2021-07-15T23:16:28,616 Created temporary directory: /tmp/pip-ephem-wheel-cache-9s61m2x6 2021-07-15T23:16:28,619 Created temporary directory: /tmp/pip-req-tracker-kt9_s8mc 2021-07-15T23:16:28,619 Initialized build tracking at /tmp/pip-req-tracker-kt9_s8mc 2021-07-15T23:16:28,619 Created build tracker: /tmp/pip-req-tracker-kt9_s8mc 2021-07-15T23:16:28,619 Entered build tracker: /tmp/pip-req-tracker-kt9_s8mc 2021-07-15T23:16:28,620 Created temporary directory: /tmp/pip-wheel-bqgco5o0 2021-07-15T23:16:28,649 1 location(s) to search for versions of mikado: 2021-07-15T23:16:28,649 * https://pypi.org/simple/mikado/ 2021-07-15T23:16:28,650 Fetching project page and analyzing links: https://pypi.org/simple/mikado/ 2021-07-15T23:16:28,650 Getting page https://pypi.org/simple/mikado/ 2021-07-15T23:16:28,652 Found index url https://pypi.org/simple 2021-07-15T23:16:28,751 Found link https://files.pythonhosted.org/packages/e0/9f/c6c5da77e4164c37427bc069d92e83c8269cdf779a43501403ae837a24b3/Mikado-1.0.0b5.post1.tar.gz#sha256=a0e3b57aaec61721c4288cade4cf5386aa069710cc947faaecbae6e3eddb6be6 (from https://pypi.org/simple/mikado/), version: 1.0.0b5.post1 2021-07-15T23:16:28,752 Found link https://files.pythonhosted.org/packages/8f/6c/ee9884cd930db5bfbee812ad1592a32127edbedf01cf28713eda06d5a9b1/Mikado-1.0.0b9.tar.gz#sha256=7d69a3202ee654421d1ef78b9ddabb2c60c2b830454406205c9bf253cc7c5f59 (from https://pypi.org/simple/mikado/), version: 1.0.0b9 2021-07-15T23:16:28,752 Found link https://files.pythonhosted.org/packages/7d/c9/edc669907250923ca1113fa140d1965eb25691f57aaff891642d34aaf217/Mikado-1.0.0b10.tar.gz#sha256=6062fa4c50cc8726f2fb1a37e202478142708b97fcc60d5bb33d3eaa1896d7ab (from https://pypi.org/simple/mikado/), version: 1.0.0b10 2021-07-15T23:16:28,752 Found link https://files.pythonhosted.org/packages/69/15/3551e2856f041aefdd1505656aa8af26b1af04f8e1b4c0448f133724e1f4/Mikado-1.0.tar.gz#sha256=7c4ffaf359f7a0f509f1670c0bd8c9bcd3ed84ade45df15aa55a636021280ac4 (from https://pypi.org/simple/mikado/), version: 1.0 2021-07-15T23:16:28,753 Found link https://files.pythonhosted.org/packages/c2/b9/41d0a6f2ebad5eab5bc183beca8de854b4187266c6674ae6da0d86053f63/Mikado-1.1.tar.gz#sha256=aca1a822799de45494b56a0a2bf66e7eac49eb25cde6642f5da7aeb6515e573e (from https://pypi.org/simple/mikado/), version: 1.1 2021-07-15T23:16:28,753 Found link https://files.pythonhosted.org/packages/40/3d/1158abded48d747b982a77c1badd0d718a174470cdecde82a313f3eb9d4f/Mikado-1.2.tar.gz#sha256=43b2734aee61c437fd6d2c8645e10c1a9f723fa60505e3065bfea1f4a771e44e (from https://pypi.org/simple/mikado/), version: 1.2 2021-07-15T23:16:28,753 Found link https://files.pythonhosted.org/packages/9a/07/5d0790de2c40a36826ac078bf4f7bf62e1fd5848411a784e7eef9fd673c4/Mikado-1.2.1.tar.gz#sha256=3ce7626bfe43a0753ea7a9bcfc1c47ecb59e6616efd2bb0cfe7d373b9bec22c0 (from https://pypi.org/simple/mikado/), version: 1.2.1 2021-07-15T23:16:28,754 Found link https://files.pythonhosted.org/packages/35/a8/73f0dfa3062e3744b27ba7dd4c0bfc6af9b23da38c4c0ce8c7d5b27b0757/Mikado-1.2.2.tar.gz#sha256=5bd12d1563dc85f369f002cfbcc8023b9df71094547fa68589a6339da8688e08 (from https://pypi.org/simple/mikado/), version: 1.2.2 2021-07-15T23:16:28,771 Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_7_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f6/7f/d791fd6b5667bf18f4e167803a05fe5c389722ca954dea524259e08121e1/Mikado-1.2.4-cp36-cp36m-macosx_10_7_x86_64.whl#sha256=86046d7c1d80363ae0bdea8adbaa73a499d288c1540ed7b7ef6cf2df8db2b809 (from https://pypi.org/simple/mikado/) 2021-07-15T23:16:28,772 Found link https://files.pythonhosted.org/packages/fc/2d/cc88561deaa5c1b4425855cd821253c68353ed787c7c63dc0f4ea155927e/Mikado-1.2.4.tar.gz#sha256=c0485dba3b7c285599809e058c83f33b5efa9522d20d9f980423410604207f61 (from https://pypi.org/simple/mikado/), version: 1.2.4 2021-07-15T23:16:28,772 Found link https://files.pythonhosted.org/packages/36/12/08d60892041a13f4bd13a486fb510844a8ed99961df828e7509e394904e6/Mikado-2.0rc1.tar.gz#sha256=745ffb74e62d1d1e777f1b6fc84acb8aae2f27290d40301fec0971560e6ba054 (from https://pypi.org/simple/mikado/), version: 2.0rc1 2021-07-15T23:16:28,772 Found link https://files.pythonhosted.org/packages/ba/bf/b9a01f43d67eacafe2deea77708497e8523b9cbc9c08d1da4bade64fdb99/Mikado-2.0rc2.tar.gz#sha256=3cbf2465f9e42dc7a02f8c4aff8625e5421010e3df7a6b3f98d87e82f5534e26 (from https://pypi.org/simple/mikado/), version: 2.0rc2 2021-07-15T23:16:28,773 Found link https://files.pythonhosted.org/packages/86/6d/f8b099f9637b38fd94c3f164f2c996765b579d2eae62cda48a04f108edb1/Mikado-2.0.tar.gz#sha256=f4736adb1014c70758f12904bf7dfe10e153b9497bdb82903d231540a23b8d57 (from https://pypi.org/simple/mikado/) (requires-python:>=3.6), version: 2.0 2021-07-15T23:16:28,773 Found link https://files.pythonhosted.org/packages/2e/33/25f4ffb7a3fb20eb2d68ebbb4547dc7c2a26f6c5576a29cca8ba3981a753/Mikado-2.0.1.tar.gz#sha256=d77bf5ca843d8cea35208c52750d014d704d46889633d5ac0f12edba6b5aa131 (from https://pypi.org/simple/mikado/) (requires-python:>=3.6), version: 2.0.1 2021-07-15T23:16:28,774 Found link https://files.pythonhosted.org/packages/3a/6e/c589e961b797498aa99fe23634edda75166679cd2a381b0354a2d1d7b46f/Mikado-2.0.2.tar.gz#sha256=6c58ccab055f95cdbb0fb0273397ce72186ff7d99fd5ba4bdeb812ea4c18f1a6 (from https://pypi.org/simple/mikado/) (requires-python:>=3.6), version: 2.0.2 2021-07-15T23:16:28,775 Found link https://files.pythonhosted.org/packages/96/ff/815427acc6fb277fe387f6bf7509ad8e374be65f557bbf1f8c7741b21e02/Mikado-2.1.0.tar.gz#sha256=b8ca7cecead9e30430de2c205e65c961b3d704d9351b85d6108577f9ffaba58f (from https://pypi.org/simple/mikado/) (requires-python:>=3.6), version: 2.1.0 2021-07-15T23:16:28,775 Found link https://files.pythonhosted.org/packages/13/49/571306c6f821dc029a1cb70472498bd9d25525d126f2084798a774f9e4ce/Mikado-2.1.1.tar.gz#sha256=2107de041d57cac81b1ff52da2b1d029f6c66f7fde78adc66cfbafd57a5215b7 (from https://pypi.org/simple/mikado/) (requires-python:>=3.6), version: 2.1.1 2021-07-15T23:16:28,776 Found link https://files.pythonhosted.org/packages/88/25/93f4d40e98702547602916000e9e8dee101c4e072c29306fcbf9cb6a0797/Mikado-2.2.0.tar.gz#sha256=0892dce8b07c655c63918933aaf4a47292bc5602f6be4b226756106c21c53177 (from https://pypi.org/simple/mikado/) (requires-python:>=3.6), version: 2.2.0 2021-07-15T23:16:28,776 Found link https://files.pythonhosted.org/packages/f5/4a/ea11bafcbd376966836c1a70d6500fc63839fe529e8d103df8771057750a/Mikado-2.2.1.tar.gz#sha256=2f8d410340e39b0fced63ee523391eae8f18751f3a0910de1cf1a27e1129d210 (from https://pypi.org/simple/mikado/) (requires-python:>=3.6), version: 2.2.1 2021-07-15T23:16:28,777 Found link https://files.pythonhosted.org/packages/d0/ba/88df54116a8a68de82bd668d6fa2189d4a26045b7e0437cdc50bfccf7002/Mikado-2.2.2.tar.gz#sha256=cb9705ff46b6e67279e27ac1836443782e128619b6ea78676364d11a097a21a9 (from https://pypi.org/simple/mikado/) (requires-python:>=3.6), version: 2.2.2 2021-07-15T23:16:28,777 Found link https://files.pythonhosted.org/packages/28/dd/dec1ae4c7519971dc80a780dde045fce221adffba00535e3ff26de7c29ba/Mikado-2.2.3.tar.gz#sha256=bdbdbdeb56bab4a4d633a0be36aea1aac3c025763a5d6721c98982ac1bd17bf9 (from https://pypi.org/simple/mikado/) (requires-python:>=3.6), version: 2.2.3 2021-07-15T23:16:28,778 Found link https://files.pythonhosted.org/packages/26/c2/021f128fc8733aa031191d140d26c992a0f62dbd0f974913c7245f208bcf/Mikado-2.2.4.tar.gz#sha256=d7eeecb13334dcfee2e8b484e3aa4c31990a7e1f1e0001cabe5a669ef7c9f433 (from https://pypi.org/simple/mikado/) (requires-python:>3.6), version: 2.2.4 2021-07-15T23:16:28,778 Found link https://files.pythonhosted.org/packages/30/57/69347e6f46b8845741045f2782a5f59bd1a650167bb6be3ddbd38c8c73c5/Mikado-2.2.5.tar.gz#sha256=ea10960477612dd0a387b2135ed76dbc23e2957b3241c8726559541b88b9ee2e (from https://pypi.org/simple/mikado/) (requires-python:>3.6), version: 2.2.5 2021-07-15T23:16:28,779 Found link https://files.pythonhosted.org/packages/09/d8/c98c1549bcbb7f37b93d69625d4228b6b6a29a0676e9dece16e3a6061ff6/Mikado-2.3.0.tar.gz#sha256=c785197f0b6e6f8597100a63181a0d39109bec914e9691a0a972a5244da5cd32 (from https://pypi.org/simple/mikado/) (requires-python:>3.6), version: 2.3.0 2021-07-15T23:16:28,779 Skipping link: not a file: https://pypi.org/simple/mikado/ 2021-07-15T23:16:28,786 Given no hashes to check 1 links for project 'mikado': discarding no candidates 2021-07-15T23:16:28,806 Collecting mikado==2.0rc2 2021-07-15T23:16:28,807 Created temporary directory: /tmp/pip-unpack-_6b3cmby 2021-07-15T23:16:28,847 Downloading Mikado-2.0rc2.tar.gz (22.9 MB) 2021-07-15T23:16:33,170 Added mikado==2.0rc2 from https://files.pythonhosted.org/packages/ba/bf/b9a01f43d67eacafe2deea77708497e8523b9cbc9c08d1da4bade64fdb99/Mikado-2.0rc2.tar.gz#sha256=3cbf2465f9e42dc7a02f8c4aff8625e5421010e3df7a6b3f98d87e82f5534e26 to build tracker '/tmp/pip-req-tracker-kt9_s8mc' 2021-07-15T23:16:33,171 Running setup.py (path:/tmp/pip-wheel-bqgco5o0/mikado_d9f9c51442764459a61d2555ff0903ff/setup.py) egg_info for package mikado 2021-07-15T23:16:33,172 Created temporary directory: /tmp/pip-pip-egg-info-d6wjblq5 2021-07-15T23:16:33,173 Running command python setup.py egg_info 2021-07-15T23:16:53,076 Compiling Mikado/utilities/intervaltree.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-15T23:16:53,077 Compiling Mikado/serializers/blast_serializer/btop_parser.pyx because it depends on /home/piwheels/.local/lib/python3.9/site-packages/numpy/__init__.pxd. 2021-07-15T23:16:53,077 Compiling Mikado/serializers/blast_serializer/aln_string_parser.pyx because it depends on /home/piwheels/.local/lib/python3.9/site-packages/numpy/__init__.pxd. 2021-07-15T23:16:53,077 [1/3] Cythonizing Mikado/serializers/blast_serializer/aln_string_parser.pyx 2021-07-15T23:16:53,077 [2/3] Cythonizing Mikado/serializers/blast_serializer/btop_parser.pyx 2021-07-15T23:16:53,077 [3/3] Cythonizing Mikado/utilities/intervaltree.pyx 2021-07-15T23:16:53,356 running egg_info 2021-07-15T23:16:53,358 creating /tmp/pip-pip-egg-info-d6wjblq5/Mikado.egg-info 2021-07-15T23:16:53,360 writing /tmp/pip-pip-egg-info-d6wjblq5/Mikado.egg-info/PKG-INFO 2021-07-15T23:16:53,363 writing dependency_links to /tmp/pip-pip-egg-info-d6wjblq5/Mikado.egg-info/dependency_links.txt 2021-07-15T23:16:53,365 writing entry points to /tmp/pip-pip-egg-info-d6wjblq5/Mikado.egg-info/entry_points.txt 2021-07-15T23:16:53,366 writing requirements to /tmp/pip-pip-egg-info-d6wjblq5/Mikado.egg-info/requires.txt 2021-07-15T23:16:53,367 writing top-level names to /tmp/pip-pip-egg-info-d6wjblq5/Mikado.egg-info/top_level.txt 2021-07-15T23:16:53,369 writing manifest file '/tmp/pip-pip-egg-info-d6wjblq5/Mikado.egg-info/SOURCES.txt' 2021-07-15T23:16:53,685 reading manifest file '/tmp/pip-pip-egg-info-d6wjblq5/Mikado.egg-info/SOURCES.txt' 2021-07-15T23:16:53,687 reading manifest template 'MANIFEST.in' 2021-07-15T23:16:53,999 warning: no previously-included files found matching 'util/analyse_metrics.py' 2021-07-15T23:16:54,000 warning: no previously-included files found matching 'util/create_model.py' 2021-07-15T23:16:54,001 warning: no previously-included files found matching 'util/self_training.py' 2021-07-15T23:16:54,503 warning: no previously-included files matching '*' found under directory 'docs/' 2021-07-15T23:16:54,503 adding license file 'AUTHORS' 2021-07-15T23:16:54,520 writing manifest file '/tmp/pip-pip-egg-info-d6wjblq5/Mikado.egg-info/SOURCES.txt' 2021-07-15T23:16:54,931 Source in /tmp/pip-wheel-bqgco5o0/mikado_d9f9c51442764459a61d2555ff0903ff has version 2.0rc2, which satisfies requirement mikado==2.0rc2 from https://files.pythonhosted.org/packages/ba/bf/b9a01f43d67eacafe2deea77708497e8523b9cbc9c08d1da4bade64fdb99/Mikado-2.0rc2.tar.gz#sha256=3cbf2465f9e42dc7a02f8c4aff8625e5421010e3df7a6b3f98d87e82f5534e26 2021-07-15T23:16:54,932 Removed mikado==2.0rc2 from https://files.pythonhosted.org/packages/ba/bf/b9a01f43d67eacafe2deea77708497e8523b9cbc9c08d1da4bade64fdb99/Mikado-2.0rc2.tar.gz#sha256=3cbf2465f9e42dc7a02f8c4aff8625e5421010e3df7a6b3f98d87e82f5534e26 from build tracker '/tmp/pip-req-tracker-kt9_s8mc' 2021-07-15T23:16:54,937 Created temporary directory: /tmp/pip-unpack-aucgbi_u 2021-07-15T23:16:54,937 Building wheels for collected packages: mikado 2021-07-15T23:16:54,941 Created temporary directory: /tmp/pip-wheel-3seelo5_ 2021-07-15T23:16:54,941 Building wheel for mikado (setup.py): started 2021-07-15T23:16:54,942 Destination directory: /tmp/pip-wheel-3seelo5_ 2021-07-15T23:16:54,942 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-bqgco5o0/mikado_d9f9c51442764459a61d2555ff0903ff/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-bqgco5o0/mikado_d9f9c51442764459a61d2555ff0903ff/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-3seelo5_ 2021-07-15T23:16:57,582 running bdist_wheel 2021-07-15T23:16:57,587 running build 2021-07-15T23:16:57,588 running build_py 2021-07-15T23:16:57,722 creating build 2021-07-15T23:16:57,722 creating build/lib.linux-armv7l-3.9 2021-07-15T23:16:57,723 creating build/lib.linux-armv7l-3.9/Mikado 2021-07-15T23:16:57,724 copying Mikado/version.py -> build/lib.linux-armv7l-3.9/Mikado 2021-07-15T23:16:57,726 copying Mikado/__init__.py -> build/lib.linux-armv7l-3.9/Mikado 2021-07-15T23:16:57,728 copying Mikado/exceptions.py -> build/lib.linux-armv7l-3.9/Mikado 2021-07-15T23:16:57,730 creating build/lib.linux-armv7l-3.9/Mikado/preparation 2021-07-15T23:16:57,731 copying Mikado/preparation/checking.py -> build/lib.linux-armv7l-3.9/Mikado/preparation 2021-07-15T23:16:57,733 copying Mikado/preparation/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/preparation 2021-07-15T23:16:57,735 copying Mikado/preparation/annotation_parser.py -> build/lib.linux-armv7l-3.9/Mikado/preparation 2021-07-15T23:16:57,738 copying Mikado/preparation/prepare.py -> build/lib.linux-armv7l-3.9/Mikado/preparation 2021-07-15T23:16:57,742 creating build/lib.linux-armv7l-3.9/Mikado/picking 2021-07-15T23:16:57,742 copying Mikado/picking/_merge_loci_utils.py -> build/lib.linux-armv7l-3.9/Mikado/picking 2021-07-15T23:16:57,745 copying Mikado/picking/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/picking 2021-07-15T23:16:57,747 copying Mikado/picking/_locus_single_printer.py -> build/lib.linux-armv7l-3.9/Mikado/picking 2021-07-15T23:16:57,749 copying Mikado/picking/loci_processer.py -> build/lib.linux-armv7l-3.9/Mikado/picking 2021-07-15T23:16:57,751 copying Mikado/picking/_locus_line_creator.py -> build/lib.linux-armv7l-3.9/Mikado/picking 2021-07-15T23:16:57,753 copying Mikado/picking/picker.py -> build/lib.linux-armv7l-3.9/Mikado/picking 2021-07-15T23:16:57,757 copying Mikado/picking/_loci_serialiser.py -> build/lib.linux-armv7l-3.9/Mikado/picking 2021-07-15T23:16:57,760 creating build/lib.linux-armv7l-3.9/Mikado/subprograms 2021-07-15T23:16:57,760 copying Mikado/subprograms/configure.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms 2021-07-15T23:16:57,763 copying Mikado/subprograms/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms 2021-07-15T23:16:57,765 copying Mikado/subprograms/pick.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms 2021-07-15T23:16:57,768 copying Mikado/subprograms/serialise.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms 2021-07-15T23:16:57,771 copying Mikado/subprograms/compare.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms 2021-07-15T23:16:57,773 copying Mikado/subprograms/__main__.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms 2021-07-15T23:16:57,775 copying Mikado/subprograms/prepare.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms 2021-07-15T23:16:57,779 creating build/lib.linux-armv7l-3.9/Mikado/loci 2021-07-15T23:16:57,780 copying Mikado/loci/monosublocusholder.py -> build/lib.linux-armv7l-3.9/Mikado/loci 2021-07-15T23:16:57,783 copying Mikado/loci/monosublocus.py -> build/lib.linux-armv7l-3.9/Mikado/loci 2021-07-15T23:16:57,785 copying Mikado/loci/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/loci 2021-07-15T23:16:57,787 copying Mikado/loci/excluded.py -> build/lib.linux-armv7l-3.9/Mikado/loci 2021-07-15T23:16:57,789 copying Mikado/loci/locus.py -> build/lib.linux-armv7l-3.9/Mikado/loci 2021-07-15T23:16:57,793 copying Mikado/loci/reference_gene.py -> build/lib.linux-armv7l-3.9/Mikado/loci 2021-07-15T23:16:57,796 copying Mikado/loci/abstractlocus.py -> build/lib.linux-armv7l-3.9/Mikado/loci 2021-07-15T23:16:57,801 copying Mikado/loci/superlocus.py -> build/lib.linux-armv7l-3.9/Mikado/loci 2021-07-15T23:16:57,805 copying Mikado/loci/sublocus.py -> build/lib.linux-armv7l-3.9/Mikado/loci 2021-07-15T23:16:57,808 creating build/lib.linux-armv7l-3.9/Mikado/transcripts 2021-07-15T23:16:57,809 copying Mikado/transcripts/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/transcripts 2021-07-15T23:16:57,811 copying Mikado/transcripts/transcript.py -> build/lib.linux-armv7l-3.9/Mikado/transcripts 2021-07-15T23:16:57,818 copying Mikado/transcripts/transcriptchecker.py -> build/lib.linux-armv7l-3.9/Mikado/transcripts 2021-07-15T23:16:57,821 copying Mikado/transcripts/clique_methods.py -> build/lib.linux-armv7l-3.9/Mikado/transcripts 2021-07-15T23:16:57,823 copying Mikado/transcripts/transcriptcomputer.py -> build/lib.linux-armv7l-3.9/Mikado/transcripts 2021-07-15T23:16:57,826 creating build/lib.linux-armv7l-3.9/Mikado/daijin 2021-07-15T23:16:57,827 copying Mikado/daijin/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/daijin 2021-07-15T23:16:57,833 creating build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,834 copying Mikado/tests/parser_test.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,837 copying Mikado/tests/test_transcript_checker.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,840 copying Mikado/tests/test_invalid_orfs.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,842 copying Mikado/tests/test_json.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,845 copying Mikado/tests/test_blast_related.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,847 copying Mikado/tests/test_transcript_positive.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,851 copying Mikado/tests/prepare_misc_test.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,853 copying Mikado/tests/test_modifications.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,856 copying Mikado/tests/test_splitting.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,859 copying Mikado/tests/test_serialise_junctions.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,862 copying Mikado/tests/test_scores.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,865 copying Mikado/tests/test_transcript_methods.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,868 copying Mikado/tests/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,870 copying Mikado/tests/test_metrics.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,873 copying Mikado/tests/locus_test.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,882 copying Mikado/tests/test_configurators.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,884 copying Mikado/tests/test_transcript_single.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,888 copying Mikado/tests/test_db_utils.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,890 copying Mikado/tests/test_utils.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,892 copying Mikado/tests/test_clique_methods.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,893 copying Mikado/tests/test_transcript_negative.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,897 copying Mikado/tests/test_gene.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,898 copying Mikado/tests/test_bed12.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,901 copying Mikado/tests/test_external_scores.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,903 copying Mikado/tests/orf_test.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,906 copying Mikado/tests/test_system_calls.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,913 copying Mikado/tests/utilities_test.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,915 copying Mikado/tests/intervaltree_test.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,918 copying Mikado/tests/test_serialise_external.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,919 copying Mikado/tests/assigner_test.py -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:57,924 creating build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:16:57,925 copying Mikado/utilities/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:16:57,927 copying Mikado/utilities/dbutils.py -> build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:16:57,929 copying Mikado/utilities/file_type.py -> build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:16:57,931 copying Mikado/utilities/log_utils.py -> build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:16:57,934 creating build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:16:57,935 copying Mikado/scales/accountant.py -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:16:57,939 copying Mikado/scales/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:16:57,941 copying Mikado/scales/assigner.py -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:16:57,945 copying Mikado/scales/compare.py -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:16:57,948 copying Mikado/scales/resultstorer.py -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:16:57,951 copying Mikado/scales/gene_dict.py -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:16:57,953 copying Mikado/scales/class_codes.py -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:16:57,957 creating build/lib.linux-armv7l-3.9/Mikado/configuration 2021-07-15T23:16:57,957 copying Mikado/configuration/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/configuration 2021-07-15T23:16:57,960 copying Mikado/configuration/daijin_configurator.py -> build/lib.linux-armv7l-3.9/Mikado/configuration 2021-07-15T23:16:57,962 copying Mikado/configuration/configurator.py -> build/lib.linux-armv7l-3.9/Mikado/configuration 2021-07-15T23:16:57,966 creating build/lib.linux-armv7l-3.9/Mikado/serializers 2021-07-15T23:16:57,967 copying Mikado/serializers/junction.py -> build/lib.linux-armv7l-3.9/Mikado/serializers 2021-07-15T23:16:57,970 copying Mikado/serializers/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/serializers 2021-07-15T23:16:57,971 copying Mikado/serializers/external.py -> build/lib.linux-armv7l-3.9/Mikado/serializers 2021-07-15T23:16:57,974 copying Mikado/serializers/orf.py -> build/lib.linux-armv7l-3.9/Mikado/serializers 2021-07-15T23:16:57,978 creating build/lib.linux-armv7l-3.9/Mikado/parsers 2021-07-15T23:16:57,978 copying Mikado/parsers/GTF.py -> build/lib.linux-armv7l-3.9/Mikado/parsers 2021-07-15T23:16:57,981 copying Mikado/parsers/GFF.py -> build/lib.linux-armv7l-3.9/Mikado/parsers 2021-07-15T23:16:57,984 copying Mikado/parsers/blast_utils.py -> build/lib.linux-armv7l-3.9/Mikado/parsers 2021-07-15T23:16:57,986 copying Mikado/parsers/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/parsers 2021-07-15T23:16:57,988 copying Mikado/parsers/gfannotation.py -> build/lib.linux-armv7l-3.9/Mikado/parsers 2021-07-15T23:16:57,991 copying Mikado/parsers/bed12.py -> build/lib.linux-armv7l-3.9/Mikado/parsers 2021-07-15T23:16:57,996 copying Mikado/parsers/bam_parser.py -> build/lib.linux-armv7l-3.9/Mikado/parsers 2021-07-15T23:16:57,998 creating build/lib.linux-armv7l-3.9/Mikado/subprograms/util 2021-07-15T23:16:57,999 copying Mikado/subprograms/util/stats.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms/util 2021-07-15T23:16:58,002 copying Mikado/subprograms/util/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms/util 2021-07-15T23:16:58,004 copying Mikado/subprograms/util/trim.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms/util 2021-07-15T23:16:58,007 copying Mikado/subprograms/util/awk_gtf.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms/util 2021-07-15T23:16:58,009 copying Mikado/subprograms/util/grep.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms/util 2021-07-15T23:16:58,011 copying Mikado/subprograms/util/metrics.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms/util 2021-07-15T23:16:58,013 copying Mikado/subprograms/util/convert.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms/util 2021-07-15T23:16:58,015 copying Mikado/subprograms/util/class_codes.py -> build/lib.linux-armv7l-3.9/Mikado/subprograms/util 2021-07-15T23:16:58,018 creating build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods 2021-07-15T23:16:58,019 copying Mikado/transcripts/transcript_methods/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods 2021-07-15T23:16:58,021 copying Mikado/transcripts/transcript_methods/finalizing.py -> build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods 2021-07-15T23:16:58,024 copying Mikado/transcripts/transcript_methods/printing.py -> build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods 2021-07-15T23:16:58,027 copying Mikado/transcripts/transcript_methods/retrieval.py -> build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods 2021-07-15T23:16:58,030 copying Mikado/transcripts/transcript_methods/splitting.py -> build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods 2021-07-15T23:16:58,034 creating build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,035 copying Mikado/serializers/blast_serializer/xml_utils.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,038 copying Mikado/serializers/blast_serializer/__init__.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,040 copying Mikado/serializers/blast_serializer/blast_serialiser.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,043 copying Mikado/serializers/blast_serializer/hsp.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,045 copying Mikado/serializers/blast_serializer/utils.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,047 copying Mikado/serializers/blast_serializer/query.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,049 copying Mikado/serializers/blast_serializer/xml_serialiser.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,052 copying Mikado/serializers/blast_serializer/tabular_utils.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,055 copying Mikado/serializers/blast_serializer/tab_serialiser.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,056 copying Mikado/serializers/blast_serializer/target.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,058 copying Mikado/serializers/blast_serializer/hit.py -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:16:58,061 running egg_info 2021-07-15T23:16:58,076 writing Mikado.egg-info/PKG-INFO 2021-07-15T23:16:58,078 writing dependency_links to Mikado.egg-info/dependency_links.txt 2021-07-15T23:16:58,080 writing entry points to Mikado.egg-info/entry_points.txt 2021-07-15T23:16:58,082 writing requirements to Mikado.egg-info/requires.txt 2021-07-15T23:16:58,083 writing top-level names to Mikado.egg-info/top_level.txt 2021-07-15T23:16:58,103 reading manifest file 'Mikado.egg-info/SOURCES.txt' 2021-07-15T23:16:58,114 reading manifest template 'MANIFEST.in' 2021-07-15T23:16:58,410 warning: no previously-included files found matching 'util/analyse_metrics.py' 2021-07-15T23:16:58,411 warning: no previously-included files found matching 'util/create_model.py' 2021-07-15T23:16:58,413 warning: no previously-included files found matching 'util/self_training.py' 2021-07-15T23:16:58,927 warning: no previously-included files matching '*' found under directory 'docs/' 2021-07-15T23:16:58,927 adding license file 'AUTHORS' 2021-07-15T23:16:58,949 writing manifest file 'Mikado.egg-info/SOURCES.txt' 2021-07-15T23:16:58,973 copying Mikado/daijin/assemble.smk -> build/lib.linux-armv7l-3.9/Mikado/daijin 2021-07-15T23:16:58,976 copying Mikado/daijin/example_config.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin 2021-07-15T23:16:58,979 copying Mikado/daijin/hpc.json -> build/lib.linux-armv7l-3.9/Mikado/daijin 2021-07-15T23:16:58,981 copying Mikado/daijin/hpc.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin 2021-07-15T23:16:58,983 copying Mikado/daijin/mikado.smk -> build/lib.linux-armv7l-3.9/Mikado/daijin 2021-07-15T23:16:58,986 creating build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:58,986 copying Mikado/daijin/envs/blast.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:58,989 copying Mikado/daijin/envs/cufflinks.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:58,991 copying Mikado/daijin/envs/diamond.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:58,993 copying Mikado/daijin/envs/gmap.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:58,999 copying Mikado/daijin/envs/gnuplot.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,001 copying Mikado/daijin/envs/hisat2.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,004 copying Mikado/daijin/envs/portcullis.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,006 copying Mikado/daijin/envs/prodigal.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,008 copying Mikado/daijin/envs/samtools.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,010 copying Mikado/daijin/envs/scallop.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,012 copying Mikado/daijin/envs/star.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,015 copying Mikado/daijin/envs/stringtie.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,017 copying Mikado/daijin/envs/tophat2.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,020 copying Mikado/daijin/envs/transdecoder.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,022 copying Mikado/daijin/envs/trinity.yaml -> build/lib.linux-armv7l-3.9/Mikado/daijin/envs 2021-07-15T23:16:59,025 copying Mikado/tests/Chrysemys_picta_bellii_problematic.gff3 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,027 copying Mikado/tests/Chrysemys_picta_bellii_problematic.list.txt -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,030 copying Mikado/tests/Chrysemys_picta_bellii_problematic.txt -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,032 copying Mikado/tests/annotation.gff3 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,035 copying Mikado/tests/annotation.gff3.stats -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,037 copying Mikado/tests/cds_test_1.gtf -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,039 copying Mikado/tests/cds_test_2.gtf -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,042 copying Mikado/tests/check_seed.gtf -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,045 copying Mikado/tests/check_seed.yaml -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,048 copying Mikado/tests/chr5.fas.gz -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,218 copying Mikado/tests/chr5.fas.gz.fai -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,220 copying Mikado/tests/chr5.fas.gz.gzi -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,223 copying Mikado/tests/chunk-001-proteins.xml.gz -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,227 copying Mikado/tests/complete_padding.bed12 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,229 copying Mikado/tests/configuration.yaml -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,232 copying Mikado/tests/cufflinks.gtf -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,235 copying Mikado/tests/cufflinks.no_transcript.gtf -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,238 copying Mikado/tests/genome.fai -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,240 copying Mikado/tests/gtf_check.gtf.gz -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,243 copying Mikado/tests/junctions.bed -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,247 copying Mikado/tests/mikado.blast.asn.gz -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,256 copying Mikado/tests/mikado.blast.xml -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,532 copying Mikado/tests/mikado.db -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,653 copying Mikado/tests/mikado_prepared.fasta -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,659 copying Mikado/tests/mikado_prepared.fasta.fai -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,661 copying Mikado/tests/mikado_prepared.gtf -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,665 copying Mikado/tests/neg_pad.bed12 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,667 copying Mikado/tests/neg_pad.fa -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,671 copying Mikado/tests/neg_pad.fa.fai -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,673 copying Mikado/tests/pad_three_neg.bed12 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,676 copying Mikado/tests/pad_utr.bed12 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,679 copying Mikado/tests/padding_test.bed12 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,681 copying Mikado/tests/padding_test.fa -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,686 copying Mikado/tests/padding_test.fa.fai -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,689 copying Mikado/tests/padding_test.rev_compl.bed12 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,692 copying Mikado/tests/padding_test.rev_compl.fa -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,697 copying Mikado/tests/padding_test.rev_compl.fa.fai -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,699 copying Mikado/tests/phasing_padding.bed12 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,702 copying Mikado/tests/plants.suspicious_requirement.yaml -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,704 copying Mikado/tests/scoring_only_cds.yaml -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,707 copying Mikado/tests/test_mRNA.bam -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,714 copying Mikado/tests/test_truncated_cds.fa -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,717 copying Mikado/tests/test_truncated_cds.fa.fai -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,719 copying Mikado/tests/test_truncated_cds.gff3 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,722 copying Mikado/tests/transcripts.fasta.prodigal.gff3 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,726 copying Mikado/tests/trinity.bed12 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,729 copying Mikado/tests/trinity.cDNA_match.gff3 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,733 copying Mikado/tests/trinity.gff3 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,736 copying Mikado/tests/trinity.gtf -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,740 copying Mikado/tests/trinity.ids -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,742 copying Mikado/tests/trinity.match_matchpart.gff3 -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,746 copying Mikado/tests/trinity.minimap2.bam -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,749 copying Mikado/tests/trinity.no_transcript_feature.gtf -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,752 copying Mikado/tests/trinity_stats.txt -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,754 copying Mikado/tests/uniprot_sprot_plants.fasta.gz -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,895 copying Mikado/tests/uniprot_sprot_plants.fasta.gz.fai -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,921 copying Mikado/tests/uniprot_sprot_plants.fasta.gz.gzi -> build/lib.linux-armv7l-3.9/Mikado/tests 2021-07-15T23:16:59,924 creating build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,925 copying Mikado/tests/__pycache__/__init__.cpython-36.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,928 copying Mikado/tests/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,930 copying Mikado/tests/__pycache__/assigner_test.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,934 copying Mikado/tests/__pycache__/assigner_test.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,938 copying Mikado/tests/__pycache__/assigner_test.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,942 copying Mikado/tests/__pycache__/intervaltree_test.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,945 copying Mikado/tests/__pycache__/intervaltree_test.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,949 copying Mikado/tests/__pycache__/intervaltree_test.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,952 copying Mikado/tests/__pycache__/locus_test.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,959 copying Mikado/tests/__pycache__/locus_test.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,966 copying Mikado/tests/__pycache__/locus_test.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,972 copying Mikado/tests/__pycache__/orf_test.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,976 copying Mikado/tests/__pycache__/orf_test.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,979 copying Mikado/tests/__pycache__/orf_test.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,983 copying Mikado/tests/__pycache__/parser_test.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,987 copying Mikado/tests/__pycache__/prepare_misc_test.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,990 copying Mikado/tests/__pycache__/test_bed12.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,993 copying Mikado/tests/__pycache__/test_bed12.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:16:59,996 copying Mikado/tests/__pycache__/test_bed12.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,000 copying Mikado/tests/__pycache__/test_blast_related.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,003 copying Mikado/tests/__pycache__/test_blast_related.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,007 copying Mikado/tests/__pycache__/test_blast_related.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,010 copying Mikado/tests/__pycache__/test_clique_methods.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,013 copying Mikado/tests/__pycache__/test_clique_methods.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,016 copying Mikado/tests/__pycache__/test_clique_methods.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,018 copying Mikado/tests/__pycache__/test_configurators.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,021 copying Mikado/tests/__pycache__/test_db_utils.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,024 copying Mikado/tests/__pycache__/test_db_utils.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,027 copying Mikado/tests/__pycache__/test_db_utils.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,030 copying Mikado/tests/__pycache__/test_external_scores.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,033 copying Mikado/tests/__pycache__/test_external_scores.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,036 copying Mikado/tests/__pycache__/test_external_scores.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,044 copying Mikado/tests/__pycache__/test_gene.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,047 copying Mikado/tests/__pycache__/test_gene.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,050 copying Mikado/tests/__pycache__/test_gene.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,053 copying Mikado/tests/__pycache__/test_invalid_orfs.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,056 copying Mikado/tests/__pycache__/test_invalid_orfs.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,060 copying Mikado/tests/__pycache__/test_invalid_orfs.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,064 copying Mikado/tests/__pycache__/test_json.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,067 copying Mikado/tests/__pycache__/test_json.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,069 copying Mikado/tests/__pycache__/test_json.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,072 copying Mikado/tests/__pycache__/test_metrics.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,075 copying Mikado/tests/__pycache__/test_metrics.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,078 copying Mikado/tests/__pycache__/test_metrics.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,081 copying Mikado/tests/__pycache__/test_modifications.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,084 copying Mikado/tests/__pycache__/test_modifications.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,087 copying Mikado/tests/__pycache__/test_modifications.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,091 copying Mikado/tests/__pycache__/test_scores.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,094 copying Mikado/tests/__pycache__/test_scores.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,097 copying Mikado/tests/__pycache__/test_scores.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,101 copying Mikado/tests/__pycache__/test_serialise_external.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,104 copying Mikado/tests/__pycache__/test_serialise_junctions.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,107 copying Mikado/tests/__pycache__/test_serialise_junctions.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,110 copying Mikado/tests/__pycache__/test_serialise_junctions.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,114 copying Mikado/tests/__pycache__/test_splitting.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,117 copying Mikado/tests/__pycache__/test_splitting.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,121 copying Mikado/tests/__pycache__/test_splitting.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,124 copying Mikado/tests/__pycache__/test_system_calls.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,130 copying Mikado/tests/__pycache__/test_system_calls.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,135 copying Mikado/tests/__pycache__/test_system_calls.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,140 copying Mikado/tests/__pycache__/test_transcript_checker.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,145 copying Mikado/tests/__pycache__/test_transcript_checker.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,148 copying Mikado/tests/__pycache__/test_transcript_checker.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,152 copying Mikado/tests/__pycache__/test_transcript_methods.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,155 copying Mikado/tests/__pycache__/test_transcript_methods.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,159 copying Mikado/tests/__pycache__/test_transcript_methods.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,163 copying Mikado/tests/__pycache__/test_transcript_negative.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,167 copying Mikado/tests/__pycache__/test_transcript_negative.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,170 copying Mikado/tests/__pycache__/test_transcript_negative.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,174 copying Mikado/tests/__pycache__/test_transcript_positive.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,179 copying Mikado/tests/__pycache__/test_transcript_positive.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,183 copying Mikado/tests/__pycache__/test_transcript_positive.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,188 copying Mikado/tests/__pycache__/test_transcript_single.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,191 copying Mikado/tests/__pycache__/test_transcript_single.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,195 copying Mikado/tests/__pycache__/test_transcript_single.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,199 copying Mikado/tests/__pycache__/test_utils.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,202 copying Mikado/tests/__pycache__/test_utils.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,205 copying Mikado/tests/__pycache__/test_utils.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,207 copying Mikado/tests/__pycache__/utilities_test.cpython-36-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,211 copying Mikado/tests/__pycache__/utilities_test.cpython-37-pytest-5.4.1.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,214 copying Mikado/tests/__pycache__/utilities_test.cpython-37.pyc -> build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__ 2021-07-15T23:17:00,218 creating build/lib.linux-armv7l-3.9/Mikado/tests/blast_data 2021-07-15T23:17:00,219 copying Mikado/tests/blast_data/diamond.0.9.30.tsv.gz -> build/lib.linux-armv7l-3.9/Mikado/tests/blast_data 2021-07-15T23:17:00,223 copying Mikado/tests/blast_data/diamond.0.9.30.xml.gz -> build/lib.linux-armv7l-3.9/Mikado/tests/blast_data 2021-07-15T23:17:00,230 copying Mikado/tests/blast_data/transcripts.fasta -> build/lib.linux-armv7l-3.9/Mikado/tests/blast_data 2021-07-15T23:17:00,238 copying Mikado/tests/blast_data/transcripts.fasta.fai -> build/lib.linux-armv7l-3.9/Mikado/tests/blast_data 2021-07-15T23:17:00,241 creating build/lib.linux-armv7l-3.9/Mikado/tests/fusion_test 2021-07-15T23:17:00,242 copying Mikado/tests/fusion_test/fusion_test_pred.gtf -> build/lib.linux-armv7l-3.9/Mikado/tests/fusion_test 2021-07-15T23:17:00,245 copying Mikado/tests/fusion_test/fusion_test_ref.gff3 -> build/lib.linux-armv7l-3.9/Mikado/tests/fusion_test 2021-07-15T23:17:00,248 creating build/lib.linux-armv7l-3.9/Mikado/tests/test_external 2021-07-15T23:17:00,248 copying Mikado/tests/test_external/annotation_run1.metrics.testds.txt -> build/lib.linux-armv7l-3.9/Mikado/tests/test_external 2021-07-15T23:17:00,251 copying Mikado/tests/test_external/aphid.scoring.yaml -> build/lib.linux-armv7l-3.9/Mikado/tests/test_external 2021-07-15T23:17:00,254 copying Mikado/tests/test_external/mikado.configuration.testds.yaml -> build/lib.linux-armv7l-3.9/Mikado/tests/test_external 2021-07-15T23:17:00,257 copying Mikado/tests/test_external/mikado_prepared.testds.fasta -> build/lib.linux-armv7l-3.9/Mikado/tests/test_external 2021-07-15T23:17:00,260 copying Mikado/tests/test_external/mikado_prepared.testds.fasta.fai -> build/lib.linux-armv7l-3.9/Mikado/tests/test_external 2021-07-15T23:17:00,262 copying Mikado/utilities/intervaltree.cpp -> build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:17:00,286 copying Mikado/utilities/intervaltree.pxd -> build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:17:00,288 copying Mikado/utilities/intervaltree.pyx -> build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:17:00,292 copying Mikado/utilities/overlap.c -> build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:17:00,298 copying Mikado/utilities/overlap.pxd -> build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:17:00,300 copying Mikado/utilities/overlap.pyx -> build/lib.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:17:00,302 copying Mikado/scales/contrast.cpp -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:17:00,317 copying Mikado/scales/contrast.pxd -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:17:00,319 copying Mikado/scales/contrast.pyx -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:17:00,322 copying Mikado/scales/f1.c -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:17:00,329 copying Mikado/scales/f1.pxd -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:17:00,331 copying Mikado/scales/f1.pyx -> build/lib.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:17:00,333 copying Mikado/configuration/configuration_blueprint.json -> build/lib.linux-armv7l-3.9/Mikado/configuration 2021-07-15T23:17:00,336 copying Mikado/configuration/daijin_schema.json -> build/lib.linux-armv7l-3.9/Mikado/configuration 2021-07-15T23:17:00,339 copying Mikado/configuration/requirements_blueprint.json -> build/lib.linux-armv7l-3.9/Mikado/configuration 2021-07-15T23:17:00,341 copying Mikado/configuration/scoring_blueprint.json -> build/lib.linux-armv7l-3.9/Mikado/configuration 2021-07-15T23:17:00,343 creating build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files 2021-07-15T23:17:00,344 copying Mikado/configuration/scoring_files/mammalian.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files 2021-07-15T23:17:00,346 copying Mikado/configuration/scoring_files/plant.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files 2021-07-15T23:17:00,348 creating build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:17:00,349 copying Mikado/configuration/scoring_files/HISTORIC/athaliana_scoring.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:17:00,352 copying Mikado/configuration/scoring_files/HISTORIC/celegans_scoring.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:17:00,354 copying Mikado/configuration/scoring_files/HISTORIC/dmelanogaster_scoring.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:17:00,357 copying Mikado/configuration/scoring_files/HISTORIC/hsapiens_scoring.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:17:00,359 copying Mikado/configuration/scoring_files/HISTORIC/human.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:17:00,362 copying Mikado/configuration/scoring_files/HISTORIC/insects.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:17:00,364 copying Mikado/configuration/scoring_files/HISTORIC/plants.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:17:00,367 copying Mikado/configuration/scoring_files/HISTORIC/scerevisiae.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:17:00,369 copying Mikado/configuration/scoring_files/HISTORIC/worm.yaml -> build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:17:00,372 copying Mikado/serializers/blast_serializer/aln_string_parser.cpp -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:17:00,396 copying Mikado/serializers/blast_serializer/aln_string_parser.pyx -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:17:00,398 copying Mikado/serializers/blast_serializer/btop_parser.cpp -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:17:00,419 copying Mikado/serializers/blast_serializer/btop_parser.pxd -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:17:00,421 copying Mikado/serializers/blast_serializer/btop_parser.pyx -> build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:17:00,436 running build_ext 2021-07-15T23:17:00,439 building 'Mikado.utilities.overlap' extension 2021-07-15T23:17:00,527 C compiler: arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 2021-07-15T23:17:00,527 creating build/temp.linux-armv7l-3.9 2021-07-15T23:17:00,528 creating build/temp.linux-armv7l-3.9/Mikado 2021-07-15T23:17:00,528 creating build/temp.linux-armv7l-3.9/Mikado/utilities 2021-07-15T23:17:00,529 compile options: '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION -I/usr/include/python3.9 -c' 2021-07-15T23:17:00,529 arm-linux-gnueabihf-gcc: Mikado/utilities/overlap.c 2021-07-15T23:17:01,137 Mikado/utilities/overlap.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-15T23:17:01,138 Mikado/utilities/overlap.c:2860:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,139 2860 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,139 | ^ 2021-07-15T23:17:01,140 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,140 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,140 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,140 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:01,140 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:01,140 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,142 Mikado/utilities/overlap.c:2860:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,142 2860 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,142 | ^ 2021-07-15T23:17:01,143 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,143 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,143 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,143 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:01,143 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:01,143 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,145 Mikado/utilities/overlap.c:2860:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,145 2860 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,145 | ^ 2021-07-15T23:17:01,145 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,145 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,146 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,146 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:01,146 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:01,146 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,148 Mikado/utilities/overlap.c:2860:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,148 2860 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,148 | ^ 2021-07-15T23:17:01,148 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,148 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,148 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,148 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:01,149 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:01,149 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,150 Mikado/utilities/overlap.c:2860:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,150 2860 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,151 | ^ 2021-07-15T23:17:01,151 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,151 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,151 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,151 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:01,151 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:01,151 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,153 Mikado/utilities/overlap.c:2860:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,153 2860 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,153 | ^ 2021-07-15T23:17:01,153 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,154 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,154 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,154 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:01,154 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:01,154 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,156 Mikado/utilities/overlap.c:2876:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,157 2876 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,157 | ^ 2021-07-15T23:17:01,157 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,157 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,157 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,157 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:01,157 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:01,158 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,159 Mikado/utilities/overlap.c:2876:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,159 2876 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,159 | ^ 2021-07-15T23:17:01,160 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,160 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,160 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,160 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:01,160 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:01,160 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,162 Mikado/utilities/overlap.c:2876:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,162 2876 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,162 | ^ 2021-07-15T23:17:01,162 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,162 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,163 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,163 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:01,163 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:01,163 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,165 Mikado/utilities/overlap.c:2876:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,165 2876 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,165 | ^ 2021-07-15T23:17:01,165 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,165 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,165 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,165 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:01,165 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:01,166 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,167 Mikado/utilities/overlap.c:2876:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,167 2876 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,167 | ^ 2021-07-15T23:17:01,168 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,168 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,168 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,168 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:01,168 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:01,168 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:01,170 Mikado/utilities/overlap.c:2876:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:01,170 2876 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:01,170 | ^ 2021-07-15T23:17:01,170 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:01,170 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:01,171 from Mikado/utilities/overlap.c:22: 2021-07-15T23:17:01,171 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:01,171 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:01,171 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:02,942 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/Mikado/utilities/overlap.o -o build/lib.linux-armv7l-3.9/Mikado/utilities/overlap.cpython-39-arm-linux-gnueabihf.so 2021-07-15T23:17:03,070 building 'Mikado.scales.f1' extension 2021-07-15T23:17:03,070 C compiler: arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 2021-07-15T23:17:03,071 creating build/temp.linux-armv7l-3.9/Mikado/scales 2021-07-15T23:17:03,071 compile options: '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION -I/usr/include/python3.9 -c' 2021-07-15T23:17:03,072 arm-linux-gnueabihf-gcc: Mikado/scales/f1.c 2021-07-15T23:17:03,474 Mikado/scales/f1.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-15T23:17:03,475 Mikado/scales/f1.c:2699:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,475 2699 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,475 | ^ 2021-07-15T23:17:03,476 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,477 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,477 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,477 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:03,477 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:03,477 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,479 Mikado/scales/f1.c:2699:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,479 2699 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,479 | ^ 2021-07-15T23:17:03,479 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,479 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,479 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,479 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:03,480 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:03,480 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,481 Mikado/scales/f1.c:2699:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,481 2699 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,481 | ^ 2021-07-15T23:17:03,481 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,482 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,482 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,482 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:03,482 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:03,482 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,483 Mikado/scales/f1.c:2699:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,483 2699 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,483 | ^ 2021-07-15T23:17:03,483 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,483 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,483 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,483 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:03,483 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:03,483 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,484 Mikado/scales/f1.c:2699:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,484 2699 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,484 | ^ 2021-07-15T23:17:03,484 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,484 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,484 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,485 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:03,485 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:03,485 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,485 Mikado/scales/f1.c:2699:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,485 2699 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,486 | ^ 2021-07-15T23:17:03,486 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,486 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,486 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,486 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:03,486 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:03,486 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,487 Mikado/scales/f1.c:2715:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,487 2715 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,488 | ^ 2021-07-15T23:17:03,488 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,488 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,488 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,488 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:03,488 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:03,488 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,489 Mikado/scales/f1.c:2715:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,489 2715 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,489 | ^ 2021-07-15T23:17:03,489 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,489 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,489 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,489 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:03,490 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:03,490 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,490 Mikado/scales/f1.c:2715:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,490 2715 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,490 | ^ 2021-07-15T23:17:03,491 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,491 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,491 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,491 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:03,491 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:03,491 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,492 Mikado/scales/f1.c:2715:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,492 2715 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,492 | ^ 2021-07-15T23:17:03,492 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,492 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,492 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,492 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:03,492 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:03,493 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,493 Mikado/scales/f1.c:2715:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,493 2715 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,493 | ^ 2021-07-15T23:17:03,493 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,493 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,494 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,494 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:03,494 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:03,494 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:03,494 Mikado/scales/f1.c:2715:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:03,494 2715 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:03,495 | ^ 2021-07-15T23:17:03,495 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:03,495 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:03,495 from Mikado/scales/f1.c:22: 2021-07-15T23:17:03,495 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:03,495 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:03,495 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:04,777 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/Mikado/scales/f1.o -o build/lib.linux-armv7l-3.9/Mikado/scales/f1.cpython-39-arm-linux-gnueabihf.so 2021-07-15T23:17:04,894 building 'Mikado.scales.contrast' extension 2021-07-15T23:17:04,894 C compiler: arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 2021-07-15T23:17:04,895 compile options: '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION -I/usr/include/python3.9 -c' 2021-07-15T23:17:04,895 arm-linux-gnueabihf-gcc: Mikado/scales/contrast.cpp 2021-07-15T23:17:05,786 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T23:17:05,786 from /usr/include/python3.9/Python.h:97, 2021-07-15T23:17:05,786 from Mikado/scales/contrast.cpp:23: 2021-07-15T23:17:05,786 Mikado/scales/contrast.cpp: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’: 2021-07-15T23:17:05,787 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,787 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-15T23:17:05,787 | ^ 2021-07-15T23:17:05,787 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-15T23:17:05,787 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-15T23:17:05,787 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,787 Mikado/scales/contrast.cpp:9836:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,788 9836 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,788 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,788 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:05,788 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:05,788 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,788 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,788 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-15T23:17:05,789 | ^ 2021-07-15T23:17:05,789 Mikado/scales/contrast.cpp:9836:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,789 9836 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,789 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,789 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:05,789 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:05,789 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,789 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,790 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-15T23:17:05,790 | ^ 2021-07-15T23:17:05,790 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-15T23:17:05,790 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-15T23:17:05,790 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,790 Mikado/scales/contrast.cpp:9836:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,791 9836 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,791 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,791 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:05,791 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:05,791 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,791 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,791 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-15T23:17:05,791 | ^ 2021-07-15T23:17:05,792 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-15T23:17:05,792 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-15T23:17:05,792 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,792 Mikado/scales/contrast.cpp:9836:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,792 9836 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,792 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,792 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:05,793 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:05,793 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,793 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,793 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-15T23:17:05,793 | ^ 2021-07-15T23:17:05,793 Mikado/scales/contrast.cpp:9836:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,793 9836 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,793 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,794 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:05,794 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:05,794 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,794 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,794 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-15T23:17:05,794 | ^ 2021-07-15T23:17:05,794 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-15T23:17:05,794 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-15T23:17:05,795 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,795 Mikado/scales/contrast.cpp:9836:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,795 9836 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,795 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,795 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:05,795 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:05,795 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,796 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,796 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-15T23:17:05,796 | ^ 2021-07-15T23:17:05,796 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-15T23:17:05,796 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-15T23:17:05,796 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,796 Mikado/scales/contrast.cpp:9852:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,797 9852 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,797 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,797 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:05,797 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:05,797 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,797 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,797 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-15T23:17:05,797 | ^ 2021-07-15T23:17:05,798 Mikado/scales/contrast.cpp:9852:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,798 9852 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,798 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,798 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:05,798 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:05,798 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,798 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,798 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-15T23:17:05,799 | ^ 2021-07-15T23:17:05,799 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-15T23:17:05,799 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-15T23:17:05,799 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,799 Mikado/scales/contrast.cpp:9852:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,799 9852 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,799 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,799 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:05,800 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:05,800 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,800 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,800 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-15T23:17:05,800 | ^ 2021-07-15T23:17:05,800 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-15T23:17:05,800 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-15T23:17:05,801 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,801 Mikado/scales/contrast.cpp:9852:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,801 9852 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,801 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,801 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:05,801 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:05,801 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,801 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,802 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-15T23:17:05,802 | ^ 2021-07-15T23:17:05,802 Mikado/scales/contrast.cpp:9852:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,802 9852 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,802 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,802 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T23:17:05,802 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T23:17:05,802 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,803 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-15T23:17:05,803 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-15T23:17:05,803 | ^ 2021-07-15T23:17:05,803 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-15T23:17:05,803 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-15T23:17:05,803 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,803 Mikado/scales/contrast.cpp:9852:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-15T23:17:05,803 9852 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T23:17:05,804 | ^~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:05,804 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T23:17:05,804 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T23:17:05,804 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:19,865 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/Mikado/scales/contrast.o -o build/lib.linux-armv7l-3.9/Mikado/scales/contrast.cpython-39-arm-linux-gnueabihf.so 2021-07-15T23:17:20,065 building 'Mikado.utilities.intervaltree' extension 2021-07-15T23:17:20,065 C compiler: arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 2021-07-15T23:17:20,066 compile options: '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION -I/usr/include/python3.9 -c' 2021-07-15T23:17:20,066 arm-linux-gnueabihf-gcc: Mikado/utilities/intervaltree.cpp 2021-07-15T23:17:22,304 Mikado/utilities/intervaltree.cpp:10963:19: warning: ‘Py_ssize_t __pyx_pw_6Mikado_9utilities_12intervaltree_12IntervalTree_11__len__(PyObject*)’ defined but not used [-Wunused-function] 2021-07-15T23:17:22,305 10963 | static Py_ssize_t __pyx_pw_6Mikado_9utilities_12intervaltree_12IntervalTree_11__len__(PyObject *__pyx_v_self) { 2021-07-15T23:17:22,305 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T23:17:36,117 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/Mikado/utilities/intervaltree.o -o build/lib.linux-armv7l-3.9/Mikado/utilities/intervaltree.cpython-39-arm-linux-gnueabihf.so 2021-07-15T23:17:36,606 building 'Mikado.serializers.blast_serializer.btop_parser' extension 2021-07-15T23:17:36,607 C compiler: arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 2021-07-15T23:17:36,609 creating build/temp.linux-armv7l-3.9/Mikado/serializers 2021-07-15T23:17:36,609 creating build/temp.linux-armv7l-3.9/Mikado/serializers/blast_serializer 2021-07-15T23:17:36,611 compile options: '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c' 2021-07-15T23:17:36,612 arm-linux-gnueabihf-gcc: Mikado/serializers/blast_serializer/btop_parser.cpp 2021-07-15T23:17:51,290 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/Mikado/serializers/blast_serializer/btop_parser.o -o build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/btop_parser.cpython-39-arm-linux-gnueabihf.so 2021-07-15T23:17:51,689 building 'Mikado.serializers.blast_serializer.aln_string_parser' extension 2021-07-15T23:17:51,689 C compiler: arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 2021-07-15T23:17:51,690 compile options: '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c' 2021-07-15T23:17:51,690 arm-linux-gnueabihf-gcc: Mikado/serializers/blast_serializer/aln_string_parser.cpp 2021-07-15T23:18:07,518 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/Mikado/serializers/blast_serializer/aln_string_parser.o -o build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/aln_string_parser.cpython-39-arm-linux-gnueabihf.so 2021-07-15T23:18:07,877 running build_scripts 2021-07-15T23:18:07,878 creating build/scripts-3.9 2021-07-15T23:18:07,879 copying and adjusting util/bam2gtf.py -> build/scripts-3.9 2021-07-15T23:18:07,881 copying and adjusting util/convert_cdna_match_gff3.py -> build/scripts-3.9 2021-07-15T23:18:07,883 copying and adjusting util/remove_from_embl.py -> build/scripts-3.9 2021-07-15T23:18:07,884 copying and adjusting util/asm_collect.py -> build/scripts-3.9 2021-07-15T23:18:07,885 copying and adjusting util/gffjunc_to_bed12.py -> build/scripts-3.9 2021-07-15T23:18:07,887 copying and adjusting util/split_fasta.py -> build/scripts-3.9 2021-07-15T23:18:07,889 copying and adjusting util/getFastaFromIds.py -> build/scripts-3.9 2021-07-15T23:18:07,890 copying util/tease_maker_apart.py -> build/scripts-3.9 2021-07-15T23:18:07,893 copying and adjusting util/trim_long_introns.py -> build/scripts-3.9 2021-07-15T23:18:07,895 copying and adjusting util/sanitize_blast_db.py -> build/scripts-3.9 2021-07-15T23:18:07,896 copying and adjusting util/grep.py -> build/scripts-3.9 2021-07-15T23:18:07,898 copying and adjusting util/calculate_distances.py -> build/scripts-3.9 2021-07-15T23:18:07,899 copying and adjusting util/remove_utrs.py -> build/scripts-3.9 2021-07-15T23:18:07,901 copying and adjusting util/merge_junction_bed12.py -> build/scripts-3.9 2021-07-15T23:18:07,903 copying and adjusting util/class_run.py -> build/scripts-3.9 2021-07-15T23:18:07,905 copying and adjusting util/add_transcript_feature_to_gtf.py -> build/scripts-3.9 2021-07-15T23:18:07,907 copying and adjusting util/extract_promoter_regions.py -> build/scripts-3.9 2021-07-15T23:18:07,909 copying and adjusting util/align_collect.py -> build/scripts-3.9 2021-07-15T23:18:07,910 changing mode of build/scripts-3.9/bam2gtf.py from 644 to 755 2021-07-15T23:18:07,910 changing mode of build/scripts-3.9/convert_cdna_match_gff3.py from 644 to 755 2021-07-15T23:18:07,911 changing mode of build/scripts-3.9/remove_from_embl.py from 644 to 755 2021-07-15T23:18:07,911 changing mode of build/scripts-3.9/asm_collect.py from 644 to 755 2021-07-15T23:18:07,911 changing mode of build/scripts-3.9/gffjunc_to_bed12.py from 644 to 755 2021-07-15T23:18:07,912 changing mode of build/scripts-3.9/split_fasta.py from 644 to 755 2021-07-15T23:18:07,912 changing mode of build/scripts-3.9/getFastaFromIds.py from 644 to 755 2021-07-15T23:18:07,912 changing mode of build/scripts-3.9/trim_long_introns.py from 644 to 755 2021-07-15T23:18:07,913 changing mode of build/scripts-3.9/sanitize_blast_db.py from 644 to 755 2021-07-15T23:18:07,913 changing mode of build/scripts-3.9/grep.py from 644 to 755 2021-07-15T23:18:07,913 changing mode of build/scripts-3.9/calculate_distances.py from 644 to 755 2021-07-15T23:18:07,913 changing mode of build/scripts-3.9/remove_utrs.py from 644 to 755 2021-07-15T23:18:07,914 changing mode of build/scripts-3.9/merge_junction_bed12.py from 644 to 755 2021-07-15T23:18:07,914 changing mode of build/scripts-3.9/class_run.py from 644 to 755 2021-07-15T23:18:07,914 changing mode of build/scripts-3.9/add_transcript_feature_to_gtf.py from 644 to 755 2021-07-15T23:18:07,915 changing mode of build/scripts-3.9/extract_promoter_regions.py from 644 to 755 2021-07-15T23:18:07,915 changing mode of build/scripts-3.9/align_collect.py from 644 to 755 2021-07-15T23:18:07,920 installing to build/bdist.linux-armv7l/wheel 2021-07-15T23:18:07,920 running install 2021-07-15T23:18:07,921 running install_lib 2021-07-15T23:18:07,927 creating build/bdist.linux-armv7l 2021-07-15T23:18:07,927 creating build/bdist.linux-armv7l/wheel 2021-07-15T23:18:07,929 creating build/bdist.linux-armv7l/wheel/Mikado 2021-07-15T23:18:07,930 copying build/lib.linux-armv7l-3.9/Mikado/version.py -> build/bdist.linux-armv7l/wheel/Mikado 2021-07-15T23:18:07,933 creating build/bdist.linux-armv7l/wheel/Mikado/preparation 2021-07-15T23:18:07,934 copying build/lib.linux-armv7l-3.9/Mikado/preparation/checking.py -> build/bdist.linux-armv7l/wheel/Mikado/preparation 2021-07-15T23:18:07,936 copying build/lib.linux-armv7l-3.9/Mikado/preparation/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/preparation 2021-07-15T23:18:07,938 copying build/lib.linux-armv7l-3.9/Mikado/preparation/annotation_parser.py -> build/bdist.linux-armv7l/wheel/Mikado/preparation 2021-07-15T23:18:07,942 copying build/lib.linux-armv7l-3.9/Mikado/preparation/prepare.py -> build/bdist.linux-armv7l/wheel/Mikado/preparation 2021-07-15T23:18:07,945 copying build/lib.linux-armv7l-3.9/Mikado/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado 2021-07-15T23:18:07,948 creating build/bdist.linux-armv7l/wheel/Mikado/picking 2021-07-15T23:18:07,949 copying build/lib.linux-armv7l-3.9/Mikado/picking/_merge_loci_utils.py -> build/bdist.linux-armv7l/wheel/Mikado/picking 2021-07-15T23:18:07,951 copying build/lib.linux-armv7l-3.9/Mikado/picking/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/picking 2021-07-15T23:18:07,953 copying build/lib.linux-armv7l-3.9/Mikado/picking/_locus_single_printer.py -> build/bdist.linux-armv7l/wheel/Mikado/picking 2021-07-15T23:18:07,955 copying build/lib.linux-armv7l-3.9/Mikado/picking/loci_processer.py -> build/bdist.linux-armv7l/wheel/Mikado/picking 2021-07-15T23:18:07,958 copying build/lib.linux-armv7l-3.9/Mikado/picking/_locus_line_creator.py -> build/bdist.linux-armv7l/wheel/Mikado/picking 2021-07-15T23:18:07,959 copying build/lib.linux-armv7l-3.9/Mikado/picking/picker.py -> build/bdist.linux-armv7l/wheel/Mikado/picking 2021-07-15T23:18:07,963 copying build/lib.linux-armv7l-3.9/Mikado/picking/_loci_serialiser.py -> build/bdist.linux-armv7l/wheel/Mikado/picking 2021-07-15T23:18:07,966 creating build/bdist.linux-armv7l/wheel/Mikado/subprograms 2021-07-15T23:18:07,967 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/configure.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms 2021-07-15T23:18:07,970 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms 2021-07-15T23:18:07,972 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/pick.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms 2021-07-15T23:18:07,975 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/serialise.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms 2021-07-15T23:18:07,978 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/compare.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms 2021-07-15T23:18:07,981 creating build/bdist.linux-armv7l/wheel/Mikado/subprograms/util 2021-07-15T23:18:07,982 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/util/stats.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms/util 2021-07-15T23:18:07,985 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/util/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms/util 2021-07-15T23:18:07,987 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/util/trim.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms/util 2021-07-15T23:18:07,990 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/util/awk_gtf.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms/util 2021-07-15T23:18:07,992 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/util/grep.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms/util 2021-07-15T23:18:07,994 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/util/metrics.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms/util 2021-07-15T23:18:07,997 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/util/convert.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms/util 2021-07-15T23:18:07,999 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/util/class_codes.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms/util 2021-07-15T23:18:08,001 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/__main__.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms 2021-07-15T23:18:08,003 copying build/lib.linux-armv7l-3.9/Mikado/subprograms/prepare.py -> build/bdist.linux-armv7l/wheel/Mikado/subprograms 2021-07-15T23:18:08,006 creating build/bdist.linux-armv7l/wheel/Mikado/loci 2021-07-15T23:18:08,007 copying build/lib.linux-armv7l-3.9/Mikado/loci/monosublocusholder.py -> build/bdist.linux-armv7l/wheel/Mikado/loci 2021-07-15T23:18:08,011 copying build/lib.linux-armv7l-3.9/Mikado/loci/monosublocus.py -> build/bdist.linux-armv7l/wheel/Mikado/loci 2021-07-15T23:18:08,013 copying build/lib.linux-armv7l-3.9/Mikado/loci/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/loci 2021-07-15T23:18:08,015 copying build/lib.linux-armv7l-3.9/Mikado/loci/excluded.py -> build/bdist.linux-armv7l/wheel/Mikado/loci 2021-07-15T23:18:08,017 copying build/lib.linux-armv7l-3.9/Mikado/loci/locus.py -> build/bdist.linux-armv7l/wheel/Mikado/loci 2021-07-15T23:18:08,021 copying build/lib.linux-armv7l-3.9/Mikado/loci/reference_gene.py -> build/bdist.linux-armv7l/wheel/Mikado/loci 2021-07-15T23:18:08,024 copying build/lib.linux-armv7l-3.9/Mikado/loci/abstractlocus.py -> build/bdist.linux-armv7l/wheel/Mikado/loci 2021-07-15T23:18:08,028 copying build/lib.linux-armv7l-3.9/Mikado/loci/superlocus.py -> build/bdist.linux-armv7l/wheel/Mikado/loci 2021-07-15T23:18:08,032 copying build/lib.linux-armv7l-3.9/Mikado/loci/sublocus.py -> build/bdist.linux-armv7l/wheel/Mikado/loci 2021-07-15T23:18:08,035 creating build/bdist.linux-armv7l/wheel/Mikado/transcripts 2021-07-15T23:18:08,037 creating build/bdist.linux-armv7l/wheel/Mikado/transcripts/transcript_methods 2021-07-15T23:18:08,038 copying build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/transcripts/transcript_methods 2021-07-15T23:18:08,040 copying build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods/finalizing.py -> build/bdist.linux-armv7l/wheel/Mikado/transcripts/transcript_methods 2021-07-15T23:18:08,043 copying build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods/printing.py -> build/bdist.linux-armv7l/wheel/Mikado/transcripts/transcript_methods 2021-07-15T23:18:08,046 copying build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods/retrieval.py -> build/bdist.linux-armv7l/wheel/Mikado/transcripts/transcript_methods 2021-07-15T23:18:08,049 copying build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript_methods/splitting.py -> build/bdist.linux-armv7l/wheel/Mikado/transcripts/transcript_methods 2021-07-15T23:18:08,052 copying build/lib.linux-armv7l-3.9/Mikado/transcripts/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/transcripts 2021-07-15T23:18:08,054 copying build/lib.linux-armv7l-3.9/Mikado/transcripts/transcript.py -> build/bdist.linux-armv7l/wheel/Mikado/transcripts 2021-07-15T23:18:08,060 copying build/lib.linux-armv7l-3.9/Mikado/transcripts/transcriptchecker.py -> build/bdist.linux-armv7l/wheel/Mikado/transcripts 2021-07-15T23:18:08,063 copying build/lib.linux-armv7l-3.9/Mikado/transcripts/clique_methods.py -> build/bdist.linux-armv7l/wheel/Mikado/transcripts 2021-07-15T23:18:08,065 copying build/lib.linux-armv7l-3.9/Mikado/transcripts/transcriptcomputer.py -> build/bdist.linux-armv7l/wheel/Mikado/transcripts 2021-07-15T23:18:08,067 creating build/bdist.linux-armv7l/wheel/Mikado/daijin 2021-07-15T23:18:08,068 copying build/lib.linux-armv7l-3.9/Mikado/daijin/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/daijin 2021-07-15T23:18:08,072 creating build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,073 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/diamond.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,075 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/hisat2.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,077 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/prodigal.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,078 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/cufflinks.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,080 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/gnuplot.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,082 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/star.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,084 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/tophat2.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,086 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/blast.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,088 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/gmap.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,091 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/samtools.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,093 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/stringtie.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,095 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/portcullis.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,097 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/trinity.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,099 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/transdecoder.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,101 copying build/lib.linux-armv7l-3.9/Mikado/daijin/envs/scallop.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin/envs 2021-07-15T23:18:08,102 copying build/lib.linux-armv7l-3.9/Mikado/daijin/hpc.json -> build/bdist.linux-armv7l/wheel/Mikado/daijin 2021-07-15T23:18:08,104 copying build/lib.linux-armv7l-3.9/Mikado/daijin/example_config.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin 2021-07-15T23:18:08,107 copying build/lib.linux-armv7l-3.9/Mikado/daijin/assemble.smk -> build/bdist.linux-armv7l/wheel/Mikado/daijin 2021-07-15T23:18:08,111 copying build/lib.linux-armv7l-3.9/Mikado/daijin/mikado.smk -> build/bdist.linux-armv7l/wheel/Mikado/daijin 2021-07-15T23:18:08,113 copying build/lib.linux-armv7l-3.9/Mikado/daijin/hpc.yaml -> build/bdist.linux-armv7l/wheel/Mikado/daijin 2021-07-15T23:18:08,115 copying build/lib.linux-armv7l-3.9/Mikado/exceptions.py -> build/bdist.linux-armv7l/wheel/Mikado 2021-07-15T23:18:08,120 creating build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,121 copying build/lib.linux-armv7l-3.9/Mikado/tests/mikado_prepared.fasta -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,128 copying build/lib.linux-armv7l-3.9/Mikado/tests/parser_test.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,131 copying build/lib.linux-armv7l-3.9/Mikado/tests/uniprot_sprot_plants.fasta.gz.fai -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,164 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_transcript_checker.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,166 copying build/lib.linux-armv7l-3.9/Mikado/tests/mikado_prepared.gtf -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,171 copying build/lib.linux-armv7l-3.9/Mikado/tests/scoring_only_cds.yaml -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,173 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_invalid_orfs.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,175 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_json.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,177 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_blast_related.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,180 copying build/lib.linux-armv7l-3.9/Mikado/tests/chr5.fas.gz.gzi -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,182 copying build/lib.linux-armv7l-3.9/Mikado/tests/padding_test.fa.fai -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,184 copying build/lib.linux-armv7l-3.9/Mikado/tests/gtf_check.gtf.gz -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,187 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_transcript_positive.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,191 copying build/lib.linux-armv7l-3.9/Mikado/tests/prepare_misc_test.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,194 copying build/lib.linux-armv7l-3.9/Mikado/tests/mikado.blast.xml -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,564 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_modifications.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,566 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_splitting.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,569 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_serialise_junctions.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,572 copying build/lib.linux-armv7l-3.9/Mikado/tests/transcripts.fasta.prodigal.gff3 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,575 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_scores.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,577 copying build/lib.linux-armv7l-3.9/Mikado/tests/padding_test.bed12 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,580 copying build/lib.linux-armv7l-3.9/Mikado/tests/genome.fai -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,582 creating build/bdist.linux-armv7l/wheel/Mikado/tests/test_external 2021-07-15T23:18:08,584 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_external/annotation_run1.metrics.testds.txt -> build/bdist.linux-armv7l/wheel/Mikado/tests/test_external 2021-07-15T23:18:08,586 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_external/mikado_prepared.testds.fasta.fai -> build/bdist.linux-armv7l/wheel/Mikado/tests/test_external 2021-07-15T23:18:08,588 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_external/mikado_prepared.testds.fasta -> build/bdist.linux-armv7l/wheel/Mikado/tests/test_external 2021-07-15T23:18:08,591 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_external/aphid.scoring.yaml -> build/bdist.linux-armv7l/wheel/Mikado/tests/test_external 2021-07-15T23:18:08,595 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_external/mikado.configuration.testds.yaml -> build/bdist.linux-armv7l/wheel/Mikado/tests/test_external 2021-07-15T23:18:08,644 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_transcript_methods.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,650 copying build/lib.linux-armv7l-3.9/Mikado/tests/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,653 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_metrics.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,656 copying build/lib.linux-armv7l-3.9/Mikado/tests/neg_pad.fa -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,660 copying build/lib.linux-armv7l-3.9/Mikado/tests/cds_test_2.gtf -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,662 copying build/lib.linux-armv7l-3.9/Mikado/tests/complete_padding.bed12 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,664 copying build/lib.linux-armv7l-3.9/Mikado/tests/cds_test_1.gtf -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,666 copying build/lib.linux-armv7l-3.9/Mikado/tests/locus_test.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,675 copying build/lib.linux-armv7l-3.9/Mikado/tests/Chrysemys_picta_bellii_problematic.list.txt -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,676 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_configurators.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,678 copying build/lib.linux-armv7l-3.9/Mikado/tests/Chrysemys_picta_bellii_problematic.gff3 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,680 copying build/lib.linux-armv7l-3.9/Mikado/tests/trinity.ids -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,682 creating build/bdist.linux-armv7l/wheel/Mikado/tests/fusion_test 2021-07-15T23:18:08,683 copying build/lib.linux-armv7l-3.9/Mikado/tests/fusion_test/fusion_test_pred.gtf -> build/bdist.linux-armv7l/wheel/Mikado/tests/fusion_test 2021-07-15T23:18:08,685 copying build/lib.linux-armv7l-3.9/Mikado/tests/fusion_test/fusion_test_ref.gff3 -> build/bdist.linux-armv7l/wheel/Mikado/tests/fusion_test 2021-07-15T23:18:08,688 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_transcript_single.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,691 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_db_utils.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,693 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_utils.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,695 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_clique_methods.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,696 copying build/lib.linux-armv7l-3.9/Mikado/tests/mikado.blast.asn.gz -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,703 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_transcript_negative.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,706 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_truncated_cds.fa.fai -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,708 copying build/lib.linux-armv7l-3.9/Mikado/tests/padding_test.rev_compl.bed12 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,710 copying build/lib.linux-armv7l-3.9/Mikado/tests/pad_three_neg.bed12 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,712 copying build/lib.linux-armv7l-3.9/Mikado/tests/trinity.no_transcript_feature.gtf -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,714 copying build/lib.linux-armv7l-3.9/Mikado/tests/trinity_stats.txt -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,716 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_gene.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,718 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_bed12.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,721 copying build/lib.linux-armv7l-3.9/Mikado/tests/cufflinks.gtf -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,723 copying build/lib.linux-armv7l-3.9/Mikado/tests/neg_pad.fa.fai -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,726 copying build/lib.linux-armv7l-3.9/Mikado/tests/trinity.bed12 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,728 copying build/lib.linux-armv7l-3.9/Mikado/tests/padding_test.fa -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,732 copying build/lib.linux-armv7l-3.9/Mikado/tests/mikado.db -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,867 copying build/lib.linux-armv7l-3.9/Mikado/tests/check_seed.yaml -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,869 copying build/lib.linux-armv7l-3.9/Mikado/tests/trinity.cDNA_match.gff3 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,871 copying build/lib.linux-armv7l-3.9/Mikado/tests/Chrysemys_picta_bellii_problematic.txt -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,873 copying build/lib.linux-armv7l-3.9/Mikado/tests/pad_utr.bed12 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,875 copying build/lib.linux-armv7l-3.9/Mikado/tests/trinity.gtf -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,877 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_external_scores.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,879 copying build/lib.linux-armv7l-3.9/Mikado/tests/orf_test.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:08,882 copying build/lib.linux-armv7l-3.9/Mikado/tests/chr5.fas.gz -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,053 creating build/bdist.linux-armv7l/wheel/Mikado/tests/blast_data 2021-07-15T23:18:09,054 copying build/lib.linux-armv7l-3.9/Mikado/tests/blast_data/diamond.0.9.30.xml.gz -> build/bdist.linux-armv7l/wheel/Mikado/tests/blast_data 2021-07-15T23:18:09,059 copying build/lib.linux-armv7l-3.9/Mikado/tests/blast_data/diamond.0.9.30.tsv.gz -> build/bdist.linux-armv7l/wheel/Mikado/tests/blast_data 2021-07-15T23:18:09,062 copying build/lib.linux-armv7l-3.9/Mikado/tests/blast_data/transcripts.fasta -> build/bdist.linux-armv7l/wheel/Mikado/tests/blast_data 2021-07-15T23:18:09,068 copying build/lib.linux-armv7l-3.9/Mikado/tests/blast_data/transcripts.fasta.fai -> build/bdist.linux-armv7l/wheel/Mikado/tests/blast_data 2021-07-15T23:18:09,070 copying build/lib.linux-armv7l-3.9/Mikado/tests/chunk-001-proteins.xml.gz -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,073 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_system_calls.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,079 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_truncated_cds.fa -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,081 copying build/lib.linux-armv7l-3.9/Mikado/tests/uniprot_sprot_plants.fasta.gz.gzi -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,084 copying build/lib.linux-armv7l-3.9/Mikado/tests/utilities_test.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,086 copying build/lib.linux-armv7l-3.9/Mikado/tests/padding_test.rev_compl.fa.fai -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,088 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_mRNA.bam -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,093 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_truncated_cds.gff3 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,095 copying build/lib.linux-armv7l-3.9/Mikado/tests/trinity.minimap2.bam -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,097 copying build/lib.linux-armv7l-3.9/Mikado/tests/phasing_padding.bed12 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,099 copying build/lib.linux-armv7l-3.9/Mikado/tests/intervaltree_test.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,102 copying build/lib.linux-armv7l-3.9/Mikado/tests/junctions.bed -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,105 copying build/lib.linux-armv7l-3.9/Mikado/tests/mikado_prepared.fasta.fai -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,107 copying build/lib.linux-armv7l-3.9/Mikado/tests/cufflinks.no_transcript.gtf -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,109 copying build/lib.linux-armv7l-3.9/Mikado/tests/test_serialise_external.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,111 copying build/lib.linux-armv7l-3.9/Mikado/tests/trinity.gff3 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,114 copying build/lib.linux-armv7l-3.9/Mikado/tests/plants.suspicious_requirement.yaml -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,119 creating build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,119 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_blast_related.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,122 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_negative.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,125 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/locus_test.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,131 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/intervaltree_test.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,134 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_external_scores.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,136 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_blast_related.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,138 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_metrics.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,140 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_external_scores.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,142 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_negative.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,145 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_json.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,148 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/intervaltree_test.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,150 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_db_utils.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,153 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_clique_methods.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,155 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_db_utils.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,158 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_positive.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,162 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/locus_test.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,168 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_utils.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,170 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/orf_test.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,173 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/assigner_test.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,177 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_db_utils.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,179 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_splitting.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,181 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/prepare_misc_test.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,184 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/orf_test.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,187 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/orf_test.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,190 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_splitting.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,193 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/utilities_test.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,196 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_methods.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,199 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_invalid_orfs.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,202 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_modifications.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,205 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_single.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,208 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/__init__.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,210 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_single.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,213 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/utilities_test.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,216 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/utilities_test.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,218 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_positive.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,224 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_gene.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,226 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/locus_test.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,232 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_serialise_junctions.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,248 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_invalid_orfs.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,253 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_modifications.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,256 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_utils.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,259 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_scores.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,265 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_single.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,270 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_bed12.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,278 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/__init__.cpython-36.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,282 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_modifications.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,284 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/intervaltree_test.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,287 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_external_scores.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,290 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/parser_test.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,293 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_checker.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,297 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_json.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,299 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_utils.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,302 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_json.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,304 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_positive.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,308 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_clique_methods.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,310 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_scores.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,313 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_splitting.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,316 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_checker.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,319 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_serialise_external.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,322 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_serialise_junctions.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,325 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_methods.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,328 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_clique_methods.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,330 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_scores.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,333 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_invalid_orfs.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,336 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_system_calls.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,340 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/assigner_test.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,344 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_bed12.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,346 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_gene.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,349 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_gene.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,351 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_bed12.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,354 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_configurators.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,356 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_checker.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,360 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/assigner_test.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,367 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_blast_related.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,370 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_serialise_junctions.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,373 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_metrics.cpython-36-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,375 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_system_calls.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,380 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_negative.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,384 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_system_calls.cpython-37-pytest-5.4.1.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,389 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_metrics.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,392 copying build/lib.linux-armv7l-3.9/Mikado/tests/__pycache__/test_transcript_methods.cpython-37.pyc -> build/bdist.linux-armv7l/wheel/Mikado/tests/__pycache__ 2021-07-15T23:18:09,396 copying build/lib.linux-armv7l-3.9/Mikado/tests/annotation.gff3.stats -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,398 copying build/lib.linux-armv7l-3.9/Mikado/tests/trinity.match_matchpart.gff3 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,401 copying build/lib.linux-armv7l-3.9/Mikado/tests/check_seed.gtf -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,404 copying build/lib.linux-armv7l-3.9/Mikado/tests/assigner_test.py -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,407 copying build/lib.linux-armv7l-3.9/Mikado/tests/annotation.gff3 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,409 copying build/lib.linux-armv7l-3.9/Mikado/tests/chr5.fas.gz.fai -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,412 copying build/lib.linux-armv7l-3.9/Mikado/tests/configuration.yaml -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,415 copying build/lib.linux-armv7l-3.9/Mikado/tests/uniprot_sprot_plants.fasta.gz -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,555 copying build/lib.linux-armv7l-3.9/Mikado/tests/neg_pad.bed12 -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,556 copying build/lib.linux-armv7l-3.9/Mikado/tests/padding_test.rev_compl.fa -> build/bdist.linux-armv7l/wheel/Mikado/tests 2021-07-15T23:18:09,561 creating build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,562 copying build/lib.linux-armv7l-3.9/Mikado/utilities/intervaltree.pxd -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,564 copying build/lib.linux-armv7l-3.9/Mikado/utilities/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,566 copying build/lib.linux-armv7l-3.9/Mikado/utilities/overlap.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,572 copying build/lib.linux-armv7l-3.9/Mikado/utilities/dbutils.py -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,574 copying build/lib.linux-armv7l-3.9/Mikado/utilities/intervaltree.cpp -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,599 copying build/lib.linux-armv7l-3.9/Mikado/utilities/overlap.pyx -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,601 copying build/lib.linux-armv7l-3.9/Mikado/utilities/overlap.c -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,607 copying build/lib.linux-armv7l-3.9/Mikado/utilities/file_type.py -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,609 copying build/lib.linux-armv7l-3.9/Mikado/utilities/overlap.pxd -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,611 copying build/lib.linux-armv7l-3.9/Mikado/utilities/log_utils.py -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,612 copying build/lib.linux-armv7l-3.9/Mikado/utilities/intervaltree.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,637 copying build/lib.linux-armv7l-3.9/Mikado/utilities/intervaltree.pyx -> build/bdist.linux-armv7l/wheel/Mikado/utilities 2021-07-15T23:18:09,641 creating build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,641 copying build/lib.linux-armv7l-3.9/Mikado/scales/f1.pxd -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,643 copying build/lib.linux-armv7l-3.9/Mikado/scales/accountant.py -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,647 copying build/lib.linux-armv7l-3.9/Mikado/scales/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,648 copying build/lib.linux-armv7l-3.9/Mikado/scales/contrast.cpp -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,661 copying build/lib.linux-armv7l-3.9/Mikado/scales/f1.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,665 copying build/lib.linux-armv7l-3.9/Mikado/scales/assigner.py -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,669 copying build/lib.linux-armv7l-3.9/Mikado/scales/contrast.pyx -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,672 copying build/lib.linux-armv7l-3.9/Mikado/scales/f1.c -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,677 copying build/lib.linux-armv7l-3.9/Mikado/scales/compare.py -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,680 copying build/lib.linux-armv7l-3.9/Mikado/scales/resultstorer.py -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,683 copying build/lib.linux-armv7l-3.9/Mikado/scales/gene_dict.py -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,685 copying build/lib.linux-armv7l-3.9/Mikado/scales/f1.pyx -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,687 copying build/lib.linux-armv7l-3.9/Mikado/scales/class_codes.py -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,690 copying build/lib.linux-armv7l-3.9/Mikado/scales/contrast.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,708 copying build/lib.linux-armv7l-3.9/Mikado/scales/contrast.pxd -> build/bdist.linux-armv7l/wheel/Mikado/scales 2021-07-15T23:18:09,711 creating build/bdist.linux-armv7l/wheel/Mikado/configuration 2021-07-15T23:18:09,712 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_blueprint.json -> build/bdist.linux-armv7l/wheel/Mikado/configuration 2021-07-15T23:18:09,714 copying build/lib.linux-armv7l-3.9/Mikado/configuration/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/configuration 2021-07-15T23:18:09,716 copying build/lib.linux-armv7l-3.9/Mikado/configuration/configuration_blueprint.json -> build/bdist.linux-armv7l/wheel/Mikado/configuration 2021-07-15T23:18:09,719 copying build/lib.linux-armv7l-3.9/Mikado/configuration/daijin_schema.json -> build/bdist.linux-armv7l/wheel/Mikado/configuration 2021-07-15T23:18:09,721 copying build/lib.linux-armv7l-3.9/Mikado/configuration/requirements_blueprint.json -> build/bdist.linux-armv7l/wheel/Mikado/configuration 2021-07-15T23:18:09,723 copying build/lib.linux-armv7l-3.9/Mikado/configuration/daijin_configurator.py -> build/bdist.linux-armv7l/wheel/Mikado/configuration 2021-07-15T23:18:09,726 copying build/lib.linux-armv7l-3.9/Mikado/configuration/configurator.py -> build/bdist.linux-armv7l/wheel/Mikado/configuration 2021-07-15T23:18:09,729 creating build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files 2021-07-15T23:18:09,730 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/plant.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files 2021-07-15T23:18:09,733 creating build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:18:09,734 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC/dmelanogaster_scoring.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:18:09,737 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC/hsapiens_scoring.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:18:09,739 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC/plants.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:18:09,741 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC/human.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:18:09,743 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC/insects.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:18:09,745 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC/scerevisiae.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:18:09,747 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC/worm.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:18:09,749 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC/athaliana_scoring.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:18:09,751 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/HISTORIC/celegans_scoring.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files/HISTORIC 2021-07-15T23:18:09,753 copying build/lib.linux-armv7l-3.9/Mikado/configuration/scoring_files/mammalian.yaml -> build/bdist.linux-armv7l/wheel/Mikado/configuration/scoring_files 2021-07-15T23:18:09,756 creating build/bdist.linux-armv7l/wheel/Mikado/serializers 2021-07-15T23:18:09,757 copying build/lib.linux-armv7l-3.9/Mikado/serializers/junction.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers 2021-07-15T23:18:09,761 creating build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,762 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/aln_string_parser.pyx -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,764 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/xml_utils.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,766 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,768 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/blast_serialiser.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,771 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/hsp.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,774 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/btop_parser.pyx -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,776 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/utils.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,778 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/btop_parser.pxd -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,780 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/query.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,782 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/btop_parser.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,811 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/btop_parser.cpp -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,831 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/aln_string_parser.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,855 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/xml_serialiser.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,858 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/tabular_utils.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,860 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/tab_serialiser.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,862 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/target.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,864 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/hit.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,867 copying build/lib.linux-armv7l-3.9/Mikado/serializers/blast_serializer/aln_string_parser.cpp -> build/bdist.linux-armv7l/wheel/Mikado/serializers/blast_serializer 2021-07-15T23:18:09,895 copying build/lib.linux-armv7l-3.9/Mikado/serializers/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers 2021-07-15T23:18:09,896 copying build/lib.linux-armv7l-3.9/Mikado/serializers/external.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers 2021-07-15T23:18:09,899 copying build/lib.linux-armv7l-3.9/Mikado/serializers/orf.py -> build/bdist.linux-armv7l/wheel/Mikado/serializers 2021-07-15T23:18:09,902 creating build/bdist.linux-armv7l/wheel/Mikado/parsers 2021-07-15T23:18:09,903 copying build/lib.linux-armv7l-3.9/Mikado/parsers/GTF.py -> build/bdist.linux-armv7l/wheel/Mikado/parsers 2021-07-15T23:18:09,905 copying build/lib.linux-armv7l-3.9/Mikado/parsers/GFF.py -> build/bdist.linux-armv7l/wheel/Mikado/parsers 2021-07-15T23:18:09,908 copying build/lib.linux-armv7l-3.9/Mikado/parsers/blast_utils.py -> build/bdist.linux-armv7l/wheel/Mikado/parsers 2021-07-15T23:18:09,910 copying build/lib.linux-armv7l-3.9/Mikado/parsers/__init__.py -> build/bdist.linux-armv7l/wheel/Mikado/parsers 2021-07-15T23:18:09,913 copying build/lib.linux-armv7l-3.9/Mikado/parsers/gfannotation.py -> build/bdist.linux-armv7l/wheel/Mikado/parsers 2021-07-15T23:18:09,916 copying build/lib.linux-armv7l-3.9/Mikado/parsers/bed12.py -> build/bdist.linux-armv7l/wheel/Mikado/parsers 2021-07-15T23:18:09,920 copying build/lib.linux-armv7l-3.9/Mikado/parsers/bam_parser.py -> build/bdist.linux-armv7l/wheel/Mikado/parsers 2021-07-15T23:18:09,922 running install_egg_info 2021-07-15T23:18:09,925 Copying Mikado.egg-info to build/bdist.linux-armv7l/wheel/Mikado-2.0rc2-py3.9.egg-info 2021-07-15T23:18:09,943 running install_scripts 2021-07-15T23:18:09,944 creating build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data 2021-07-15T23:18:09,945 creating build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,946 copying build/scripts-3.9/bam2gtf.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,948 copying build/scripts-3.9/convert_cdna_match_gff3.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,950 copying build/scripts-3.9/remove_from_embl.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,952 copying build/scripts-3.9/asm_collect.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,954 copying build/scripts-3.9/gffjunc_to_bed12.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,956 copying build/scripts-3.9/split_fasta.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,958 copying build/scripts-3.9/getFastaFromIds.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,961 copying build/scripts-3.9/tease_maker_apart.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,963 copying build/scripts-3.9/trim_long_introns.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,965 copying build/scripts-3.9/sanitize_blast_db.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,967 copying build/scripts-3.9/grep.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,969 copying build/scripts-3.9/calculate_distances.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,972 copying build/scripts-3.9/remove_utrs.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,974 copying build/scripts-3.9/merge_junction_bed12.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,976 copying build/scripts-3.9/class_run.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,979 copying build/scripts-3.9/add_transcript_feature_to_gtf.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,981 copying build/scripts-3.9/extract_promoter_regions.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,984 copying build/scripts-3.9/align_collect.py -> build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts 2021-07-15T23:18:09,985 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/bam2gtf.py to 755 2021-07-15T23:18:09,986 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/convert_cdna_match_gff3.py to 755 2021-07-15T23:18:09,986 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/remove_from_embl.py to 755 2021-07-15T23:18:09,986 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/asm_collect.py to 755 2021-07-15T23:18:09,987 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/gffjunc_to_bed12.py to 755 2021-07-15T23:18:09,987 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/split_fasta.py to 755 2021-07-15T23:18:09,987 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/getFastaFromIds.py to 755 2021-07-15T23:18:09,987 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/tease_maker_apart.py to 755 2021-07-15T23:18:09,988 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/trim_long_introns.py to 755 2021-07-15T23:18:09,988 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/sanitize_blast_db.py to 755 2021-07-15T23:18:09,988 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/grep.py to 755 2021-07-15T23:18:09,989 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/calculate_distances.py to 755 2021-07-15T23:18:09,989 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/remove_utrs.py to 755 2021-07-15T23:18:09,989 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/merge_junction_bed12.py to 755 2021-07-15T23:18:09,990 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/class_run.py to 755 2021-07-15T23:18:09,990 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/add_transcript_feature_to_gtf.py to 755 2021-07-15T23:18:09,990 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/extract_promoter_regions.py to 755 2021-07-15T23:18:09,991 changing mode of build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.data/scripts/align_collect.py to 755 2021-07-15T23:18:10,049 adding license file "AUTHORS" (matched pattern "AUTHORS*") 2021-07-15T23:18:10,053 creating build/bdist.linux-armv7l/wheel/Mikado-2.0rc2.dist-info/WHEEL 2021-07-15T23:18:10,056 creating '/tmp/pip-wheel-3seelo5_/Mikado-2.0rc2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-15T23:18:10,060 adding 'Mikado/__init__.py' 2021-07-15T23:18:10,061 adding 'Mikado/exceptions.py' 2021-07-15T23:18:10,062 adding 'Mikado/version.py' 2021-07-15T23:18:10,066 adding 'Mikado/configuration/__init__.py' 2021-07-15T23:18:10,070 adding 'Mikado/configuration/configuration_blueprint.json' 2021-07-15T23:18:10,074 adding 'Mikado/configuration/configurator.py' 2021-07-15T23:18:10,076 adding 'Mikado/configuration/daijin_configurator.py' 2021-07-15T23:18:10,078 adding 'Mikado/configuration/daijin_schema.json' 2021-07-15T23:18:10,080 adding 'Mikado/configuration/requirements_blueprint.json' 2021-07-15T23:18:10,081 adding 'Mikado/configuration/scoring_blueprint.json' 2021-07-15T23:18:10,083 adding 'Mikado/configuration/scoring_files/mammalian.yaml' 2021-07-15T23:18:10,084 adding 'Mikado/configuration/scoring_files/plant.yaml' 2021-07-15T23:18:10,086 adding 'Mikado/configuration/scoring_files/HISTORIC/athaliana_scoring.yaml' 2021-07-15T23:18:10,087 adding 'Mikado/configuration/scoring_files/HISTORIC/celegans_scoring.yaml' 2021-07-15T23:18:10,089 adding 'Mikado/configuration/scoring_files/HISTORIC/dmelanogaster_scoring.yaml' 2021-07-15T23:18:10,090 adding 'Mikado/configuration/scoring_files/HISTORIC/hsapiens_scoring.yaml' 2021-07-15T23:18:10,092 adding 'Mikado/configuration/scoring_files/HISTORIC/human.yaml' 2021-07-15T23:18:10,093 adding 'Mikado/configuration/scoring_files/HISTORIC/insects.yaml' 2021-07-15T23:18:10,094 adding 'Mikado/configuration/scoring_files/HISTORIC/plants.yaml' 2021-07-15T23:18:10,095 adding 'Mikado/configuration/scoring_files/HISTORIC/scerevisiae.yaml' 2021-07-15T23:18:10,097 adding 'Mikado/configuration/scoring_files/HISTORIC/worm.yaml' 2021-07-15T23:18:10,101 adding 'Mikado/daijin/__init__.py' 2021-07-15T23:18:10,105 adding 'Mikado/daijin/assemble.smk' 2021-07-15T23:18:10,107 adding 'Mikado/daijin/example_config.yaml' 2021-07-15T23:18:10,109 adding 'Mikado/daijin/hpc.json' 2021-07-15T23:18:10,110 adding 'Mikado/daijin/hpc.yaml' 2021-07-15T23:18:10,112 adding 'Mikado/daijin/mikado.smk' 2021-07-15T23:18:10,114 adding 'Mikado/daijin/envs/blast.yaml' 2021-07-15T23:18:10,115 adding 'Mikado/daijin/envs/cufflinks.yaml' 2021-07-15T23:18:10,116 adding 'Mikado/daijin/envs/diamond.yaml' 2021-07-15T23:18:10,117 adding 'Mikado/daijin/envs/gmap.yaml' 2021-07-15T23:18:10,118 adding 'Mikado/daijin/envs/gnuplot.yaml' 2021-07-15T23:18:10,120 adding 'Mikado/daijin/envs/hisat2.yaml' 2021-07-15T23:18:10,121 adding 'Mikado/daijin/envs/portcullis.yaml' 2021-07-15T23:18:10,122 adding 'Mikado/daijin/envs/prodigal.yaml' 2021-07-15T23:18:10,123 adding 'Mikado/daijin/envs/samtools.yaml' 2021-07-15T23:18:10,124 adding 'Mikado/daijin/envs/scallop.yaml' 2021-07-15T23:18:10,125 adding 'Mikado/daijin/envs/star.yaml' 2021-07-15T23:18:10,126 adding 'Mikado/daijin/envs/stringtie.yaml' 2021-07-15T23:18:10,127 adding 'Mikado/daijin/envs/tophat2.yaml' 2021-07-15T23:18:10,128 adding 'Mikado/daijin/envs/transdecoder.yaml' 2021-07-15T23:18:10,129 adding 'Mikado/daijin/envs/trinity.yaml' 2021-07-15T23:18:10,131 adding 'Mikado/loci/__init__.py' 2021-07-15T23:18:10,141 adding 'Mikado/loci/abstractlocus.py' 2021-07-15T23:18:10,143 adding 'Mikado/loci/excluded.py' 2021-07-15T23:18:10,152 adding 'Mikado/loci/locus.py' 2021-07-15T23:18:10,154 adding 'Mikado/loci/monosublocus.py' 2021-07-15T23:18:10,157 adding 'Mikado/loci/monosublocusholder.py' 2021-07-15T23:18:10,160 adding 'Mikado/loci/reference_gene.py' 2021-07-15T23:18:10,162 adding 'Mikado/loci/sublocus.py' 2021-07-15T23:18:10,170 adding 'Mikado/loci/superlocus.py' 2021-07-15T23:18:10,173 adding 'Mikado/parsers/GFF.py' 2021-07-15T23:18:10,175 adding 'Mikado/parsers/GTF.py' 2021-07-15T23:18:10,176 adding 'Mikado/parsers/__init__.py' 2021-07-15T23:18:10,177 adding 'Mikado/parsers/bam_parser.py' 2021-07-15T23:18:10,185 adding 'Mikado/parsers/bed12.py' 2021-07-15T23:18:10,187 adding 'Mikado/parsers/blast_utils.py' 2021-07-15T23:18:10,189 adding 'Mikado/parsers/gfannotation.py' 2021-07-15T23:18:10,191 adding 'Mikado/picking/__init__.py' 2021-07-15T23:18:10,193 adding 'Mikado/picking/_loci_serialiser.py' 2021-07-15T23:18:10,194 adding 'Mikado/picking/_locus_line_creator.py' 2021-07-15T23:18:10,195 adding 'Mikado/picking/_locus_single_printer.py' 2021-07-15T23:18:10,197 adding 'Mikado/picking/_merge_loci_utils.py' 2021-07-15T23:18:10,200 adding 'Mikado/picking/loci_processer.py' 2021-07-15T23:18:10,206 adding 'Mikado/picking/picker.py' 2021-07-15T23:18:10,208 adding 'Mikado/preparation/__init__.py' 2021-07-15T23:18:10,211 adding 'Mikado/preparation/annotation_parser.py' 2021-07-15T23:18:10,214 adding 'Mikado/preparation/checking.py' 2021-07-15T23:18:10,217 adding 'Mikado/preparation/prepare.py' 2021-07-15T23:18:10,220 adding 'Mikado/scales/__init__.py' 2021-07-15T23:18:10,225 adding 'Mikado/scales/accountant.py' 2021-07-15T23:18:10,231 adding 'Mikado/scales/assigner.py' 2021-07-15T23:18:10,233 adding 'Mikado/scales/class_codes.py' 2021-07-15T23:18:10,238 adding 'Mikado/scales/compare.py' 2021-07-15T23:18:10,277 adding 'Mikado/scales/contrast.cpp' 2021-07-15T23:18:10,422 adding 'Mikado/scales/contrast.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T23:18:10,428 adding 'Mikado/scales/contrast.pxd' 2021-07-15T23:18:10,431 adding 'Mikado/scales/contrast.pyx' 2021-07-15T23:18:10,446 adding 'Mikado/scales/f1.c' 2021-07-15T23:18:10,467 adding 'Mikado/scales/f1.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T23:18:10,469 adding 'Mikado/scales/f1.pxd' 2021-07-15T23:18:10,470 adding 'Mikado/scales/f1.pyx' 2021-07-15T23:18:10,472 adding 'Mikado/scales/gene_dict.py' 2021-07-15T23:18:10,473 adding 'Mikado/scales/resultstorer.py' 2021-07-15T23:18:10,475 adding 'Mikado/serializers/__init__.py' 2021-07-15T23:18:10,477 adding 'Mikado/serializers/external.py' 2021-07-15T23:18:10,479 adding 'Mikado/serializers/junction.py' 2021-07-15T23:18:10,482 adding 'Mikado/serializers/orf.py' 2021-07-15T23:18:10,484 adding 'Mikado/serializers/blast_serializer/__init__.py' 2021-07-15T23:18:10,561 adding 'Mikado/serializers/blast_serializer/aln_string_parser.cpp' 2021-07-15T23:18:10,777 adding 'Mikado/serializers/blast_serializer/aln_string_parser.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T23:18:10,786 adding 'Mikado/serializers/blast_serializer/aln_string_parser.pyx' 2021-07-15T23:18:10,788 adding 'Mikado/serializers/blast_serializer/blast_serialiser.py' 2021-07-15T23:18:10,862 adding 'Mikado/serializers/blast_serializer/btop_parser.cpp' 2021-07-15T23:18:11,063 adding 'Mikado/serializers/blast_serializer/btop_parser.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T23:18:11,071 adding 'Mikado/serializers/blast_serializer/btop_parser.pxd' 2021-07-15T23:18:11,073 adding 'Mikado/serializers/blast_serializer/btop_parser.pyx' 2021-07-15T23:18:11,075 adding 'Mikado/serializers/blast_serializer/hit.py' 2021-07-15T23:18:11,077 adding 'Mikado/serializers/blast_serializer/hsp.py' 2021-07-15T23:18:11,078 adding 'Mikado/serializers/blast_serializer/query.py' 2021-07-15T23:18:11,079 adding 'Mikado/serializers/blast_serializer/tab_serialiser.py' 2021-07-15T23:18:11,082 adding 'Mikado/serializers/blast_serializer/tabular_utils.py' 2021-07-15T23:18:11,083 adding 'Mikado/serializers/blast_serializer/target.py' 2021-07-15T23:18:11,084 adding 'Mikado/serializers/blast_serializer/utils.py' 2021-07-15T23:18:11,086 adding 'Mikado/serializers/blast_serializer/xml_serialiser.py' 2021-07-15T23:18:11,088 adding 'Mikado/serializers/blast_serializer/xml_utils.py' 2021-07-15T23:18:11,090 adding 'Mikado/subprograms/__init__.py' 2021-07-15T23:18:11,091 adding 'Mikado/subprograms/__main__.py' 2021-07-15T23:18:11,092 adding 'Mikado/subprograms/compare.py' 2021-07-15T23:18:11,095 adding 'Mikado/subprograms/configure.py' 2021-07-15T23:18:11,098 adding 'Mikado/subprograms/pick.py' 2021-07-15T23:18:11,100 adding 'Mikado/subprograms/prepare.py' 2021-07-15T23:18:11,103 adding 'Mikado/subprograms/serialise.py' 2021-07-15T23:18:11,105 adding 'Mikado/subprograms/util/__init__.py' 2021-07-15T23:18:11,106 adding 'Mikado/subprograms/util/awk_gtf.py' 2021-07-15T23:18:11,108 adding 'Mikado/subprograms/util/class_codes.py' 2021-07-15T23:18:11,109 adding 'Mikado/subprograms/util/convert.py' 2021-07-15T23:18:11,111 adding 'Mikado/subprograms/util/grep.py' 2021-07-15T23:18:11,113 adding 'Mikado/subprograms/util/metrics.py' 2021-07-15T23:18:11,117 adding 'Mikado/subprograms/util/stats.py' 2021-07-15T23:18:11,119 adding 'Mikado/subprograms/util/trim.py' 2021-07-15T23:18:11,123 adding 'Mikado/tests/Chrysemys_picta_bellii_problematic.gff3' 2021-07-15T23:18:11,124 adding 'Mikado/tests/Chrysemys_picta_bellii_problematic.list.txt' 2021-07-15T23:18:11,125 adding 'Mikado/tests/Chrysemys_picta_bellii_problematic.txt' 2021-07-15T23:18:11,126 adding 'Mikado/tests/__init__.py' 2021-07-15T23:18:11,128 adding 'Mikado/tests/annotation.gff3' 2021-07-15T23:18:11,129 adding 'Mikado/tests/annotation.gff3.stats' 2021-07-15T23:18:11,133 adding 'Mikado/tests/assigner_test.py' 2021-07-15T23:18:11,134 adding 'Mikado/tests/cds_test_1.gtf' 2021-07-15T23:18:11,136 adding 'Mikado/tests/cds_test_2.gtf' 2021-07-15T23:18:11,137 adding 'Mikado/tests/check_seed.gtf' 2021-07-15T23:18:11,139 adding 'Mikado/tests/check_seed.yaml' 2021-07-15T23:18:12,036 adding 'Mikado/tests/chr5.fas.gz' 2021-07-15T23:18:12,106 adding 'Mikado/tests/chr5.fas.gz.fai' 2021-07-15T23:18:12,112 adding 'Mikado/tests/chr5.fas.gz.gzi' 2021-07-15T23:18:12,123 adding 'Mikado/tests/chunk-001-proteins.xml.gz' 2021-07-15T23:18:12,125 adding 'Mikado/tests/complete_padding.bed12' 2021-07-15T23:18:12,127 adding 'Mikado/tests/configuration.yaml' 2021-07-15T23:18:12,130 adding 'Mikado/tests/cufflinks.gtf' 2021-07-15T23:18:12,132 adding 'Mikado/tests/cufflinks.no_transcript.gtf' 2021-07-15T23:18:12,133 adding 'Mikado/tests/genome.fai' 2021-07-15T23:18:12,135 adding 'Mikado/tests/gtf_check.gtf.gz' 2021-07-15T23:18:12,136 adding 'Mikado/tests/intervaltree_test.py' 2021-07-15T23:18:12,142 adding 'Mikado/tests/junctions.bed' 2021-07-15T23:18:12,156 adding 'Mikado/tests/locus_test.py' 2021-07-15T23:18:12,182 adding 'Mikado/tests/mikado.blast.asn.gz' 2021-07-15T23:18:13,560 adding 'Mikado/tests/mikado.blast.xml' 2021-07-15T23:18:15,005 adding 'Mikado/tests/mikado.db' 2021-07-15T23:18:15,086 adding 'Mikado/tests/mikado_prepared.fasta' 2021-07-15T23:18:15,088 adding 'Mikado/tests/mikado_prepared.fasta.fai' 2021-07-15T23:18:15,093 adding 'Mikado/tests/mikado_prepared.gtf' 2021-07-15T23:18:15,095 adding 'Mikado/tests/neg_pad.bed12' 2021-07-15T23:18:15,113 adding 'Mikado/tests/neg_pad.fa' 2021-07-15T23:18:15,115 adding 'Mikado/tests/neg_pad.fa.fai' 2021-07-15T23:18:15,122 adding 'Mikado/tests/orf_test.py' 2021-07-15T23:18:15,123 adding 'Mikado/tests/pad_three_neg.bed12' 2021-07-15T23:18:15,125 adding 'Mikado/tests/pad_utr.bed12' 2021-07-15T23:18:15,126 adding 'Mikado/tests/padding_test.bed12' 2021-07-15T23:18:15,161 adding 'Mikado/tests/padding_test.fa' 2021-07-15T23:18:15,163 adding 'Mikado/tests/padding_test.fa.fai' 2021-07-15T23:18:15,164 adding 'Mikado/tests/padding_test.rev_compl.bed12' 2021-07-15T23:18:15,199 adding 'Mikado/tests/padding_test.rev_compl.fa' 2021-07-15T23:18:15,201 adding 'Mikado/tests/padding_test.rev_compl.fa.fai' 2021-07-15T23:18:15,203 adding 'Mikado/tests/parser_test.py' 2021-07-15T23:18:15,204 adding 'Mikado/tests/phasing_padding.bed12' 2021-07-15T23:18:15,205 adding 'Mikado/tests/plants.suspicious_requirement.yaml' 2021-07-15T23:18:15,207 adding 'Mikado/tests/prepare_misc_test.py' 2021-07-15T23:18:15,209 adding 'Mikado/tests/scoring_only_cds.yaml' 2021-07-15T23:18:15,211 adding 'Mikado/tests/test_bed12.py' 2021-07-15T23:18:15,213 adding 'Mikado/tests/test_blast_related.py' 2021-07-15T23:18:15,215 adding 'Mikado/tests/test_clique_methods.py' 2021-07-15T23:18:15,217 adding 'Mikado/tests/test_configurators.py' 2021-07-15T23:18:15,218 adding 'Mikado/tests/test_db_utils.py' 2021-07-15T23:18:15,220 adding 'Mikado/tests/test_external_scores.py' 2021-07-15T23:18:15,221 adding 'Mikado/tests/test_gene.py' 2021-07-15T23:18:15,223 adding 'Mikado/tests/test_invalid_orfs.py' 2021-07-15T23:18:15,224 adding 'Mikado/tests/test_json.py' 2021-07-15T23:18:15,240 adding 'Mikado/tests/test_mRNA.bam' 2021-07-15T23:18:15,242 adding 'Mikado/tests/test_metrics.py' 2021-07-15T23:18:15,245 adding 'Mikado/tests/test_modifications.py' 2021-07-15T23:18:15,247 adding 'Mikado/tests/test_scores.py' 2021-07-15T23:18:15,249 adding 'Mikado/tests/test_serialise_external.py' 2021-07-15T23:18:15,251 adding 'Mikado/tests/test_serialise_junctions.py' 2021-07-15T23:18:15,253 adding 'Mikado/tests/test_splitting.py' 2021-07-15T23:18:15,262 adding 'Mikado/tests/test_system_calls.py' 2021-07-15T23:18:15,266 adding 'Mikado/tests/test_transcript_checker.py' 2021-07-15T23:18:15,269 adding 'Mikado/tests/test_transcript_methods.py' 2021-07-15T23:18:15,272 adding 'Mikado/tests/test_transcript_negative.py' 2021-07-15T23:18:15,276 adding 'Mikado/tests/test_transcript_positive.py' 2021-07-15T23:18:15,280 adding 'Mikado/tests/test_transcript_single.py' 2021-07-15T23:18:15,283 adding 'Mikado/tests/test_truncated_cds.fa' 2021-07-15T23:18:15,285 adding 'Mikado/tests/test_truncated_cds.fa.fai' 2021-07-15T23:18:15,286 adding 'Mikado/tests/test_truncated_cds.gff3' 2021-07-15T23:18:15,287 adding 'Mikado/tests/test_utils.py' 2021-07-15T23:18:15,292 adding 'Mikado/tests/transcripts.fasta.prodigal.gff3' 2021-07-15T23:18:15,294 adding 'Mikado/tests/trinity.bed12' 2021-07-15T23:18:15,296 adding 'Mikado/tests/trinity.cDNA_match.gff3' 2021-07-15T23:18:15,299 adding 'Mikado/tests/trinity.gff3' 2021-07-15T23:18:15,301 adding 'Mikado/tests/trinity.gtf' 2021-07-15T23:18:15,303 adding 'Mikado/tests/trinity.ids' 2021-07-15T23:18:15,305 adding 'Mikado/tests/trinity.match_matchpart.gff3' 2021-07-15T23:18:15,308 adding 'Mikado/tests/trinity.minimap2.bam' 2021-07-15T23:18:15,310 adding 'Mikado/tests/trinity.no_transcript_feature.gtf' 2021-07-15T23:18:15,311 adding 'Mikado/tests/trinity_stats.txt' 2021-07-15T23:18:16,065 adding 'Mikado/tests/uniprot_sprot_plants.fasta.gz' 2021-07-15T23:18:16,343 adding 'Mikado/tests/uniprot_sprot_plants.fasta.gz.fai' 2021-07-15T23:18:16,353 adding 'Mikado/tests/uniprot_sprot_plants.fasta.gz.gzi' 2021-07-15T23:18:16,355 adding 'Mikado/tests/utilities_test.py' 2021-07-15T23:18:16,358 adding 'Mikado/tests/__pycache__/__init__.cpython-36.pyc' 2021-07-15T23:18:16,359 adding 'Mikado/tests/__pycache__/__init__.cpython-37.pyc' 2021-07-15T23:18:16,363 adding 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adding 'Mikado/tests/__pycache__/test_gene.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,489 adding 'Mikado/tests/__pycache__/test_gene.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,490 adding 'Mikado/tests/__pycache__/test_gene.cpython-37.pyc' 2021-07-15T23:18:16,492 adding 'Mikado/tests/__pycache__/test_invalid_orfs.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,494 adding 'Mikado/tests/__pycache__/test_invalid_orfs.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,495 adding 'Mikado/tests/__pycache__/test_invalid_orfs.cpython-37.pyc' 2021-07-15T23:18:16,497 adding 'Mikado/tests/__pycache__/test_json.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,498 adding 'Mikado/tests/__pycache__/test_json.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,500 adding 'Mikado/tests/__pycache__/test_json.cpython-37.pyc' 2021-07-15T23:18:16,501 adding 'Mikado/tests/__pycache__/test_metrics.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,503 adding 'Mikado/tests/__pycache__/test_metrics.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,504 adding 'Mikado/tests/__pycache__/test_metrics.cpython-37.pyc' 2021-07-15T23:18:16,507 adding 'Mikado/tests/__pycache__/test_modifications.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,509 adding 'Mikado/tests/__pycache__/test_modifications.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,511 adding 'Mikado/tests/__pycache__/test_modifications.cpython-37.pyc' 2021-07-15T23:18:16,513 adding 'Mikado/tests/__pycache__/test_scores.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,515 adding 'Mikado/tests/__pycache__/test_scores.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,518 adding 'Mikado/tests/__pycache__/test_scores.cpython-37.pyc' 2021-07-15T23:18:16,519 adding 'Mikado/tests/__pycache__/test_serialise_external.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,521 adding 'Mikado/tests/__pycache__/test_serialise_junctions.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,523 adding 'Mikado/tests/__pycache__/test_serialise_junctions.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,525 adding 'Mikado/tests/__pycache__/test_serialise_junctions.cpython-37.pyc' 2021-07-15T23:18:16,528 adding 'Mikado/tests/__pycache__/test_splitting.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,531 adding 'Mikado/tests/__pycache__/test_splitting.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,534 adding 'Mikado/tests/__pycache__/test_splitting.cpython-37.pyc' 2021-07-15T23:18:16,546 adding 'Mikado/tests/__pycache__/test_system_calls.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,557 adding 'Mikado/tests/__pycache__/test_system_calls.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,568 adding 'Mikado/tests/__pycache__/test_system_calls.cpython-37.pyc' 2021-07-15T23:18:16,572 adding 'Mikado/tests/__pycache__/test_transcript_checker.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,575 adding 'Mikado/tests/__pycache__/test_transcript_checker.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,578 adding 'Mikado/tests/__pycache__/test_transcript_checker.cpython-37.pyc' 2021-07-15T23:18:16,583 adding 'Mikado/tests/__pycache__/test_transcript_methods.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,587 adding 'Mikado/tests/__pycache__/test_transcript_methods.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,591 adding 'Mikado/tests/__pycache__/test_transcript_methods.cpython-37.pyc' 2021-07-15T23:18:16,595 adding 'Mikado/tests/__pycache__/test_transcript_negative.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,598 adding 'Mikado/tests/__pycache__/test_transcript_negative.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,601 adding 'Mikado/tests/__pycache__/test_transcript_negative.cpython-37.pyc' 2021-07-15T23:18:16,606 adding 'Mikado/tests/__pycache__/test_transcript_positive.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,611 adding 'Mikado/tests/__pycache__/test_transcript_positive.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,616 adding 'Mikado/tests/__pycache__/test_transcript_positive.cpython-37.pyc' 2021-07-15T23:18:16,620 adding 'Mikado/tests/__pycache__/test_transcript_single.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,624 adding 'Mikado/tests/__pycache__/test_transcript_single.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,627 adding 'Mikado/tests/__pycache__/test_transcript_single.cpython-37.pyc' 2021-07-15T23:18:16,629 adding 'Mikado/tests/__pycache__/test_utils.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,630 adding 'Mikado/tests/__pycache__/test_utils.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,631 adding 'Mikado/tests/__pycache__/test_utils.cpython-37.pyc' 2021-07-15T23:18:16,633 adding 'Mikado/tests/__pycache__/utilities_test.cpython-36-pytest-5.4.1.pyc' 2021-07-15T23:18:16,635 adding 'Mikado/tests/__pycache__/utilities_test.cpython-37-pytest-5.4.1.pyc' 2021-07-15T23:18:16,636 adding 'Mikado/tests/__pycache__/utilities_test.cpython-37.pyc' 2021-07-15T23:18:16,641 adding 'Mikado/tests/blast_data/diamond.0.9.30.tsv.gz' 2021-07-15T23:18:16,653 adding 'Mikado/tests/blast_data/diamond.0.9.30.xml.gz' 2021-07-15T23:18:16,689 adding 'Mikado/tests/blast_data/transcripts.fasta' 2021-07-15T23:18:16,692 adding 'Mikado/tests/blast_data/transcripts.fasta.fai' 2021-07-15T23:18:16,694 adding 'Mikado/tests/fusion_test/fusion_test_pred.gtf' 2021-07-15T23:18:16,696 adding 'Mikado/tests/fusion_test/fusion_test_ref.gff3' 2021-07-15T23:18:16,698 adding 'Mikado/tests/test_external/annotation_run1.metrics.testds.txt' 2021-07-15T23:18:16,699 adding 'Mikado/tests/test_external/aphid.scoring.yaml' 2021-07-15T23:18:16,701 adding 'Mikado/tests/test_external/mikado.configuration.testds.yaml' 2021-07-15T23:18:16,703 adding 'Mikado/tests/test_external/mikado_prepared.testds.fasta' 2021-07-15T23:18:16,705 adding 'Mikado/tests/test_external/mikado_prepared.testds.fasta.fai' 2021-07-15T23:18:16,707 adding 'Mikado/transcripts/__init__.py' 2021-07-15T23:18:16,708 adding 'Mikado/transcripts/clique_methods.py' 2021-07-15T23:18:16,724 adding 'Mikado/transcripts/transcript.py' 2021-07-15T23:18:16,728 adding 'Mikado/transcripts/transcriptchecker.py' 2021-07-15T23:18:16,730 adding 'Mikado/transcripts/transcriptcomputer.py' 2021-07-15T23:18:16,731 adding 'Mikado/transcripts/transcript_methods/__init__.py' 2021-07-15T23:18:16,736 adding 'Mikado/transcripts/transcript_methods/finalizing.py' 2021-07-15T23:18:16,738 adding 'Mikado/transcripts/transcript_methods/printing.py' 2021-07-15T23:18:16,742 adding 'Mikado/transcripts/transcript_methods/retrieval.py' 2021-07-15T23:18:16,747 adding 'Mikado/transcripts/transcript_methods/splitting.py' 2021-07-15T23:18:16,750 adding 'Mikado/utilities/__init__.py' 2021-07-15T23:18:16,751 adding 'Mikado/utilities/dbutils.py' 2021-07-15T23:18:16,753 adding 'Mikado/utilities/file_type.py' 2021-07-15T23:18:16,819 adding 'Mikado/utilities/intervaltree.cpp' 2021-07-15T23:18:17,042 adding 'Mikado/utilities/intervaltree.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T23:18:17,052 adding 'Mikado/utilities/intervaltree.pxd' 2021-07-15T23:18:17,055 adding 'Mikado/utilities/intervaltree.pyx' 2021-07-15T23:18:17,056 adding 'Mikado/utilities/log_utils.py' 2021-07-15T23:18:17,071 adding 'Mikado/utilities/overlap.c' 2021-07-15T23:18:17,100 adding 'Mikado/utilities/overlap.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T23:18:17,102 adding 'Mikado/utilities/overlap.pxd' 2021-07-15T23:18:17,103 adding 'Mikado/utilities/overlap.pyx' 2021-07-15T23:18:17,106 adding 'Mikado-2.0rc2.data/scripts/add_transcript_feature_to_gtf.py' 2021-07-15T23:18:17,107 adding 'Mikado-2.0rc2.data/scripts/align_collect.py' 2021-07-15T23:18:17,108 adding 'Mikado-2.0rc2.data/scripts/asm_collect.py' 2021-07-15T23:18:17,110 adding 'Mikado-2.0rc2.data/scripts/bam2gtf.py' 2021-07-15T23:18:17,111 adding 'Mikado-2.0rc2.data/scripts/calculate_distances.py' 2021-07-15T23:18:17,113 adding 'Mikado-2.0rc2.data/scripts/class_run.py' 2021-07-15T23:18:17,114 adding 'Mikado-2.0rc2.data/scripts/convert_cdna_match_gff3.py' 2021-07-15T23:18:17,116 adding 'Mikado-2.0rc2.data/scripts/extract_promoter_regions.py' 2021-07-15T23:18:17,117 adding 'Mikado-2.0rc2.data/scripts/getFastaFromIds.py' 2021-07-15T23:18:17,119 adding 'Mikado-2.0rc2.data/scripts/gffjunc_to_bed12.py' 2021-07-15T23:18:17,120 adding 'Mikado-2.0rc2.data/scripts/grep.py' 2021-07-15T23:18:17,122 adding 'Mikado-2.0rc2.data/scripts/merge_junction_bed12.py' 2021-07-15T23:18:17,123 adding 'Mikado-2.0rc2.data/scripts/remove_from_embl.py' 2021-07-15T23:18:17,124 adding 'Mikado-2.0rc2.data/scripts/remove_utrs.py' 2021-07-15T23:18:17,125 adding 'Mikado-2.0rc2.data/scripts/sanitize_blast_db.py' 2021-07-15T23:18:17,127 adding 'Mikado-2.0rc2.data/scripts/split_fasta.py' 2021-07-15T23:18:17,128 adding 'Mikado-2.0rc2.data/scripts/tease_maker_apart.py' 2021-07-15T23:18:17,130 adding 'Mikado-2.0rc2.data/scripts/trim_long_introns.py' 2021-07-15T23:18:17,132 adding 'Mikado-2.0rc2.dist-info/AUTHORS' 2021-07-15T23:18:17,133 adding 'Mikado-2.0rc2.dist-info/METADATA' 2021-07-15T23:18:17,135 adding 'Mikado-2.0rc2.dist-info/WHEEL' 2021-07-15T23:18:17,136 adding 'Mikado-2.0rc2.dist-info/entry_points.txt' 2021-07-15T23:18:17,136 adding 'Mikado-2.0rc2.dist-info/top_level.txt' 2021-07-15T23:18:17,143 adding 'Mikado-2.0rc2.dist-info/RECORD' 2021-07-15T23:18:17,506 removing build/bdist.linux-armv7l/wheel 2021-07-15T23:18:17,814 Building wheel for mikado (setup.py): finished with status 'done' 2021-07-15T23:18:18,123 Created wheel for mikado: filename=Mikado-2.0rc2-cp39-cp39-linux_armv7l.whl size=24765298 sha256=27d920e52482eb28c4c4915cd13022c57b6a2e9b24ab9cbb9c6fb84a57c86006 2021-07-15T23:18:18,124 Stored in directory: /tmp/pip-ephem-wheel-cache-9s61m2x6/wheels/9f/f2/da/0c32e3be43796e23607d2c322952da8b4a1bb8200690e64b9f 2021-07-15T23:18:18,157 Successfully built mikado 2021-07-15T23:18:18,861 Removed build tracker: '/tmp/pip-req-tracker-kt9_s8mc'