2021-09-28T18:57:55,287 Created temporary directory: /tmp/pip-ephem-wheel-cache-5sugva7m
2021-09-28T18:57:55,293 Created temporary directory: /tmp/pip-req-tracker-84mistzr
2021-09-28T18:57:55,294 Initialized build tracking at /tmp/pip-req-tracker-84mistzr
2021-09-28T18:57:55,295 Created build tracker: /tmp/pip-req-tracker-84mistzr
2021-09-28T18:57:55,295 Entered build tracker: /tmp/pip-req-tracker-84mistzr
2021-09-28T18:57:55,296 Created temporary directory: /tmp/pip-wheel-sviip7_m
2021-09-28T18:57:55,361 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2021-09-28T18:57:55,364 2 location(s) to search for versions of cap2:
2021-09-28T18:57:55,364 * https://pypi.org/simple/cap2/
2021-09-28T18:57:55,364 * https://www.piwheels.org/simple/cap2/
2021-09-28T18:57:55,365 Fetching project page and analyzing links: https://pypi.org/simple/cap2/
2021-09-28T18:57:55,367 Getting page https://pypi.org/simple/cap2/
2021-09-28T18:57:55,371 Found index url https://pypi.org/simple
2021-09-28T18:57:55,710   Skipping link: No binaries permitted for cap2: https://files.pythonhosted.org/packages/b3/52/8ec289ae38ebaf48b632b5972427bac8e590605f49d9a24403bede4869a3/cap2-0.1.0-py3-none-any.whl#sha256=a71b837f29490868951049dc7e0677c1c8e1eac524e5d7669640a5bcd1dcf46c (from https://pypi.org/simple/cap2/)
2021-09-28T18:57:55,711   Skipping link: No binaries permitted for cap2: https://files.pythonhosted.org/packages/2b/e3/4e5a3484f1b24f8b128015933e046b143208edc6d36085c8b1eb4d472784/cap2-0.4.0-py3-none-any.whl#sha256=fdfd158c594bd09595d3c91a5c5c338e17fb0c9f0a4fc4f4effd3288ec3cdf7f (from https://pypi.org/simple/cap2/)
2021-09-28T18:57:55,713   Found link https://files.pythonhosted.org/packages/0c/52/9a4d2d4d476655e99333d99a87077870ea43dd2416bdd32e7f3ed01d477a/cap2-0.4.0.macosx-11.0-arm64.tar.gz#sha256=0461f41e1cb527d4bf5261f967f4fd774e66eb03b4c777d6cfb9aac45b4171c2 (from https://pypi.org/simple/cap2/), version: 0.4.0.macosx-11.0-arm64
2021-09-28T18:57:55,714   Skipping link: No binaries permitted for cap2: https://files.pythonhosted.org/packages/da/6b/b6ab60092c2a2c310f1a65d1d508a21b6cac14804cd966593e3114c14a32/cap2-0.4.1-py3-none-any.whl#sha256=470d08715fe6a19389e8cd7ee952098a38409413fedce5e96798de75069e9fd1 (from https://pypi.org/simple/cap2/)
2021-09-28T18:57:55,715   Found link https://files.pythonhosted.org/packages/85/78/9c4622c999e03476c68fa557dfa0c57dd070728355194dbbe59382449fc5/cap2-0.4.1.tar.gz#sha256=8f52279a38fbf5e9866b65f91b072c8e0a4effacc4cbcaae00b9be57adc8338b (from https://pypi.org/simple/cap2/), version: 0.4.1
2021-09-28T18:57:55,716   Found link https://files.pythonhosted.org/packages/4c/c1/1f57ea79725c84d9a89c7161d059bd2c23682d4b2e8cd8de9a9f8b8e37f2/cap2-0.5.0.tar.gz#sha256=a343ba402ebb91919c54ba90492432f59f0906e5eaf4469663851508d6314e75 (from https://pypi.org/simple/cap2/), version: 0.5.0
2021-09-28T18:57:55,718   Found link https://files.pythonhosted.org/packages/42/0a/8123696bb01d00ce7c7151bd6ca3607822a68e6cf568378be7716e2cf20c/cap2-0.5.1.tar.gz#sha256=cf487e8f2e798f276dc00b19c57840bb0f9e432143f0343e182dbc071b2b125d (from https://pypi.org/simple/cap2/), version: 0.5.1
2021-09-28T18:57:55,719   Found link https://files.pythonhosted.org/packages/84/0e/13298d3b562eba44ff02eaa3d101cc8054bd3b14f7ec61d831999af9c7b0/cap2-0.5.2.tar.gz#sha256=b49d96e3c614975123e49190bcf3037a3ca73c126e3233d30f53a0bce30501f7 (from https://pypi.org/simple/cap2/), version: 0.5.2
2021-09-28T18:57:55,720   Found link https://files.pythonhosted.org/packages/d2/c8/0c9bd5ba6f986a7c814e429c89fbf9e940ed67e0bb9093fafcdfb2cd664b/cap2-0.5.3.tar.gz#sha256=d0a21afeaeda8e4cfbf514629b04236689c473f1135e702a9306d243fedf146e (from https://pypi.org/simple/cap2/), version: 0.5.3
2021-09-28T18:57:55,721 Fetching project page and analyzing links: https://www.piwheels.org/simple/cap2/
2021-09-28T18:57:55,722 Getting page https://www.piwheels.org/simple/cap2/
2021-09-28T18:57:55,725 Found index url https://www.piwheels.org/simple
2021-09-28T18:57:55,890   Skipping link: No binaries permitted for cap2: https://www.piwheels.org/simple/cap2/cap2-0.4.1-py3-none-any.whl#sha256=2c3f9a43fc7583e80720736ac32c3bd96d3ee5c9a77b0d6a957c5da1d02b797a (from https://www.piwheels.org/simple/cap2/)
2021-09-28T18:57:55,891   Skipping link: No binaries permitted for cap2: https://www.piwheels.org/simple/cap2/cap2-0.5.0-py3-none-any.whl#sha256=603e0f03c6032e54849c0a8573190d882dc2b4ae464698c1961d40c5c2927bd5 (from https://www.piwheels.org/simple/cap2/)
2021-09-28T18:57:55,892   Skipping link: No binaries permitted for cap2: https://www.piwheels.org/simple/cap2/cap2-0.5.1-py3-none-any.whl#sha256=fa1a09db21904f0b54ebf151dff5f853ca9fb0b645b20a5142c8eaf64f76d04f (from https://www.piwheels.org/simple/cap2/)
2021-09-28T18:57:55,893   Skipping link: No binaries permitted for cap2: https://www.piwheels.org/simple/cap2/cap2-0.5.2-py3-none-any.whl#sha256=648c5d557bf7909f6c526187792d2a5120228db432fec248593d0f5441aea890 (from https://www.piwheels.org/simple/cap2/)
2021-09-28T18:57:55,924 Given no hashes to check 1 links for project 'cap2': discarding no candidates
2021-09-28T18:57:55,956 Collecting cap2==0.5.3
2021-09-28T18:57:55,960   Created temporary directory: /tmp/pip-unpack-udsioygr
2021-09-28T18:57:56,176   Downloading cap2-0.5.3.tar.gz (79 kB)
2021-09-28T18:57:57,096   Added cap2==0.5.3 from https://files.pythonhosted.org/packages/d2/c8/0c9bd5ba6f986a7c814e429c89fbf9e940ed67e0bb9093fafcdfb2cd664b/cap2-0.5.3.tar.gz#sha256=d0a21afeaeda8e4cfbf514629b04236689c473f1135e702a9306d243fedf146e to build tracker '/tmp/pip-req-tracker-84mistzr'
2021-09-28T18:57:57,098     Running setup.py (path:/tmp/pip-wheel-sviip7_m/cap2_cca9872900b345c3b833a7050c3d9fc6/setup.py) egg_info for package cap2
2021-09-28T18:57:57,099     Created temporary directory: /tmp/pip-pip-egg-info-mjox4816
2021-09-28T18:57:57,100     Running command python setup.py egg_info
2021-09-28T18:57:59,118     running egg_info
2021-09-28T18:57:59,123     creating /tmp/pip-pip-egg-info-mjox4816/cap2.egg-info
2021-09-28T18:57:59,125     writing /tmp/pip-pip-egg-info-mjox4816/cap2.egg-info/PKG-INFO
2021-09-28T18:57:59,130     writing top-level names to /tmp/pip-pip-egg-info-mjox4816/cap2.egg-info/top_level.txt
2021-09-28T18:57:59,133     writing requirements to /tmp/pip-pip-egg-info-mjox4816/cap2.egg-info/requires.txt
2021-09-28T18:57:59,135     writing entry points to /tmp/pip-pip-egg-info-mjox4816/cap2.egg-info/entry_points.txt
2021-09-28T18:57:59,137     writing dependency_links to /tmp/pip-pip-egg-info-mjox4816/cap2.egg-info/dependency_links.txt
2021-09-28T18:57:59,141     writing manifest file '/tmp/pip-pip-egg-info-mjox4816/cap2.egg-info/SOURCES.txt'
2021-09-28T18:57:59,535     reading manifest file '/tmp/pip-pip-egg-info-mjox4816/cap2.egg-info/SOURCES.txt'
2021-09-28T18:57:59,555     writing manifest file '/tmp/pip-pip-egg-info-mjox4816/cap2.egg-info/SOURCES.txt'
2021-09-28T18:57:59,689   Source in /tmp/pip-wheel-sviip7_m/cap2_cca9872900b345c3b833a7050c3d9fc6 has version 0.5.3, which satisfies requirement cap2==0.5.3 from https://files.pythonhosted.org/packages/d2/c8/0c9bd5ba6f986a7c814e429c89fbf9e940ed67e0bb9093fafcdfb2cd664b/cap2-0.5.3.tar.gz#sha256=d0a21afeaeda8e4cfbf514629b04236689c473f1135e702a9306d243fedf146e
2021-09-28T18:57:59,691   Removed cap2==0.5.3 from https://files.pythonhosted.org/packages/d2/c8/0c9bd5ba6f986a7c814e429c89fbf9e940ed67e0bb9093fafcdfb2cd664b/cap2-0.5.3.tar.gz#sha256=d0a21afeaeda8e4cfbf514629b04236689c473f1135e702a9306d243fedf146e from build tracker '/tmp/pip-req-tracker-84mistzr'
2021-09-28T18:57:59,699 Created temporary directory: /tmp/pip-unpack-g9e5a_pu
2021-09-28T18:57:59,700 Building wheels for collected packages: cap2
2021-09-28T18:57:59,709   Created temporary directory: /tmp/pip-wheel-0rg19d_o
2021-09-28T18:57:59,710   Building wheel for cap2 (setup.py): started
2021-09-28T18:57:59,711   Destination directory: /tmp/pip-wheel-0rg19d_o
2021-09-28T18:57:59,711   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-sviip7_m/cap2_cca9872900b345c3b833a7050c3d9fc6/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-sviip7_m/cap2_cca9872900b345c3b833a7050c3d9fc6/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-0rg19d_o
2021-09-28T18:58:01,828   running bdist_wheel
2021-09-28T18:58:01,843   running build
2021-09-28T18:58:01,843   running build_py
2021-09-28T18:58:02,187   creating build
2021-09-28T18:58:02,188   creating build/lib
2021-09-28T18:58:02,189   creating build/lib/tests
2021-09-28T18:58:02,192   copying tests/test_pangea.py -> build/lib/tests
2021-09-28T18:58:02,198   copying tests/test_api.py -> build/lib/tests
2021-09-28T18:58:02,203   copying tests/test_assembly.py -> build/lib/tests
2021-09-28T18:58:02,207   copying tests/test_strainotyping.py -> build/lib/tests
2021-09-28T18:58:02,211   copying tests/test_versions.py -> build/lib/tests
2021-09-28T18:58:02,216   copying tests/test_pipeline_preprocessing.py -> build/lib/tests
2021-09-28T18:58:02,223   copying tests/test_tcems.py -> build/lib/tests
2021-09-28T18:58:02,228   copying tests/__init__.py -> build/lib/tests
2021-09-28T18:58:02,233   copying tests/test_experimental_strain.py -> build/lib/tests
2021-09-28T18:58:02,239   copying tests/test_experimental_covid.py -> build/lib/tests
2021-09-28T18:58:02,246   copying tests/test_databases.py -> build/lib/tests
2021-09-28T18:58:02,252   copying tests/test_short_read.py -> build/lib/tests
2021-09-28T18:58:02,260   creating build/lib/cap2
2021-09-28T18:58:02,262   copying cap2/cli.py -> build/lib/cap2
2021-09-28T18:58:02,267   copying cap2/api.py -> build/lib/cap2
2021-09-28T18:58:02,271   copying cap2/exceptions.py -> build/lib/cap2
2021-09-28T18:58:02,275   copying cap2/setup_logging.py -> build/lib/cap2
2021-09-28T18:58:02,280   copying cap2/utils.py -> build/lib/cap2
2021-09-28T18:58:02,285   copying cap2/constants.py -> build/lib/cap2
2021-09-28T18:58:02,290   copying cap2/__init__.py -> build/lib/cap2
2021-09-28T18:58:02,295   copying cap2/sample.py -> build/lib/cap2
2021-09-28T18:58:02,301   creating build/lib/cap2/extensions
2021-09-28T18:58:02,303   copying cap2/extensions/cli.py -> build/lib/cap2/extensions
2021-09-28T18:58:02,306   copying cap2/extensions/__init__.py -> build/lib/cap2/extensions
2021-09-28T18:58:02,311   creating build/lib/cap2/pangea
2021-09-28T18:58:02,313   copying cap2/pangea/cli.py -> build/lib/cap2/pangea
2021-09-28T18:58:02,318   copying cap2/pangea/cli_utils.py -> build/lib/cap2/pangea
2021-09-28T18:58:02,325   copying cap2/pangea/api.py -> build/lib/cap2/pangea
2021-09-28T18:58:02,332   copying cap2/pangea/sra_utils.py -> build/lib/cap2/pangea
2021-09-28T18:58:02,337   copying cap2/pangea/load_task.py -> build/lib/cap2/pangea
2021-09-28T18:58:02,345   copying cap2/pangea/utils.py -> build/lib/cap2/pangea
2021-09-28T18:58:02,350   copying cap2/pangea/download_reads.py -> build/lib/cap2/pangea
2021-09-28T18:58:02,355   copying cap2/pangea/pangea_sample.py -> build/lib/cap2/pangea
2021-09-28T18:58:02,362   copying cap2/pangea/constants.py -> build/lib/cap2/pangea
2021-09-28T18:58:02,367   copying cap2/pangea/__init__.py -> build/lib/cap2/pangea
2021-09-28T18:58:02,374   creating build/lib/cap2/capalyzer
2021-09-28T18:58:02,376   copying cap2/capalyzer/parsers.py -> build/lib/cap2/capalyzer
2021-09-28T18:58:02,381   copying cap2/capalyzer/cli.py -> build/lib/cap2/capalyzer
2021-09-28T18:58:02,385   copying cap2/capalyzer/version.py -> build/lib/cap2/capalyzer
2021-09-28T18:58:02,389   copying cap2/capalyzer/exceptions.py -> build/lib/cap2/capalyzer
2021-09-28T18:58:02,393   copying cap2/capalyzer/__init__.py -> build/lib/cap2/capalyzer
2021-09-28T18:58:02,398   creating build/lib/cap2/pipeline
2021-09-28T18:58:02,400   copying cap2/pipeline/full_pipeline.py -> build/lib/cap2/pipeline
2021-09-28T18:58:02,406   copying cap2/pipeline/constants.py -> build/lib/cap2/pipeline
2021-09-28T18:58:02,411   copying cap2/pipeline/__init__.py -> build/lib/cap2/pipeline
2021-09-28T18:58:02,416   copying cap2/pipeline/config.py -> build/lib/cap2/pipeline
2021-09-28T18:58:02,422   creating build/lib/cap2/extensions/experimental
2021-09-28T18:58:02,424   copying cap2/extensions/experimental/cli.py -> build/lib/cap2/extensions/experimental
2021-09-28T18:58:02,428   copying cap2/extensions/experimental/__init__.py -> build/lib/cap2/extensions/experimental
2021-09-28T18:58:02,434   creating build/lib/cap2/extensions/experimental/covid
2021-09-28T18:58:02,436   copying cap2/extensions/experimental/covid/make_pileup.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:58:02,440   copying cap2/extensions/experimental/covid/covid_genome_db.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:58:02,446   copying cap2/extensions/experimental/covid/cli.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:58:02,453   copying cap2/extensions/experimental/covid/align_to_covid_genome.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:58:02,459   copying cap2/extensions/experimental/covid/make_covid_consensus_seq.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:58:02,465   copying cap2/extensions/experimental/covid/genome_coverage.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:58:02,470   copying cap2/extensions/experimental/covid/fast_detect.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:58:02,476   copying cap2/extensions/experimental/covid/__init__.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:58:02,481   copying cap2/extensions/experimental/covid/call_covid_variants.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:58:02,487   creating build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:58:02,489   copying cap2/extensions/experimental/tcems/cli.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:58:02,494   copying cap2/extensions/experimental/tcems/tcem_repertoire.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:58:02,499   copying cap2/extensions/experimental/tcems/__init__.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:58:02,503   copying cap2/extensions/experimental/tcems/tcem_aa_db.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:58:02,510   copying cap2/extensions/experimental/tcems/mixcr.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:58:02,519   creating build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:58:02,522   copying cap2/extensions/experimental/preclassify/cli.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:58:02,527   copying cap2/extensions/experimental/preclassify/preclassify_db.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:58:02,531   copying cap2/extensions/experimental/preclassify/dynamic_pipeline.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:58:02,535   copying cap2/extensions/experimental/preclassify/preclassify.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:58:02,540   copying cap2/extensions/experimental/preclassify/__init__.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:58:02,548   creating build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,551   copying cap2/extensions/experimental/strains/make_pileup.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,557   copying cap2/extensions/experimental/strains/align_to_genome.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,564   copying cap2/extensions/experimental/strains/cli.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,569   copying cap2/extensions/experimental/strains/bacterial_genome_getter.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,573   copying cap2/extensions/experimental/strains/make_snp_graph.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,578   copying cap2/extensions/experimental/strains/merge_snp_graph.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,582   copying cap2/extensions/experimental/strains/merge_snp_clusters.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,587   copying cap2/extensions/experimental/strains/tasks.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,593   copying cap2/extensions/experimental/strains/make_snp_clusters.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,599   copying cap2/extensions/experimental/strains/utils.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,605   copying cap2/extensions/experimental/strains/get_microbial_genome.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,609   copying cap2/extensions/experimental/strains/make_snp_table.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,613   copying cap2/extensions/experimental/strains/align_to_genome_db.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,617   copying cap2/extensions/experimental/strains/__init__.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:58:02,623   creating build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:02,626   copying cap2/extensions/experimental/strains/strainotyping/cli.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:02,632   copying cap2/extensions/experimental/strains/strainotyping/api.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:02,641   copying cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:02,647   copying cap2/extensions/experimental/strains/strainotyping/graphs.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:02,653   copying cap2/extensions/experimental/strains/strainotyping/io.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:02,659   copying cap2/extensions/experimental/strains/strainotyping/__init__.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:02,665   copying cap2/extensions/experimental/strains/strainotyping/clustering.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:02,670   creating build/lib/cap2/capalyzer/table_builder
2021-09-28T18:58:02,672   copying cap2/capalyzer/table_builder/parsers.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T18:58:02,677   copying cap2/capalyzer/table_builder/base_module.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T18:58:02,681   copying cap2/capalyzer/table_builder/cap_table_builder.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T18:58:02,687   copying cap2/capalyzer/table_builder/__init__.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T18:58:02,695   creating build/lib/cap2/capalyzer/table_parser
2021-09-28T18:58:02,699   copying cap2/capalyzer/table_parser/analysis_utils.py -> build/lib/cap2/capalyzer/table_parser
2021-09-28T18:58:02,708   copying cap2/capalyzer/table_parser/cap_table_parser.py -> build/lib/cap2/capalyzer/table_parser
2021-09-28T18:58:02,713   copying cap2/capalyzer/table_parser/__init__.py -> build/lib/cap2/capalyzer/table_parser
2021-09-28T18:58:02,719   creating build/lib/cap2/capalyzer/pangea
2021-09-28T18:58:02,722   copying cap2/capalyzer/pangea/parsers.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:58:02,727   copying cap2/capalyzer/pangea/cli.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:58:02,732   copying cap2/capalyzer/pangea/api.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:58:02,737   copying cap2/capalyzer/pangea/pangea_file_uploader.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:58:02,743   copying cap2/capalyzer/pangea/pangea_file_source.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:58:02,748   copying cap2/capalyzer/pangea/utils.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:58:02,752   copying cap2/capalyzer/pangea/__init__.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:58:02,759   creating build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:02,762   copying cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:02,767   copying cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:02,773   copying cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:02,777   copying cap2/capalyzer/table_builder/modules/__init__.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:02,782   copying cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:02,787   copying cap2/capalyzer/table_builder/modules/covid_variant_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:02,793   copying cap2/capalyzer/table_builder/modules/basic_stats_summary.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:02,799   creating build/lib/cap2/pipeline/utils
2021-09-28T18:58:02,802   copying cap2/pipeline/utils/cap_task.py -> build/lib/cap2/pipeline/utils
2021-09-28T18:58:02,809   copying cap2/pipeline/utils/conda.py -> build/lib/cap2/pipeline/utils
2021-09-28T18:58:02,815   copying cap2/pipeline/utils/utils.py -> build/lib/cap2/pipeline/utils
2021-09-28T18:58:02,820   copying cap2/pipeline/utils/__init__.py -> build/lib/cap2/pipeline/utils
2021-09-28T18:58:02,828   creating build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,831   copying cap2/pipeline/short_read/processed_reads.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,839   copying cap2/pipeline/short_read/read_stats.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,844   copying cap2/pipeline/short_read/amrs.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,851   copying cap2/pipeline/short_read/hmp_comparison.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,858   copying cap2/pipeline/short_read/mash.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,865   copying cap2/pipeline/short_read/__init__.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,872   copying cap2/pipeline/short_read/jellyfish.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,878   copying cap2/pipeline/short_read/humann2.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,884   copying cap2/pipeline/short_read/microbe_census.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,891   copying cap2/pipeline/short_read/kraken2.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:58:02,901   creating build/lib/cap2/pipeline/databases
2021-09-28T18:58:02,905   copying cap2/pipeline/databases/human_removal_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:58:02,912   copying cap2/pipeline/databases/kraken2_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:58:02,923   copying cap2/pipeline/databases/amr_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:58:02,929   copying cap2/pipeline/databases/__init__.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:58:02,935   copying cap2/pipeline/databases/hmp_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:58:02,941   copying cap2/pipeline/databases/mouse_removal_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:58:02,947   copying cap2/pipeline/databases/taxonomic_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:58:02,953   copying cap2/pipeline/databases/fast_kraken2_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:58:02,957   copying cap2/pipeline/databases/uniref.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:58:02,963   creating build/lib/cap2/pipeline/contigs
2021-09-28T18:58:02,965   copying cap2/pipeline/contigs/amr_identification.py -> build/lib/cap2/pipeline/contigs
2021-09-28T18:58:02,970   copying cap2/pipeline/contigs/__init__.py -> build/lib/cap2/pipeline/contigs
2021-09-28T18:58:02,974   copying cap2/pipeline/contigs/prodigal.py -> build/lib/cap2/pipeline/contigs
2021-09-28T18:58:02,981   creating build/lib/cap2/pipeline/assembly
2021-09-28T18:58:02,984   copying cap2/pipeline/assembly/metaspades.py -> build/lib/cap2/pipeline/assembly
2021-09-28T18:58:02,991   copying cap2/pipeline/assembly/clean_contigs.py -> build/lib/cap2/pipeline/assembly
2021-09-28T18:58:02,996   copying cap2/pipeline/assembly/metabat2.py -> build/lib/cap2/pipeline/assembly
2021-09-28T18:58:03,000   copying cap2/pipeline/assembly/__init__.py -> build/lib/cap2/pipeline/assembly
2021-09-28T18:58:03,007   creating build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,009   copying cap2/pipeline/preprocessing/count_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,013   copying cap2/pipeline/preprocessing/fastqc.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,018   copying cap2/pipeline/preprocessing/clean_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,024   copying cap2/pipeline/preprocessing/remove_adapters.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,030   copying cap2/pipeline/preprocessing/control_sample_abundances.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,037   copying cap2/pipeline/preprocessing/fast_taxa.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,043   copying cap2/pipeline/preprocessing/basic_sample_stats.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,048   copying cap2/pipeline/preprocessing/map_to_human.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,054   copying cap2/pipeline/preprocessing/map_to_mouse.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,059   copying cap2/pipeline/preprocessing/error_correct_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,064   copying cap2/pipeline/preprocessing/base_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,067   copying cap2/pipeline/preprocessing/__init__.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,071   copying cap2/pipeline/preprocessing/multiqc.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:58:03,122   installing to build/bdist.linux-armv7l/wheel
2021-09-28T18:58:03,123   running install
2021-09-28T18:58:03,124   running install_lib
2021-09-28T18:58:03,133   creating build/bdist.linux-armv7l
2021-09-28T18:58:03,134   creating build/bdist.linux-armv7l/wheel
2021-09-28T18:58:03,138   creating build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,140   copying build/lib/tests/test_pangea.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,145   copying build/lib/tests/test_api.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,149   copying build/lib/tests/test_assembly.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,153   copying build/lib/tests/test_strainotyping.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,157   copying build/lib/tests/test_versions.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,162   copying build/lib/tests/test_pipeline_preprocessing.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,168   copying build/lib/tests/test_tcems.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,173   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,178   copying build/lib/tests/test_experimental_strain.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,184   copying build/lib/tests/test_experimental_covid.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,189   copying build/lib/tests/test_databases.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,193   copying build/lib/tests/test_short_read.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:58:03,199   creating build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:58:03,201   copying build/lib/cap2/cli.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:58:03,207   copying build/lib/cap2/api.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:58:03,214   creating build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-28T18:58:03,216   copying build/lib/cap2/extensions/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-28T18:58:03,223   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-28T18:58:03,225   copying build/lib/cap2/extensions/experimental/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-28T18:58:03,230   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:58:03,232   copying build/lib/cap2/extensions/experimental/covid/make_pileup.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:58:03,236   copying build/lib/cap2/extensions/experimental/covid/covid_genome_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:58:03,240   copying build/lib/cap2/extensions/experimental/covid/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:58:03,247   copying build/lib/cap2/extensions/experimental/covid/align_to_covid_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:58:03,253   copying build/lib/cap2/extensions/experimental/covid/make_covid_consensus_seq.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:58:03,259   copying build/lib/cap2/extensions/experimental/covid/genome_coverage.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:58:03,264   copying build/lib/cap2/extensions/experimental/covid/fast_detect.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:58:03,268   copying build/lib/cap2/extensions/experimental/covid/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:58:03,272   copying build/lib/cap2/extensions/experimental/covid/call_covid_variants.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:58:03,277   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:58:03,279   copying build/lib/cap2/extensions/experimental/tcems/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:58:03,285   copying build/lib/cap2/extensions/experimental/tcems/tcem_repertoire.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:58:03,291   copying build/lib/cap2/extensions/experimental/tcems/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:58:03,296   copying build/lib/cap2/extensions/experimental/tcems/tcem_aa_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:58:03,303   copying build/lib/cap2/extensions/experimental/tcems/mixcr.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:58:03,310   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:58:03,312   copying build/lib/cap2/extensions/experimental/preclassify/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:58:03,317   copying build/lib/cap2/extensions/experimental/preclassify/preclassify_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:58:03,321   copying build/lib/cap2/extensions/experimental/preclassify/dynamic_pipeline.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:58:03,325   copying build/lib/cap2/extensions/experimental/preclassify/preclassify.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:58:03,332   copying build/lib/cap2/extensions/experimental/preclassify/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:58:03,338   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,341   copying build/lib/cap2/extensions/experimental/strains/make_pileup.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,347   copying build/lib/cap2/extensions/experimental/strains/align_to_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,352   copying build/lib/cap2/extensions/experimental/strains/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,359   copying build/lib/cap2/extensions/experimental/strains/bacterial_genome_getter.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,364   copying build/lib/cap2/extensions/experimental/strains/make_snp_graph.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,369   copying build/lib/cap2/extensions/experimental/strains/merge_snp_graph.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,376   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:03,378   copying build/lib/cap2/extensions/experimental/strains/strainotyping/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:03,384   copying build/lib/cap2/extensions/experimental/strains/strainotyping/api.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:03,389   copying build/lib/cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:03,394   copying build/lib/cap2/extensions/experimental/strains/strainotyping/graphs.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:03,398   copying build/lib/cap2/extensions/experimental/strains/strainotyping/io.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:03,402   copying build/lib/cap2/extensions/experimental/strains/strainotyping/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:03,406   copying build/lib/cap2/extensions/experimental/strains/strainotyping/clustering.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:58:03,410   copying build/lib/cap2/extensions/experimental/strains/merge_snp_clusters.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,416   copying build/lib/cap2/extensions/experimental/strains/tasks.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,422   copying build/lib/cap2/extensions/experimental/strains/make_snp_clusters.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,427   copying build/lib/cap2/extensions/experimental/strains/utils.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,431   copying build/lib/cap2/extensions/experimental/strains/get_microbial_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,436   copying build/lib/cap2/extensions/experimental/strains/make_snp_table.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,440   copying build/lib/cap2/extensions/experimental/strains/align_to_genome_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,444   copying build/lib/cap2/extensions/experimental/strains/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:58:03,448   copying build/lib/cap2/extensions/experimental/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-28T18:58:03,453   copying build/lib/cap2/extensions/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-28T18:58:03,457   copying build/lib/cap2/exceptions.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:58:03,465   creating build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,467   copying build/lib/cap2/pangea/cli.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,473   copying build/lib/cap2/pangea/cli_utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,478   copying build/lib/cap2/pangea/api.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,483   copying build/lib/cap2/pangea/sra_utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,487   copying build/lib/cap2/pangea/load_task.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,494   copying build/lib/cap2/pangea/utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,499   copying build/lib/cap2/pangea/download_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,504   copying build/lib/cap2/pangea/pangea_sample.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,511   copying build/lib/cap2/pangea/constants.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,515   copying build/lib/cap2/pangea/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:58:03,518   copying build/lib/cap2/setup_logging.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:58:03,522   copying build/lib/cap2/utils.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:58:03,527   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:58:03,529   copying build/lib/cap2/capalyzer/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:58:03,535   copying build/lib/cap2/capalyzer/cli.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:58:03,542   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T18:58:03,544   copying build/lib/cap2/capalyzer/table_builder/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T18:58:03,552   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:03,554   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:03,558   copying build/lib/cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:03,562   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:03,566   copying build/lib/cap2/capalyzer/table_builder/modules/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:03,570   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:03,576   copying build/lib/cap2/capalyzer/table_builder/modules/covid_variant_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:03,581   copying build/lib/cap2/capalyzer/table_builder/modules/basic_stats_summary.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:58:03,587   copying build/lib/cap2/capalyzer/table_builder/base_module.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T18:58:03,592   copying build/lib/cap2/capalyzer/table_builder/cap_table_builder.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T18:58:03,597   copying build/lib/cap2/capalyzer/table_builder/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T18:58:03,601   copying build/lib/cap2/capalyzer/version.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:58:03,606   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T18:58:03,608   copying build/lib/cap2/capalyzer/table_parser/analysis_utils.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T18:58:03,615   copying build/lib/cap2/capalyzer/table_parser/cap_table_parser.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T18:58:03,620   copying build/lib/cap2/capalyzer/table_parser/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T18:58:03,626   copying build/lib/cap2/capalyzer/exceptions.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:58:03,633   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:58:03,635   copying build/lib/cap2/capalyzer/pangea/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:58:03,639   copying build/lib/cap2/capalyzer/pangea/cli.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:58:03,643   copying build/lib/cap2/capalyzer/pangea/api.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:58:03,647   copying build/lib/cap2/capalyzer/pangea/pangea_file_uploader.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:58:03,651   copying build/lib/cap2/capalyzer/pangea/pangea_file_source.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:58:03,657   copying build/lib/cap2/capalyzer/pangea/utils.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:58:03,662   copying build/lib/cap2/capalyzer/pangea/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:58:03,668   copying build/lib/cap2/capalyzer/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:58:03,673   copying build/lib/cap2/constants.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:58:03,677   copying build/lib/cap2/__init__.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:58:03,680   copying build/lib/cap2/sample.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:58:03,686   creating build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T18:58:03,689   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T18:58:03,691   copying build/lib/cap2/pipeline/utils/cap_task.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T18:58:03,698   copying build/lib/cap2/pipeline/utils/conda.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T18:58:03,705   copying build/lib/cap2/pipeline/utils/utils.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T18:58:03,710   copying build/lib/cap2/pipeline/utils/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T18:58:03,717   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,719   copying build/lib/cap2/pipeline/short_read/processed_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,723   copying build/lib/cap2/pipeline/short_read/read_stats.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,728   copying build/lib/cap2/pipeline/short_read/amrs.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,733   copying build/lib/cap2/pipeline/short_read/hmp_comparison.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,738   copying build/lib/cap2/pipeline/short_read/mash.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,743   copying build/lib/cap2/pipeline/short_read/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,749   copying build/lib/cap2/pipeline/short_read/jellyfish.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,754   copying build/lib/cap2/pipeline/short_read/humann2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,760   copying build/lib/cap2/pipeline/short_read/microbe_census.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,764   copying build/lib/cap2/pipeline/short_read/kraken2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:58:03,769   copying build/lib/cap2/pipeline/full_pipeline.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T18:58:03,774   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:58:03,777   copying build/lib/cap2/pipeline/databases/human_removal_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:58:03,783   copying build/lib/cap2/pipeline/databases/kraken2_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:58:03,789   copying build/lib/cap2/pipeline/databases/amr_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:58:03,795   copying build/lib/cap2/pipeline/databases/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:58:03,799   copying build/lib/cap2/pipeline/databases/hmp_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:58:03,804   copying build/lib/cap2/pipeline/databases/mouse_removal_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:58:03,808   copying build/lib/cap2/pipeline/databases/taxonomic_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:58:03,812   copying build/lib/cap2/pipeline/databases/fast_kraken2_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:58:03,816   copying build/lib/cap2/pipeline/databases/uniref.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:58:03,824   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T18:58:03,827   copying build/lib/cap2/pipeline/contigs/amr_identification.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T18:58:03,834   copying build/lib/cap2/pipeline/contigs/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T18:58:03,840   copying build/lib/cap2/pipeline/contigs/prodigal.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T18:58:03,845   copying build/lib/cap2/pipeline/constants.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T18:58:03,849   copying build/lib/cap2/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T18:58:03,854   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T18:58:03,857   copying build/lib/cap2/pipeline/assembly/metaspades.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T18:58:03,862   copying build/lib/cap2/pipeline/assembly/clean_contigs.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T18:58:03,867   copying build/lib/cap2/pipeline/assembly/metabat2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T18:58:03,872   copying build/lib/cap2/pipeline/assembly/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T18:58:03,877   copying build/lib/cap2/pipeline/config.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T18:58:03,883   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,885   copying build/lib/cap2/pipeline/preprocessing/count_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,891   copying build/lib/cap2/pipeline/preprocessing/fastqc.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,895   copying build/lib/cap2/pipeline/preprocessing/clean_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,900   copying build/lib/cap2/pipeline/preprocessing/remove_adapters.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,905   copying build/lib/cap2/pipeline/preprocessing/control_sample_abundances.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,911   copying build/lib/cap2/pipeline/preprocessing/fast_taxa.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,916   copying build/lib/cap2/pipeline/preprocessing/basic_sample_stats.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,922   copying build/lib/cap2/pipeline/preprocessing/map_to_human.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,929   copying build/lib/cap2/pipeline/preprocessing/map_to_mouse.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,936   copying build/lib/cap2/pipeline/preprocessing/error_correct_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,943   copying build/lib/cap2/pipeline/preprocessing/base_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,947   copying build/lib/cap2/pipeline/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,952   copying build/lib/cap2/pipeline/preprocessing/multiqc.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:58:03,956   running install_egg_info
2021-09-28T18:58:04,002   running egg_info
2021-09-28T18:58:04,005   writing entry points to cap2.egg-info/entry_points.txt
2021-09-28T18:58:04,008   writing dependency_links to cap2.egg-info/dependency_links.txt
2021-09-28T18:58:04,011   writing top-level names to cap2.egg-info/top_level.txt
2021-09-28T18:58:04,015   writing requirements to cap2.egg-info/requires.txt
2021-09-28T18:58:04,018   writing cap2.egg-info/PKG-INFO
2021-09-28T18:58:04,062   reading manifest file 'cap2.egg-info/SOURCES.txt'
2021-09-28T18:58:04,099   writing manifest file 'cap2.egg-info/SOURCES.txt'
2021-09-28T18:58:04,103   Copying cap2.egg-info to build/bdist.linux-armv7l/wheel/cap2-0.5.3-py3.5.egg-info
2021-09-28T18:58:04,131   running install_scripts
2021-09-28T18:58:04,368   creating build/bdist.linux-armv7l/wheel/cap2-0.5.3.dist-info/WHEEL
2021-09-28T18:58:05,226   Building wheel for cap2 (setup.py): finished with status 'done'
2021-09-28T18:58:05,233   Created wheel for cap2: filename=cap2-0.5.3-py3-none-any.whl size=142401 sha256=0f689f840659451d88ed6dbd56954500688017ca202def8d699806d020b8c931
2021-09-28T18:58:05,233   Stored in directory: /tmp/pip-ephem-wheel-cache-5sugva7m/wheels/b1/8e/45/4d717c4f6f1f000ce7de65907ad51debd4efc9c08050abe16c
2021-09-28T18:58:05,264 Successfully built cap2
2021-09-28T18:58:05,293 Removed build tracker: '/tmp/pip-req-tracker-84mistzr'