2021-09-28T18:08:58,029 Created temporary directory: /tmp/pip-ephem-wheel-cache-jxnzul5c
2021-09-28T18:08:58,036 Created temporary directory: /tmp/pip-req-tracker-n4c33io7
2021-09-28T18:08:58,036 Initialized build tracking at /tmp/pip-req-tracker-n4c33io7
2021-09-28T18:08:58,037 Created build tracker: /tmp/pip-req-tracker-n4c33io7
2021-09-28T18:08:58,037 Entered build tracker: /tmp/pip-req-tracker-n4c33io7
2021-09-28T18:08:58,039 Created temporary directory: /tmp/pip-wheel-f8zfpir1
2021-09-28T18:08:58,104 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2021-09-28T18:08:58,108 2 location(s) to search for versions of cap2:
2021-09-28T18:08:58,108 * https://pypi.org/simple/cap2/
2021-09-28T18:08:58,108 * https://www.piwheels.org/simple/cap2/
2021-09-28T18:08:58,108 Fetching project page and analyzing links: https://pypi.org/simple/cap2/
2021-09-28T18:08:58,111 Getting page https://pypi.org/simple/cap2/
2021-09-28T18:08:58,115 Found index url https://pypi.org/simple
2021-09-28T18:08:58,451   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/)
2021-09-28T18:08:58,452   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/)
2021-09-28T18:08:58,453   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
2021-09-28T18:08:58,454   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/)
2021-09-28T18:08:58,455   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
2021-09-28T18:08:58,456   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
2021-09-28T18:08:58,457   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
2021-09-28T18:08:58,457 Fetching project page and analyzing links: https://www.piwheels.org/simple/cap2/
2021-09-28T18:08:58,458 Getting page https://www.piwheels.org/simple/cap2/
2021-09-28T18:08:58,461 Found index url https://www.piwheels.org/simple
2021-09-28T18:08:58,617   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/)
2021-09-28T18:08:58,618   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/)
2021-09-28T18:08:58,649 Given no hashes to check 1 links for project 'cap2': discarding no candidates
2021-09-28T18:08:58,681 Collecting cap2==0.5.1
2021-09-28T18:08:58,684   Created temporary directory: /tmp/pip-unpack-j4444wfh
2021-09-28T18:08:58,901   Downloading cap2-0.5.1.tar.gz (79 kB)
2021-09-28T18:08:59,797   Added cap2==0.5.1 from https://files.pythonhosted.org/packages/42/0a/8123696bb01d00ce7c7151bd6ca3607822a68e6cf568378be7716e2cf20c/cap2-0.5.1.tar.gz#sha256=cf487e8f2e798f276dc00b19c57840bb0f9e432143f0343e182dbc071b2b125d to build tracker '/tmp/pip-req-tracker-n4c33io7'
2021-09-28T18:08:59,799     Running setup.py (path:/tmp/pip-wheel-f8zfpir1/cap2_f5479fe84c134402b898c4982f35f712/setup.py) egg_info for package cap2
2021-09-28T18:08:59,800     Created temporary directory: /tmp/pip-pip-egg-info-l1qf_3f6
2021-09-28T18:08:59,801     Running command python setup.py egg_info
2021-09-28T18:09:01,868     running egg_info
2021-09-28T18:09:01,875     creating /tmp/pip-pip-egg-info-l1qf_3f6/cap2.egg-info
2021-09-28T18:09:01,880     writing /tmp/pip-pip-egg-info-l1qf_3f6/cap2.egg-info/PKG-INFO
2021-09-28T18:09:01,887     writing entry points to /tmp/pip-pip-egg-info-l1qf_3f6/cap2.egg-info/entry_points.txt
2021-09-28T18:09:01,890     writing requirements to /tmp/pip-pip-egg-info-l1qf_3f6/cap2.egg-info/requires.txt
2021-09-28T18:09:01,894     writing top-level names to /tmp/pip-pip-egg-info-l1qf_3f6/cap2.egg-info/top_level.txt
2021-09-28T18:09:01,897     writing dependency_links to /tmp/pip-pip-egg-info-l1qf_3f6/cap2.egg-info/dependency_links.txt
2021-09-28T18:09:01,902     writing manifest file '/tmp/pip-pip-egg-info-l1qf_3f6/cap2.egg-info/SOURCES.txt'
2021-09-28T18:09:02,306     reading manifest file '/tmp/pip-pip-egg-info-l1qf_3f6/cap2.egg-info/SOURCES.txt'
2021-09-28T18:09:02,327     writing manifest file '/tmp/pip-pip-egg-info-l1qf_3f6/cap2.egg-info/SOURCES.txt'
2021-09-28T18:09:02,461   Source in /tmp/pip-wheel-f8zfpir1/cap2_f5479fe84c134402b898c4982f35f712 has version 0.5.1, which satisfies requirement cap2==0.5.1 from https://files.pythonhosted.org/packages/42/0a/8123696bb01d00ce7c7151bd6ca3607822a68e6cf568378be7716e2cf20c/cap2-0.5.1.tar.gz#sha256=cf487e8f2e798f276dc00b19c57840bb0f9e432143f0343e182dbc071b2b125d
2021-09-28T18:09:02,463   Removed cap2==0.5.1 from https://files.pythonhosted.org/packages/42/0a/8123696bb01d00ce7c7151bd6ca3607822a68e6cf568378be7716e2cf20c/cap2-0.5.1.tar.gz#sha256=cf487e8f2e798f276dc00b19c57840bb0f9e432143f0343e182dbc071b2b125d from build tracker '/tmp/pip-req-tracker-n4c33io7'
2021-09-28T18:09:02,471 Created temporary directory: /tmp/pip-unpack-cx_uh9ag
2021-09-28T18:09:02,472 Building wheels for collected packages: cap2
2021-09-28T18:09:02,480   Created temporary directory: /tmp/pip-wheel-oeosd3ng
2021-09-28T18:09:02,481   Building wheel for cap2 (setup.py): started
2021-09-28T18:09:02,482   Destination directory: /tmp/pip-wheel-oeosd3ng
2021-09-28T18:09:02,483   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-f8zfpir1/cap2_f5479fe84c134402b898c4982f35f712/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-f8zfpir1/cap2_f5479fe84c134402b898c4982f35f712/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-oeosd3ng
2021-09-28T18:09:04,480   running bdist_wheel
2021-09-28T18:09:04,494   running build
2021-09-28T18:09:04,495   running build_py
2021-09-28T18:09:04,834   creating build
2021-09-28T18:09:04,835   creating build/lib
2021-09-28T18:09:04,836   creating build/lib/tests
2021-09-28T18:09:04,839   copying tests/test_experimental_strain.py -> build/lib/tests
2021-09-28T18:09:04,845   copying tests/test_versions.py -> build/lib/tests
2021-09-28T18:09:04,850   copying tests/test_experimental_covid.py -> build/lib/tests
2021-09-28T18:09:04,855   copying tests/test_strainotyping.py -> build/lib/tests
2021-09-28T18:09:04,859   copying tests/test_assembly.py -> build/lib/tests
2021-09-28T18:09:04,863   copying tests/test_tcems.py -> build/lib/tests
2021-09-28T18:09:04,868   copying tests/test_short_read.py -> build/lib/tests
2021-09-28T18:09:04,874   copying tests/__init__.py -> build/lib/tests
2021-09-28T18:09:04,879   copying tests/test_pipeline_preprocessing.py -> build/lib/tests
2021-09-28T18:09:04,886   copying tests/test_databases.py -> build/lib/tests
2021-09-28T18:09:04,891   copying tests/test_pangea.py -> build/lib/tests
2021-09-28T18:09:04,897   copying tests/test_api.py -> build/lib/tests
2021-09-28T18:09:04,903   creating build/lib/cap2
2021-09-28T18:09:04,906   copying cap2/setup_logging.py -> build/lib/cap2
2021-09-28T18:09:04,912   copying cap2/api.py -> build/lib/cap2
2021-09-28T18:09:04,917   copying cap2/constants.py -> build/lib/cap2
2021-09-28T18:09:04,922   copying cap2/cli.py -> build/lib/cap2
2021-09-28T18:09:04,927   copying cap2/__init__.py -> build/lib/cap2
2021-09-28T18:09:04,931   copying cap2/utils.py -> build/lib/cap2
2021-09-28T18:09:04,936   copying cap2/exceptions.py -> build/lib/cap2
2021-09-28T18:09:04,940   copying cap2/sample.py -> build/lib/cap2
2021-09-28T18:09:04,947   creating build/lib/cap2/pipeline
2021-09-28T18:09:04,950   copying cap2/pipeline/config.py -> build/lib/cap2/pipeline
2021-09-28T18:09:04,955   copying cap2/pipeline/constants.py -> build/lib/cap2/pipeline
2021-09-28T18:09:04,960   copying cap2/pipeline/__init__.py -> build/lib/cap2/pipeline
2021-09-28T18:09:04,964   copying cap2/pipeline/full_pipeline.py -> build/lib/cap2/pipeline
2021-09-28T18:09:04,970   creating build/lib/cap2/capalyzer
2021-09-28T18:09:04,973   copying cap2/capalyzer/parsers.py -> build/lib/cap2/capalyzer
2021-09-28T18:09:04,979   copying cap2/capalyzer/cli.py -> build/lib/cap2/capalyzer
2021-09-28T18:09:04,983   copying cap2/capalyzer/__init__.py -> build/lib/cap2/capalyzer
2021-09-28T18:09:04,988   copying cap2/capalyzer/version.py -> build/lib/cap2/capalyzer
2021-09-28T18:09:04,993   copying cap2/capalyzer/exceptions.py -> build/lib/cap2/capalyzer
2021-09-28T18:09:05,000   creating build/lib/cap2/extensions
2021-09-28T18:09:05,003   copying cap2/extensions/cli.py -> build/lib/cap2/extensions
2021-09-28T18:09:05,008   copying cap2/extensions/__init__.py -> build/lib/cap2/extensions
2021-09-28T18:09:05,014   creating build/lib/cap2/pangea
2021-09-28T18:09:05,016   copying cap2/pangea/cli_utils.py -> build/lib/cap2/pangea
2021-09-28T18:09:05,021   copying cap2/pangea/api.py -> build/lib/cap2/pangea
2021-09-28T18:09:05,026   copying cap2/pangea/constants.py -> build/lib/cap2/pangea
2021-09-28T18:09:05,030   copying cap2/pangea/sra_utils.py -> build/lib/cap2/pangea
2021-09-28T18:09:05,034   copying cap2/pangea/download_reads.py -> build/lib/cap2/pangea
2021-09-28T18:09:05,038   copying cap2/pangea/load_task.py -> build/lib/cap2/pangea
2021-09-28T18:09:05,044   copying cap2/pangea/cli.py -> build/lib/cap2/pangea
2021-09-28T18:09:05,050   copying cap2/pangea/pangea_sample.py -> build/lib/cap2/pangea
2021-09-28T18:09:05,058   copying cap2/pangea/__init__.py -> build/lib/cap2/pangea
2021-09-28T18:09:05,064   copying cap2/pangea/utils.py -> build/lib/cap2/pangea
2021-09-28T18:09:05,072   creating build/lib/cap2/pipeline/utils
2021-09-28T18:09:05,075   copying cap2/pipeline/utils/cap_task.py -> build/lib/cap2/pipeline/utils
2021-09-28T18:09:05,081   copying cap2/pipeline/utils/__init__.py -> build/lib/cap2/pipeline/utils
2021-09-28T18:09:05,086   copying cap2/pipeline/utils/utils.py -> build/lib/cap2/pipeline/utils
2021-09-28T18:09:05,091   copying cap2/pipeline/utils/conda.py -> build/lib/cap2/pipeline/utils
2021-09-28T18:09:05,098   creating build/lib/cap2/pipeline/contigs
2021-09-28T18:09:05,101   copying cap2/pipeline/contigs/prodigal.py -> build/lib/cap2/pipeline/contigs
2021-09-28T18:09:05,106   copying cap2/pipeline/contigs/__init__.py -> build/lib/cap2/pipeline/contigs
2021-09-28T18:09:05,111   copying cap2/pipeline/contigs/amr_identification.py -> build/lib/cap2/pipeline/contigs
2021-09-28T18:09:05,118   creating build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,121   copying cap2/pipeline/preprocessing/control_sample_abundances.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,127   copying cap2/pipeline/preprocessing/fast_taxa.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,132   copying cap2/pipeline/preprocessing/count_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,137   copying cap2/pipeline/preprocessing/basic_sample_stats.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,142   copying cap2/pipeline/preprocessing/map_to_mouse.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,148   copying cap2/pipeline/preprocessing/remove_adapters.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,153   copying cap2/pipeline/preprocessing/fastqc.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,158   copying cap2/pipeline/preprocessing/error_correct_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,163   copying cap2/pipeline/preprocessing/clean_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,168   copying cap2/pipeline/preprocessing/__init__.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,173   copying cap2/pipeline/preprocessing/base_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,178   copying cap2/pipeline/preprocessing/map_to_human.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,183   copying cap2/pipeline/preprocessing/multiqc.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T18:09:05,189   creating build/lib/cap2/pipeline/assembly
2021-09-28T18:09:05,192   copying cap2/pipeline/assembly/metaspades.py -> build/lib/cap2/pipeline/assembly
2021-09-28T18:09:05,197   copying cap2/pipeline/assembly/__init__.py -> build/lib/cap2/pipeline/assembly
2021-09-28T18:09:05,202   copying cap2/pipeline/assembly/clean_contigs.py -> build/lib/cap2/pipeline/assembly
2021-09-28T18:09:05,207   copying cap2/pipeline/assembly/metabat2.py -> build/lib/cap2/pipeline/assembly
2021-09-28T18:09:05,214   creating build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,217   copying cap2/pipeline/short_read/kraken2.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,223   copying cap2/pipeline/short_read/amrs.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,229   copying cap2/pipeline/short_read/mash.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,234   copying cap2/pipeline/short_read/hmp_comparison.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,238   copying cap2/pipeline/short_read/__init__.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,243   copying cap2/pipeline/short_read/processed_reads.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,248   copying cap2/pipeline/short_read/jellyfish.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,252   copying cap2/pipeline/short_read/microbe_census.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,258   copying cap2/pipeline/short_read/humann2.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,264   copying cap2/pipeline/short_read/read_stats.py -> build/lib/cap2/pipeline/short_read
2021-09-28T18:09:05,273   creating build/lib/cap2/pipeline/databases
2021-09-28T18:09:05,276   copying cap2/pipeline/databases/taxonomic_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:09:05,282   copying cap2/pipeline/databases/human_removal_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:09:05,288   copying cap2/pipeline/databases/fast_kraken2_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:09:05,293   copying cap2/pipeline/databases/mouse_removal_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:09:05,298   copying cap2/pipeline/databases/uniref.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:09:05,302   copying cap2/pipeline/databases/hmp_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:09:05,306   copying cap2/pipeline/databases/__init__.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:09:05,310   copying cap2/pipeline/databases/kraken2_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:09:05,317   copying cap2/pipeline/databases/amr_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T18:09:05,325   creating build/lib/cap2/capalyzer/table_parser
2021-09-28T18:09:05,327   copying cap2/capalyzer/table_parser/cap_table_parser.py -> build/lib/cap2/capalyzer/table_parser
2021-09-28T18:09:05,334   copying cap2/capalyzer/table_parser/analysis_utils.py -> build/lib/cap2/capalyzer/table_parser
2021-09-28T18:09:05,339   copying cap2/capalyzer/table_parser/__init__.py -> build/lib/cap2/capalyzer/table_parser
2021-09-28T18:09:05,344   creating build/lib/cap2/capalyzer/pangea
2021-09-28T18:09:05,346   copying cap2/capalyzer/pangea/parsers.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:09:05,351   copying cap2/capalyzer/pangea/api.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:09:05,356   copying cap2/capalyzer/pangea/cli.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:09:05,361   copying cap2/capalyzer/pangea/__init__.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:09:05,367   copying cap2/capalyzer/pangea/pangea_file_uploader.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:09:05,373   copying cap2/capalyzer/pangea/pangea_file_source.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:09:05,378   copying cap2/capalyzer/pangea/utils.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T18:09:05,383   creating build/lib/cap2/capalyzer/table_builder
2021-09-28T18:09:05,385   copying cap2/capalyzer/table_builder/parsers.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T18:09:05,389   copying cap2/capalyzer/table_builder/__init__.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T18:09:05,393   copying cap2/capalyzer/table_builder/base_module.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T18:09:05,399   copying cap2/capalyzer/table_builder/cap_table_builder.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T18:09:05,408   creating build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:05,411   copying cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:05,417   copying cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:05,422   copying cap2/capalyzer/table_builder/modules/basic_stats_summary.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:05,427   copying cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:05,431   copying cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:05,436   copying cap2/capalyzer/table_builder/modules/__init__.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:05,442   copying cap2/capalyzer/table_builder/modules/covid_variant_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:05,451   creating build/lib/cap2/extensions/experimental
2021-09-28T18:09:05,454   copying cap2/extensions/experimental/cli.py -> build/lib/cap2/extensions/experimental
2021-09-28T18:09:05,459   copying cap2/extensions/experimental/__init__.py -> build/lib/cap2/extensions/experimental
2021-09-28T18:09:05,465   creating build/lib/cap2/extensions/experimental/covid
2021-09-28T18:09:05,467   copying cap2/extensions/experimental/covid/covid_genome_db.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:09:05,473   copying cap2/extensions/experimental/covid/make_covid_consensus_seq.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:09:05,478   copying cap2/extensions/experimental/covid/align_to_covid_genome.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:09:05,485   copying cap2/extensions/experimental/covid/genome_coverage.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:09:05,491   copying cap2/extensions/experimental/covid/fast_detect.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:09:05,498   copying cap2/extensions/experimental/covid/cli.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:09:05,505   copying cap2/extensions/experimental/covid/make_pileup.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:09:05,511   copying cap2/extensions/experimental/covid/__init__.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:09:05,517   copying cap2/extensions/experimental/covid/call_covid_variants.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T18:09:05,526   creating build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:09:05,529   copying cap2/extensions/experimental/preclassify/preclassify.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:09:05,536   copying cap2/extensions/experimental/preclassify/dynamic_pipeline.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:09:05,540   copying cap2/extensions/experimental/preclassify/cli.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:09:05,545   copying cap2/extensions/experimental/preclassify/__init__.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:09:05,548   copying cap2/extensions/experimental/preclassify/preclassify_db.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T18:09:05,555   creating build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,557   copying cap2/extensions/experimental/strains/merge_snp_graph.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,563   copying cap2/extensions/experimental/strains/align_to_genome.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,569   copying cap2/extensions/experimental/strains/get_microbial_genome.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,575   copying cap2/extensions/experimental/strains/tasks.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,581   copying cap2/extensions/experimental/strains/bacterial_genome_getter.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,587   copying cap2/extensions/experimental/strains/align_to_genome_db.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,593   copying cap2/extensions/experimental/strains/cli.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,600   copying cap2/extensions/experimental/strains/make_pileup.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,605   copying cap2/extensions/experimental/strains/__init__.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,611   copying cap2/extensions/experimental/strains/make_snp_table.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,616   copying cap2/extensions/experimental/strains/make_snp_graph.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,621   copying cap2/extensions/experimental/strains/merge_snp_clusters.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,625   copying cap2/extensions/experimental/strains/make_snp_clusters.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,629   copying cap2/extensions/experimental/strains/utils.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T18:09:05,634   creating build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:09:05,636   copying cap2/extensions/experimental/tcems/cli.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:09:05,643   copying cap2/extensions/experimental/tcems/__init__.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:09:05,647   copying cap2/extensions/experimental/tcems/tcem_aa_db.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:09:05,655   copying cap2/extensions/experimental/tcems/tcem_repertoire.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:09:05,662   copying cap2/extensions/experimental/tcems/mixcr.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T18:09:05,671   creating build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:05,674   copying cap2/extensions/experimental/strains/strainotyping/api.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:05,680   copying cap2/extensions/experimental/strains/strainotyping/io.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:05,684   copying cap2/extensions/experimental/strains/strainotyping/graphs.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:05,688   copying cap2/extensions/experimental/strains/strainotyping/cli.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:05,692   copying cap2/extensions/experimental/strains/strainotyping/__init__.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:05,696   copying cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:05,701   copying cap2/extensions/experimental/strains/strainotyping/clustering.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:05,759   installing to build/bdist.linux-armv7l/wheel
2021-09-28T18:09:05,760   running install
2021-09-28T18:09:05,762   running install_lib
2021-09-28T18:09:05,771   creating build/bdist.linux-armv7l
2021-09-28T18:09:05,771   creating build/bdist.linux-armv7l/wheel
2021-09-28T18:09:05,775   creating build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,777   copying build/lib/tests/test_experimental_strain.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,782   copying build/lib/tests/test_versions.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,787   copying build/lib/tests/test_experimental_covid.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,792   copying build/lib/tests/test_strainotyping.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,796   copying build/lib/tests/test_assembly.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,800   copying build/lib/tests/test_tcems.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,805   copying build/lib/tests/test_short_read.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,811   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,816   copying build/lib/tests/test_pipeline_preprocessing.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,823   copying build/lib/tests/test_databases.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,828   copying build/lib/tests/test_pangea.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,833   copying build/lib/tests/test_api.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T18:09:05,838   creating build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:09:05,840   copying build/lib/cap2/setup_logging.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:09:05,845   copying build/lib/cap2/api.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:09:05,850   copying build/lib/cap2/constants.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:09:05,857   creating build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T18:09:05,861   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T18:09:05,864   copying build/lib/cap2/pipeline/utils/cap_task.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T18:09:05,870   copying build/lib/cap2/pipeline/utils/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T18:09:05,874   copying build/lib/cap2/pipeline/utils/utils.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T18:09:05,878   copying build/lib/cap2/pipeline/utils/conda.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T18:09:05,883   copying build/lib/cap2/pipeline/config.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T18:09:05,889   copying build/lib/cap2/pipeline/constants.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T18:09:05,895   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T18:09:05,898   copying build/lib/cap2/pipeline/contigs/prodigal.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T18:09:05,904   copying build/lib/cap2/pipeline/contigs/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T18:09:05,908   copying build/lib/cap2/pipeline/contigs/amr_identification.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T18:09:05,913   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,915   copying build/lib/cap2/pipeline/preprocessing/control_sample_abundances.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,921   copying build/lib/cap2/pipeline/preprocessing/fast_taxa.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,925   copying build/lib/cap2/pipeline/preprocessing/count_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,930   copying build/lib/cap2/pipeline/preprocessing/basic_sample_stats.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,936   copying build/lib/cap2/pipeline/preprocessing/map_to_mouse.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,941   copying build/lib/cap2/pipeline/preprocessing/remove_adapters.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,947   copying build/lib/cap2/pipeline/preprocessing/fastqc.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,951   copying build/lib/cap2/pipeline/preprocessing/error_correct_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,955   copying build/lib/cap2/pipeline/preprocessing/clean_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,959   copying build/lib/cap2/pipeline/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,963   copying build/lib/cap2/pipeline/preprocessing/base_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,967   copying build/lib/cap2/pipeline/preprocessing/map_to_human.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,971   copying build/lib/cap2/pipeline/preprocessing/multiqc.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T18:09:05,975   copying build/lib/cap2/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T18:09:05,979   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T18:09:05,981   copying build/lib/cap2/pipeline/assembly/metaspades.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T18:09:05,986   copying build/lib/cap2/pipeline/assembly/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T18:09:05,991   copying build/lib/cap2/pipeline/assembly/clean_contigs.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T18:09:05,996   copying build/lib/cap2/pipeline/assembly/metabat2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T18:09:06,004   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,006   copying build/lib/cap2/pipeline/short_read/kraken2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,011   copying build/lib/cap2/pipeline/short_read/amrs.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,016   copying build/lib/cap2/pipeline/short_read/mash.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,020   copying build/lib/cap2/pipeline/short_read/hmp_comparison.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,024   copying build/lib/cap2/pipeline/short_read/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,029   copying build/lib/cap2/pipeline/short_read/processed_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,035   copying build/lib/cap2/pipeline/short_read/jellyfish.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,041   copying build/lib/cap2/pipeline/short_read/microbe_census.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,046   copying build/lib/cap2/pipeline/short_read/humann2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,052   copying build/lib/cap2/pipeline/short_read/read_stats.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T18:09:06,057   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:09:06,059   copying build/lib/cap2/pipeline/databases/taxonomic_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:09:06,063   copying build/lib/cap2/pipeline/databases/human_removal_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:09:06,068   copying build/lib/cap2/pipeline/databases/fast_kraken2_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:09:06,073   copying build/lib/cap2/pipeline/databases/mouse_removal_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:09:06,079   copying build/lib/cap2/pipeline/databases/uniref.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:09:06,085   copying build/lib/cap2/pipeline/databases/hmp_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:09:06,090   copying build/lib/cap2/pipeline/databases/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:09:06,094   copying build/lib/cap2/pipeline/databases/kraken2_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:09:06,099   copying build/lib/cap2/pipeline/databases/amr_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T18:09:06,103   copying build/lib/cap2/pipeline/full_pipeline.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T18:09:06,108   copying build/lib/cap2/cli.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:09:06,115   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:09:06,118   copying build/lib/cap2/capalyzer/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:09:06,124   copying build/lib/cap2/capalyzer/cli.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:09:06,129   copying build/lib/cap2/capalyzer/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:09:06,133   copying build/lib/cap2/capalyzer/version.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:09:06,138   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T18:09:06,139   copying build/lib/cap2/capalyzer/table_parser/cap_table_parser.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T18:09:06,144   copying build/lib/cap2/capalyzer/table_parser/analysis_utils.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T18:09:06,149   copying build/lib/cap2/capalyzer/table_parser/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T18:09:06,155   copying build/lib/cap2/capalyzer/exceptions.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T18:09:06,162   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:09:06,164   copying build/lib/cap2/capalyzer/pangea/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:09:06,170   copying build/lib/cap2/capalyzer/pangea/api.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:09:06,174   copying build/lib/cap2/capalyzer/pangea/cli.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:09:06,178   copying build/lib/cap2/capalyzer/pangea/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:09:06,182   copying build/lib/cap2/capalyzer/pangea/pangea_file_uploader.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:09:06,187   copying build/lib/cap2/capalyzer/pangea/pangea_file_source.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:09:06,191   copying build/lib/cap2/capalyzer/pangea/utils.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T18:09:06,198   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T18:09:06,201   copying build/lib/cap2/capalyzer/table_builder/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T18:09:06,214   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:06,216   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:06,222   copying build/lib/cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:06,227   copying build/lib/cap2/capalyzer/table_builder/modules/basic_stats_summary.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:06,232   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:06,242   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:06,246   copying build/lib/cap2/capalyzer/table_builder/modules/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:06,250   copying build/lib/cap2/capalyzer/table_builder/modules/covid_variant_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T18:09:06,255   copying build/lib/cap2/capalyzer/table_builder/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T18:09:06,261   copying build/lib/cap2/capalyzer/table_builder/base_module.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T18:09:06,266   copying build/lib/cap2/capalyzer/table_builder/cap_table_builder.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T18:09:06,274   creating build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-28T18:09:06,277   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-28T18:09:06,280   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:09:06,282   copying build/lib/cap2/extensions/experimental/covid/covid_genome_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:09:06,287   copying build/lib/cap2/extensions/experimental/covid/make_covid_consensus_seq.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:09:06,291   copying build/lib/cap2/extensions/experimental/covid/align_to_covid_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:09:06,298   copying build/lib/cap2/extensions/experimental/covid/genome_coverage.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:09:06,303   copying build/lib/cap2/extensions/experimental/covid/fast_detect.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:09:06,309   copying build/lib/cap2/extensions/experimental/covid/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:09:06,315   copying build/lib/cap2/extensions/experimental/covid/make_pileup.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:09:06,319   copying build/lib/cap2/extensions/experimental/covid/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:09:06,323   copying build/lib/cap2/extensions/experimental/covid/call_covid_variants.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T18:09:06,327   copying build/lib/cap2/extensions/experimental/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-28T18:09:06,332   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:09:06,335   copying build/lib/cap2/extensions/experimental/preclassify/preclassify.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:09:06,342   copying build/lib/cap2/extensions/experimental/preclassify/dynamic_pipeline.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:09:06,348   copying build/lib/cap2/extensions/experimental/preclassify/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:09:06,354   copying build/lib/cap2/extensions/experimental/preclassify/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:09:06,357   copying build/lib/cap2/extensions/experimental/preclassify/preclassify_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T18:09:06,362   copying build/lib/cap2/extensions/experimental/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-28T18:09:06,367   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,368   copying build/lib/cap2/extensions/experimental/strains/merge_snp_graph.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,373   copying build/lib/cap2/extensions/experimental/strains/align_to_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,377   copying build/lib/cap2/extensions/experimental/strains/get_microbial_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,382   copying build/lib/cap2/extensions/experimental/strains/tasks.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,386   copying build/lib/cap2/extensions/experimental/strains/bacterial_genome_getter.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,390   copying build/lib/cap2/extensions/experimental/strains/align_to_genome_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,395   copying build/lib/cap2/extensions/experimental/strains/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,401   copying build/lib/cap2/extensions/experimental/strains/make_pileup.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,407   copying build/lib/cap2/extensions/experimental/strains/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,412   copying build/lib/cap2/extensions/experimental/strains/make_snp_table.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,417   copying build/lib/cap2/extensions/experimental/strains/make_snp_graph.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,421   copying build/lib/cap2/extensions/experimental/strains/merge_snp_clusters.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,425   copying build/lib/cap2/extensions/experimental/strains/make_snp_clusters.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,429   copying build/lib/cap2/extensions/experimental/strains/utils.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T18:09:06,435   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:06,437   copying build/lib/cap2/extensions/experimental/strains/strainotyping/api.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:06,443   copying build/lib/cap2/extensions/experimental/strains/strainotyping/io.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:06,448   copying build/lib/cap2/extensions/experimental/strains/strainotyping/graphs.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:06,454   copying build/lib/cap2/extensions/experimental/strains/strainotyping/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:06,458   copying build/lib/cap2/extensions/experimental/strains/strainotyping/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:06,462   copying build/lib/cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:06,466   copying build/lib/cap2/extensions/experimental/strains/strainotyping/clustering.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T18:09:06,472   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:09:06,473   copying build/lib/cap2/extensions/experimental/tcems/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:09:06,479   copying build/lib/cap2/extensions/experimental/tcems/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:09:06,482   copying build/lib/cap2/extensions/experimental/tcems/tcem_aa_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:09:06,487   copying build/lib/cap2/extensions/experimental/tcems/tcem_repertoire.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:09:06,492   copying build/lib/cap2/extensions/experimental/tcems/mixcr.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T18:09:06,498   copying build/lib/cap2/extensions/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-28T18:09:06,503   copying build/lib/cap2/extensions/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-28T18:09:06,507   copying build/lib/cap2/__init__.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:09:06,512   copying build/lib/cap2/utils.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:09:06,516   copying build/lib/cap2/exceptions.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:09:06,521   creating build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,523   copying build/lib/cap2/pangea/cli_utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,528   copying build/lib/cap2/pangea/api.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,533   copying build/lib/cap2/pangea/constants.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,538   copying build/lib/cap2/pangea/sra_utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,544   copying build/lib/cap2/pangea/download_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,548   copying build/lib/cap2/pangea/load_task.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,556   copying build/lib/cap2/pangea/cli.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,561   copying build/lib/cap2/pangea/pangea_sample.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,566   copying build/lib/cap2/pangea/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,569   copying build/lib/cap2/pangea/utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T18:09:06,573   copying build/lib/cap2/sample.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T18:09:06,576   running install_egg_info
2021-09-28T18:09:06,632   running egg_info
2021-09-28T18:09:06,634   writing entry points to cap2.egg-info/entry_points.txt
2021-09-28T18:09:06,636   writing top-level names to cap2.egg-info/top_level.txt
2021-09-28T18:09:06,638   writing dependency_links to cap2.egg-info/dependency_links.txt
2021-09-28T18:09:06,641   writing requirements to cap2.egg-info/requires.txt
2021-09-28T18:09:06,643   writing cap2.egg-info/PKG-INFO
2021-09-28T18:09:06,689   reading manifest file 'cap2.egg-info/SOURCES.txt'
2021-09-28T18:09:06,725   writing manifest file 'cap2.egg-info/SOURCES.txt'
2021-09-28T18:09:06,729   Copying cap2.egg-info to build/bdist.linux-armv7l/wheel/cap2-0.5.1-py3.5.egg-info
2021-09-28T18:09:06,760   running install_scripts
2021-09-28T18:09:06,987   creating build/bdist.linux-armv7l/wheel/cap2-0.5.1.dist-info/WHEEL
2021-09-28T18:09:07,843   Building wheel for cap2 (setup.py): finished with status 'done'
2021-09-28T18:09:07,850   Created wheel for cap2: filename=cap2-0.5.1-py3-none-any.whl size=142405 sha256=fa1a09db21904f0b54ebf151dff5f853ca9fb0b645b20a5142c8eaf64f76d04f
2021-09-28T18:09:07,851   Stored in directory: /tmp/pip-ephem-wheel-cache-jxnzul5c/wheels/89/a5/a9/be3c52801938c7ac63feba97c54f2d9986e8445f30295f63de
2021-09-28T18:09:07,881 Successfully built cap2
2021-09-28T18:09:07,910 Removed build tracker: '/tmp/pip-req-tracker-n4c33io7'