Created temporary directory: /tmp/pip-ephem-wheel-cache-yhugdkmm Created temporary directory: /tmp/pip-req-tracker-lp1of782 Created requirements tracker '/tmp/pip-req-tracker-lp1of782' Created temporary directory: /tmp/pip-wheel-2lsyz5gh Collecting mgatk==0.5.5 1 location(s) to search for versions of mgatk: * https://pypi.org/simple/mgatk/ Getting page https://pypi.org/simple/mgatk/ Analyzing links from page https://pypi.org/simple/mgatk/ Found link https://files.pythonhosted.org/packages/8f/0c/47da433403828d2e53de436d7689af32d8ee5130dc1c748ce0175d0f2eb1/mgatk-0.0.1.tar.gz#sha256=f0a66229c6057d0cc66db65b33141cd22a3ebc0a4ede501e4887014b5a56643b (from https://pypi.org/simple/mgatk/), version: 0.0.1 Found link https://files.pythonhosted.org/packages/f7/7f/f09842055b19e670fbc309415123b423d30cc0fd1a8c430785bd1754827f/mgatk-0.1.0.tar.gz#sha256=bcfea43a3fb2d22b7c5cbecf59fd3989ef03250f87378b33e889b4054e275166 (from https://pypi.org/simple/mgatk/), version: 0.1.0 Found link https://files.pythonhosted.org/packages/b7/8e/ac9ab509199f852d88097608e3fb60fc85232c87a36a062a041043ea869d/mgatk-0.2.5.tar.gz#sha256=b16329f84786ef87490379db121816b103fe5339ed90fb395e0a9c4ef5028d6e (from https://pypi.org/simple/mgatk/), version: 0.2.5 Found link https://files.pythonhosted.org/packages/74/28/da183d0b56f401dec7f3bded24c50a02396e56c4f995fd50a3cf21c4381d/mgatk-0.5.0.tar.gz#sha256=61ee4d3c18cf696ecfbea6ab5dd9bfebf9791c368a04cfc2d1afcdfe16a6d3ca (from https://pypi.org/simple/mgatk/), version: 0.5.0 Found link https://files.pythonhosted.org/packages/96/e8/e35c039eac8d418ca9213b1db69c4176b59783ca43638a75e824b475197d/mgatk-0.5.1.tar.gz#sha256=518ef6a1d25d9f889a306514eaf1ade02146fce28a43866a60dc6f1dad81b54c (from https://pypi.org/simple/mgatk/), version: 0.5.1 Found link https://files.pythonhosted.org/packages/b6/16/d11afe05a803f23995d04af8fd832473fa1d21f73f242340f6086eb97183/mgatk-0.5.3.tar.gz#sha256=d9b78751af0fe8c31d22508a24ef061d7478c8a2c6283eded971f8802f060f79 (from https://pypi.org/simple/mgatk/), version: 0.5.3 Found link https://files.pythonhosted.org/packages/be/5f/896adc0419fad47b3434866dd68deb7b93a1328916be0eb1f0827393633e/mgatk-0.5.5.tar.gz#sha256=bcc0470b4d01e5cd5d5e67f87720101fc4db889a0c5a4ef35c7d7224989d60a7 (from https://pypi.org/simple/mgatk/), version: 0.5.5 Using version 0.5.5 (newest of versions: 0.5.5) Created temporary directory: /tmp/pip-unpack-6cu960bd Downloading https://files.pythonhosted.org/packages/be/5f/896adc0419fad47b3434866dd68deb7b93a1328916be0eb1f0827393633e/mgatk-0.5.5.tar.gz (14.3MB) Downloading from URL https://files.pythonhosted.org/packages/be/5f/896adc0419fad47b3434866dd68deb7b93a1328916be0eb1f0827393633e/mgatk-0.5.5.tar.gz#sha256=bcc0470b4d01e5cd5d5e67f87720101fc4db889a0c5a4ef35c7d7224989d60a7 (from https://pypi.org/simple/mgatk/) Added mgatk==0.5.5 from https://files.pythonhosted.org/packages/be/5f/896adc0419fad47b3434866dd68deb7b93a1328916be0eb1f0827393633e/mgatk-0.5.5.tar.gz#sha256=bcc0470b4d01e5cd5d5e67f87720101fc4db889a0c5a4ef35c7d7224989d60a7 to build tracker '/tmp/pip-req-tracker-lp1of782' Running setup.py (path:/tmp/pip-wheel-2lsyz5gh/mgatk/setup.py) egg_info for package mgatk Running command python setup.py egg_info running egg_info creating pip-egg-info/mgatk.egg-info writing pip-egg-info/mgatk.egg-info/PKG-INFO writing dependency_links to pip-egg-info/mgatk.egg-info/dependency_links.txt writing entry points to pip-egg-info/mgatk.egg-info/entry_points.txt writing requirements to pip-egg-info/mgatk.egg-info/requires.txt writing top-level names to pip-egg-info/mgatk.egg-info/top_level.txt writing manifest file 'pip-egg-info/mgatk.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/mgatk.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching 'mgatk.egg-info/' no previously-included directories found matching 'tests/' no previously-included directories found matching '*.DS_Store' writing manifest file 'pip-egg-info/mgatk.egg-info/SOURCES.txt' Source in /tmp/pip-wheel-2lsyz5gh/mgatk has version 0.5.5, which satisfies requirement mgatk==0.5.5 from https://files.pythonhosted.org/packages/be/5f/896adc0419fad47b3434866dd68deb7b93a1328916be0eb1f0827393633e/mgatk-0.5.5.tar.gz#sha256=bcc0470b4d01e5cd5d5e67f87720101fc4db889a0c5a4ef35c7d7224989d60a7 Removed mgatk==0.5.5 from https://files.pythonhosted.org/packages/be/5f/896adc0419fad47b3434866dd68deb7b93a1328916be0eb1f0827393633e/mgatk-0.5.5.tar.gz#sha256=bcc0470b4d01e5cd5d5e67f87720101fc4db889a0c5a4ef35c7d7224989d60a7 from build tracker '/tmp/pip-req-tracker-lp1of782' Building wheels for collected packages: mgatk Created temporary directory: /tmp/pip-wheel-z424n5dn Running setup.py bdist_wheel for mgatk: started Destination directory: /tmp/pip-wheel-z424n5dn Running command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-wheel-2lsyz5gh/mgatk/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-z424n5dn running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/mgatk copying mgatk/cli.py -> build/lib/mgatk copying mgatk/__init__.py -> build/lib/mgatk copying mgatk/mgatkHelp.py -> build/lib/mgatk running egg_info writing dependency_links to mgatk.egg-info/dependency_links.txt writing requirements to mgatk.egg-info/requires.txt writing mgatk.egg-info/PKG-INFO writing entry points to mgatk.egg-info/entry_points.txt writing top-level names to mgatk.egg-info/top_level.txt reading manifest file 'mgatk.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching 'tests/' no previously-included directories found matching '*.DS_Store' writing manifest file 'mgatk.egg-info/SOURCES.txt' copying mgatk/.DS_Store -> build/lib/mgatk copying mgatk/devnotes.md -> build/lib/mgatk creating build/lib/mgatk/__pycache__ copying mgatk/__pycache__/__init__.cpython-36.pyc -> build/lib/mgatk/__pycache__ copying mgatk/__pycache__/cli.cpython-36.pyc -> build/lib/mgatk/__pycache__ copying mgatk/__pycache__/mgatkHelp.cpython-36.pyc -> build/lib/mgatk/__pycache__ creating build/lib/mgatk/bin copying mgatk/bin/.DS_Store -> build/lib/mgatk/bin copying mgatk/bin/picard.jar -> build/lib/mgatk/bin creating build/lib/mgatk/bin/R copying mgatk/bin/R/toRDS.R -> build/lib/mgatk/bin/R creating build/lib/mgatk/bin/anno creating build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/GRCh37.fasta -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/GRCh38.fasta -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/GRCh38.fasta.fai -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/GRCm38.fasta -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/GRCz10.fasta -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/NC_012920.fasta -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/hg19.fasta -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/hg19_chrM.fasta -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/hg38.fasta -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/mm10.fasta -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/mm9.fasta -> build/lib/mgatk/bin/anno/fasta copying mgatk/bin/anno/fasta/rCRS.fasta -> build/lib/mgatk/bin/anno/fasta creating build/lib/mgatk/bin/python copying mgatk/bin/python/chunk_barcoded_bam.py -> build/lib/mgatk/bin/python copying mgatk/bin/python/filterClipBam.py -> build/lib/mgatk/bin/python copying mgatk/bin/python/find_barcodes.py -> build/lib/mgatk/bin/python copying mgatk/bin/python/oneSample.py -> build/lib/mgatk/bin/python copying mgatk/bin/python/split_barcoded_bam.py -> build/lib/mgatk/bin/python copying mgatk/bin/python/sumstatsBP.py -> build/lib/mgatk/bin/python copying mgatk/bin/python/sumstatsBPmem.py -> build/lib/mgatk/bin/python creating build/lib/mgatk/bin/snake copying mgatk/bin/snake/Snakefile.Gather -> build/lib/mgatk/bin/snake copying mgatk/bin/snake/Snakefile.Scatter -> build/lib/mgatk/bin/snake copying mgatk/bin/snake/Snakefile.mem -> build/lib/mgatk/bin/snake creating build/lib/mgatk/del copying mgatk/del/.DS_Store -> build/lib/mgatk/del copying mgatk/del/clidel.py -> build/lib/mgatk/del copying mgatk/del/clifind.py -> build/lib/mgatk/del creating build/lib/mgatk/del/__pycache__ copying mgatk/del/__pycache__/clidel.cpython-36.pyc -> build/lib/mgatk/del/__pycache__ copying mgatk/del/__pycache__/clifind.cpython-36.pyc -> build/lib/mgatk/del/__pycache__ creating build/lib/mgatk/del/bulk_del copying mgatk/del/bulk_del/plot_deletion_breaks_bulk.R -> build/lib/mgatk/del/bulk_del creating build/lib/mgatk/del/singles_del copying mgatk/del/singles_del/01_process_cell_reads.py -> build/lib/mgatk/del/singles_del copying mgatk/del/singles_del/02_heteroplasmy_del_singles.R -> build/lib/mgatk/del/singles_del copying mgatk/del/singles_del/Snakefile.delSingles -> build/lib/mgatk/del/singles_del 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/mgatk creating build/bdist.linux-armv7l/wheel/mgatk/del copying build/lib/mgatk/del/.DS_Store -> build/bdist.linux-armv7l/wheel/mgatk/del creating build/bdist.linux-armv7l/wheel/mgatk/del/__pycache__ copying build/lib/mgatk/del/__pycache__/clidel.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/mgatk/del/__pycache__ copying build/lib/mgatk/del/__pycache__/clifind.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/mgatk/del/__pycache__ creating build/bdist.linux-armv7l/wheel/mgatk/del/bulk_del copying build/lib/mgatk/del/bulk_del/plot_deletion_breaks_bulk.R -> build/bdist.linux-armv7l/wheel/mgatk/del/bulk_del copying build/lib/mgatk/del/clifind.py -> build/bdist.linux-armv7l/wheel/mgatk/del copying build/lib/mgatk/del/clidel.py -> build/bdist.linux-armv7l/wheel/mgatk/del creating build/bdist.linux-armv7l/wheel/mgatk/del/singles_del copying build/lib/mgatk/del/singles_del/01_process_cell_reads.py -> build/bdist.linux-armv7l/wheel/mgatk/del/singles_del copying build/lib/mgatk/del/singles_del/02_heteroplasmy_del_singles.R -> build/bdist.linux-armv7l/wheel/mgatk/del/singles_del copying build/lib/mgatk/del/singles_del/Snakefile.delSingles -> build/bdist.linux-armv7l/wheel/mgatk/del/singles_del copying build/lib/mgatk/cli.py -> build/bdist.linux-armv7l/wheel/mgatk copying build/lib/mgatk/.DS_Store -> build/bdist.linux-armv7l/wheel/mgatk creating build/bdist.linux-armv7l/wheel/mgatk/__pycache__ copying build/lib/mgatk/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/mgatk/__pycache__ copying build/lib/mgatk/__pycache__/cli.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/mgatk/__pycache__ copying build/lib/mgatk/__pycache__/mgatkHelp.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/mgatk/__pycache__ creating build/bdist.linux-armv7l/wheel/mgatk/bin creating build/bdist.linux-armv7l/wheel/mgatk/bin/anno creating build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/mm9.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/hg19_chrM.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/GRCz10.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/rCRS.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/mm10.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/hg19.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/hg38.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/GRCh38.fasta.fai -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/NC_012920.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/GRCh38.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/GRCm38.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta copying build/lib/mgatk/bin/anno/fasta/GRCh37.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta creating build/bdist.linux-armv7l/wheel/mgatk/bin/snake copying build/lib/mgatk/bin/snake/Snakefile.Scatter -> build/bdist.linux-armv7l/wheel/mgatk/bin/snake copying build/lib/mgatk/bin/snake/Snakefile.mem -> build/bdist.linux-armv7l/wheel/mgatk/bin/snake copying build/lib/mgatk/bin/snake/Snakefile.Gather -> build/bdist.linux-armv7l/wheel/mgatk/bin/snake copying build/lib/mgatk/bin/.DS_Store -> build/bdist.linux-armv7l/wheel/mgatk/bin copying build/lib/mgatk/bin/picard.jar -> build/bdist.linux-armv7l/wheel/mgatk/bin creating build/bdist.linux-armv7l/wheel/mgatk/bin/R copying build/lib/mgatk/bin/R/toRDS.R -> build/bdist.linux-armv7l/wheel/mgatk/bin/R creating build/bdist.linux-armv7l/wheel/mgatk/bin/python copying build/lib/mgatk/bin/python/split_barcoded_bam.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python copying build/lib/mgatk/bin/python/sumstatsBPmem.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python copying build/lib/mgatk/bin/python/chunk_barcoded_bam.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python copying build/lib/mgatk/bin/python/find_barcodes.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python copying build/lib/mgatk/bin/python/filterClipBam.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python copying build/lib/mgatk/bin/python/oneSample.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python copying build/lib/mgatk/bin/python/sumstatsBP.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python copying build/lib/mgatk/__init__.py -> build/bdist.linux-armv7l/wheel/mgatk copying build/lib/mgatk/devnotes.md -> build/bdist.linux-armv7l/wheel/mgatk copying build/lib/mgatk/mgatkHelp.py -> build/bdist.linux-armv7l/wheel/mgatk running install_egg_info Copying mgatk.egg-info to build/bdist.linux-armv7l/wheel/mgatk-0.5.5-py3.4.egg-info running install_scripts adding license file "LICENSE.txt" (matched pattern "LICEN[CS]E*") creating build/bdist.linux-armv7l/wheel/mgatk-0.5.5.dist-info/WHEEL creating '/tmp/pip-wheel-z424n5dn/mgatk-0.5.5-py2.py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it adding 'mgatk/.DS_Store' adding 'mgatk/__init__.py' adding 'mgatk/cli.py' adding 'mgatk/devnotes.md' adding 'mgatk/mgatkHelp.py' adding 'mgatk/__pycache__/__init__.cpython-36.pyc' adding 'mgatk/__pycache__/cli.cpython-36.pyc' adding 'mgatk/__pycache__/mgatkHelp.cpython-36.pyc' adding 'mgatk/bin/.DS_Store' adding 'mgatk/bin/picard.jar' adding 'mgatk/bin/R/toRDS.R' adding 'mgatk/bin/anno/fasta/GRCh37.fasta' adding 'mgatk/bin/anno/fasta/GRCh38.fasta' adding 'mgatk/bin/anno/fasta/GRCh38.fasta.fai' adding 'mgatk/bin/anno/fasta/GRCm38.fasta' adding 'mgatk/bin/anno/fasta/GRCz10.fasta' adding 'mgatk/bin/anno/fasta/NC_012920.fasta' adding 'mgatk/bin/anno/fasta/hg19.fasta' adding 'mgatk/bin/anno/fasta/hg19_chrM.fasta' adding 'mgatk/bin/anno/fasta/hg38.fasta' adding 'mgatk/bin/anno/fasta/mm10.fasta' adding 'mgatk/bin/anno/fasta/mm9.fasta' adding 'mgatk/bin/anno/fasta/rCRS.fasta' adding 'mgatk/bin/python/chunk_barcoded_bam.py' adding 'mgatk/bin/python/filterClipBam.py' adding 'mgatk/bin/python/find_barcodes.py' adding 'mgatk/bin/python/oneSample.py' adding 'mgatk/bin/python/split_barcoded_bam.py' adding 'mgatk/bin/python/sumstatsBP.py' adding 'mgatk/bin/python/sumstatsBPmem.py' adding 'mgatk/bin/snake/Snakefile.Gather' adding 'mgatk/bin/snake/Snakefile.Scatter' adding 'mgatk/bin/snake/Snakefile.mem' adding 'mgatk/del/.DS_Store' adding 'mgatk/del/clidel.py' adding 'mgatk/del/clifind.py' adding 'mgatk/del/__pycache__/clidel.cpython-36.pyc' adding 'mgatk/del/__pycache__/clifind.cpython-36.pyc' adding 'mgatk/del/bulk_del/plot_deletion_breaks_bulk.R' adding 'mgatk/del/singles_del/01_process_cell_reads.py' adding 'mgatk/del/singles_del/02_heteroplasmy_del_singles.R' adding 'mgatk/del/singles_del/Snakefile.delSingles' adding 'mgatk-0.5.5.dist-info/LICENSE.txt' adding 'mgatk-0.5.5.dist-info/METADATA' adding 'mgatk-0.5.5.dist-info/WHEEL' adding 'mgatk-0.5.5.dist-info/entry_points.txt' adding 'mgatk-0.5.5.dist-info/top_level.txt' adding 'mgatk-0.5.5.dist-info/RECORD' removing build/bdist.linux-armv7l/wheel Running setup.py bdist_wheel for mgatk: finished with status 'done' Stored in directory: /tmp/tmpxhntmse9 Successfully built mgatk Cleaning up... Removing source in /tmp/pip-wheel-2lsyz5gh/mgatk Removed build tracker '/tmp/pip-req-tracker-lp1of782'