gimmemotif&bioframefailure.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "d1a9bb3b-94c5-4aeb-b373-de447b626123",
   "metadata": {},
   "source": [
    "# Testing to see Gimmemotifs & Bioframe Issue "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "99938f4a-56c7-4957-b389-c67197a77b15",
   "metadata": {},
   "outputs": [
    {
     "ename": "ModuleNotFoundError",
     "evalue": "No module named 'gimmemotifs'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
      "\u001b[0;32m/tmp/SLURM_8560109/ipykernel_23204/1862538731.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mgimmemotifs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mbioframe\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpandas\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'gimmemotifs'"
     ]
    }
   ],
   "source": [
    "import gimmemotifs\n",
    "import bioframe\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "b5565b0b-9c46-4125-b1d1-f5887734cc89",
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'pd' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m/tmp/SLURM_8560109/ipykernel_23204/1997899844.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m##Test Case\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m df1 = pd.DataFrame([\n\u001b[0m\u001b[1;32m      3\u001b[0m     \u001b[0;34m[\u001b[0m\u001b[0;34m'chr1'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m5\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      4\u001b[0m     \u001b[0;34m[\u001b[0m\u001b[0;34m'chr1'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m3\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m8\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      5\u001b[0m     \u001b[0;34m[\u001b[0m\u001b[0;34m'chr1'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m8\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m10\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;31mNameError\u001b[0m: name 'pd' is not defined"
     ]
    }
   ],
   "source": [
    "##Test Case\n",
    "df1 = pd.DataFrame([\n",
    "    ['chr1', 1, 5],\n",
    "    ['chr1', 3, 8],\n",
    "    ['chr1', 8, 10],\n",
    "    ['chr1', 12, 14]],\n",
    "    columns=['chrom', 'start', 'end']\n",
    ")\n",
    "display(df1.columns)\n",
    "\n",
    "\n",
    "df2 = pd.DataFrame([\n",
    "    ['chr1', 1, 5],\n",
    "    ['chr1', 3, 8],\n",
    "    ['chr1', 8, 10],\n",
    "    ['chr1', 12, 14]],\n",
    "    columns=['chrom', 'start', 'end']\n",
    ")\n",
    "display(df2.columns)\n",
    "\n",
    "import bioframe as bf\n",
    "\n",
    "overlapping_intervals = bf.overlap(df1, df2, how = 'inner', suffixes = ('_1', '_2'))\n",
    "display (overlapping_intervals)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "21a37ebe-2290-4387-b1ac-d257f706d32b",
   "metadata": {},
   "source": [
    "# The issue with trying to download both into one Conda environment "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "453bb73a-9258-4ed3-b08e-f26a26ec186d",
   "metadata": {},
   "outputs": [],
   "source": [
    "   ERROR: Command errored out with exit status 1:\n",
    "     command: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/bin/python3.9 -c 'import sys, setuptools, tokenize; sys.argv[0] = '\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pysam_9297d049b06448d3a32e44f03d1f0b5e/setup.py'\"'\"'; __file__='\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pysam_9297d049b06448d3a32e44f03d1f0b5e/setup.py'\"'\"';f=getattr(tokenize, '\"'\"'open'\"'\"', open)(__file__);code=f.read().replace('\"'\"'\\r\\n'\"'\"', '\"'\"'\\n'\"'\"');f.close();exec(compile(code, __file__, '\"'\"'exec'\"'\"'))' egg_info --egg-base /tmp/SLURM_8560109/pip-pip-egg-info-zmuwgkfv\n",
    "         cwd: /tmp/SLURM_8560109/pip-install-sgql4to3/pysam_9297d049b06448d3a32e44f03d1f0b5e/\n",
    "    Complete output (126 lines):\n",
    "    # pysam: cython is available - using cythonize if necessary\n",
    "    # pysam: htslib mode is shared\n",
    "    # pysam: HTSLIB_CONFIGURE_OPTIONS=None\n",
    "    # pysam: (sysconfig) CC=/spack/apps/gcc/8.3.0/bin/gcc -pthread\n",
    "    # pysam: (sysconfig) CFLAGS=-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC\n",
    "    # pysam: (sysconfig) LDFLAGS=-L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/gettext-0.20.1-xk2yprlbovytt6sd54xjhbzsz2erz7gg/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/readline-8.0-odh3n6nbrw6ffkpsjcnwpv7tlyxpregx/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/ncurses-6.1-akiyo4qrgzlzxw3hggkc42nvv7hz2evj/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/openssl-1.1.1d-d7a46dreyvyazopzpgcwerqvjfmy2grd/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/sqlite-3.30.1-law2rzqeabsqggz3c74aydhnkjsozab2/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/gdbm-1.18.1-vmpezmonnso5wltqaaz5huflaqswzvec/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/libnsl-1.2.0-dwvt6mwkaqgyibvqcjpiz27cjwtquj7g/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/zlib-1.2.11-dp3wfr26pumq5x4dltujahr4qse4agnk/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/bzip2-1.0.8-b65almiioh2l4xgr3ulcr7bftjvo5m2u/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/xz-5.2.4-k3s7isvxg4uuldajdbyu6lbmkhm2ntxm/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/expat-2.2.9-ope3awavw2mgzmhncl5tqddb4ewhj4zh/lib -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/libffi-3.2.1-5zm7fbrppbfnsdztrda267dtlcelq7rx/lib64 -L/spack/apps/linux-centos7-x86_64/gcc-8.3.0/libuuid-1.0.3-heivksfaa2zlycd2sxxezhyeo3tojhyt/lib\n",
    "    checking for gcc... /spack/apps/gcc/8.3.0/bin/gcc -pthread\n",
    "    checking whether the C compiler works... yes\n",
    "    checking for C compiler default output file name... a.out\n",
    "    checking for suffix of executables...\n",
    "    checking whether we are cross compiling... no\n",
    "    checking for suffix of object files... o\n",
    "    checking whether we are using the GNU C compiler... yes\n",
    "    checking whether /spack/apps/gcc/8.3.0/bin/gcc -pthread accepts -g... yes\n",
    "    checking for /spack/apps/gcc/8.3.0/bin/gcc -pthread option to accept ISO C89... none needed\n",
    "    checking for ranlib... ranlib\n",
    "    checking for grep that handles long lines and -e... /bin/grep\n",
    "    checking for C compiler warning flags... unknown\n",
    "    checking for pkg-config... /bin/pkg-config\n",
    "    checking pkg-config is at least version 0.9.0... yes\n",
    "    checking for special C compiler options needed for large files... no\n",
    "    checking for _FILE_OFFSET_BITS value needed for large files... no\n",
    "    checking shared library type for unknown-Linux... plain .so\n",
    "    checking whether the compiler accepts -fvisibility=hidden... yes\n",
    "    checking how to run the C preprocessor... /spack/apps/gcc/8.3.0/bin/gcc -pthread -E\n",
    "    checking for egrep... /bin/grep -E\n",
    "    checking for ANSI C header files... yes\n",
    "    checking for sys/types.h... yes\n",
    "    checking for sys/stat.h... yes\n",
    "    checking for stdlib.h... yes\n",
    "    checking for string.h... yes\n",
    "    checking for memory.h... yes\n",
    "    checking for strings.h... yes\n",
    "    checking for inttypes.h... yes\n",
    "    checking for stdint.h... yes\n",
    "    checking for unistd.h... yes\n",
    "    checking for stdlib.h... (cached) yes\n",
    "    checking for unistd.h... (cached) yes\n",
    "    checking for sys/param.h... yes\n",
    "    checking for getpagesize... yes\n",
    "    checking for working mmap... yes\n",
    "    checking for gmtime_r... yes\n",
    "    checking for fsync... yes\n",
    "    checking for drand48... yes\n",
    "    checking for srand48_deterministic... no\n",
    "    checking whether fdatasync is declared... yes\n",
    "    checking for fdatasync... yes\n",
    "    checking for library containing log... -lm\n",
    "    checking for zlib.h... no\n",
    "    checking for inflate in -lz... yes\n",
    "    configure: error: zlib development files not found\n",
    "    \n",
    "    HTSlib uses compression routines from the zlib library <http://zlib.net>.\n",
    "    Building HTSlib requires zlib development files to be installed on the build\n",
    "    machine; you may need to ensure a package such as zlib1g-dev (on Debian or\n",
    "    Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions or Cygwin)\n",
    "    is installed.\n",
    "    \n",
    "    FAILED.  This error must be resolved in order to build HTSlib successfully.\n",
    "    checking for gcc... /spack/apps/gcc/8.3.0/bin/gcc -pthread\n",
    "    checking whether the C compiler works... yes\n",
    "    checking for C compiler default output file name... a.out\n",
    "    checking for suffix of executables...\n",
    "    checking whether we are cross compiling... no\n",
    "    checking for suffix of object files... o\n",
    "    checking whether we are using the GNU C compiler... yes\n",
    "    checking whether /spack/apps/gcc/8.3.0/bin/gcc -pthread accepts -g... yes\n",
    "    checking for /spack/apps/gcc/8.3.0/bin/gcc -pthread option to accept ISO C89... none needed\n",
    "    checking for ranlib... ranlib\n",
    "    checking for grep that handles long lines and -e... /bin/grep\n",
    "    checking for C compiler warning flags... unknown\n",
    "    checking for pkg-config... /bin/pkg-config\n",
    "    checking pkg-config is at least version 0.9.0... yes\n",
    "    checking for special C compiler options needed for large files... no\n",
    "    checking for _FILE_OFFSET_BITS value needed for large files... no\n",
    "    checking shared library type for unknown-Linux... plain .so\n",
    "    checking whether the compiler accepts -fvisibility=hidden... yes\n",
    "    checking how to run the C preprocessor... /spack/apps/gcc/8.3.0/bin/gcc -pthread -E\n",
    "    checking for egrep... /bin/grep -E\n",
    "    checking for ANSI C header files... yes\n",
    "    checking for sys/types.h... yes\n",
    "    checking for sys/stat.h... yes\n",
    "    checking for stdlib.h... yes\n",
    "    checking for string.h... yes\n",
    "    checking for memory.h... yes\n",
    "    checking for strings.h... yes\n",
    "    checking for inttypes.h... yes\n",
    "    checking for stdint.h... yes\n",
    "    checking for unistd.h... yes\n",
    "    checking for stdlib.h... (cached) yes\n",
    "    checking for unistd.h... (cached) yes\n",
    "    checking for sys/param.h... yes\n",
    "    checking for getpagesize... yes\n",
    "    checking for working mmap... yes\n",
    "    checking for gmtime_r... yes\n",
    "    checking for fsync... yes\n",
    "    checking for drand48... yes\n",
    "    checking for srand48_deterministic... no\n",
    "    checking whether fdatasync is declared... yes\n",
    "    checking for fdatasync... yes\n",
    "    checking for library containing log... -lm\n",
    "    checking for zlib.h... no\n",
    "    checking for inflate in -lz... yes\n",
    "    configure: error: zlib development files not found\n",
    "    \n",
    "    HTSlib uses compression routines from the zlib library <http://zlib.net>.\n",
    "    Building HTSlib requires zlib development files to be installed on the build\n",
    "    machine; you may need to ensure a package such as zlib1g-dev (on Debian or\n",
    "    Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions or Cygwin)\n",
    "    is installed.\n",
    "    \n",
    "    FAILED.  This error must be resolved in order to build HTSlib successfully.\n",
    "    Makefile:122: htscodecs.mk: No such file or directory\n",
    "    config.mk:2: *** Resolve configure error first.  Stop.\n",
    "    Traceback (most recent call last):\n",
    "      File \"<string>\", line 1, in <module>\n",
    "      File \"/tmp/SLURM_8560109/pip-install-sgql4to3/pysam_9297d049b06448d3a32e44f03d1f0b5e/setup.py\", line 375, in <module>\n",
    "        htslib_make_options = run_make_print_config()\n",
    "      File \"/tmp/SLURM_8560109/pip-install-sgql4to3/pysam_9297d049b06448d3a32e44f03d1f0b5e/setup.py\", line 74, in run_make_print_config\n",
    "        stdout = subprocess.check_output([\"make\", \"-s\", \"print-config\"])\n",
    "      File \"/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/subprocess.py\", line 424, in check_output\n",
    "        return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,\n",
    "      File \"/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/subprocess.py\", line 528, in run\n",
    "        raise CalledProcessError(retcode, process.args,\n",
    "    subprocess.CalledProcessError: Command '['make', '-s', 'print-config']' returned non-zero exit status 2.\n",
    "    # pysam: htslib configure options: None\n",
    "    ----------------------------------------\n",
    "WARNING: Discarding https://files.pythonhosted.org/packages/a0/10/f6d705984838f8620ff597dd99d3904aea7727b4824bee22de8f44b4ebd4/pysam-0.19.1.tar.gz#sha256=dee403cbdf232170c1e11cc24c76e7dd748fc672ad38eb0414f3b9d569b1448f (from https://pypi.org/simple/pysam/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.\n",
    "  Downloading pysam-0.19.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)\n",
    "     |████████████████████████████████| 15.7 MB 38.7 MB/s \n",
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    "     |████████████████████████████████| 255.9 MB 29 kB/s \n",
    "Collecting xdg\n",
    "  Using cached xdg-5.1.1-py3-none-any.whl (5.0 kB)\n",
    "Collecting diskcache\n",
    "  Using cached diskcache-5.4.0-py3-none-any.whl (44 kB)\n",
    "Collecting xxhash\n",
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    "     |████████████████████████████████| 80 kB 11.9 MB/s \n",
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    "     |████████████████████████████████| 78 kB 8.6 MB/s \n",
    "Requirement already satisfied: pillow in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from gimmemotifs) (8.1.2)\n",
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    "Requirement already satisfied: requests in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from genomepy>=0.8.3->gimmemotifs) (2.25.1)\n",
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    "Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from matplotlib>=2->gimmemotifs) (2.4.7)\n",
    "Requirement already satisfied: cycler>=0.10 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from matplotlib>=2->gimmemotifs) (0.10.0)\n",
    "Requirement already satisfied: kiwisolver>=1.0.1 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from matplotlib>=2->gimmemotifs) (1.3.1)\n",
    "Requirement already satisfied: python-dateutil>=2.1 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from matplotlib>=2->gimmemotifs) (2.8.1)\n",
    "Requirement already satisfied: six in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from cycler>=0.10->matplotlib>=2->gimmemotifs) (1.15.0)\n",
    "Collecting nose\n",
    "  Using cached nose-1.3.7-py3-none-any.whl (154 kB)\n",
    "Requirement already satisfied: pytz>=2017.3 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from pandas>=1.1->gimmemotifs) (2021.1)\n",
    "Collecting HTSeq\n",
    "  Downloading HTSeq-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.9 MB)\n",
    "     |████████████████████████████████| 1.9 MB 48.3 MB/s \n",
    "Collecting palettable\n",
    "  Using cached palettable-3.3.0-py2.py3-none-any.whl (111 kB)\n",
    "Collecting pyBigWig\n",
    "  Using cached pyBigWig-0.3.18.tar.gz (64 kB)\n",
    "Requirement already satisfied: MarkupSafe>=0.23 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from jinja2->gimmemotifs) (1.1.1)\n",
    "Collecting biothings-client>=0.2.6\n",
    "  Using cached biothings_client-0.2.6-py2.py3-none-any.whl (37 kB)\n",
    "Requirement already satisfied: chardet<5,>=3.0.2 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from requests->genomepy>=0.8.3->gimmemotifs) (4.0.0)\n",
    "Requirement already satisfied: urllib3<1.27,>=1.21.1 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from requests->genomepy>=0.8.3->gimmemotifs) (1.26.4)\n",
    "Requirement already satisfied: idna<3,>=2.5 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from requests->genomepy>=0.8.3->gimmemotifs) (2.10)\n",
    "Requirement already satisfied: certifi>=2017.4.17 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from requests->genomepy>=0.8.3->gimmemotifs) (2020.12.5)\n",
    "Requirement already satisfied: protobuf<=3.20.1,>=3.11.0 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from mysql-connector-python->genomepy>=0.8.3->gimmemotifs) (3.15.8)\n",
    "Collecting numba\n",
    "  Downloading numba-0.56.2-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)\n",
    "     |████████████████████████████████| 3.5 MB 36.0 MB/s \n",
    "Collecting llvmlite<0.40,>=0.39.0dev0\n",
    "  Downloading llvmlite-0.39.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.6 MB)\n",
    "     |████████████████████████████████| 34.6 MB 48.4 MB/s \n",
    "Collecting threadpoolctl>=2.0.0\n",
    "  Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB)\n",
    "Requirement already satisfied: joblib>=1.0.0 in /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages (from scikit-learn->gimmemotifs) (1.0.1)\n",
    "Collecting patsy>=0.5.2\n",
    "  Using cached patsy-0.5.2-py2.py3-none-any.whl (233 kB)\n",
    "Collecting packaging>=21.3\n",
    "  Using cached packaging-21.3-py3-none-any.whl (40 kB)\n",
    "Building wheels for collected packages: gimmemotifs, norns, pyfaidx, biofluff, pybedtools, pyBigWig\n",
    "  Building wheel for gimmemotifs (setup.py) ... done\n",
    "  Created wheel for gimmemotifs: filename=gimmemotifs-0.17.0-cp39-cp39-linux_x86_64.whl size=10671869 sha256=7c9470bc9922e68e719d8baf0681bf0d2b4774683197e66990051cf3be4597c7\n",
    "  Stored in directory: /home1/chavali/.cache/pip/wheels/ea/7f/a9/38a0ea47979bb8a0b5ebf27b7a61213cf29d957ff32ccab70c\n",
    "  Building wheel for norns (setup.py) ... done\n",
    "  Created wheel for norns: filename=norns-0.1.6-py3-none-any.whl size=3999 sha256=e246f5a84e81e1c6830b29aff3669d97fd118298393b3335797a360aa013b570\n",
    "  Stored in directory: /home1/chavali/.cache/pip/wheels/28/d5/41/7ea06b4e7b36840cd8ef8997f13a5f68632c96dfd438aa5298\n",
    "  Building wheel for pyfaidx (setup.py) ... done\n",
    "  Created wheel for pyfaidx: filename=pyfaidx-0.7.1-py3-none-any.whl size=27719 sha256=b75575d6176d3b4be3daf86d927dee920fd08a3f08906d715866daadf05404bc\n",
    "  Stored in directory: /home1/chavali/.cache/pip/wheels/69/0e/15/54b1d49d19da55e1a65ef570fb7b2f240bf995e58640cb0842\n",
    "  Building wheel for biofluff (setup.py) ... done\n",
    "  Created wheel for biofluff: filename=biofluff-3.0.4-py3-none-any.whl size=31255 sha256=4699768c3b2a7447f4120c18e12417702773aad47a24c562b3fcbbccfb6492d2\n",
    "  Stored in directory: /home1/chavali/.cache/pip/wheels/ca/56/a8/dfb75e81a751b8aed5e0ccdfd8b4eea2d3a18dd660aa4f6936\n",
    "  Building wheel for pybedtools (setup.py) ... error\n",
    "ERROR: Command errored out with exit status 1:\n",
    "   command: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pybedtools_bb3df649c30f4cc1a07ccb8ff010f5bd/setup.py'\"'\"'; __file__='\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pybedtools_bb3df649c30f4cc1a07ccb8ff010f5bd/setup.py'\"'\"';f=getattr(tokenize, '\"'\"'open'\"'\"', open)(__file__);code=f.read().replace('\"'\"'\\r\\n'\"'\"', '\"'\"'\\n'\"'\"');f.close();exec(compile(code, __file__, '\"'\"'exec'\"'\"'))' bdist_wheel -d /tmp/SLURM_8560109/pip-wheel-ei7gvy8g\n",
    "       cwd: /tmp/SLURM_8560109/pip-install-sgql4to3/pybedtools_bb3df649c30f4cc1a07ccb8ff010f5bd/\n",
    "  Complete output (144 lines):\n",
    "  running bdist_wheel\n",
    "  The [wheel] section is deprecated. Use [bdist_wheel] instead.\n",
    "  running build\n",
    "  running build_py\n",
    "  creating build\n",
    "  creating build/lib.linux-x86_64-3.9\n",
    "  creating build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/version.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/stats.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/settings.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/paths.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/parallel.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/logger.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/helpers.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/filenames.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/bedtool.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/__init__.py -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  creating build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/tfuncs.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/test_pathlib.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/test_len_leak.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/test_issues.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/test_helpers.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/test_contrib.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/test_1.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/genomepy_integration.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  copying pybedtools/test/__init__.py -> build/lib.linux-x86_64-3.9/pybedtools/test\n",
    "  creating build/lib.linux-x86_64-3.9/pybedtools/contrib\n",
    "  copying pybedtools/contrib/venn_maker.py -> build/lib.linux-x86_64-3.9/pybedtools/contrib\n",
    "  copying pybedtools/contrib/plotting.py -> build/lib.linux-x86_64-3.9/pybedtools/contrib\n",
    "  copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-x86_64-3.9/pybedtools/contrib\n",
    "  copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-3.9/pybedtools/contrib\n",
    "  copying pybedtools/contrib/bigwig.py -> build/lib.linux-x86_64-3.9/pybedtools/contrib\n",
    "  copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-3.9/pybedtools/contrib\n",
    "  copying pybedtools/contrib/__init__.py -> build/lib.linux-x86_64-3.9/pybedtools/contrib\n",
    "  creating build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/__init__.py -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  running egg_info\n",
    "  creating pybedtools.egg-info\n",
    "  writing pybedtools.egg-info/PKG-INFO\n",
    "  writing dependency_links to pybedtools.egg-info/dependency_links.txt\n",
    "  writing requirements to pybedtools.egg-info/requires.txt\n",
    "  writing top-level names to pybedtools.egg-info/top_level.txt\n",
    "  writing manifest file 'pybedtools.egg-info/SOURCES.txt'\n",
    "  adding license file 'LICENSE.txt' (matched pattern 'LICEN[CS]E*')\n",
    "  reading manifest file 'pybedtools.egg-info/SOURCES.txt'\n",
    "  writing manifest file 'pybedtools.egg-info/SOURCES.txt'\n",
    "  copying pybedtools/cbedtools.cpp -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/featurefuncs.cpp -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  creating build/lib.linux-x86_64-3.9/pybedtools/include\n",
    "  copying pybedtools/include/bedFile.cpp -> build/lib.linux-x86_64-3.9/pybedtools/include\n",
    "  copying pybedtools/include/fileType.cpp -> build/lib.linux-x86_64-3.9/pybedtools/include\n",
    "  copying pybedtools/include/gzstream.cpp -> build/lib.linux-x86_64-3.9/pybedtools/include\n",
    "  copying pybedtools/test/data/y.bam -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/x.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/x.bam -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/venn.c.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/venn.b.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/v.vcf -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/test.fa -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/small.fastq -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/small.bam -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/reads.bam -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/m1.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/issue_121.bam -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/issue319.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/genome.fa -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.gff -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.cram -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.bam -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/expand_test.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/exons.gff -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/d.gff -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/c.gff -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/bedpe.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/b.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/a.links.html -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/a.igv_script -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/a.bed.gz.tbi -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/a.bed.gz -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/164.gtf -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-x86_64-3.9/pybedtools/test/data\n",
    "  copying pybedtools/featurefuncs.pyx -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/cbedtools.pyx -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/_Window.pyx -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  copying pybedtools/cbedtools.pxd -> build/lib.linux-x86_64-3.9/pybedtools\n",
    "  running build_ext\n",
    "  building 'pybedtools.cbedtools' extension\n",
    "  creating build/temp.linux-x86_64-3.9\n",
    "  creating build/temp.linux-x86_64-3.9/pybedtools\n",
    "  creating build/temp.linux-x86_64-3.9/pybedtools/include\n",
    "  /spack/apps/gcc/8.3.0/bin/gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -fPIC -Ipybedtools/include/ -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/include/python3.9 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-3.9/pybedtools/cbedtools.o\n",
    "  In file included from pybedtools/include/bedFile.h:16,\n",
    "                   from pybedtools/cbedtools.cpp:731:\n",
    "  pybedtools/include/gzstream.h:35:10: fatal error: zlib.h: No such file or directory\n",
    "   #include <zlib.h>\n",
    "            ^~~~~~~~\n",
    "  compilation terminated.\n",
    "  error: command '/spack/apps/gcc/8.3.0/bin/gcc' failed with exit code 1\n",
    "  ----------------------------------------\n",
    "  ERROR: Failed building wheel for pybedtools\n",
    "  Running setup.py clean for pybedtools\n",
    "  ERROR: Command errored out with exit status 1:\n",
    "   command: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pybedtools_bb3df649c30f4cc1a07ccb8ff010f5bd/setup.py'\"'\"'; __file__='\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pybedtools_bb3df649c30f4cc1a07ccb8ff010f5bd/setup.py'\"'\"';f=getattr(tokenize, '\"'\"'open'\"'\"', open)(__file__);code=f.read().replace('\"'\"'\\r\\n'\"'\"', '\"'\"'\\n'\"'\"');f.close();exec(compile(code, __file__, '\"'\"'exec'\"'\"'))' clean --all\n",
    "       cwd: /tmp/SLURM_8560109/pip-install-sgql4to3/pybedtools_bb3df649c30f4cc1a07ccb8ff010f5bd\n",
    "  Complete output (6 lines):\n",
    "  usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]\n",
    "     or: setup.py --help [cmd1 cmd2 ...]\n",
    "     or: setup.py --help-commands\n",
    "     or: setup.py cmd --help\n",
    "  \n",
    "  error: option --all not recognized\n",
    "  ----------------------------------------\n",
    "  ERROR: Failed cleaning build dir for pybedtools\n",
    "  Building wheel for pyBigWig (setup.py) ... error\n",
    "  ERROR: Command errored out with exit status 1:\n",
    "   command: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pybigwig_d9538d38b1e14b23b89986765b7022c2/setup.py'\"'\"'; __file__='\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pybigwig_d9538d38b1e14b23b89986765b7022c2/setup.py'\"'\"';f=getattr(tokenize, '\"'\"'open'\"'\"', open)(__file__);code=f.read().replace('\"'\"'\\r\\n'\"'\"', '\"'\"'\\n'\"'\"');f.close();exec(compile(code, __file__, '\"'\"'exec'\"'\"'))' bdist_wheel -d /tmp/SLURM_8560109/pip-wheel-j_i3djqp\n",
    "       cwd: /tmp/SLURM_8560109/pip-install-sgql4to3/pybigwig_d9538d38b1e14b23b89986765b7022c2/\n",
    "  Complete output (74 lines):\n",
    "  /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages/setuptools/dist.py:642: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead\n",
    "    warnings.warn(\n",
    "  /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier'\n",
    "    warnings.warn(msg)\n",
    "  running bdist_wheel\n",
    "  running build\n",
    "  running build_py\n",
    "  creating build\n",
    "  creating build/lib.linux-x86_64-3.9\n",
    "  creating build/lib.linux-x86_64-3.9/pyBigWigTest\n",
    "  copying pyBigWigTest/test.py -> build/lib.linux-x86_64-3.9/pyBigWigTest\n",
    "  copying pyBigWigTest/__init__.py -> build/lib.linux-x86_64-3.9/pyBigWigTest\n",
    "  running egg_info\n",
    "  writing pyBigWig.egg-info/PKG-INFO\n",
    "  writing dependency_links to pyBigWig.egg-info/dependency_links.txt\n",
    "  writing requirements to pyBigWig.egg-info/requires.txt\n",
    "  writing top-level names to pyBigWig.egg-info/top_level.txt\n",
    "  adding license file 'LICENSE.txt' (matched pattern 'LICEN[CS]E*')\n",
    "  reading manifest file 'pyBigWig.egg-info/SOURCES.txt'\n",
    "  reading manifest template 'MANIFEST.in'\n",
    "  writing manifest file 'pyBigWig.egg-info/SOURCES.txt'\n",
    "  copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-3.9/pyBigWigTest\n",
    "  copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-3.9/pyBigWigTest\n",
    "  running build_ext\n",
    "  building 'pyBigWig' extension\n",
    "  Warning: Can't read registry to find the necessary compiler setting\n",
    "  Make sure that Python modules winreg, win32api or win32con are installed.\n",
    "  C compiler: /spack/apps/gcc/8.3.0/bin/gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -fPIC\n",
    "  \n",
    "  creating build/temp.linux-x86_64-3.9\n",
    "  creating build/temp.linux-x86_64-3.9/libBigWig\n",
    "  compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/include/python3.9 -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages/numpy/core/include -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/include/python3.9 -c'\n",
    "  gcc: libBigWig/bwRead.cgcc: libBigWig/bwStats.c\n",
    "  \n",
    "  gcc: libBigWig/bwValues.cgcc: libBigWig/bwWrite.c\n",
    "  \n",
    "  gcc: libBigWig/io.c\n",
    "  gcc: pyBigWig.c\n",
    "  In file included from libBigWig/bigWig.h:4,\n",
    "                   from libBigWig/bwStats.c:1:\n",
    "  libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory\n",
    "   #include <curl/curl.h>\n",
    "            ^~~~~~~~~~~~~\n",
    "  compilation terminated.\n",
    "  libBigWig/io.c:2:10: fatal error: curl/curl.h: No such file or directory\n",
    "   #include <curl/curl.h>\n",
    "            ^~~~~~~~~~~~~\n",
    "  compilation terminated.\n",
    "  In file included from libBigWig/bigWig.h:4,\n",
    "                   from libBigWig/bwValues.c:1:\n",
    "  libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory\n",
    "   #include <curl/curl.h>\n",
    "            ^~~~~~~~~~~~~\n",
    "  compilation terminated.\n",
    "  In file included from libBigWig/bigWig.h:4,\n",
    "                   from libBigWig/bwRead.c:1:\n",
    "  libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory\n",
    "   #include <curl/curl.h>\n",
    "            ^~~~~~~~~~~~~\n",
    "  compilation terminated.\n",
    "  In file included from libBigWig/bigWig.h:4,\n",
    "                   from libBigWig/bwWrite.c:6:\n",
    "  libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory\n",
    "   #include <curl/curl.h>\n",
    "            ^~~~~~~~~~~~~\n",
    "  compilation terminated.\n",
    "  In file included from libBigWig/bigWig.h:4,\n",
    "                   from pyBigWig.h:3,\n",
    "                   from pyBigWig.c:3:\n",
    "  libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory\n",
    "   #include <curl/curl.h>\n",
    "            ^~~~~~~~~~~~~\n",
    "  compilation terminated.\n",
    "  error: Command \"/spack/apps/gcc/8.3.0/bin/gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/include/python3.9 -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages/numpy/core/include -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/include/python3.9 -c libBigWig/bwStats.c -o build/temp.linux-x86_64-3.9/libBigWig/bwStats.o\" failed with exit status 1\n",
    "  ----------------------------------------\n",
    "  ERROR: Failed building wheel for pyBigWig\n",
    "  Running setup.py clean for pyBigWig\n",
    "Successfully built gimmemotifs norns pyfaidx biofluff\n",
    "Failed to build pybedtools pyBigWig\n",
    "Installing collected packages: threadpoolctl, scipy, pysam, nose, llvmlite, biothings-client, tqdm, scikit-learn, pyfaidx, pyBigWig, pybedtools, patsy, palettable, packaging, numba, norns, mysql-connector-python, mygene, loguru, HTSeq, filelock, diskcache, colorama, click, biopython, xxhash, xgboost, xdg, statsmodels, seaborn, qnorm, pyarrow, logomaker, iteround, genomepy, configparser, biofluff, gimmemotifs\n",
    "    Running setup.py install for pyBigWig ... error\n",
    "    ERROR: Command errored out with exit status 1:\n",
    "     command: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pybigwig_d9538d38b1e14b23b89986765b7022c2/setup.py'\"'\"'; __file__='\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pybigwig_d9538d38b1e14b23b89986765b7022c2/setup.py'\"'\"';f=getattr(tokenize, '\"'\"'open'\"'\"', open)(__file__);code=f.read().replace('\"'\"'\\r\\n'\"'\"', '\"'\"'\\n'\"'\"');f.close();exec(compile(code, __file__, '\"'\"'exec'\"'\"'))' install --record /tmp/SLURM_8560109/pip-record-sppyp97d/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home1/chavali/.local/include/python3.9/pyBigWig\n",
    "         cwd: /tmp/SLURM_8560109/pip-install-sgql4to3/pybigwig_d9538d38b1e14b23b89986765b7022c2/\n",
    "    Complete output (74 lines):\n",
    "    /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages/setuptools/dist.py:642: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead\n",
    "      warnings.warn(\n",
    "    /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier'\n",
    "      warnings.warn(msg)\n",
    "    running install\n",
    "    running build\n",
    "    running build_py\n",
    "    creating build\n",
    "    creating build/lib.linux-x86_64-3.9\n",
    "    creating build/lib.linux-x86_64-3.9/pyBigWigTest\n",
    "    copying pyBigWigTest/test.py -> build/lib.linux-x86_64-3.9/pyBigWigTest\n",
    "    copying pyBigWigTest/__init__.py -> build/lib.linux-x86_64-3.9/pyBigWigTest\n",
    "    running egg_info\n",
    "    writing pyBigWig.egg-info/PKG-INFO\n",
    "    writing dependency_links to pyBigWig.egg-info/dependency_links.txt\n",
    "    writing requirements to pyBigWig.egg-info/requires.txt\n",
    "    writing top-level names to pyBigWig.egg-info/top_level.txt\n",
    "    adding license file 'LICENSE.txt' (matched pattern 'LICEN[CS]E*')\n",
    "    reading manifest file 'pyBigWig.egg-info/SOURCES.txt'\n",
    "    reading manifest template 'MANIFEST.in'\n",
    "    writing manifest file 'pyBigWig.egg-info/SOURCES.txt'\n",
    "    copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-3.9/pyBigWigTest\n",
    "    copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-3.9/pyBigWigTest\n",
    "    running build_ext\n",
    "    building 'pyBigWig' extension\n",
    "    Warning: Can't read registry to find the necessary compiler setting\n",
    "    Make sure that Python modules winreg, win32api or win32con are installed.\n",
    "    C compiler: /spack/apps/gcc/8.3.0/bin/gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -fPIC\n",
    "    \n",
    "    creating build/temp.linux-x86_64-3.9\n",
    "    creating build/temp.linux-x86_64-3.9/libBigWig\n",
    "    compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/include/python3.9 -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages/numpy/core/include -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/include/python3.9 -c'\n",
    "    gcc: libBigWig/bwRead.cgcc: libBigWig/bwStats.c\n",
    "    \n",
    "    gcc: libBigWig/bwValues.cgcc: libBigWig/bwWrite.c\n",
    "    \n",
    "    gcc: libBigWig/io.cgcc: pyBigWig.c\n",
    "    \n",
    "    In file included from libBigWig/bigWig.h:4,\n",
    "                     from libBigWig/bwStats.c:1:\n",
    "    libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory\n",
    "     #include <curl/curl.h>\n",
    "              ^~~~~~~~~~~~~\n",
    "    compilation terminated.\n",
    "    In file included from libBigWig/bigWig.h:4,\n",
    "                     from libBigWig/bwRead.c:1:\n",
    "    libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory\n",
    "     #include <curl/curl.h>\n",
    "              ^~~~~~~~~~~~~\n",
    "    compilation terminated.\n",
    "    In file included from libBigWig/bigWig.h:4,\n",
    "                     from libBigWig/bwValues.c:1:\n",
    "    libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory\n",
    "     #include <curl/curl.h>\n",
    "              ^~~~~~~~~~~~~\n",
    "    compilation terminated.\n",
    "    libBigWig/io.c:2:10: fatal error: curl/curl.h: No such file or directory\n",
    "     #include <curl/curl.h>\n",
    "              ^~~~~~~~~~~~~\n",
    "    compilation terminated.\n",
    "    In file included from libBigWig/bigWig.h:4,\n",
    "                     from libBigWig/bwWrite.c:6:\n",
    "    libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory\n",
    "     #include <curl/curl.h>\n",
    "              ^~~~~~~~~~~~~\n",
    "    compilation terminated.\n",
    "    In file included from libBigWig/bigWig.h:4,\n",
    "                     from pyBigWig.h:3,\n",
    "                     from pyBigWig.c:3:\n",
    "    libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory\n",
    "     #include <curl/curl.h>\n",
    "              ^~~~~~~~~~~~~\n",
    "    compilation terminated.\n",
    "    error: Command \"/spack/apps/gcc/8.3.0/bin/gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/include/python3.9 -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/site-packages/numpy/core/include -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/include/python3.9 -c libBigWig/bwStats.c -o build/temp.linux-x86_64-3.9/libBigWig/bwStats.o\" failed with exit status 1\n",
    "    ----------------------------------------\n",
    "ERROR: Command errored out with exit status 1: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pybigwig_d9538d38b1e14b23b89986765b7022c2/setup.py'\"'\"'; __file__='\"'\"'/tmp/SLURM_8560109/pip-install-sgql4to3/pybigwig_d9538d38b1e14b23b89986765b7022c2/setup.py'\"'\"';f=getattr(tokenize, '\"'\"'open'\"'\"', open)(__file__);code=f.read().replace('\"'\"'\\r\\n'\"'\"', '\"'\"'\\n'\"'\"');f.close();exec(compile(code, __file__, '\"'\"'exec'\"'\"'))' install --record /tmp/SLURM_8560109/pip-record-sppyp97d/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home1/chavali/.local/include/python3.9/pyBigWig Check the logs for full command output.\n",
    "WARNING: You are using pip version 21.0.1; however, version 22.2.2 is available.\n",
    "You should consider upgrading via the '/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/bin/python3.9 -m pip install --upgrade pip' command.\n",
    " "
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "testgb_",
   "language": "python",
   "name": "testgb"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.2"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}