2021-09-28T18:36:25,588 Created temporary directory: /tmp/pip-ephem-wheel-cache-dfnbl5r4 2021-09-28T18:36:25,594 Created temporary directory: /tmp/pip-req-tracker-ey8i2ofj 2021-09-28T18:36:25,595 Initialized build tracking at /tmp/pip-req-tracker-ey8i2ofj 2021-09-28T18:36:25,596 Created build tracker: /tmp/pip-req-tracker-ey8i2ofj 2021-09-28T18:36:25,596 Entered build tracker: /tmp/pip-req-tracker-ey8i2ofj 2021-09-28T18:36:25,597 Created temporary directory: /tmp/pip-wheel-yyx2yz6x 2021-09-28T18:36:25,665 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2021-09-28T18:36:25,668 2 location(s) to search for versions of cap2: 2021-09-28T18:36:25,668 * https://pypi.org/simple/cap2/ 2021-09-28T18:36:25,668 * https://www.piwheels.org/simple/cap2/ 2021-09-28T18:36:25,669 Fetching project page and analyzing links: https://pypi.org/simple/cap2/ 2021-09-28T18:36:25,671 Getting page https://pypi.org/simple/cap2/ 2021-09-28T18:36:25,675 Found index url https://pypi.org/simple 2021-09-28T18:36:26,012 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/) 2021-09-28T18:36:26,013 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/) 2021-09-28T18:36:26,014 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 2021-09-28T18:36:26,015 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/) 2021-09-28T18:36:26,016 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 2021-09-28T18:36:26,017 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 2021-09-28T18:36:26,018 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 2021-09-28T18:36:26,018 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 2021-09-28T18:36:26,019 Fetching project page and analyzing links: https://www.piwheels.org/simple/cap2/ 2021-09-28T18:36:26,020 Getting page https://www.piwheels.org/simple/cap2/ 2021-09-28T18:36:26,023 Found index url https://www.piwheels.org/simple 2021-09-28T18:36:26,184 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/) 2021-09-28T18:36:26,185 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/) 2021-09-28T18:36:26,186 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/) 2021-09-28T18:36:26,217 Given no hashes to check 1 links for project 'cap2': discarding no candidates 2021-09-28T18:36:26,249 Collecting cap2==0.5.2 2021-09-28T18:36:26,253 Created temporary directory: /tmp/pip-unpack-5bqq6s3p 2021-09-28T18:36:26,468 Downloading cap2-0.5.2.tar.gz (79 kB) 2021-09-28T18:36:27,380 Added cap2==0.5.2 from https://files.pythonhosted.org/packages/84/0e/13298d3b562eba44ff02eaa3d101cc8054bd3b14f7ec61d831999af9c7b0/cap2-0.5.2.tar.gz#sha256=b49d96e3c614975123e49190bcf3037a3ca73c126e3233d30f53a0bce30501f7 to build tracker '/tmp/pip-req-tracker-ey8i2ofj' 2021-09-28T18:36:27,382 Running setup.py (path:/tmp/pip-wheel-yyx2yz6x/cap2_40792b6dffa14155b61e194b8b9804ec/setup.py) egg_info for package cap2 2021-09-28T18:36:27,384 Created temporary directory: /tmp/pip-pip-egg-info-a82ibclv 2021-09-28T18:36:27,384 Running command python setup.py egg_info 2021-09-28T18:36:29,373 running egg_info 2021-09-28T18:36:29,379 creating /tmp/pip-pip-egg-info-a82ibclv/cap2.egg-info 2021-09-28T18:36:29,380 writing dependency_links to /tmp/pip-pip-egg-info-a82ibclv/cap2.egg-info/dependency_links.txt 2021-09-28T18:36:29,384 writing entry points to /tmp/pip-pip-egg-info-a82ibclv/cap2.egg-info/entry_points.txt 2021-09-28T18:36:29,386 writing /tmp/pip-pip-egg-info-a82ibclv/cap2.egg-info/PKG-INFO 2021-09-28T18:36:29,390 writing top-level names to /tmp/pip-pip-egg-info-a82ibclv/cap2.egg-info/top_level.txt 2021-09-28T18:36:29,392 writing requirements to /tmp/pip-pip-egg-info-a82ibclv/cap2.egg-info/requires.txt 2021-09-28T18:36:29,396 writing manifest file '/tmp/pip-pip-egg-info-a82ibclv/cap2.egg-info/SOURCES.txt' 2021-09-28T18:36:29,786 reading manifest file '/tmp/pip-pip-egg-info-a82ibclv/cap2.egg-info/SOURCES.txt' 2021-09-28T18:36:29,806 writing manifest file '/tmp/pip-pip-egg-info-a82ibclv/cap2.egg-info/SOURCES.txt' 2021-09-28T18:36:29,940 Source in /tmp/pip-wheel-yyx2yz6x/cap2_40792b6dffa14155b61e194b8b9804ec has version 0.5.2, which satisfies requirement cap2==0.5.2 from https://files.pythonhosted.org/packages/84/0e/13298d3b562eba44ff02eaa3d101cc8054bd3b14f7ec61d831999af9c7b0/cap2-0.5.2.tar.gz#sha256=b49d96e3c614975123e49190bcf3037a3ca73c126e3233d30f53a0bce30501f7 2021-09-28T18:36:29,942 Removed cap2==0.5.2 from https://files.pythonhosted.org/packages/84/0e/13298d3b562eba44ff02eaa3d101cc8054bd3b14f7ec61d831999af9c7b0/cap2-0.5.2.tar.gz#sha256=b49d96e3c614975123e49190bcf3037a3ca73c126e3233d30f53a0bce30501f7 from build tracker '/tmp/pip-req-tracker-ey8i2ofj' 2021-09-28T18:36:29,950 Created temporary directory: /tmp/pip-unpack-6q_u65wc 2021-09-28T18:36:29,951 Building wheels for collected packages: cap2 2021-09-28T18:36:29,959 Created temporary directory: /tmp/pip-wheel-vw_4wslz 2021-09-28T18:36:29,960 Building wheel for cap2 (setup.py): started 2021-09-28T18:36:29,961 Destination directory: /tmp/pip-wheel-vw_4wslz 2021-09-28T18:36:29,962 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-yyx2yz6x/cap2_40792b6dffa14155b61e194b8b9804ec/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-yyx2yz6x/cap2_40792b6dffa14155b61e194b8b9804ec/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-vw_4wslz 2021-09-28T18:36:31,990 running bdist_wheel 2021-09-28T18:36:32,004 running build 2021-09-28T18:36:32,005 running build_py 2021-09-28T18:36:32,346 creating build 2021-09-28T18:36:32,347 creating build/lib 2021-09-28T18:36:32,348 creating build/lib/tests 2021-09-28T18:36:32,351 copying tests/test_pangea.py -> build/lib/tests 2021-09-28T18:36:32,357 copying tests/test_api.py -> build/lib/tests 2021-09-28T18:36:32,361 copying tests/test_assembly.py -> build/lib/tests 2021-09-28T18:36:32,365 copying tests/test_strainotyping.py -> build/lib/tests 2021-09-28T18:36:32,369 copying tests/test_versions.py -> build/lib/tests 2021-09-28T18:36:32,375 copying tests/test_pipeline_preprocessing.py -> build/lib/tests 2021-09-28T18:36:32,382 copying tests/test_tcems.py -> build/lib/tests 2021-09-28T18:36:32,387 copying tests/__init__.py -> build/lib/tests 2021-09-28T18:36:32,391 copying tests/test_experimental_strain.py -> build/lib/tests 2021-09-28T18:36:32,397 copying tests/test_experimental_covid.py -> build/lib/tests 2021-09-28T18:36:32,402 copying tests/test_databases.py -> build/lib/tests 2021-09-28T18:36:32,407 copying tests/test_short_read.py -> build/lib/tests 2021-09-28T18:36:32,414 creating build/lib/cap2 2021-09-28T18:36:32,418 copying cap2/cli.py -> build/lib/cap2 2021-09-28T18:36:32,424 copying cap2/api.py -> build/lib/cap2 2021-09-28T18:36:32,430 copying cap2/exceptions.py -> build/lib/cap2 2021-09-28T18:36:32,435 copying cap2/setup_logging.py -> build/lib/cap2 2021-09-28T18:36:32,439 copying cap2/utils.py -> build/lib/cap2 2021-09-28T18:36:32,443 copying cap2/constants.py -> build/lib/cap2 2021-09-28T18:36:32,447 copying cap2/__init__.py -> build/lib/cap2 2021-09-28T18:36:32,450 copying cap2/sample.py -> build/lib/cap2 2021-09-28T18:36:32,455 creating build/lib/cap2/extensions 2021-09-28T18:36:32,458 copying cap2/extensions/cli.py -> build/lib/cap2/extensions 2021-09-28T18:36:32,463 copying cap2/extensions/__init__.py -> build/lib/cap2/extensions 2021-09-28T18:36:32,471 creating build/lib/cap2/pangea 2021-09-28T18:36:32,473 copying cap2/pangea/cli.py -> build/lib/cap2/pangea 2021-09-28T18:36:32,479 copying cap2/pangea/cli_utils.py -> build/lib/cap2/pangea 2021-09-28T18:36:32,484 copying cap2/pangea/api.py -> build/lib/cap2/pangea 2021-09-28T18:36:32,489 copying cap2/pangea/sra_utils.py -> build/lib/cap2/pangea 2021-09-28T18:36:32,493 copying cap2/pangea/load_task.py -> build/lib/cap2/pangea 2021-09-28T18:36:32,501 copying cap2/pangea/utils.py -> build/lib/cap2/pangea 2021-09-28T18:36:32,506 copying cap2/pangea/download_reads.py -> build/lib/cap2/pangea 2021-09-28T18:36:32,511 copying cap2/pangea/pangea_sample.py -> build/lib/cap2/pangea 2021-09-28T18:36:32,517 copying cap2/pangea/constants.py -> build/lib/cap2/pangea 2021-09-28T18:36:32,521 copying cap2/pangea/__init__.py -> build/lib/cap2/pangea 2021-09-28T18:36:32,525 creating build/lib/cap2/capalyzer 2021-09-28T18:36:32,527 copying cap2/capalyzer/parsers.py -> build/lib/cap2/capalyzer 2021-09-28T18:36:32,532 copying cap2/capalyzer/cli.py -> build/lib/cap2/capalyzer 2021-09-28T18:36:32,536 copying cap2/capalyzer/version.py -> build/lib/cap2/capalyzer 2021-09-28T18:36:32,541 copying cap2/capalyzer/exceptions.py -> build/lib/cap2/capalyzer 2021-09-28T18:36:32,546 copying cap2/capalyzer/__init__.py -> build/lib/cap2/capalyzer 2021-09-28T18:36:32,553 creating build/lib/cap2/pipeline 2021-09-28T18:36:32,556 copying cap2/pipeline/full_pipeline.py -> build/lib/cap2/pipeline 2021-09-28T18:36:32,561 copying cap2/pipeline/constants.py -> build/lib/cap2/pipeline 2021-09-28T18:36:32,564 copying cap2/pipeline/__init__.py -> build/lib/cap2/pipeline 2021-09-28T18:36:32,568 copying cap2/pipeline/config.py -> build/lib/cap2/pipeline 2021-09-28T18:36:32,573 creating build/lib/cap2/extensions/experimental 2021-09-28T18:36:32,575 copying cap2/extensions/experimental/cli.py -> build/lib/cap2/extensions/experimental 2021-09-28T18:36:32,580 copying cap2/extensions/experimental/__init__.py -> build/lib/cap2/extensions/experimental 2021-09-28T18:36:32,588 creating build/lib/cap2/extensions/experimental/covid 2021-09-28T18:36:32,590 copying cap2/extensions/experimental/covid/make_pileup.py -> build/lib/cap2/extensions/experimental/covid 2021-09-28T18:36:32,597 copying cap2/extensions/experimental/covid/covid_genome_db.py -> build/lib/cap2/extensions/experimental/covid 2021-09-28T18:36:32,601 copying cap2/extensions/experimental/covid/cli.py -> build/lib/cap2/extensions/experimental/covid 2021-09-28T18:36:32,606 copying cap2/extensions/experimental/covid/align_to_covid_genome.py -> build/lib/cap2/extensions/experimental/covid 2021-09-28T18:36:32,611 copying cap2/extensions/experimental/covid/make_covid_consensus_seq.py -> build/lib/cap2/extensions/experimental/covid 2021-09-28T18:36:32,615 copying cap2/extensions/experimental/covid/genome_coverage.py -> build/lib/cap2/extensions/experimental/covid 2021-09-28T18:36:32,621 copying cap2/extensions/experimental/covid/fast_detect.py -> build/lib/cap2/extensions/experimental/covid 2021-09-28T18:36:32,627 copying cap2/extensions/experimental/covid/__init__.py -> build/lib/cap2/extensions/experimental/covid 2021-09-28T18:36:32,632 copying cap2/extensions/experimental/covid/call_covid_variants.py -> build/lib/cap2/extensions/experimental/covid 2021-09-28T18:36:32,640 creating build/lib/cap2/extensions/experimental/tcems 2021-09-28T18:36:32,642 copying cap2/extensions/experimental/tcems/cli.py -> build/lib/cap2/extensions/experimental/tcems 2021-09-28T18:36:32,648 copying cap2/extensions/experimental/tcems/tcem_repertoire.py -> build/lib/cap2/extensions/experimental/tcems 2021-09-28T18:36:32,653 copying cap2/extensions/experimental/tcems/__init__.py -> build/lib/cap2/extensions/experimental/tcems 2021-09-28T18:36:32,657 copying cap2/extensions/experimental/tcems/tcem_aa_db.py -> build/lib/cap2/extensions/experimental/tcems 2021-09-28T18:36:32,664 copying cap2/extensions/experimental/tcems/mixcr.py -> build/lib/cap2/extensions/experimental/tcems 2021-09-28T18:36:32,673 creating build/lib/cap2/extensions/experimental/preclassify 2021-09-28T18:36:32,676 copying cap2/extensions/experimental/preclassify/cli.py -> build/lib/cap2/extensions/experimental/preclassify 2021-09-28T18:36:32,684 copying cap2/extensions/experimental/preclassify/preclassify_db.py -> build/lib/cap2/extensions/experimental/preclassify 2021-09-28T18:36:32,688 copying cap2/extensions/experimental/preclassify/dynamic_pipeline.py -> build/lib/cap2/extensions/experimental/preclassify 2021-09-28T18:36:32,692 copying cap2/extensions/experimental/preclassify/preclassify.py -> build/lib/cap2/extensions/experimental/preclassify 2021-09-28T18:36:32,697 copying cap2/extensions/experimental/preclassify/__init__.py -> build/lib/cap2/extensions/experimental/preclassify 2021-09-28T18:36:32,703 creating build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,706 copying cap2/extensions/experimental/strains/make_pileup.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,712 copying cap2/extensions/experimental/strains/align_to_genome.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,718 copying cap2/extensions/experimental/strains/cli.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,725 copying cap2/extensions/experimental/strains/bacterial_genome_getter.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,729 copying cap2/extensions/experimental/strains/make_snp_graph.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,733 copying cap2/extensions/experimental/strains/merge_snp_graph.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,737 copying cap2/extensions/experimental/strains/merge_snp_clusters.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,742 copying cap2/extensions/experimental/strains/tasks.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,747 copying cap2/extensions/experimental/strains/make_snp_clusters.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,753 copying cap2/extensions/experimental/strains/utils.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,759 copying cap2/extensions/experimental/strains/get_microbial_genome.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,764 copying cap2/extensions/experimental/strains/make_snp_table.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,768 copying cap2/extensions/experimental/strains/align_to_genome_db.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,772 copying cap2/extensions/experimental/strains/__init__.py -> build/lib/cap2/extensions/experimental/strains 2021-09-28T18:36:32,778 creating build/lib/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:32,780 copying cap2/extensions/experimental/strains/strainotyping/cli.py -> build/lib/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:32,785 copying cap2/extensions/experimental/strains/strainotyping/api.py -> build/lib/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:32,790 copying cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py -> build/lib/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:32,796 copying cap2/extensions/experimental/strains/strainotyping/graphs.py -> build/lib/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:32,802 copying cap2/extensions/experimental/strains/strainotyping/io.py -> build/lib/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:32,806 copying cap2/extensions/experimental/strains/strainotyping/__init__.py -> build/lib/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:32,810 copying cap2/extensions/experimental/strains/strainotyping/clustering.py -> build/lib/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:32,816 creating build/lib/cap2/capalyzer/table_builder 2021-09-28T18:36:32,818 copying cap2/capalyzer/table_builder/parsers.py -> build/lib/cap2/capalyzer/table_builder 2021-09-28T18:36:32,822 copying cap2/capalyzer/table_builder/base_module.py -> build/lib/cap2/capalyzer/table_builder 2021-09-28T18:36:32,827 copying cap2/capalyzer/table_builder/cap_table_builder.py -> build/lib/cap2/capalyzer/table_builder 2021-09-28T18:36:32,833 copying cap2/capalyzer/table_builder/__init__.py -> build/lib/cap2/capalyzer/table_builder 2021-09-28T18:36:32,840 creating build/lib/cap2/capalyzer/table_parser 2021-09-28T18:36:32,843 copying cap2/capalyzer/table_parser/analysis_utils.py -> build/lib/cap2/capalyzer/table_parser 2021-09-28T18:36:32,850 copying cap2/capalyzer/table_parser/cap_table_parser.py -> build/lib/cap2/capalyzer/table_parser 2021-09-28T18:36:32,853 copying cap2/capalyzer/table_parser/__init__.py -> build/lib/cap2/capalyzer/table_parser 2021-09-28T18:36:32,859 creating build/lib/cap2/capalyzer/pangea 2021-09-28T18:36:32,861 copying cap2/capalyzer/pangea/parsers.py -> build/lib/cap2/capalyzer/pangea 2021-09-28T18:36:32,866 copying cap2/capalyzer/pangea/cli.py -> build/lib/cap2/capalyzer/pangea 2021-09-28T18:36:32,872 copying cap2/capalyzer/pangea/api.py -> build/lib/cap2/capalyzer/pangea 2021-09-28T18:36:32,878 copying cap2/capalyzer/pangea/pangea_file_uploader.py -> build/lib/cap2/capalyzer/pangea 2021-09-28T18:36:32,884 copying cap2/capalyzer/pangea/pangea_file_source.py -> build/lib/cap2/capalyzer/pangea 2021-09-28T18:36:32,889 copying cap2/capalyzer/pangea/utils.py -> build/lib/cap2/capalyzer/pangea 2021-09-28T18:36:32,893 copying cap2/capalyzer/pangea/__init__.py -> build/lib/cap2/capalyzer/pangea 2021-09-28T18:36:32,899 creating build/lib/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:32,901 copying cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py -> build/lib/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:32,905 copying cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py -> build/lib/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:32,911 copying cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py -> build/lib/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:32,916 copying cap2/capalyzer/table_builder/modules/__init__.py -> build/lib/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:32,922 copying cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py -> build/lib/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:32,927 copying cap2/capalyzer/table_builder/modules/covid_variant_table.py -> build/lib/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:32,932 copying cap2/capalyzer/table_builder/modules/basic_stats_summary.py -> build/lib/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:32,937 creating build/lib/cap2/pipeline/utils 2021-09-28T18:36:32,939 copying cap2/pipeline/utils/cap_task.py -> build/lib/cap2/pipeline/utils 2021-09-28T18:36:32,945 copying cap2/pipeline/utils/conda.py -> build/lib/cap2/pipeline/utils 2021-09-28T18:36:32,951 copying cap2/pipeline/utils/utils.py -> build/lib/cap2/pipeline/utils 2021-09-28T18:36:32,956 copying cap2/pipeline/utils/__init__.py -> build/lib/cap2/pipeline/utils 2021-09-28T18:36:32,965 creating build/lib/cap2/pipeline/short_read 2021-09-28T18:36:32,968 copying cap2/pipeline/short_read/processed_reads.py -> build/lib/cap2/pipeline/short_read 2021-09-28T18:36:32,972 copying cap2/pipeline/short_read/read_stats.py -> build/lib/cap2/pipeline/short_read 2021-09-28T18:36:32,976 copying cap2/pipeline/short_read/amrs.py -> build/lib/cap2/pipeline/short_read 2021-09-28T18:36:32,981 copying cap2/pipeline/short_read/hmp_comparison.py -> build/lib/cap2/pipeline/short_read 2021-09-28T18:36:32,985 copying cap2/pipeline/short_read/mash.py -> build/lib/cap2/pipeline/short_read 2021-09-28T18:36:32,990 copying cap2/pipeline/short_read/__init__.py -> build/lib/cap2/pipeline/short_read 2021-09-28T18:36:32,995 copying cap2/pipeline/short_read/jellyfish.py -> build/lib/cap2/pipeline/short_read 2021-09-28T18:36:33,001 copying cap2/pipeline/short_read/humann2.py -> build/lib/cap2/pipeline/short_read 2021-09-28T18:36:33,007 copying cap2/pipeline/short_read/microbe_census.py -> build/lib/cap2/pipeline/short_read 2021-09-28T18:36:33,012 copying cap2/pipeline/short_read/kraken2.py -> build/lib/cap2/pipeline/short_read 2021-09-28T18:36:33,018 creating build/lib/cap2/pipeline/databases 2021-09-28T18:36:33,020 copying cap2/pipeline/databases/human_removal_db.py -> build/lib/cap2/pipeline/databases 2021-09-28T18:36:33,025 copying cap2/pipeline/databases/kraken2_db.py -> build/lib/cap2/pipeline/databases 2021-09-28T18:36:33,031 copying cap2/pipeline/databases/amr_db.py -> build/lib/cap2/pipeline/databases 2021-09-28T18:36:33,037 copying cap2/pipeline/databases/__init__.py -> build/lib/cap2/pipeline/databases 2021-09-28T18:36:33,042 copying cap2/pipeline/databases/hmp_db.py -> build/lib/cap2/pipeline/databases 2021-09-28T18:36:33,048 copying cap2/pipeline/databases/mouse_removal_db.py -> build/lib/cap2/pipeline/databases 2021-09-28T18:36:33,053 copying cap2/pipeline/databases/taxonomic_db.py -> build/lib/cap2/pipeline/databases 2021-09-28T18:36:33,059 copying cap2/pipeline/databases/fast_kraken2_db.py -> build/lib/cap2/pipeline/databases 2021-09-28T18:36:33,065 copying cap2/pipeline/databases/uniref.py -> build/lib/cap2/pipeline/databases 2021-09-28T18:36:33,071 creating build/lib/cap2/pipeline/contigs 2021-09-28T18:36:33,073 copying cap2/pipeline/contigs/amr_identification.py -> build/lib/cap2/pipeline/contigs 2021-09-28T18:36:33,077 copying cap2/pipeline/contigs/__init__.py -> build/lib/cap2/pipeline/contigs 2021-09-28T18:36:33,081 copying cap2/pipeline/contigs/prodigal.py -> build/lib/cap2/pipeline/contigs 2021-09-28T18:36:33,087 creating build/lib/cap2/pipeline/assembly 2021-09-28T18:36:33,089 copying cap2/pipeline/assembly/metaspades.py -> build/lib/cap2/pipeline/assembly 2021-09-28T18:36:33,096 copying cap2/pipeline/assembly/clean_contigs.py -> build/lib/cap2/pipeline/assembly 2021-09-28T18:36:33,102 copying cap2/pipeline/assembly/metabat2.py -> build/lib/cap2/pipeline/assembly 2021-09-28T18:36:33,107 copying cap2/pipeline/assembly/__init__.py -> build/lib/cap2/pipeline/assembly 2021-09-28T18:36:33,117 creating build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,119 copying cap2/pipeline/preprocessing/count_reads.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,126 copying cap2/pipeline/preprocessing/fastqc.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,131 copying cap2/pipeline/preprocessing/clean_reads.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,135 copying cap2/pipeline/preprocessing/remove_adapters.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,139 copying cap2/pipeline/preprocessing/control_sample_abundances.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,144 copying cap2/pipeline/preprocessing/fast_taxa.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,149 copying cap2/pipeline/preprocessing/basic_sample_stats.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,155 copying cap2/pipeline/preprocessing/map_to_human.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,161 copying cap2/pipeline/preprocessing/map_to_mouse.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,167 copying cap2/pipeline/preprocessing/error_correct_reads.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,173 copying cap2/pipeline/preprocessing/base_reads.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,178 copying cap2/pipeline/preprocessing/__init__.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,184 copying cap2/pipeline/preprocessing/multiqc.py -> build/lib/cap2/pipeline/preprocessing 2021-09-28T18:36:33,237 installing to build/bdist.linux-armv7l/wheel 2021-09-28T18:36:33,238 running install 2021-09-28T18:36:33,241 running install_lib 2021-09-28T18:36:33,248 creating build/bdist.linux-armv7l 2021-09-28T18:36:33,249 creating build/bdist.linux-armv7l/wheel 2021-09-28T18:36:33,253 creating build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,255 copying build/lib/tests/test_pangea.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,260 copying build/lib/tests/test_api.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,264 copying build/lib/tests/test_assembly.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,268 copying build/lib/tests/test_strainotyping.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,272 copying build/lib/tests/test_versions.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,279 copying build/lib/tests/test_pipeline_preprocessing.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,285 copying build/lib/tests/test_tcems.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,290 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,295 copying build/lib/tests/test_experimental_strain.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,301 copying build/lib/tests/test_experimental_covid.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,307 copying build/lib/tests/test_databases.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,313 copying build/lib/tests/test_short_read.py -> build/bdist.linux-armv7l/wheel/tests 2021-09-28T18:36:33,321 creating build/bdist.linux-armv7l/wheel/cap2 2021-09-28T18:36:33,324 copying build/lib/cap2/cli.py -> build/bdist.linux-armv7l/wheel/cap2 2021-09-28T18:36:33,329 copying build/lib/cap2/api.py -> build/bdist.linux-armv7l/wheel/cap2 2021-09-28T18:36:33,336 creating build/bdist.linux-armv7l/wheel/cap2/extensions 2021-09-28T18:36:33,338 copying build/lib/cap2/extensions/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions 2021-09-28T18:36:33,345 creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental 2021-09-28T18:36:33,347 copying build/lib/cap2/extensions/experimental/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental 2021-09-28T18:36:33,355 creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid 2021-09-28T18:36:33,357 copying build/lib/cap2/extensions/experimental/covid/make_pileup.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid 2021-09-28T18:36:33,361 copying build/lib/cap2/extensions/experimental/covid/covid_genome_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid 2021-09-28T18:36:33,365 copying build/lib/cap2/extensions/experimental/covid/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid 2021-09-28T18:36:33,370 copying build/lib/cap2/extensions/experimental/covid/align_to_covid_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid 2021-09-28T18:36:33,375 copying build/lib/cap2/extensions/experimental/covid/make_covid_consensus_seq.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid 2021-09-28T18:36:33,380 copying build/lib/cap2/extensions/experimental/covid/genome_coverage.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid 2021-09-28T18:36:33,385 copying build/lib/cap2/extensions/experimental/covid/fast_detect.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid 2021-09-28T18:36:33,391 copying build/lib/cap2/extensions/experimental/covid/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid 2021-09-28T18:36:33,396 copying build/lib/cap2/extensions/experimental/covid/call_covid_variants.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid 2021-09-28T18:36:33,403 creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems 2021-09-28T18:36:33,405 copying build/lib/cap2/extensions/experimental/tcems/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems 2021-09-28T18:36:33,412 copying build/lib/cap2/extensions/experimental/tcems/tcem_repertoire.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems 2021-09-28T18:36:33,418 copying build/lib/cap2/extensions/experimental/tcems/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems 2021-09-28T18:36:33,421 copying build/lib/cap2/extensions/experimental/tcems/tcem_aa_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems 2021-09-28T18:36:33,426 copying build/lib/cap2/extensions/experimental/tcems/mixcr.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems 2021-09-28T18:36:33,432 creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify 2021-09-28T18:36:33,434 copying build/lib/cap2/extensions/experimental/preclassify/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify 2021-09-28T18:36:33,440 copying build/lib/cap2/extensions/experimental/preclassify/preclassify_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify 2021-09-28T18:36:33,446 copying build/lib/cap2/extensions/experimental/preclassify/dynamic_pipeline.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify 2021-09-28T18:36:33,451 copying build/lib/cap2/extensions/experimental/preclassify/preclassify.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify 2021-09-28T18:36:33,458 copying build/lib/cap2/extensions/experimental/preclassify/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify 2021-09-28T18:36:33,464 creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,466 copying build/lib/cap2/extensions/experimental/strains/make_pileup.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,472 copying build/lib/cap2/extensions/experimental/strains/align_to_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,478 copying build/lib/cap2/extensions/experimental/strains/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,485 copying build/lib/cap2/extensions/experimental/strains/bacterial_genome_getter.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,490 copying build/lib/cap2/extensions/experimental/strains/make_snp_graph.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,496 copying build/lib/cap2/extensions/experimental/strains/merge_snp_graph.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,503 creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:33,505 copying build/lib/cap2/extensions/experimental/strains/strainotyping/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:33,511 copying build/lib/cap2/extensions/experimental/strains/strainotyping/api.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:33,516 copying build/lib/cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:33,521 copying build/lib/cap2/extensions/experimental/strains/strainotyping/graphs.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:33,525 copying build/lib/cap2/extensions/experimental/strains/strainotyping/io.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:33,529 copying build/lib/cap2/extensions/experimental/strains/strainotyping/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:33,533 copying build/lib/cap2/extensions/experimental/strains/strainotyping/clustering.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping 2021-09-28T18:36:33,536 copying build/lib/cap2/extensions/experimental/strains/merge_snp_clusters.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,541 copying build/lib/cap2/extensions/experimental/strains/tasks.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,547 copying build/lib/cap2/extensions/experimental/strains/make_snp_clusters.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,552 copying build/lib/cap2/extensions/experimental/strains/utils.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,558 copying build/lib/cap2/extensions/experimental/strains/get_microbial_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,563 copying build/lib/cap2/extensions/experimental/strains/make_snp_table.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,568 copying build/lib/cap2/extensions/experimental/strains/align_to_genome_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,574 copying build/lib/cap2/extensions/experimental/strains/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains 2021-09-28T18:36:33,579 copying build/lib/cap2/extensions/experimental/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental 2021-09-28T18:36:33,583 copying build/lib/cap2/extensions/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions 2021-09-28T18:36:33,588 copying build/lib/cap2/exceptions.py -> build/bdist.linux-armv7l/wheel/cap2 2021-09-28T18:36:33,595 creating build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,597 copying build/lib/cap2/pangea/cli.py -> build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,603 copying build/lib/cap2/pangea/cli_utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,608 copying build/lib/cap2/pangea/api.py -> build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,613 copying build/lib/cap2/pangea/sra_utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,616 copying build/lib/cap2/pangea/load_task.py -> build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,624 copying build/lib/cap2/pangea/utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,629 copying build/lib/cap2/pangea/download_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,633 copying build/lib/cap2/pangea/pangea_sample.py -> build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,640 copying build/lib/cap2/pangea/constants.py -> build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,644 copying build/lib/cap2/pangea/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pangea 2021-09-28T18:36:33,647 copying build/lib/cap2/setup_logging.py -> build/bdist.linux-armv7l/wheel/cap2 2021-09-28T18:36:33,651 copying build/lib/cap2/utils.py -> build/bdist.linux-armv7l/wheel/cap2 2021-09-28T18:36:33,656 creating build/bdist.linux-armv7l/wheel/cap2/capalyzer 2021-09-28T18:36:33,658 copying build/lib/cap2/capalyzer/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer 2021-09-28T18:36:33,662 copying build/lib/cap2/capalyzer/cli.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer 2021-09-28T18:36:33,667 creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder 2021-09-28T18:36:33,669 copying build/lib/cap2/capalyzer/table_builder/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder 2021-09-28T18:36:33,674 creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:33,676 copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:33,680 copying build/lib/cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:33,686 copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:33,691 copying build/lib/cap2/capalyzer/table_builder/modules/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:33,697 copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:33,702 copying build/lib/cap2/capalyzer/table_builder/modules/covid_variant_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:33,706 copying build/lib/cap2/capalyzer/table_builder/modules/basic_stats_summary.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules 2021-09-28T18:36:33,710 copying build/lib/cap2/capalyzer/table_builder/base_module.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder 2021-09-28T18:36:33,714 copying build/lib/cap2/capalyzer/table_builder/cap_table_builder.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder 2021-09-28T18:36:33,718 copying build/lib/cap2/capalyzer/table_builder/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder 2021-09-28T18:36:33,722 copying build/lib/cap2/capalyzer/version.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer 2021-09-28T18:36:33,727 creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser 2021-09-28T18:36:33,729 copying build/lib/cap2/capalyzer/table_parser/analysis_utils.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser 2021-09-28T18:36:33,734 copying build/lib/cap2/capalyzer/table_parser/cap_table_parser.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser 2021-09-28T18:36:33,738 copying build/lib/cap2/capalyzer/table_parser/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser 2021-09-28T18:36:33,742 copying build/lib/cap2/capalyzer/exceptions.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer 2021-09-28T18:36:33,747 creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea 2021-09-28T18:36:33,748 copying build/lib/cap2/capalyzer/pangea/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea 2021-09-28T18:36:33,753 copying build/lib/cap2/capalyzer/pangea/cli.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea 2021-09-28T18:36:33,756 copying build/lib/cap2/capalyzer/pangea/api.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea 2021-09-28T18:36:33,760 copying build/lib/cap2/capalyzer/pangea/pangea_file_uploader.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea 2021-09-28T18:36:33,765 copying build/lib/cap2/capalyzer/pangea/pangea_file_source.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea 2021-09-28T18:36:33,769 copying build/lib/cap2/capalyzer/pangea/utils.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea 2021-09-28T18:36:33,772 copying build/lib/cap2/capalyzer/pangea/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea 2021-09-28T18:36:33,776 copying build/lib/cap2/capalyzer/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer 2021-09-28T18:36:33,780 copying build/lib/cap2/constants.py -> build/bdist.linux-armv7l/wheel/cap2 2021-09-28T18:36:33,783 copying build/lib/cap2/__init__.py -> build/bdist.linux-armv7l/wheel/cap2 2021-09-28T18:36:33,787 copying build/lib/cap2/sample.py -> build/bdist.linux-armv7l/wheel/cap2 2021-09-28T18:36:33,792 creating build/bdist.linux-armv7l/wheel/cap2/pipeline 2021-09-28T18:36:33,795 creating build/bdist.linux-armv7l/wheel/cap2/pipeline/utils 2021-09-28T18:36:33,797 copying build/lib/cap2/pipeline/utils/cap_task.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils 2021-09-28T18:36:33,803 copying build/lib/cap2/pipeline/utils/conda.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils 2021-09-28T18:36:33,808 copying build/lib/cap2/pipeline/utils/utils.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils 2021-09-28T18:36:33,811 copying build/lib/cap2/pipeline/utils/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils 2021-09-28T18:36:33,817 creating build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,818 copying build/lib/cap2/pipeline/short_read/processed_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,823 copying build/lib/cap2/pipeline/short_read/read_stats.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,827 copying build/lib/cap2/pipeline/short_read/amrs.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,832 copying build/lib/cap2/pipeline/short_read/hmp_comparison.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,836 copying build/lib/cap2/pipeline/short_read/mash.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,840 copying build/lib/cap2/pipeline/short_read/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,844 copying build/lib/cap2/pipeline/short_read/jellyfish.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,848 copying build/lib/cap2/pipeline/short_read/humann2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,852 copying build/lib/cap2/pipeline/short_read/microbe_census.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,856 copying build/lib/cap2/pipeline/short_read/kraken2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read 2021-09-28T18:36:33,861 copying build/lib/cap2/pipeline/full_pipeline.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline 2021-09-28T18:36:33,867 creating build/bdist.linux-armv7l/wheel/cap2/pipeline/databases 2021-09-28T18:36:33,870 copying build/lib/cap2/pipeline/databases/human_removal_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases 2021-09-28T18:36:33,876 copying build/lib/cap2/pipeline/databases/kraken2_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases 2021-09-28T18:36:33,882 copying build/lib/cap2/pipeline/databases/amr_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases 2021-09-28T18:36:33,887 copying build/lib/cap2/pipeline/databases/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases 2021-09-28T18:36:33,891 copying build/lib/cap2/pipeline/databases/hmp_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases 2021-09-28T18:36:33,895 copying build/lib/cap2/pipeline/databases/mouse_removal_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases 2021-09-28T18:36:33,900 copying build/lib/cap2/pipeline/databases/taxonomic_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases 2021-09-28T18:36:33,904 copying build/lib/cap2/pipeline/databases/fast_kraken2_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases 2021-09-28T18:36:33,909 copying build/lib/cap2/pipeline/databases/uniref.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases 2021-09-28T18:36:33,917 creating build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs 2021-09-28T18:36:33,919 copying build/lib/cap2/pipeline/contigs/amr_identification.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs 2021-09-28T18:36:33,925 copying build/lib/cap2/pipeline/contigs/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs 2021-09-28T18:36:33,929 copying build/lib/cap2/pipeline/contigs/prodigal.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs 2021-09-28T18:36:33,933 copying build/lib/cap2/pipeline/constants.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline 2021-09-28T18:36:33,937 copying build/lib/cap2/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline 2021-09-28T18:36:33,941 creating build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly 2021-09-28T18:36:33,943 copying build/lib/cap2/pipeline/assembly/metaspades.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly 2021-09-28T18:36:33,947 copying build/lib/cap2/pipeline/assembly/clean_contigs.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly 2021-09-28T18:36:33,951 copying build/lib/cap2/pipeline/assembly/metabat2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly 2021-09-28T18:36:33,955 copying build/lib/cap2/pipeline/assembly/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly 2021-09-28T18:36:33,959 copying build/lib/cap2/pipeline/config.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline 2021-09-28T18:36:33,964 creating build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:33,967 copying build/lib/cap2/pipeline/preprocessing/count_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:33,972 copying build/lib/cap2/pipeline/preprocessing/fastqc.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:33,978 copying build/lib/cap2/pipeline/preprocessing/clean_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:33,984 copying build/lib/cap2/pipeline/preprocessing/remove_adapters.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:33,991 copying build/lib/cap2/pipeline/preprocessing/control_sample_abundances.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:33,996 copying build/lib/cap2/pipeline/preprocessing/fast_taxa.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:34,000 copying build/lib/cap2/pipeline/preprocessing/basic_sample_stats.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:34,005 copying build/lib/cap2/pipeline/preprocessing/map_to_human.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:34,009 copying build/lib/cap2/pipeline/preprocessing/map_to_mouse.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:34,013 copying build/lib/cap2/pipeline/preprocessing/error_correct_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:34,017 copying build/lib/cap2/pipeline/preprocessing/base_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:34,021 copying build/lib/cap2/pipeline/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:34,025 copying build/lib/cap2/pipeline/preprocessing/multiqc.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing 2021-09-28T18:36:34,029 running install_egg_info 2021-09-28T18:36:34,085 running egg_info 2021-09-28T18:36:34,087 writing requirements to cap2.egg-info/requires.txt 2021-09-28T18:36:34,090 writing top-level names to cap2.egg-info/top_level.txt 2021-09-28T18:36:34,091 writing cap2.egg-info/PKG-INFO 2021-09-28T18:36:34,095 writing entry points to cap2.egg-info/entry_points.txt 2021-09-28T18:36:34,098 writing dependency_links to cap2.egg-info/dependency_links.txt 2021-09-28T18:36:34,141 reading manifest file 'cap2.egg-info/SOURCES.txt' 2021-09-28T18:36:34,177 writing manifest file 'cap2.egg-info/SOURCES.txt' 2021-09-28T18:36:34,181 Copying cap2.egg-info to build/bdist.linux-armv7l/wheel/cap2-0.5.2-py3.5.egg-info 2021-09-28T18:36:34,210 running install_scripts 2021-09-28T18:36:34,436 creating build/bdist.linux-armv7l/wheel/cap2-0.5.2.dist-info/WHEEL 2021-09-28T18:36:35,384 Building wheel for cap2 (setup.py): finished with status 'done' 2021-09-28T18:36:35,390 Created wheel for cap2: filename=cap2-0.5.2-py3-none-any.whl size=142396 sha256=648c5d557bf7909f6c526187792d2a5120228db432fec248593d0f5441aea890 2021-09-28T18:36:35,391 Stored in directory: /tmp/pip-ephem-wheel-cache-dfnbl5r4/wheels/76/ff/af/da1c334b08bfcdf8555e1203e522e82c929831536ccad1c216 2021-09-28T18:36:35,421 Successfully built cap2 2021-09-28T18:36:35,449 Removed build tracker: '/tmp/pip-req-tracker-ey8i2ofj'