Created temporary directory: /tmp/pip-ephem-wheel-cache-norcgt0f Created temporary directory: /tmp/pip-req-tracker-amj9qb4d Created requirements tracker '/tmp/pip-req-tracker-amj9qb4d' Created temporary directory: /tmp/pip-wheel-5k17j7zp Collecting mitopipeline==1.1.post1 1 location(s) to search for versions of mitopipeline: * https://pypi.org/simple/mitopipeline/ Getting page https://pypi.org/simple/mitopipeline/ Analyzing links from page https://pypi.org/simple/mitopipeline/ Found link https://files.pythonhosted.org/packages/5d/9b/8337beabd1834f4d3430189ac176944d11a8d44d5dae2785bd24bff4bb8d/MitoPipeline-0.1.tar.gz#sha256=d56911bcaebe3d2e83487e01c3f431bf48b0a1dae8c068a319f1474bce0d5d79 (from https://pypi.org/simple/mitopipeline/), version: 0.1 Found link https://files.pythonhosted.org/packages/cf/69/ffd813111460b31f8fc6da0c774ff3b0600c02a3e4711609109338372513/mitopipeline-0.11.tar.gz#sha256=680d7b9f2df46e04d9f9e635bf850eb4528f6472a2bb4ea17f8a64e11fbfa4cb (from https://pypi.org/simple/mitopipeline/), version: 0.11 Found link https://files.pythonhosted.org/packages/3b/d0/b6f7bdd90188537d6e72e08cd3cf16be42ed5fbda99072d97e12e548e52b/mitopipeline-0.12.tar.gz#sha256=e584c0e7d38043a3f39214859ed5f4e3cb2e410b077d8c899769d76f514d7a97 (from https://pypi.org/simple/mitopipeline/), version: 0.12 Found link https://files.pythonhosted.org/packages/89/a1/28523ab054e9d0357bd2363c9651150f5a1d53aadd5d2a1aa5df6a41f7d1/mitopipeline-0.13.tar.gz#sha256=17a23b0c03791e566a939ec23a405b2560ff1e68e36f511e305ad9dafe2014ac (from https://pypi.org/simple/mitopipeline/), version: 0.13 Found link https://files.pythonhosted.org/packages/08/db/d5629c98955a06c4216a438b30a4c69030f531094596aa83f0ed484e1396/mitopipeline-1.0.tar.gz#sha256=73fa17138aba695edbbf1923a795e6051306f97acdf1f00317857ef6af2d165c (from https://pypi.org/simple/mitopipeline/), version: 1.0 Found link https://files.pythonhosted.org/packages/f3/76/90790504070e7627fe0de968484415752b27d95c359c56018c6b534d49f6/mitopipeline-1.0.post1.tar.gz#sha256=5b603c61e07f96c066823550e45e0446cf04f58b8096b4fe29801d261831813d (from https://pypi.org/simple/mitopipeline/), version: 1.0.post1 Skipping link https://files.pythonhosted.org/packages/aa/20/435aaf4fcbda8e3eb247da9007832c4a41688a2dff5f4348b4a15b8211cc/mitopipeline-1.0.post2-py3.6.egg#sha256=fe4ac3118728b9c62b2b8500eb9bd8594c8822c296237c9db40ed30e7812e996 (from https://pypi.org/simple/mitopipeline/); unsupported archive format: .egg Found link https://files.pythonhosted.org/packages/59/06/853ea3900a7b6ae5ad5b2cc7c5efe9136ca8042d86ddbabfb425048e8fbf/mitopipeline-1.0.post2.tar.gz#sha256=78356b2d55babe29c27d46beaa5df03083861873ddb046b921798a980868048f (from https://pypi.org/simple/mitopipeline/), version: 1.0.post2 Found link https://files.pythonhosted.org/packages/81/aa/5df89bda98a25867b208ff7929aa52d06f48a5e0e9460449bb874273f63e/mitopipeline-1.1.tar.gz#sha256=717f5c823af92aa154745fa8932f1dad8d297bc92710257f8fbda7aeef33ba87 (from https://pypi.org/simple/mitopipeline/), version: 1.1 Found link https://files.pythonhosted.org/packages/d3/a6/3c067b7dd13ed7b5af914ba984ea758a17db888c2873a0315df911d49f53/mitopipeline-1.1.post1.tar.gz#sha256=dc05a5ba6ad1b4f6a5ccd3304eb2053dd044f19495fbf3ffd76d6e82c05f1ce2 (from https://pypi.org/simple/mitopipeline/), version: 1.1.post1 Found link https://files.pythonhosted.org/packages/0f/d4/b5c973d094a1b2bedf9d1c16e72f3a1aa0d312952074c787b2240dc65756/mitopipeline-1.1.post2.tar.gz#sha256=40d5756e50ef694e608a686518a5f56f5df42a1cd4d4be59e074f52b0881bb12 (from https://pypi.org/simple/mitopipeline/), version: 1.1.post2 Found link https://files.pythonhosted.org/packages/65/21/be471082d6bbbfc5ac4f57b1edd34b31016804a167c31d231888dee68bf7/mitopipeline-1.1.post3.tar.gz#sha256=07a2441272a7d90b05e2a46da2ddb9cba34636788908c5e8d3e9851fcbeb0987 (from https://pypi.org/simple/mitopipeline/), version: 1.1.post3 Found link https://files.pythonhosted.org/packages/8c/cd/22b4a9114f182218ff352dba4219c8ade23808e6a688803cf91d263fbba6/mitopipeline-1.1.post4.tar.gz#sha256=e6e890f44ca519276d40b2fa3fba99a2a9a17ceec563c559c49852849ae81262 (from https://pypi.org/simple/mitopipeline/), version: 1.1.post4 Found link https://files.pythonhosted.org/packages/1a/e5/3ae059daaeabb018ab04d7ae88c1deffcacc19a8b2abe6d55a955537d00c/mitopipeline-1.1.post5.tar.gz#sha256=9090d339da8a4243046d4043ea41c865d200304e9a08abd66a1dc4fc6cf3ec8a (from https://pypi.org/simple/mitopipeline/), version: 1.1.post5 Using version 1.1.post1 (newest of versions: 1.1.post1) Created temporary directory: /tmp/pip-unpack-g_5vo5io Downloading https://files.pythonhosted.org/packages/d3/a6/3c067b7dd13ed7b5af914ba984ea758a17db888c2873a0315df911d49f53/mitopipeline-1.1.post1.tar.gz (72.6MB) Downloading from URL https://files.pythonhosted.org/packages/d3/a6/3c067b7dd13ed7b5af914ba984ea758a17db888c2873a0315df911d49f53/mitopipeline-1.1.post1.tar.gz#sha256=dc05a5ba6ad1b4f6a5ccd3304eb2053dd044f19495fbf3ffd76d6e82c05f1ce2 (from https://pypi.org/simple/mitopipeline/) Added mitopipeline==1.1.post1 from https://files.pythonhosted.org/packages/d3/a6/3c067b7dd13ed7b5af914ba984ea758a17db888c2873a0315df911d49f53/mitopipeline-1.1.post1.tar.gz#sha256=dc05a5ba6ad1b4f6a5ccd3304eb2053dd044f19495fbf3ffd76d6e82c05f1ce2 to build tracker '/tmp/pip-req-tracker-amj9qb4d' Running setup.py (path:/tmp/pip-wheel-5k17j7zp/mitopipeline/setup.py) egg_info for package mitopipeline Running command python setup.py egg_info zip_safe flag not set; analyzing archive contents... luigi.__pycache__.server.cpython-35: module references __file__ luigi.__pycache__.six.cpython-35: module references __path__ luigi.contrib.__pycache__.hadoop.cpython-35: module references __file__ luigi.contrib.__pycache__.hadoop.cpython-35: module references __path__ luigi.contrib.__pycache__.lsf.cpython-35: module references __file__ luigi.contrib.__pycache__.sge.cpython-35: module references __file__ luigi.contrib.__pycache__.spark.cpython-35: module references __file__ luigi.contrib.__pycache__.spark.cpython-35: module references __path__ Installed /tmp/pip-wheel-5k17j7zp/mitopipeline/.eggs/luigi-2.8.7-py3.5.egg Searching for python-dateutil<3,>=2.7.5 Reading https://pypi.org/simple/python-dateutil/ Downloading https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl#sha256=7e6584c74aeed623791615e26efd690f29817a27c73085b78e4bad02493df2fb Best match: python-dateutil 2.8.0 Processing python_dateutil-2.8.0-py2.py3-none-any.whl Installing python_dateutil-2.8.0-py2.py3-none-any.whl to /tmp/pip-wheel-5k17j7zp/mitopipeline/.eggs writing requirements to /tmp/pip-wheel-5k17j7zp/mitopipeline/.eggs/python_dateutil-2.8.0-py3.5.egg/EGG-INFO/requires.txt Installed /tmp/pip-wheel-5k17j7zp/mitopipeline/.eggs/python_dateutil-2.8.0-py3.5.egg Searching for python-daemon<2.2.0 Reading https://pypi.org/simple/python-daemon/ Downloading https://files.pythonhosted.org/packages/f4/59/816004688f8e8602526553cd96226f34657ce4a86daa2240c3eebb0568a3/python_daemon-2.1.2-py2.py3-none-any.whl#sha256=53da55aec3bb67b576e13a8091a2181f99b395c2eec32a5a0d91d347a5c420a7 Best match: python-daemon 2.1.2 Processing python_daemon-2.1.2-py2.py3-none-any.whl Installing python_daemon-2.1.2-py2.py3-none-any.whl to /tmp/pip-wheel-5k17j7zp/mitopipeline/.eggs writing requirements to /tmp/pip-wheel-5k17j7zp/mitopipeline/.eggs/python_daemon-2.1.2-py3.5.egg/EGG-INFO/requires.txt Installed /tmp/pip-wheel-5k17j7zp/mitopipeline/.eggs/python_daemon-2.1.2-py3.5.egg Searching for lockfile>=0.10 Reading https://pypi.org/simple/lockfile/ Downloading https://files.pythonhosted.org/packages/c8/22/9460e311f340cb62d26a38c419b1381b8593b0bb6b5d1f056938b086d362/lockfile-0.12.2-py2.py3-none-any.whl#sha256=6c3cb24f344923d30b2785d5ad75182c8ea7ac1b6171b08657258ec7429d50fa Best match: lockfile 0.12.2 Processing lockfile-0.12.2-py2.py3-none-any.whl Installing lockfile-0.12.2-py2.py3-none-any.whl to /tmp/pip-wheel-5k17j7zp/mitopipeline/.eggs Installed /tmp/pip-wheel-5k17j7zp/mitopipeline/.eggs/lockfile-0.12.2-py3.5.egg running egg_info creating pip-egg-info/mitopipeline.egg-info writing requirements to pip-egg-info/mitopipeline.egg-info/requires.txt writing pip-egg-info/mitopipeline.egg-info/PKG-INFO writing top-level names to pip-egg-info/mitopipeline.egg-info/top_level.txt writing dependency_links to pip-egg-info/mitopipeline.egg-info/dependency_links.txt writing entry points to pip-egg-info/mitopipeline.egg-info/entry_points.txt writing manifest file 'pip-egg-info/mitopipeline.egg-info/SOURCES.txt' /usr/local/lib/python3.5/dist-packages/setuptools/dist.py:470: UserWarning: Normalizing '1.1post1' to '1.1.post1' normalized_version, file mitopipeline.py (for module mitopipeline) not found reading manifest file 'pip-egg-info/mitopipeline.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'mitopipeline/tools/*' writing manifest file 'pip-egg-info/mitopipeline.egg-info/SOURCES.txt' Source in /tmp/pip-wheel-5k17j7zp/mitopipeline has version 1.1.post1, which satisfies requirement mitopipeline==1.1.post1 from https://files.pythonhosted.org/packages/d3/a6/3c067b7dd13ed7b5af914ba984ea758a17db888c2873a0315df911d49f53/mitopipeline-1.1.post1.tar.gz#sha256=dc05a5ba6ad1b4f6a5ccd3304eb2053dd044f19495fbf3ffd76d6e82c05f1ce2 Removed mitopipeline==1.1.post1 from https://files.pythonhosted.org/packages/d3/a6/3c067b7dd13ed7b5af914ba984ea758a17db888c2873a0315df911d49f53/mitopipeline-1.1.post1.tar.gz#sha256=dc05a5ba6ad1b4f6a5ccd3304eb2053dd044f19495fbf3ffd76d6e82c05f1ce2 from build tracker '/tmp/pip-req-tracker-amj9qb4d' Building wheels for collected packages: mitopipeline Created temporary directory: /tmp/pip-wheel-9v591f0n Running setup.py bdist_wheel for mitopipeline: started Destination directory: /tmp/pip-wheel-9v591f0n Running command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-wheel-5k17j7zp/mitopipeline/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/pip-wheel-9v591f0n /usr/local/lib/python3.5/dist-packages/setuptools/dist.py:470: UserWarning: Normalizing '1.1post1' to '1.1.post1' normalized_version, running bdist_wheel running build running build_py file mitopipeline.py (for module mitopipeline) not found creating build creating build/lib creating build/lib/mitopipeline copying mitopipeline/config.py -> build/lib/mitopipeline copying mitopipeline/cmdline.py -> build/lib/mitopipeline copying mitopipeline/downloader.py -> build/lib/mitopipeline copying mitopipeline/templates.py -> build/lib/mitopipeline copying mitopipeline/util.py -> build/lib/mitopipeline copying mitopipeline/pipeline_builder.py -> build/lib/mitopipeline copying mitopipeline/logging.py -> build/lib/mitopipeline copying mitopipeline/cmdline_parser.py -> build/lib/mitopipeline copying mitopipeline/pipeline_runner.py -> build/lib/mitopipeline copying mitopipeline/__init__.py -> build/lib/mitopipeline creating build/lib/mitopipeline/steps copying mitopipeline/steps/splitgap.sh -> build/lib/mitopipeline/steps copying mitopipeline/steps/gatk.sh -> build/lib/mitopipeline/steps copying mitopipeline/steps/annovar.sh -> build/lib/mitopipeline/steps copying mitopipeline/steps/downsample.sh -> build/lib/mitopipeline/steps copying mitopipeline/steps/removenumts.sh -> build/lib/mitopipeline/steps copying mitopipeline/steps/split_bams.py -> build/lib/mitopipeline/steps copying mitopipeline/steps/submit_job.sh -> build/lib/mitopipeline/steps copying mitopipeline/steps/remove_numts_no_split_gap.sh -> build/lib/mitopipeline/steps copying mitopipeline/steps/snpeff.sh -> build/lib/mitopipeline/steps copying mitopipeline/steps/read_depths.py -> build/lib/mitopipeline/steps copying mitopipeline/steps/extractmito.sh -> build/lib/mitopipeline/steps copying mitopipeline/steps/clipping.sh -> build/lib/mitopipeline/steps creating build/lib/mitopipeline/steps/dbsnp copying mitopipeline/steps/dbsnp/mtONLY.vcf -> build/lib/mitopipeline/steps/dbsnp copying mitopipeline/steps/dbsnp/mtONLY.vcf.idx -> build/lib/mitopipeline/steps/dbsnp creating build/lib/mitopipeline/steps/tools copying mitopipeline/steps/tools/AddOrReplaceReadGroups.jar -> build/lib/mitopipeline/steps/tools copying mitopipeline/steps/tools/FixMateInformation.jar -> build/lib/mitopipeline/steps/tools copying mitopipeline/steps/tools/SamToFastq.jar -> build/lib/mitopipeline/steps/tools copying mitopipeline/steps/tools/MarkDuplicates.jar -> build/lib/mitopipeline/steps/tools file mitopipeline.py (for module mitopipeline) not found installing to build/bdist.linux-armv7l/wheel running install running install_lib creating build/bdist.linux-armv7l creating build/bdist.linux-armv7l/wheel creating build/bdist.linux-armv7l/wheel/mitopipeline copying build/lib/mitopipeline/config.py -> build/bdist.linux-armv7l/wheel/mitopipeline creating build/bdist.linux-armv7l/wheel/mitopipeline/steps creating build/bdist.linux-armv7l/wheel/mitopipeline/steps/tools copying build/lib/mitopipeline/steps/tools/AddOrReplaceReadGroups.jar -> build/bdist.linux-armv7l/wheel/mitopipeline/steps/tools copying build/lib/mitopipeline/steps/tools/FixMateInformation.jar -> build/bdist.linux-armv7l/wheel/mitopipeline/steps/tools copying build/lib/mitopipeline/steps/tools/SamToFastq.jar -> build/bdist.linux-armv7l/wheel/mitopipeline/steps/tools copying build/lib/mitopipeline/steps/tools/MarkDuplicates.jar -> build/bdist.linux-armv7l/wheel/mitopipeline/steps/tools copying build/lib/mitopipeline/steps/splitgap.sh -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/steps/gatk.sh -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/steps/annovar.sh -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/steps/downsample.sh -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/steps/removenumts.sh -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/steps/split_bams.py -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/steps/submit_job.sh -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/steps/remove_numts_no_split_gap.sh -> build/bdist.linux-armv7l/wheel/mitopipeline/steps creating build/bdist.linux-armv7l/wheel/mitopipeline/steps/dbsnp copying build/lib/mitopipeline/steps/dbsnp/mtONLY.vcf -> build/bdist.linux-armv7l/wheel/mitopipeline/steps/dbsnp copying build/lib/mitopipeline/steps/dbsnp/mtONLY.vcf.idx -> build/bdist.linux-armv7l/wheel/mitopipeline/steps/dbsnp copying build/lib/mitopipeline/steps/snpeff.sh -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/steps/read_depths.py -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/steps/extractmito.sh -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/steps/clipping.sh -> build/bdist.linux-armv7l/wheel/mitopipeline/steps copying build/lib/mitopipeline/cmdline.py -> build/bdist.linux-armv7l/wheel/mitopipeline copying build/lib/mitopipeline/downloader.py -> build/bdist.linux-armv7l/wheel/mitopipeline copying build/lib/mitopipeline/templates.py -> build/bdist.linux-armv7l/wheel/mitopipeline copying build/lib/mitopipeline/util.py -> build/bdist.linux-armv7l/wheel/mitopipeline copying build/lib/mitopipeline/pipeline_builder.py -> build/bdist.linux-armv7l/wheel/mitopipeline copying build/lib/mitopipeline/logging.py -> build/bdist.linux-armv7l/wheel/mitopipeline copying build/lib/mitopipeline/cmdline_parser.py -> build/bdist.linux-armv7l/wheel/mitopipeline copying build/lib/mitopipeline/pipeline_runner.py -> build/bdist.linux-armv7l/wheel/mitopipeline copying build/lib/mitopipeline/__init__.py -> build/bdist.linux-armv7l/wheel/mitopipeline running install_egg_info running egg_info writing top-level names to mitopipeline.egg-info/top_level.txt writing entry points to mitopipeline.egg-info/entry_points.txt writing dependency_links to mitopipeline.egg-info/dependency_links.txt writing mitopipeline.egg-info/PKG-INFO writing requirements to mitopipeline.egg-info/requires.txt file mitopipeline.py (for module mitopipeline) not found reading manifest file 'mitopipeline.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'mitopipeline/tools/*' writing manifest file 'mitopipeline.egg-info/SOURCES.txt' Copying mitopipeline.egg-info to build/bdist.linux-armv7l/wheel/mitopipeline-1.1.post1-py3.5.egg-info running install_scripts adding license file "LICENSE.txt" (matched pattern "LICEN[CS]E*") creating build/bdist.linux-armv7l/wheel/mitopipeline-1.1.post1.dist-info/WHEEL creating '/tmp/pip-wheel-9v591f0n/mitopipeline-1.1.post1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it adding 'mitopipeline/__init__.py' adding 'mitopipeline/cmdline.py' adding 'mitopipeline/cmdline_parser.py' adding 'mitopipeline/config.py' adding 'mitopipeline/downloader.py' adding 'mitopipeline/logging.py' adding 'mitopipeline/pipeline_builder.py' adding 'mitopipeline/pipeline_runner.py' adding 'mitopipeline/templates.py' adding 'mitopipeline/util.py' adding 'mitopipeline/steps/annovar.sh' adding 'mitopipeline/steps/clipping.sh' adding 'mitopipeline/steps/downsample.sh' adding 'mitopipeline/steps/extractmito.sh' adding 'mitopipeline/steps/gatk.sh' adding 'mitopipeline/steps/read_depths.py' adding 'mitopipeline/steps/remove_numts_no_split_gap.sh' adding 'mitopipeline/steps/removenumts.sh' adding 'mitopipeline/steps/snpeff.sh' adding 'mitopipeline/steps/split_bams.py' adding 'mitopipeline/steps/splitgap.sh' adding 'mitopipeline/steps/submit_job.sh' adding 'mitopipeline/steps/dbsnp/mtONLY.vcf' adding 'mitopipeline/steps/dbsnp/mtONLY.vcf.idx' adding 'mitopipeline/steps/tools/AddOrReplaceReadGroups.jar' adding 'mitopipeline/steps/tools/FixMateInformation.jar' adding 'mitopipeline/steps/tools/MarkDuplicates.jar' adding 'mitopipeline/steps/tools/SamToFastq.jar' adding 'mitopipeline-1.1.post1.dist-info/LICENSE.txt' adding 'mitopipeline-1.1.post1.dist-info/METADATA' adding 'mitopipeline-1.1.post1.dist-info/WHEEL' adding 'mitopipeline-1.1.post1.dist-info/entry_points.txt' adding 'mitopipeline-1.1.post1.dist-info/top_level.txt' adding 'mitopipeline-1.1.post1.dist-info/RECORD' removing build/bdist.linux-armv7l/wheel Running setup.py bdist_wheel for mitopipeline: finished with status 'done' Stored in directory: /tmp/tmpdhelrcmq Successfully built mitopipeline Cleaning up... Removing source in /tmp/pip-wheel-5k17j7zp/mitopipeline Removed build tracker '/tmp/pip-req-tracker-amj9qb4d'