2020-12-14T20:58:21,464 DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
2020-12-14T20:58:22,187 Created temporary directory: /tmp/pip-ephem-wheel-cache-ig1t071r
2020-12-14T20:58:22,191 Created temporary directory: /tmp/pip-req-tracker-i3p061rx
2020-12-14T20:58:22,192 Initialized build tracking at /tmp/pip-req-tracker-i3p061rx
2020-12-14T20:58:22,193 Created build tracker: /tmp/pip-req-tracker-i3p061rx
2020-12-14T20:58:22,193 Entered build tracker: /tmp/pip-req-tracker-i3p061rx
2020-12-14T20:58:22,195 Created temporary directory: /tmp/pip-wheel-uvh6lu9l
2020-12-14T20:58:22,214 Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com
2020-12-14T20:58:22,216 2 location(s) to search for versions of novartis-pisces:
2020-12-14T20:58:22,216 * https://pypi.org/simple/novartis-pisces/
2020-12-14T20:58:22,216 * https://pypi.ngc.nvidia.com/novartis-pisces/
2020-12-14T20:58:22,217 Fetching project page and analyzing links: https://pypi.org/simple/novartis-pisces/
2020-12-14T20:58:22,219 Getting page https://pypi.org/simple/novartis-pisces/
2020-12-14T20:58:22,223 Found index url https://pypi.org/simple
2020-12-14T20:58:22,816   Found link https://files.pythonhosted.org/packages/7a/69/6e62653f167dfe6d2fa7f2f6527efa22825fecf80941f3190b20b8c0b972/novartis-pisces-0.1.1.tar.gz#sha256=b41fa61940d3517b258f8d1387453bd73814aad7e987ac21641a81dba5165460 (from https://pypi.org/simple/novartis-pisces/), version: 0.1.1
2020-12-14T20:58:22,817   Found link https://files.pythonhosted.org/packages/88/19/cdb5149b3ea5580bafffd7f6b2b18807bdd1cf364154be052bfb17b7a392/novartis-pisces-0.1.2.tar.gz#sha256=f334f331f7f9b29892fe2aa993e75b7d5fb372e7864fcc98c0e32c5b11225e00 (from https://pypi.org/simple/novartis-pisces/), version: 0.1.2
2020-12-14T20:58:22,818   Found link https://files.pythonhosted.org/packages/b6/72/9686797df03a1087913e92f359e09d7f35458b06c9503d27cbfce69959d6/novartis-pisces-0.1.3.tar.gz#sha256=4840853713bdf9cf9c9993c1e2b3cded285f50797868c6321bce2ef669c54ced (from https://pypi.org/simple/novartis-pisces/), version: 0.1.3
2020-12-14T20:58:22,819   Found link https://files.pythonhosted.org/packages/63/0c/bd21a99df2f38fc359ec3531b30c5439dbdd1d22e06cfeadf657af9be952/novartis-pisces-0.1.3.1.tar.gz#sha256=db8e4c9270d9b269f6dac35e7c48197f27c3127ec750b42e68d359dcaac54b39 (from https://pypi.org/simple/novartis-pisces/), version: 0.1.3.1
2020-12-14T20:58:22,820 Fetching project page and analyzing links: https://pypi.ngc.nvidia.com/novartis-pisces/
2020-12-14T20:58:22,820 Getting page https://pypi.ngc.nvidia.com/novartis-pisces/
2020-12-14T20:58:22,823 Found index url https://pypi.ngc.nvidia.com
2020-12-14T20:58:23,476 Could not fetch URL https://pypi.ngc.nvidia.com/novartis-pisces/: 404 Client Error: Not Found for url: https://developer.download.nvidia.com/compute/redist/novartis-pisces/ - skipping
2020-12-14T20:58:23,495 Given no hashes to check 1 links for project 'novartis-pisces': discarding no candidates
2020-12-14T20:58:23,497 Using version 0.1.3.1 (newest of versions: 0.1.3.1)
2020-12-14T20:58:23,507 Collecting novartis-pisces==0.1.3.1
2020-12-14T20:58:23,512   Created temporary directory: /tmp/pip-unpack-b30zdghq
2020-12-14T20:58:24,646   Downloading novartis-pisces-0.1.3.1.tar.gz (18.4 MB)
2020-12-14T20:58:33,452   Added novartis-pisces==0.1.3.1 from https://files.pythonhosted.org/packages/63/0c/bd21a99df2f38fc359ec3531b30c5439dbdd1d22e06cfeadf657af9be952/novartis-pisces-0.1.3.1.tar.gz#sha256=db8e4c9270d9b269f6dac35e7c48197f27c3127ec750b42e68d359dcaac54b39 to build tracker '/tmp/pip-req-tracker-i3p061rx'
2020-12-14T20:58:33,458     Running setup.py (path:/tmp/pip-wheel-uvh6lu9l/novartis-pisces/setup.py) egg_info for package novartis-pisces
2020-12-14T20:58:33,461     Created temporary directory: /tmp/pip-pip-egg-info-hko6i5j0
2020-12-14T20:58:33,462     Running command python setup.py egg_info
2020-12-14T20:58:39,550     DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
2020-12-14T20:58:43,449     running egg_info
2020-12-14T20:58:43,455     creating /tmp/pip-pip-egg-info-hko6i5j0/novartis_pisces.egg-info
2020-12-14T20:58:43,457     writing dependency_links to /tmp/pip-pip-egg-info-hko6i5j0/novartis_pisces.egg-info/dependency_links.txt
2020-12-14T20:58:43,461     writing requirements to /tmp/pip-pip-egg-info-hko6i5j0/novartis_pisces.egg-info/requires.txt
2020-12-14T20:58:43,463     writing /tmp/pip-pip-egg-info-hko6i5j0/novartis_pisces.egg-info/PKG-INFO
2020-12-14T20:58:43,467     writing entry points to /tmp/pip-pip-egg-info-hko6i5j0/novartis_pisces.egg-info/entry_points.txt
2020-12-14T20:58:43,470     writing top-level names to /tmp/pip-pip-egg-info-hko6i5j0/novartis_pisces.egg-info/top_level.txt
2020-12-14T20:58:43,475     writing manifest file '/tmp/pip-pip-egg-info-hko6i5j0/novartis_pisces.egg-info/SOURCES.txt'
2020-12-14T20:58:43,867     reading manifest file '/tmp/pip-pip-egg-info-hko6i5j0/novartis_pisces.egg-info/SOURCES.txt'
2020-12-14T20:58:43,871     reading manifest template 'MANIFEST.in'
2020-12-14T20:58:43,899     writing manifest file '/tmp/pip-pip-egg-info-hko6i5j0/novartis_pisces.egg-info/SOURCES.txt'
2020-12-14T20:58:44,067   Source in /tmp/pip-wheel-uvh6lu9l/novartis-pisces has version 0.1.3.1, which satisfies requirement novartis-pisces==0.1.3.1 from https://files.pythonhosted.org/packages/63/0c/bd21a99df2f38fc359ec3531b30c5439dbdd1d22e06cfeadf657af9be952/novartis-pisces-0.1.3.1.tar.gz#sha256=db8e4c9270d9b269f6dac35e7c48197f27c3127ec750b42e68d359dcaac54b39
2020-12-14T20:58:44,069   Removed novartis-pisces==0.1.3.1 from https://files.pythonhosted.org/packages/63/0c/bd21a99df2f38fc359ec3531b30c5439dbdd1d22e06cfeadf657af9be952/novartis-pisces-0.1.3.1.tar.gz#sha256=db8e4c9270d9b269f6dac35e7c48197f27c3127ec750b42e68d359dcaac54b39 from build tracker '/tmp/pip-req-tracker-i3p061rx'
2020-12-14T20:58:44,073 Building wheels for collected packages: novartis-pisces
2020-12-14T20:58:44,082   Created temporary directory: /tmp/pip-wheel-zlz24vl8
2020-12-14T20:58:44,083   Building wheel for novartis-pisces (setup.py): started
2020-12-14T20:58:44,083   Destination directory: /tmp/pip-wheel-zlz24vl8
2020-12-14T20:58:44,084   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-uvh6lu9l/novartis-pisces/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-uvh6lu9l/novartis-pisces/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-zlz24vl8
2020-12-14T20:58:47,483   running bdist_wheel
2020-12-14T20:58:47,491   running build
2020-12-14T20:58:47,492   running build_py
2020-12-14T20:58:47,813   creating build
2020-12-14T20:58:47,814   creating build/lib
2020-12-14T20:58:47,815   creating build/lib/pisces
2020-12-14T20:58:47,818   copying pisces/cli.py -> build/lib/pisces
2020-12-14T20:58:47,824   copying pisces/qc.py -> build/lib/pisces
2020-12-14T20:58:47,829   copying pisces/run.py -> build/lib/pisces
2020-12-14T20:58:47,834   copying pisces/submit.py -> build/lib/pisces
2020-12-14T20:58:47,840   copying pisces/index.py -> build/lib/pisces
2020-12-14T20:58:47,848   copying pisces/__init__.py -> build/lib/pisces
2020-12-14T20:58:47,855   copying pisces/fastq.py -> build/lib/pisces
2020-12-14T20:58:47,860   running egg_info
2020-12-14T20:58:47,873   writing dependency_links to novartis_pisces.egg-info/dependency_links.txt
2020-12-14T20:58:47,877   writing entry points to novartis_pisces.egg-info/entry_points.txt
2020-12-14T20:58:47,880   writing novartis_pisces.egg-info/PKG-INFO
2020-12-14T20:58:47,884   writing top-level names to novartis_pisces.egg-info/top_level.txt
2020-12-14T20:58:47,886   writing requirements to novartis_pisces.egg-info/requires.txt
2020-12-14T20:58:47,927   reading manifest file 'novartis_pisces.egg-info/SOURCES.txt'
2020-12-14T20:58:47,965   reading manifest template 'MANIFEST.in'
2020-12-14T20:58:48,000   writing manifest file 'novartis_pisces.egg-info/SOURCES.txt'
2020-12-14T20:58:48,011   copying pisces/.DS_Store -> build/lib/pisces
2020-12-14T20:58:48,017   copying pisces/config.json -> build/lib/pisces
2020-12-14T20:58:48,023   creating build/lib/pisces/R
2020-12-14T20:58:48,025   copying pisces/R/.DS_Store -> build/lib/pisces/R
2020-12-14T20:58:48,032   copying pisces/R/.Rprofile -> build/lib/pisces/R
2020-12-14T20:58:48,038   copying pisces/R/.gitignore -> build/lib/pisces/R
2020-12-14T20:58:48,044   copying pisces/R/make_expression_matrix.R -> build/lib/pisces/R
2020-12-14T20:58:48,054   copying pisces/R/set_up_dependencies.R -> build/lib/pisces/R
2020-12-14T20:58:48,060   creating build/lib/pisces/R/renv
2020-12-14T20:58:48,063   copying pisces/R/renv/activate.R -> build/lib/pisces/R/renv
2020-12-14T20:58:48,072   creating build/lib/pisces/data
2020-12-14T20:58:48,074   copying pisces/data/fp_kmers.txt -> build/lib/pisces/data
2020-12-14T20:58:48,089   copying pisces/data/fp_kmers_col1.txt -> build/lib/pisces/data
2020-12-14T20:58:48,095   creating build/lib/pisces/scripts
2020-12-14T20:58:48,097   copying pisces/scripts/.DS_Store -> build/lib/pisces/scripts
2020-12-14T20:58:48,103   copying pisces/scripts/create_sample_sets_stripped.py -> build/lib/pisces/scripts
2020-12-14T20:58:48,111   copying pisces/scripts/kmer_counts_to_fingerprint_strand_and_pcthuman.py -> build/lib/pisces/scripts
2020-12-14T20:58:48,120   creating build/lib/pisces/tests
2020-12-14T20:58:48,122   copying pisces/tests/test_cli.py -> build/lib/pisces/tests
2020-12-14T20:58:48,134   installing to build/bdist.linux-armv7l/wheel
2020-12-14T20:58:48,135   running install
2020-12-14T20:58:48,137   running install_lib
2020-12-14T20:58:48,146   creating build/bdist.linux-armv7l
2020-12-14T20:58:48,147   creating build/bdist.linux-armv7l/wheel
2020-12-14T20:58:48,151   creating build/bdist.linux-armv7l/wheel/pisces
2020-12-14T20:58:48,153   copying build/lib/pisces/config.json -> build/bdist.linux-armv7l/wheel/pisces
2020-12-14T20:58:48,158   copying build/lib/pisces/cli.py -> build/bdist.linux-armv7l/wheel/pisces
2020-12-14T20:58:48,165   creating build/bdist.linux-armv7l/wheel/pisces/scripts
2020-12-14T20:58:48,167   copying build/lib/pisces/scripts/.DS_Store -> build/bdist.linux-armv7l/wheel/pisces/scripts
2020-12-14T20:58:48,172   copying build/lib/pisces/scripts/create_sample_sets_stripped.py -> build/bdist.linux-armv7l/wheel/pisces/scripts
2020-12-14T20:58:48,180   copying build/lib/pisces/scripts/kmer_counts_to_fingerprint_strand_and_pcthuman.py -> build/bdist.linux-armv7l/wheel/pisces/scripts
2020-12-14T20:58:48,188   copying build/lib/pisces/.DS_Store -> build/bdist.linux-armv7l/wheel/pisces
2020-12-14T20:58:48,198   creating build/bdist.linux-armv7l/wheel/pisces/R
2020-12-14T20:58:48,200   copying build/lib/pisces/R/.Rprofile -> build/bdist.linux-armv7l/wheel/pisces/R
2020-12-14T20:58:48,207   copying build/lib/pisces/R/make_expression_matrix.R -> build/bdist.linux-armv7l/wheel/pisces/R
2020-12-14T20:58:48,218   creating build/bdist.linux-armv7l/wheel/pisces/R/renv
2020-12-14T20:58:48,221   copying build/lib/pisces/R/renv/activate.R -> build/bdist.linux-armv7l/wheel/pisces/R/renv
2020-12-14T20:58:48,228   copying build/lib/pisces/R/.DS_Store -> build/bdist.linux-armv7l/wheel/pisces/R
2020-12-14T20:58:48,235   copying build/lib/pisces/R/.gitignore -> build/bdist.linux-armv7l/wheel/pisces/R
2020-12-14T20:58:48,240   copying build/lib/pisces/R/set_up_dependencies.R -> build/bdist.linux-armv7l/wheel/pisces/R
2020-12-14T20:58:48,247   creating build/bdist.linux-armv7l/wheel/pisces/tests
2020-12-14T20:58:48,250   copying build/lib/pisces/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/pisces/tests
2020-12-14T20:58:48,257   creating build/bdist.linux-armv7l/wheel/pisces/data
2020-12-14T20:58:48,260   copying build/lib/pisces/data/fp_kmers.txt -> build/bdist.linux-armv7l/wheel/pisces/data
2020-12-14T20:58:48,272   copying build/lib/pisces/data/fp_kmers_col1.txt -> build/bdist.linux-armv7l/wheel/pisces/data
2020-12-14T20:58:48,281   copying build/lib/pisces/qc.py -> build/bdist.linux-armv7l/wheel/pisces
2020-12-14T20:58:48,287   copying build/lib/pisces/run.py -> build/bdist.linux-armv7l/wheel/pisces
2020-12-14T20:58:48,294   copying build/lib/pisces/submit.py -> build/bdist.linux-armv7l/wheel/pisces
2020-12-14T20:58:48,301   copying build/lib/pisces/index.py -> build/bdist.linux-armv7l/wheel/pisces
2020-12-14T20:58:48,309   copying build/lib/pisces/__init__.py -> build/bdist.linux-armv7l/wheel/pisces
2020-12-14T20:58:48,316   copying build/lib/pisces/fastq.py -> build/bdist.linux-armv7l/wheel/pisces
2020-12-14T20:58:48,323   running install_egg_info
2020-12-14T20:58:48,331   Copying novartis_pisces.egg-info to build/bdist.linux-armv7l/wheel/novartis_pisces-0.1.3.1-py3.5.egg-info
2020-12-14T20:58:48,365   running install_scripts
2020-12-14T20:58:48,940   Installing salmon
2020-12-14T20:59:16,642   creating build/bdist.linux-armv7l/wheel/novartis_pisces-0.1.3.1.dist-info/WHEEL
2020-12-14T20:59:17,022   Building wheel for novartis-pisces (setup.py): finished with status 'done'
2020-12-14T20:59:17,029   Created wheel for novartis-pisces: filename=novartis_pisces-0.1.3.1-py3-none-any.whl size=59130 sha256=01160ead2aa7f47bfe8a6b47b1989993ec6cc55701d98eb00b283a7dd2c005a0
2020-12-14T20:59:17,030   Stored in directory: /tmp/pip-ephem-wheel-cache-ig1t071r/wheels/8a/24/e6/c87556988457be5501b3cf691d264459ec96ab2d49c256a133
2020-12-14T20:59:17,034 Successfully built novartis-pisces
2020-12-14T20:59:17,051 Removed build tracker: '/tmp/pip-req-tracker-i3p061rx'