04:56 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_15\n",
      "Fri Dec 20 20:04:56 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_15\n",
      "Fri Dec 20 20:04:59 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_16\n",
      "Fri Dec 20 20:04:59 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_16\n",
      "Fri Dec 20 20:05:02 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_17\n",
      "Fri Dec 20 20:05:02 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_17\n",
      "Fri Dec 20 20:05:06 2019\n",
      "\n",
      "Splitting allc files for chromosome Scaffold_18\n",
      "Fri Dec 20 20:05:06 2019\n",
      "\n",
      "Running rms tests for chromosome Scaffold_18\n",
      "Fri Dec 20 20:05:09 2019\n",
      "\n",
      "Merging sorted day10_AllpH_DMR250bp_MCmax25_cov5x_rms_results.tsv files.\n",
      "Fri Dec 20 20:07:24 2019\n",
      "\n",
      "Begin FDR Correction\n",
      "Fri Dec 20 20:07:25 2019\n",
      "\n",
      "m0 estimate for iteration 0: 11885\n",
      "Histogram FDR correction did not converge. Using the smallest p-value 0.0003333333333333333 as cutoff.\n",
      "\n",
      "Calculating Residual Cutoff\n",
      "Fri Dec 20 20:07:25 2019\n",
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "gsl: discrete.c:238: ERROR: probabilities must be non-negative\n",
      "Default GSL error handler invoked.\n",
      "Traceback (most recent call last):\n",
      "  File \"/Users/strigg/anaconda3/bin/methylpy\", line 5, in <module>\n",
      "    parse_args()\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/parser.py\", line 71, in parse_args\n",
      "    seed=args.seed)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 274, in DMRfind\n",
      "    convergence_diff=convergence_diff)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 319, in merge_DMS_to_DMR\n",
      "    input_rms_file)\n",
      "  File \"/Users/strigg/anaconda3/lib/python3.6/site-packages/methylpy/DMRfind.py\", line 482, in get_resid_cutoff\n",
      "    residuals.append(float(resid))\n",
      "ValueError: could not convert string to float: '-0.0Scaffold_01'\n"
     ]
    },
    {
     "ename": "CalledProcessError",
     "evalue": "Command 'b'methylpy DMRfind \\\\\\n--allc-files EPI-103_S27_L005_5xmerg_allc.tsv \\\\\\nEPI-104_S28_L005_5xmerg_allc.tsv \\\\\\nEPI-111_S29_L005_5xmerg_allc.tsv \\\\\\nEPI-113_S30_L005_5xmerg_allc.tsv \\\\\\nEPI-119_S31_L005_5xmerg_allc.tsv \\\\\\nEPI-120_S32_L005_5xmerg_allc.tsv \\\\\\nEPI-135_S35_L005_5xmerg_allc.tsv \\\\\\nEPI-136_S36_L005_5xmerg_allc.tsv \\\\\\nEPI-127_S33_L005_5xmerg_allc.tsv \\\\\\nEPI-128_S34_L005_5xmerg_allc.tsv \\\\\\nEPI-143_S37_L005_5xmerg_allc.tsv \\\\\\nEPI-145_S38_L005_5xmerg_allc.tsv \\\\\\n--samples EPI-103 EPI-104 EPI-111 EPI-113 EPI-119 EPI-120 EPI-135 EPI-136 EPI-127 EPI-128 EPI-143 EPI-145 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day10_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 1 1 2 2 2 2 0 0 1 1 \\n'' returned non-zero exit status 1.",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mCalledProcessError\u001b[0m                        Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-24-cb2bc52d326b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_cell_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'bash'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'methylpy DMRfind \\\\\\n--allc-files EPI-103_S27_L005_5xmerg_allc.tsv \\\\\\nEPI-104_S28_L005_5xmerg_allc.tsv \\\\\\nEPI-111_S29_L005_5xmerg_allc.tsv \\\\\\nEPI-113_S30_L005_5xmerg_allc.tsv \\\\\\nEPI-119_S31_L005_5xmerg_allc.tsv \\\\\\nEPI-120_S32_L005_5xmerg_allc.tsv \\\\\\nEPI-135_S35_L005_5xmerg_allc.tsv \\\\\\nEPI-136_S36_L005_5xmerg_allc.tsv \\\\\\nEPI-127_S33_L005_5xmerg_allc.tsv \\\\\\nEPI-128_S34_L005_5xmerg_allc.tsv \\\\\\nEPI-143_S37_L005_5xmerg_allc.tsv \\\\\\nEPI-145_S38_L005_5xmerg_allc.tsv \\\\\\n--samples EPI-103 EPI-104 EPI-111 EPI-113 EPI-119 EPI-120 EPI-135 EPI-136 EPI-127 EPI-128 EPI-143 EPI-145 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day10_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 1 1 2 2 2 2 0 0 1 1 \\n'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py\u001b[0m in \u001b[0;36mrun_cell_magic\u001b[0;34m(self, magic_name, line, cell)\u001b[0m\n\u001b[1;32m   2356\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2357\u001b[0m                 \u001b[0margs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2358\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2359\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2360\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/anaconda3/lib/python3.6/site-packages/IPython/core/magics/script.py\u001b[0m in \u001b[0;36mnamed_script_magic\u001b[0;34m(line, cell)\u001b[0m\n\u001b[1;32m    140\u001b[0m             \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    141\u001b[0m                 \u001b[0mline\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mscript\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 142\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshebang\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mline\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    143\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    144\u001b[0m         \u001b[0;31m# write a basic docstring:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m</Users/strigg/anaconda3/lib/python3.6/site-packages/decorator.py:decorator-gen-110>\u001b[0m in \u001b[0;36mshebang\u001b[0;34m(self, line, cell)\u001b[0m\n",
      "\u001b[0;32m~/anaconda3/lib/python3.6/site-packages/IPython/core/magic.py\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m    185\u001b[0m     \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    186\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 187\u001b[0;31m         \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    188\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    189\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/anaconda3/lib/python3.6/site-packages/IPython/core/magics/script.py\u001b[0m in \u001b[0;36mshebang\u001b[0;34m(self, line, cell)\u001b[0m\n\u001b[1;32m    243\u001b[0m             \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstderr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mflush\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    244\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraise_error\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreturncode\u001b[0m\u001b[0;34m!=\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 245\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mCalledProcessError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreturncode\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mout\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstderr\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0merr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    246\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    247\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_run_script\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mto_close\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mCalledProcessError\u001b[0m: Command 'b'methylpy DMRfind \\\\\\n--allc-files EPI-103_S27_L005_5xmerg_allc.tsv \\\\\\nEPI-104_S28_L005_5xmerg_allc.tsv \\\\\\nEPI-111_S29_L005_5xmerg_allc.tsv \\\\\\nEPI-113_S30_L005_5xmerg_allc.tsv \\\\\\nEPI-119_S31_L005_5xmerg_allc.tsv \\\\\\nEPI-120_S32_L005_5xmerg_allc.tsv \\\\\\nEPI-135_S35_L005_5xmerg_allc.tsv \\\\\\nEPI-136_S36_L005_5xmerg_allc.tsv \\\\\\nEPI-127_S33_L005_5xmerg_allc.tsv \\\\\\nEPI-128_S34_L005_5xmerg_allc.tsv \\\\\\nEPI-143_S37_L005_5xmerg_allc.tsv \\\\\\nEPI-145_S38_L005_5xmerg_allc.tsv \\\\\\n--samples EPI-103 EPI-104 EPI-111 EPI-113 EPI-119 EPI-120 EPI-135 EPI-136 EPI-127 EPI-128 EPI-143 EPI-145 \\\\\\n--mc-type \"CGN\" \\\\\\n--num-procs 8 \\\\\\n--output-prefix day10_AllpH_DMR250bp_MCmax25_cov5x \\\\\\n--mc-max-dist 25 \\\\\\n--dmr-max-dist 250 \\\\\\n--min-num-dms 3 \\\\\\n--sample-category 0 0 1 1 2 2 2 2 0 0 1 1 \\n'' returned non-zero exit status 1."
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "methylpy DMRfind \\\n",
    "--allc-files EPI-103_S27_L005_5xmerg_allc.tsv \\\n",
    "EPI-104_S28_L005_5xmerg_allc.tsv \\\n",
    "EPI-111_S29_L005_5xmerg_allc.tsv \\\n",
    "EPI-113_S30_L005_5xmerg_allc.tsv \\\n",
    "EPI-119_S31_L005_5xmerg_allc.tsv \\\n",
    "EPI-120_S32_L005_5xmerg_allc.tsv \\\n",
    "EPI-135_S35_L005_5xmerg_allc.tsv \\\n",
    "EPI-136_S36_L005_5xmerg_allc.tsv \\\n",
    "EPI-127_S33_L005_5xmerg_allc.tsv \\\n",
    "EPI-128_S34_L005_5xmerg_allc.tsv \\\n",
    "EPI-143_S37_L005_5xmerg_allc.tsv \\\n",
    "EPI-145_S38_L005_5xmerg_allc.tsv \\\n",
    "--samples EPI-103 EPI-104 EPI-111 EPI-113 EPI-119 EPI-120 EPI-135 EPI-136 EPI-127 EPI-128 EPI-143 EPI-145 \\\n",
    "--mc-type \"CGN\" \\\n",
    "--num-procs 8 \\\n",
    "--output-prefix day10_AllpH_DMR250bp_MCmax25_cov5x \\\n",
    "--mc-max-dist 25 \\\n",
    "--dmr-max-dist 250 \\\n",
    "--min-num-dms 3 \\\n",
    "--sample-category 0 0 1 1 2 2 2 2 0 0 1 1 "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#still fails and fails on mox, so must be a problem with my files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#count number of fields in all files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1351629 7\n",
      "2227491 7\n",
      "2000000 7\n",
      "1884056 7\n",
      "2198895 7\n",
      "1839968 7\n",
      "1581613 7\n",
      "1827135 7\n",
      "1971800 7\n",
      "1918998 7\n",
      "1351709 7\n",
      "1823309 7\n",
      "1058959 7\n",
      "1369561 7\n",
      "871227 7\n",
      "907153 7\n",
      "483679 7\n",
      "1297463 7\n",
      "678676 7\n",
      "680182 7\n",
      "1104567 7\n",
      "859394 7\n",
      "777627 7\n",
      "1010358 7\n",
      "1232823 7\n",
      "1731088 7\n",
      "1384747 7\n",
      "1815201 7\n",
      "762495 7\n",
      "161152 7\n",
      "1074861 7\n",
      "662217 7\n",
      "1119439 7\n",
      "1633878 7\n",
      "424431 7\n",
      "1013497 7\n",
      "442695 7\n",
      "834196 7\n",
      "1162246 7\n",
      "1418332 7\n",
      "1371534 7\n",
      "846755 7\n",
      "418787 7\n",
      "488239 7\n",
      "314881 7\n",
      "391764 7\n",
      "719055 7\n",
      "922429 7\n",
      "814194 7\n",
      "1365139 7\n",
      "835719 7\n",
      "401401 7\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "for f in *_5xmerg_allc.tsv\n",
    "do\n",
    "awk -F'\\t' '{print NF}' ${f} | sort | uniq -c \n",
    "done"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#they all have 7 fields in every"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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