2021-09-28T15:42:35,420 Created temporary directory: /tmp/pip-ephem-wheel-cache-qkwso070
2021-09-28T15:42:35,426 Created temporary directory: /tmp/pip-req-tracker-f5f_kexp
2021-09-28T15:42:35,427 Initialized build tracking at /tmp/pip-req-tracker-f5f_kexp
2021-09-28T15:42:35,427 Created build tracker: /tmp/pip-req-tracker-f5f_kexp
2021-09-28T15:42:35,427 Entered build tracker: /tmp/pip-req-tracker-f5f_kexp
2021-09-28T15:42:35,429 Created temporary directory: /tmp/pip-wheel-w5iz1ccj
2021-09-28T15:42:35,494 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2021-09-28T15:42:35,497 2 location(s) to search for versions of cap2:
2021-09-28T15:42:35,497 * https://pypi.org/simple/cap2/
2021-09-28T15:42:35,497 * https://www.piwheels.org/simple/cap2/
2021-09-28T15:42:35,498 Fetching project page and analyzing links: https://pypi.org/simple/cap2/
2021-09-28T15:42:35,500 Getting page https://pypi.org/simple/cap2/
2021-09-28T15:42:35,504 Found index url https://pypi.org/simple
2021-09-28T15:42:35,835   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/)
2021-09-28T15:42:35,836   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/)
2021-09-28T15:42:35,837   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
2021-09-28T15:42:35,838   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/)
2021-09-28T15:42:35,838   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
2021-09-28T15:42:35,839   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
2021-09-28T15:42:35,840 Fetching project page and analyzing links: https://www.piwheels.org/simple/cap2/
2021-09-28T15:42:35,841 Getting page https://www.piwheels.org/simple/cap2/
2021-09-28T15:42:35,843 Found index url https://www.piwheels.org/simple
2021-09-28T15:42:36,013   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/)
2021-09-28T15:42:36,043 Given no hashes to check 1 links for project 'cap2': discarding no candidates
2021-09-28T15:42:36,075 Collecting cap2==0.5.0
2021-09-28T15:42:36,078   Created temporary directory: /tmp/pip-unpack-rvelxp56
2021-09-28T15:42:36,302   Downloading cap2-0.5.0.tar.gz (79 kB)
2021-09-28T15:42:37,224   Added cap2==0.5.0 from https://files.pythonhosted.org/packages/4c/c1/1f57ea79725c84d9a89c7161d059bd2c23682d4b2e8cd8de9a9f8b8e37f2/cap2-0.5.0.tar.gz#sha256=a343ba402ebb91919c54ba90492432f59f0906e5eaf4469663851508d6314e75 to build tracker '/tmp/pip-req-tracker-f5f_kexp'
2021-09-28T15:42:37,226     Running setup.py (path:/tmp/pip-wheel-w5iz1ccj/cap2_f09403b489354d15b6463c09393d40c0/setup.py) egg_info for package cap2
2021-09-28T15:42:37,227     Created temporary directory: /tmp/pip-pip-egg-info-jkv9v4ib
2021-09-28T15:42:37,228     Running command python setup.py egg_info
2021-09-28T15:42:39,293     running egg_info
2021-09-28T15:42:39,299     creating /tmp/pip-pip-egg-info-jkv9v4ib/cap2.egg-info
2021-09-28T15:42:39,302     writing top-level names to /tmp/pip-pip-egg-info-jkv9v4ib/cap2.egg-info/top_level.txt
2021-09-28T15:42:39,306     writing dependency_links to /tmp/pip-pip-egg-info-jkv9v4ib/cap2.egg-info/dependency_links.txt
2021-09-28T15:42:39,311     writing /tmp/pip-pip-egg-info-jkv9v4ib/cap2.egg-info/PKG-INFO
2021-09-28T15:42:39,315     writing requirements to /tmp/pip-pip-egg-info-jkv9v4ib/cap2.egg-info/requires.txt
2021-09-28T15:42:39,318     writing entry points to /tmp/pip-pip-egg-info-jkv9v4ib/cap2.egg-info/entry_points.txt
2021-09-28T15:42:39,323     writing manifest file '/tmp/pip-pip-egg-info-jkv9v4ib/cap2.egg-info/SOURCES.txt'
2021-09-28T15:42:39,734     reading manifest file '/tmp/pip-pip-egg-info-jkv9v4ib/cap2.egg-info/SOURCES.txt'
2021-09-28T15:42:39,755     writing manifest file '/tmp/pip-pip-egg-info-jkv9v4ib/cap2.egg-info/SOURCES.txt'
2021-09-28T15:42:39,890   Source in /tmp/pip-wheel-w5iz1ccj/cap2_f09403b489354d15b6463c09393d40c0 has version 0.5.0, which satisfies requirement cap2==0.5.0 from https://files.pythonhosted.org/packages/4c/c1/1f57ea79725c84d9a89c7161d059bd2c23682d4b2e8cd8de9a9f8b8e37f2/cap2-0.5.0.tar.gz#sha256=a343ba402ebb91919c54ba90492432f59f0906e5eaf4469663851508d6314e75
2021-09-28T15:42:39,892   Removed cap2==0.5.0 from https://files.pythonhosted.org/packages/4c/c1/1f57ea79725c84d9a89c7161d059bd2c23682d4b2e8cd8de9a9f8b8e37f2/cap2-0.5.0.tar.gz#sha256=a343ba402ebb91919c54ba90492432f59f0906e5eaf4469663851508d6314e75 from build tracker '/tmp/pip-req-tracker-f5f_kexp'
2021-09-28T15:42:39,900 Created temporary directory: /tmp/pip-unpack-16ousvvf
2021-09-28T15:42:39,901 Building wheels for collected packages: cap2
2021-09-28T15:42:39,910   Created temporary directory: /tmp/pip-wheel-z0sdzwsk
2021-09-28T15:42:39,911   Building wheel for cap2 (setup.py): started
2021-09-28T15:42:39,911   Destination directory: /tmp/pip-wheel-z0sdzwsk
2021-09-28T15:42:39,912   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-w5iz1ccj/cap2_f09403b489354d15b6463c09393d40c0/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-w5iz1ccj/cap2_f09403b489354d15b6463c09393d40c0/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-z0sdzwsk
2021-09-28T15:42:41,939   running bdist_wheel
2021-09-28T15:42:41,953   running build
2021-09-28T15:42:41,954   running build_py
2021-09-28T15:42:42,296   creating build
2021-09-28T15:42:42,297   creating build/lib
2021-09-28T15:42:42,298   creating build/lib/tests
2021-09-28T15:42:42,301   copying tests/test_pangea.py -> build/lib/tests
2021-09-28T15:42:42,307   copying tests/test_experimental_covid.py -> build/lib/tests
2021-09-28T15:42:42,312   copying tests/test_tcems.py -> build/lib/tests
2021-09-28T15:42:42,316   copying tests/test_short_read.py -> build/lib/tests
2021-09-28T15:42:42,321   copying tests/__init__.py -> build/lib/tests
2021-09-28T15:42:42,324   copying tests/test_assembly.py -> build/lib/tests
2021-09-28T15:42:42,328   copying tests/test_versions.py -> build/lib/tests
2021-09-28T15:42:42,335   copying tests/test_experimental_strain.py -> build/lib/tests
2021-09-28T15:42:42,342   copying tests/test_api.py -> build/lib/tests
2021-09-28T15:42:42,347   copying tests/test_databases.py -> build/lib/tests
2021-09-28T15:42:42,353   copying tests/test_strainotyping.py -> build/lib/tests
2021-09-28T15:42:42,357   copying tests/test_pipeline_preprocessing.py -> build/lib/tests
2021-09-28T15:42:42,364   creating build/lib/cap2
2021-09-28T15:42:42,366   copying cap2/utils.py -> build/lib/cap2
2021-09-28T15:42:42,371   copying cap2/cli.py -> build/lib/cap2
2021-09-28T15:42:42,376   copying cap2/constants.py -> build/lib/cap2
2021-09-28T15:42:42,382   copying cap2/api.py -> build/lib/cap2
2021-09-28T15:42:42,387   copying cap2/__init__.py -> build/lib/cap2
2021-09-28T15:42:42,391   copying cap2/sample.py -> build/lib/cap2
2021-09-28T15:42:42,395   copying cap2/exceptions.py -> build/lib/cap2
2021-09-28T15:42:42,399   copying cap2/setup_logging.py -> build/lib/cap2
2021-09-28T15:42:42,405   creating build/lib/cap2/capalyzer
2021-09-28T15:42:42,407   copying cap2/capalyzer/version.py -> build/lib/cap2/capalyzer
2021-09-28T15:42:42,411   copying cap2/capalyzer/cli.py -> build/lib/cap2/capalyzer
2021-09-28T15:42:42,415   copying cap2/capalyzer/__init__.py -> build/lib/cap2/capalyzer
2021-09-28T15:42:42,419   copying cap2/capalyzer/exceptions.py -> build/lib/cap2/capalyzer
2021-09-28T15:42:42,423   copying cap2/capalyzer/parsers.py -> build/lib/cap2/capalyzer
2021-09-28T15:42:42,429   creating build/lib/cap2/pangea
2021-09-28T15:42:42,431   copying cap2/pangea/utils.py -> build/lib/cap2/pangea
2021-09-28T15:42:42,435   copying cap2/pangea/cli.py -> build/lib/cap2/pangea
2021-09-28T15:42:42,440   copying cap2/pangea/constants.py -> build/lib/cap2/pangea
2021-09-28T15:42:42,444   copying cap2/pangea/api.py -> build/lib/cap2/pangea
2021-09-28T15:42:42,449   copying cap2/pangea/__init__.py -> build/lib/cap2/pangea
2021-09-28T15:42:42,453   copying cap2/pangea/download_reads.py -> build/lib/cap2/pangea
2021-09-28T15:42:42,458   copying cap2/pangea/load_task.py -> build/lib/cap2/pangea
2021-09-28T15:42:42,466   copying cap2/pangea/cli_utils.py -> build/lib/cap2/pangea
2021-09-28T15:42:42,472   copying cap2/pangea/pangea_sample.py -> build/lib/cap2/pangea
2021-09-28T15:42:42,477   copying cap2/pangea/sra_utils.py -> build/lib/cap2/pangea
2021-09-28T15:42:42,483   creating build/lib/cap2/pipeline
2021-09-28T15:42:42,485   copying cap2/pipeline/constants.py -> build/lib/cap2/pipeline
2021-09-28T15:42:42,489   copying cap2/pipeline/__init__.py -> build/lib/cap2/pipeline
2021-09-28T15:42:42,492   copying cap2/pipeline/config.py -> build/lib/cap2/pipeline
2021-09-28T15:42:42,496   copying cap2/pipeline/full_pipeline.py -> build/lib/cap2/pipeline
2021-09-28T15:42:42,502   creating build/lib/cap2/extensions
2021-09-28T15:42:42,504   copying cap2/extensions/cli.py -> build/lib/cap2/extensions
2021-09-28T15:42:42,507   copying cap2/extensions/__init__.py -> build/lib/cap2/extensions
2021-09-28T15:42:42,512   creating build/lib/cap2/capalyzer/table_builder
2021-09-28T15:42:42,514   copying cap2/capalyzer/table_builder/base_module.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T15:42:42,518   copying cap2/capalyzer/table_builder/__init__.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T15:42:42,522   copying cap2/capalyzer/table_builder/cap_table_builder.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T15:42:42,527   copying cap2/capalyzer/table_builder/parsers.py -> build/lib/cap2/capalyzer/table_builder
2021-09-28T15:42:42,533   creating build/lib/cap2/capalyzer/pangea
2021-09-28T15:42:42,535   copying cap2/capalyzer/pangea/pangea_file_source.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T15:42:42,539   copying cap2/capalyzer/pangea/utils.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T15:42:42,543   copying cap2/capalyzer/pangea/cli.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T15:42:42,548   copying cap2/capalyzer/pangea/api.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T15:42:42,552   copying cap2/capalyzer/pangea/__init__.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T15:42:42,556   copying cap2/capalyzer/pangea/pangea_file_uploader.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T15:42:42,560   copying cap2/capalyzer/pangea/parsers.py -> build/lib/cap2/capalyzer/pangea
2021-09-28T15:42:42,566   creating build/lib/cap2/capalyzer/table_parser
2021-09-28T15:42:42,568   copying cap2/capalyzer/table_parser/analysis_utils.py -> build/lib/cap2/capalyzer/table_parser
2021-09-28T15:42:42,573   copying cap2/capalyzer/table_parser/__init__.py -> build/lib/cap2/capalyzer/table_parser
2021-09-28T15:42:42,579   copying cap2/capalyzer/table_parser/cap_table_parser.py -> build/lib/cap2/capalyzer/table_parser
2021-09-28T15:42:42,588   creating build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:42,591   copying cap2/capalyzer/table_builder/modules/basic_stats_summary.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:42,596   copying cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:42,600   copying cap2/capalyzer/table_builder/modules/__init__.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:42,604   copying cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:42,608   copying cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:42,613   copying cap2/capalyzer/table_builder/modules/covid_variant_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:42,617   copying cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:42,623   creating build/lib/cap2/pipeline/assembly
2021-09-28T15:42:42,625   copying cap2/pipeline/assembly/metabat2.py -> build/lib/cap2/pipeline/assembly
2021-09-28T15:42:42,629   copying cap2/pipeline/assembly/__init__.py -> build/lib/cap2/pipeline/assembly
2021-09-28T15:42:42,633   copying cap2/pipeline/assembly/clean_contigs.py -> build/lib/cap2/pipeline/assembly
2021-09-28T15:42:42,638   copying cap2/pipeline/assembly/metaspades.py -> build/lib/cap2/pipeline/assembly
2021-09-28T15:42:42,643   creating build/lib/cap2/pipeline/contigs
2021-09-28T15:42:42,645   copying cap2/pipeline/contigs/__init__.py -> build/lib/cap2/pipeline/contigs
2021-09-28T15:42:42,649   copying cap2/pipeline/contigs/amr_identification.py -> build/lib/cap2/pipeline/contigs
2021-09-28T15:42:42,654   copying cap2/pipeline/contigs/prodigal.py -> build/lib/cap2/pipeline/contigs
2021-09-28T15:42:42,660   creating build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,662   copying cap2/pipeline/short_read/humann2.py -> build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,668   copying cap2/pipeline/short_read/jellyfish.py -> build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,672   copying cap2/pipeline/short_read/microbe_census.py -> build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,677   copying cap2/pipeline/short_read/processed_reads.py -> build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,681   copying cap2/pipeline/short_read/read_stats.py -> build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,685   copying cap2/pipeline/short_read/kraken2.py -> build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,690   copying cap2/pipeline/short_read/__init__.py -> build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,694   copying cap2/pipeline/short_read/hmp_comparison.py -> build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,700   copying cap2/pipeline/short_read/amrs.py -> build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,707   copying cap2/pipeline/short_read/mash.py -> build/lib/cap2/pipeline/short_read
2021-09-28T15:42:42,717   creating build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,719   copying cap2/pipeline/preprocessing/basic_sample_stats.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,724   copying cap2/pipeline/preprocessing/fastqc.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,729   copying cap2/pipeline/preprocessing/count_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,733   copying cap2/pipeline/preprocessing/fast_taxa.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,737   copying cap2/pipeline/preprocessing/multiqc.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,743   copying cap2/pipeline/preprocessing/map_to_human.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,749   copying cap2/pipeline/preprocessing/__init__.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,755   copying cap2/pipeline/preprocessing/control_sample_abundances.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,761   copying cap2/pipeline/preprocessing/error_correct_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,765   copying cap2/pipeline/preprocessing/remove_adapters.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,770   copying cap2/pipeline/preprocessing/map_to_mouse.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,774   copying cap2/pipeline/preprocessing/base_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,779   copying cap2/pipeline/preprocessing/clean_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-28T15:42:42,787   creating build/lib/cap2/pipeline/utils
2021-09-28T15:42:42,790   copying cap2/pipeline/utils/utils.py -> build/lib/cap2/pipeline/utils
2021-09-28T15:42:42,796   copying cap2/pipeline/utils/__init__.py -> build/lib/cap2/pipeline/utils
2021-09-28T15:42:42,801   copying cap2/pipeline/utils/cap_task.py -> build/lib/cap2/pipeline/utils
2021-09-28T15:42:42,807   copying cap2/pipeline/utils/conda.py -> build/lib/cap2/pipeline/utils
2021-09-28T15:42:42,814   creating build/lib/cap2/pipeline/databases
2021-09-28T15:42:42,816   copying cap2/pipeline/databases/amr_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T15:42:42,822   copying cap2/pipeline/databases/taxonomic_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T15:42:42,828   copying cap2/pipeline/databases/mouse_removal_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T15:42:42,834   copying cap2/pipeline/databases/uniref.py -> build/lib/cap2/pipeline/databases
2021-09-28T15:42:42,840   copying cap2/pipeline/databases/__init__.py -> build/lib/cap2/pipeline/databases
2021-09-28T15:42:42,844   copying cap2/pipeline/databases/kraken2_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T15:42:42,850   copying cap2/pipeline/databases/human_removal_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T15:42:42,854   copying cap2/pipeline/databases/hmp_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T15:42:42,858   copying cap2/pipeline/databases/fast_kraken2_db.py -> build/lib/cap2/pipeline/databases
2021-09-28T15:42:42,865   creating build/lib/cap2/extensions/experimental
2021-09-28T15:42:42,868   copying cap2/extensions/experimental/cli.py -> build/lib/cap2/extensions/experimental
2021-09-28T15:42:42,874   copying cap2/extensions/experimental/__init__.py -> build/lib/cap2/extensions/experimental
2021-09-28T15:42:42,881   creating build/lib/cap2/extensions/experimental/tcems
2021-09-28T15:42:42,883   copying cap2/extensions/experimental/tcems/cli.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T15:42:42,888   copying cap2/extensions/experimental/tcems/__init__.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T15:42:42,892   copying cap2/extensions/experimental/tcems/tcem_aa_db.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T15:42:42,898   copying cap2/extensions/experimental/tcems/tcem_repertoire.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T15:42:42,903   copying cap2/extensions/experimental/tcems/mixcr.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-28T15:42:42,914   creating build/lib/cap2/extensions/experimental/covid
2021-09-28T15:42:42,916   copying cap2/extensions/experimental/covid/make_pileup.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T15:42:42,923   copying cap2/extensions/experimental/covid/cli.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T15:42:42,927   copying cap2/extensions/experimental/covid/__init__.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T15:42:42,931   copying cap2/extensions/experimental/covid/make_covid_consensus_seq.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T15:42:42,936   copying cap2/extensions/experimental/covid/align_to_covid_genome.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T15:42:42,941   copying cap2/extensions/experimental/covid/fast_detect.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T15:42:42,946   copying cap2/extensions/experimental/covid/covid_genome_db.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T15:42:42,952   copying cap2/extensions/experimental/covid/genome_coverage.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T15:42:42,958   copying cap2/extensions/experimental/covid/call_covid_variants.py -> build/lib/cap2/extensions/experimental/covid
2021-09-28T15:42:42,966   creating build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:42,968   copying cap2/extensions/experimental/strains/make_pileup.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:42,972   copying cap2/extensions/experimental/strains/utils.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:42,976   copying cap2/extensions/experimental/strains/make_snp_graph.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:42,981   copying cap2/extensions/experimental/strains/make_snp_table.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:42,986   copying cap2/extensions/experimental/strains/cli.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:42,993   copying cap2/extensions/experimental/strains/bacterial_genome_getter.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:42,999   copying cap2/extensions/experimental/strains/merge_snp_clusters.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:43,005   copying cap2/extensions/experimental/strains/merge_snp_graph.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:43,009   copying cap2/extensions/experimental/strains/__init__.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:43,013   copying cap2/extensions/experimental/strains/align_to_genome.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:43,018   copying cap2/extensions/experimental/strains/make_snp_clusters.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:43,022   copying cap2/extensions/experimental/strains/tasks.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:43,027   copying cap2/extensions/experimental/strains/align_to_genome_db.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:43,033   copying cap2/extensions/experimental/strains/get_microbial_genome.py -> build/lib/cap2/extensions/experimental/strains
2021-09-28T15:42:43,041   creating build/lib/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,044   copying cap2/extensions/experimental/preclassify/dynamic_pipeline.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,049   copying cap2/extensions/experimental/preclassify/cli.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,054   copying cap2/extensions/experimental/preclassify/__init__.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,057   copying cap2/extensions/experimental/preclassify/preclassify_db.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,061   copying cap2/extensions/experimental/preclassify/preclassify.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,070   creating build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,072   copying cap2/extensions/experimental/strains/strainotyping/cli.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,078   copying cap2/extensions/experimental/strains/strainotyping/api.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,084   copying cap2/extensions/experimental/strains/strainotyping/clustering.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,088   copying cap2/extensions/experimental/strains/strainotyping/__init__.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,092   copying cap2/extensions/experimental/strains/strainotyping/graphs.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,096   copying cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,100   copying cap2/extensions/experimental/strains/strainotyping/io.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,149   installing to build/bdist.linux-armv7l/wheel
2021-09-28T15:42:43,150   running install
2021-09-28T15:42:43,153   running install_lib
2021-09-28T15:42:43,160   creating build/bdist.linux-armv7l
2021-09-28T15:42:43,161   creating build/bdist.linux-armv7l/wheel
2021-09-28T15:42:43,165   creating build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,167   copying build/lib/tests/test_pangea.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,173   copying build/lib/tests/test_experimental_covid.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,178   copying build/lib/tests/test_tcems.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,182   copying build/lib/tests/test_short_read.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,186   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,190   copying build/lib/tests/test_assembly.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,195   copying build/lib/tests/test_versions.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,201   copying build/lib/tests/test_experimental_strain.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,208   copying build/lib/tests/test_api.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,212   copying build/lib/tests/test_databases.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,217   copying build/lib/tests/test_strainotyping.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,221   copying build/lib/tests/test_pipeline_preprocessing.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-28T15:42:43,228   creating build/bdist.linux-armv7l/wheel/cap2
2021-09-28T15:42:43,229   copying build/lib/cap2/utils.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T15:42:43,234   copying build/lib/cap2/cli.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T15:42:43,240   copying build/lib/cap2/constants.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T15:42:43,245   copying build/lib/cap2/api.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T15:42:43,250   copying build/lib/cap2/__init__.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T15:42:43,255   copying build/lib/cap2/sample.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T15:42:43,261   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T15:42:43,264   copying build/lib/cap2/capalyzer/version.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T15:42:43,269   copying build/lib/cap2/capalyzer/cli.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T15:42:43,275   copying build/lib/cap2/capalyzer/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T15:42:43,281   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T15:42:43,285   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:43,288   copying build/lib/cap2/capalyzer/table_builder/modules/basic_stats_summary.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:43,294   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:43,300   copying build/lib/cap2/capalyzer/table_builder/modules/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:43,305   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:43,311   copying build/lib/cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:43,316   copying build/lib/cap2/capalyzer/table_builder/modules/covid_variant_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:43,321   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-28T15:42:43,327   copying build/lib/cap2/capalyzer/table_builder/base_module.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T15:42:43,332   copying build/lib/cap2/capalyzer/table_builder/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T15:42:43,337   copying build/lib/cap2/capalyzer/table_builder/cap_table_builder.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T15:42:43,343   copying build/lib/cap2/capalyzer/table_builder/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-28T15:42:43,349   copying build/lib/cap2/capalyzer/exceptions.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T15:42:43,356   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T15:42:43,358   copying build/lib/cap2/capalyzer/pangea/pangea_file_source.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T15:42:43,364   copying build/lib/cap2/capalyzer/pangea/utils.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T15:42:43,370   copying build/lib/cap2/capalyzer/pangea/cli.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T15:42:43,375   copying build/lib/cap2/capalyzer/pangea/api.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T15:42:43,379   copying build/lib/cap2/capalyzer/pangea/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T15:42:43,383   copying build/lib/cap2/capalyzer/pangea/pangea_file_uploader.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T15:42:43,387   copying build/lib/cap2/capalyzer/pangea/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-28T15:42:43,391   copying build/lib/cap2/capalyzer/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-28T15:42:43,397   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T15:42:43,400   copying build/lib/cap2/capalyzer/table_parser/analysis_utils.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T15:42:43,407   copying build/lib/cap2/capalyzer/table_parser/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T15:42:43,412   copying build/lib/cap2/capalyzer/table_parser/cap_table_parser.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-28T15:42:43,417   copying build/lib/cap2/exceptions.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T15:42:43,422   creating build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,424   copying build/lib/cap2/pangea/utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,428   copying build/lib/cap2/pangea/cli.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,433   copying build/lib/cap2/pangea/constants.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,438   copying build/lib/cap2/pangea/api.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,445   copying build/lib/cap2/pangea/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,449   copying build/lib/cap2/pangea/download_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,454   copying build/lib/cap2/pangea/load_task.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,461   copying build/lib/cap2/pangea/cli_utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,468   copying build/lib/cap2/pangea/pangea_sample.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,474   copying build/lib/cap2/pangea/sra_utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-28T15:42:43,478   copying build/lib/cap2/setup_logging.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-28T15:42:43,484   creating build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T15:42:43,485   copying build/lib/cap2/pipeline/constants.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T15:42:43,491   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T15:42:43,492   copying build/lib/cap2/pipeline/assembly/metabat2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T15:42:43,498   copying build/lib/cap2/pipeline/assembly/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T15:42:43,503   copying build/lib/cap2/pipeline/assembly/clean_contigs.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T15:42:43,509   copying build/lib/cap2/pipeline/assembly/metaspades.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-28T15:42:43,516   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T15:42:43,518   copying build/lib/cap2/pipeline/contigs/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T15:42:43,524   copying build/lib/cap2/pipeline/contigs/amr_identification.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T15:42:43,529   copying build/lib/cap2/pipeline/contigs/prodigal.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-28T15:42:43,535   copying build/lib/cap2/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T15:42:43,538   copying build/lib/cap2/pipeline/config.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T15:42:43,544   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,545   copying build/lib/cap2/pipeline/short_read/humann2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,550   copying build/lib/cap2/pipeline/short_read/jellyfish.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,554   copying build/lib/cap2/pipeline/short_read/microbe_census.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,559   copying build/lib/cap2/pipeline/short_read/processed_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,565   copying build/lib/cap2/pipeline/short_read/read_stats.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,570   copying build/lib/cap2/pipeline/short_read/kraken2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,576   copying build/lib/cap2/pipeline/short_read/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,582   copying build/lib/cap2/pipeline/short_read/hmp_comparison.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,587   copying build/lib/cap2/pipeline/short_read/amrs.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,593   copying build/lib/cap2/pipeline/short_read/mash.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-28T15:42:43,600   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,601   copying build/lib/cap2/pipeline/preprocessing/basic_sample_stats.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,606   copying build/lib/cap2/pipeline/preprocessing/fastqc.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,610   copying build/lib/cap2/pipeline/preprocessing/count_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,614   copying build/lib/cap2/pipeline/preprocessing/fast_taxa.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,619   copying build/lib/cap2/pipeline/preprocessing/multiqc.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,624   copying build/lib/cap2/pipeline/preprocessing/map_to_human.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,630   copying build/lib/cap2/pipeline/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,635   copying build/lib/cap2/pipeline/preprocessing/control_sample_abundances.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,640   copying build/lib/cap2/pipeline/preprocessing/error_correct_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,645   copying build/lib/cap2/pipeline/preprocessing/remove_adapters.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,649   copying build/lib/cap2/pipeline/preprocessing/map_to_mouse.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,653   copying build/lib/cap2/pipeline/preprocessing/base_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,657   copying build/lib/cap2/pipeline/preprocessing/clean_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-28T15:42:43,664   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T15:42:43,666   copying build/lib/cap2/pipeline/utils/utils.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T15:42:43,672   copying build/lib/cap2/pipeline/utils/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T15:42:43,678   copying build/lib/cap2/pipeline/utils/cap_task.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T15:42:43,685   copying build/lib/cap2/pipeline/utils/conda.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-28T15:42:43,691   copying build/lib/cap2/pipeline/full_pipeline.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-28T15:42:43,698   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T15:42:43,700   copying build/lib/cap2/pipeline/databases/amr_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T15:42:43,705   copying build/lib/cap2/pipeline/databases/taxonomic_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T15:42:43,709   copying build/lib/cap2/pipeline/databases/mouse_removal_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T15:42:43,714   copying build/lib/cap2/pipeline/databases/uniref.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T15:42:43,719   copying build/lib/cap2/pipeline/databases/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T15:42:43,724   copying build/lib/cap2/pipeline/databases/kraken2_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T15:42:43,731   copying build/lib/cap2/pipeline/databases/human_removal_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T15:42:43,737   copying build/lib/cap2/pipeline/databases/hmp_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T15:42:43,742   copying build/lib/cap2/pipeline/databases/fast_kraken2_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-28T15:42:43,749   creating build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-28T15:42:43,751   copying build/lib/cap2/extensions/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-28T15:42:43,756   copying build/lib/cap2/extensions/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-28T15:42:43,762   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-28T15:42:43,765   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T15:42:43,767   copying build/lib/cap2/extensions/experimental/tcems/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T15:42:43,772   copying build/lib/cap2/extensions/experimental/tcems/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T15:42:43,775   copying build/lib/cap2/extensions/experimental/tcems/tcem_aa_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T15:42:43,781   copying build/lib/cap2/extensions/experimental/tcems/tcem_repertoire.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T15:42:43,789   copying build/lib/cap2/extensions/experimental/tcems/mixcr.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-28T15:42:43,795   copying build/lib/cap2/extensions/experimental/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-28T15:42:43,801   copying build/lib/cap2/extensions/experimental/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-28T15:42:43,808   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T15:42:43,810   copying build/lib/cap2/extensions/experimental/covid/make_pileup.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T15:42:43,816   copying build/lib/cap2/extensions/experimental/covid/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T15:42:43,823   copying build/lib/cap2/extensions/experimental/covid/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T15:42:43,829   copying build/lib/cap2/extensions/experimental/covid/make_covid_consensus_seq.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T15:42:43,834   copying build/lib/cap2/extensions/experimental/covid/align_to_covid_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T15:42:43,840   copying build/lib/cap2/extensions/experimental/covid/fast_detect.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T15:42:43,845   copying build/lib/cap2/extensions/experimental/covid/covid_genome_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T15:42:43,849   copying build/lib/cap2/extensions/experimental/covid/genome_coverage.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T15:42:43,853   copying build/lib/cap2/extensions/experimental/covid/call_covid_variants.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-28T15:42:43,859   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,861   copying build/lib/cap2/extensions/experimental/strains/make_pileup.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,867   copying build/lib/cap2/extensions/experimental/strains/utils.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,872   copying build/lib/cap2/extensions/experimental/strains/make_snp_graph.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,877   copying build/lib/cap2/extensions/experimental/strains/make_snp_table.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,883   copying build/lib/cap2/extensions/experimental/strains/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,888   copying build/lib/cap2/extensions/experimental/strains/bacterial_genome_getter.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,892   copying build/lib/cap2/extensions/experimental/strains/merge_snp_clusters.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,896   copying build/lib/cap2/extensions/experimental/strains/merge_snp_graph.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,900   copying build/lib/cap2/extensions/experimental/strains/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,905   copying build/lib/cap2/extensions/experimental/strains/align_to_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,912   copying build/lib/cap2/extensions/experimental/strains/make_snp_clusters.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,917   copying build/lib/cap2/extensions/experimental/strains/tasks.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,923   copying build/lib/cap2/extensions/experimental/strains/align_to_genome_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,927   copying build/lib/cap2/extensions/experimental/strains/get_microbial_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-28T15:42:43,933   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,934   copying build/lib/cap2/extensions/experimental/strains/strainotyping/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,939   copying build/lib/cap2/extensions/experimental/strains/strainotyping/api.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,943   copying build/lib/cap2/extensions/experimental/strains/strainotyping/clustering.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,948   copying build/lib/cap2/extensions/experimental/strains/strainotyping/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,954   copying build/lib/cap2/extensions/experimental/strains/strainotyping/graphs.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,960   copying build/lib/cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,965   copying build/lib/cap2/extensions/experimental/strains/strainotyping/io.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-28T15:42:43,970   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,972   copying build/lib/cap2/extensions/experimental/preclassify/dynamic_pipeline.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,976   copying build/lib/cap2/extensions/experimental/preclassify/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,981   copying build/lib/cap2/extensions/experimental/preclassify/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,985   copying build/lib/cap2/extensions/experimental/preclassify/preclassify_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,991   copying build/lib/cap2/extensions/experimental/preclassify/preclassify.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-28T15:42:43,996   running install_egg_info
2021-09-28T15:42:44,045   running egg_info
2021-09-28T15:42:44,046   writing requirements to cap2.egg-info/requires.txt
2021-09-28T15:42:44,049   writing entry points to cap2.egg-info/entry_points.txt
2021-09-28T15:42:44,052   writing dependency_links to cap2.egg-info/dependency_links.txt
2021-09-28T15:42:44,055   writing top-level names to cap2.egg-info/top_level.txt
2021-09-28T15:42:44,057   writing cap2.egg-info/PKG-INFO
2021-09-28T15:42:44,101   reading manifest file 'cap2.egg-info/SOURCES.txt'
2021-09-28T15:42:44,136   writing manifest file 'cap2.egg-info/SOURCES.txt'
2021-09-28T15:42:44,140   Copying cap2.egg-info to build/bdist.linux-armv7l/wheel/cap2-0.5.0-py3.5.egg-info
2021-09-28T15:42:44,169   running install_scripts
2021-09-28T15:42:44,404   creating build/bdist.linux-armv7l/wheel/cap2-0.5.0.dist-info/WHEEL
2021-09-28T15:42:45,250   Building wheel for cap2 (setup.py): finished with status 'done'
2021-09-28T15:42:45,257   Created wheel for cap2: filename=cap2-0.5.0-py3-none-any.whl size=142374 sha256=603e0f03c6032e54849c0a8573190d882dc2b4ae464698c1961d40c5c2927bd5
2021-09-28T15:42:45,258   Stored in directory: /tmp/pip-ephem-wheel-cache-qkwso070/wheels/b8/41/38/10414ea5736d2e291e03030756d905eac805402454bf3f3dfe
2021-09-28T15:42:45,289 Successfully built cap2
2021-09-28T15:42:45,318 Removed build tracker: '/tmp/pip-req-tracker-f5f_kexp'