2021-09-18T12:32:24,618 Created temporary directory: /tmp/pip-ephem-wheel-cache-v2yiuycj
2021-09-18T12:32:24,624 Created temporary directory: /tmp/pip-req-tracker-vvj9cj8y
2021-09-18T12:32:24,625 Initialized build tracking at /tmp/pip-req-tracker-vvj9cj8y
2021-09-18T12:32:24,626 Created build tracker: /tmp/pip-req-tracker-vvj9cj8y
2021-09-18T12:32:24,626 Entered build tracker: /tmp/pip-req-tracker-vvj9cj8y
2021-09-18T12:32:24,627 Created temporary directory: /tmp/pip-wheel-adq_ds2t
2021-09-18T12:32:24,693 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2021-09-18T12:32:24,696 2 location(s) to search for versions of cap2:
2021-09-18T12:32:24,696 * https://pypi.org/simple/cap2/
2021-09-18T12:32:24,696 * https://www.piwheels.org/simple/cap2/
2021-09-18T12:32:24,697 Fetching project page and analyzing links: https://pypi.org/simple/cap2/
2021-09-18T12:32:24,699 Getting page https://pypi.org/simple/cap2/
2021-09-18T12:32:24,703 Found index url https://pypi.org/simple
2021-09-18T12:32:24,945   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/)
2021-09-18T12:32:24,946   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/)
2021-09-18T12:32:24,947   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
2021-09-18T12:32:24,947   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/)
2021-09-18T12:32:24,948   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
2021-09-18T12:32:24,949 Fetching project page and analyzing links: https://www.piwheels.org/simple/cap2/
2021-09-18T12:32:24,950 Getting page https://www.piwheels.org/simple/cap2/
2021-09-18T12:32:24,952 Found index url https://www.piwheels.org/simple
2021-09-18T12:32:25,147 Given no hashes to check 1 links for project 'cap2': discarding no candidates
2021-09-18T12:32:25,179 Collecting cap2==0.4.1
2021-09-18T12:32:25,183   Created temporary directory: /tmp/pip-unpack-03werh1h
2021-09-18T12:32:25,399   Downloading cap2-0.4.1.tar.gz (79 kB)
2021-09-18T12:32:26,308   Added cap2==0.4.1 from https://files.pythonhosted.org/packages/85/78/9c4622c999e03476c68fa557dfa0c57dd070728355194dbbe59382449fc5/cap2-0.4.1.tar.gz#sha256=8f52279a38fbf5e9866b65f91b072c8e0a4effacc4cbcaae00b9be57adc8338b to build tracker '/tmp/pip-req-tracker-vvj9cj8y'
2021-09-18T12:32:26,310     Running setup.py (path:/tmp/pip-wheel-adq_ds2t/cap2_bd6f79a21e7c4248b50adda30a803fbb/setup.py) egg_info for package cap2
2021-09-18T12:32:26,311     Created temporary directory: /tmp/pip-pip-egg-info-fj0xahzy
2021-09-18T12:32:26,312     Running command python setup.py egg_info
2021-09-18T12:32:28,334     running egg_info
2021-09-18T12:32:28,341     creating /tmp/pip-pip-egg-info-fj0xahzy/cap2.egg-info
2021-09-18T12:32:28,343     writing requirements to /tmp/pip-pip-egg-info-fj0xahzy/cap2.egg-info/requires.txt
2021-09-18T12:32:28,346     writing /tmp/pip-pip-egg-info-fj0xahzy/cap2.egg-info/PKG-INFO
2021-09-18T12:32:28,350     writing top-level names to /tmp/pip-pip-egg-info-fj0xahzy/cap2.egg-info/top_level.txt
2021-09-18T12:32:28,352     writing dependency_links to /tmp/pip-pip-egg-info-fj0xahzy/cap2.egg-info/dependency_links.txt
2021-09-18T12:32:28,354     writing entry points to /tmp/pip-pip-egg-info-fj0xahzy/cap2.egg-info/entry_points.txt
2021-09-18T12:32:28,359     writing manifest file '/tmp/pip-pip-egg-info-fj0xahzy/cap2.egg-info/SOURCES.txt'
2021-09-18T12:32:28,750     reading manifest file '/tmp/pip-pip-egg-info-fj0xahzy/cap2.egg-info/SOURCES.txt'
2021-09-18T12:32:28,771     writing manifest file '/tmp/pip-pip-egg-info-fj0xahzy/cap2.egg-info/SOURCES.txt'
2021-09-18T12:32:28,903   Source in /tmp/pip-wheel-adq_ds2t/cap2_bd6f79a21e7c4248b50adda30a803fbb has version 0.4.1, which satisfies requirement cap2==0.4.1 from https://files.pythonhosted.org/packages/85/78/9c4622c999e03476c68fa557dfa0c57dd070728355194dbbe59382449fc5/cap2-0.4.1.tar.gz#sha256=8f52279a38fbf5e9866b65f91b072c8e0a4effacc4cbcaae00b9be57adc8338b
2021-09-18T12:32:28,905   Removed cap2==0.4.1 from https://files.pythonhosted.org/packages/85/78/9c4622c999e03476c68fa557dfa0c57dd070728355194dbbe59382449fc5/cap2-0.4.1.tar.gz#sha256=8f52279a38fbf5e9866b65f91b072c8e0a4effacc4cbcaae00b9be57adc8338b from build tracker '/tmp/pip-req-tracker-vvj9cj8y'
2021-09-18T12:32:28,913 Created temporary directory: /tmp/pip-unpack-3r0g4vid
2021-09-18T12:32:28,914 Building wheels for collected packages: cap2
2021-09-18T12:32:28,923   Created temporary directory: /tmp/pip-wheel-k9qzmltm
2021-09-18T12:32:28,924   Building wheel for cap2 (setup.py): started
2021-09-18T12:32:28,925   Destination directory: /tmp/pip-wheel-k9qzmltm
2021-09-18T12:32:28,925   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-adq_ds2t/cap2_bd6f79a21e7c4248b50adda30a803fbb/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-adq_ds2t/cap2_bd6f79a21e7c4248b50adda30a803fbb/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-k9qzmltm
2021-09-18T12:32:30,915   running bdist_wheel
2021-09-18T12:32:30,929   running build
2021-09-18T12:32:30,930   running build_py
2021-09-18T12:32:31,265   creating build
2021-09-18T12:32:31,266   creating build/lib
2021-09-18T12:32:31,268   creating build/lib/tests
2021-09-18T12:32:31,271   copying tests/test_pangea.py -> build/lib/tests
2021-09-18T12:32:31,276   copying tests/test_experimental_covid.py -> build/lib/tests
2021-09-18T12:32:31,281   copying tests/test_tcems.py -> build/lib/tests
2021-09-18T12:32:31,285   copying tests/test_short_read.py -> build/lib/tests
2021-09-18T12:32:31,290   copying tests/__init__.py -> build/lib/tests
2021-09-18T12:32:31,295   copying tests/test_assembly.py -> build/lib/tests
2021-09-18T12:32:31,301   copying tests/test_versions.py -> build/lib/tests
2021-09-18T12:32:31,308   copying tests/test_experimental_strain.py -> build/lib/tests
2021-09-18T12:32:31,314   copying tests/test_api.py -> build/lib/tests
2021-09-18T12:32:31,319   copying tests/test_databases.py -> build/lib/tests
2021-09-18T12:32:31,326   copying tests/test_strainotyping.py -> build/lib/tests
2021-09-18T12:32:31,332   copying tests/test_pipeline_preprocessing.py -> build/lib/tests
2021-09-18T12:32:31,341   creating build/lib/cap2
2021-09-18T12:32:31,344   copying cap2/utils.py -> build/lib/cap2
2021-09-18T12:32:31,350   copying cap2/cli.py -> build/lib/cap2
2021-09-18T12:32:31,355   copying cap2/constants.py -> build/lib/cap2
2021-09-18T12:32:31,359   copying cap2/api.py -> build/lib/cap2
2021-09-18T12:32:31,362   copying cap2/__init__.py -> build/lib/cap2
2021-09-18T12:32:31,366   copying cap2/sample.py -> build/lib/cap2
2021-09-18T12:32:31,370   copying cap2/exceptions.py -> build/lib/cap2
2021-09-18T12:32:31,374   copying cap2/setup_logging.py -> build/lib/cap2
2021-09-18T12:32:31,381   creating build/lib/cap2/capalyzer
2021-09-18T12:32:31,384   copying cap2/capalyzer/version.py -> build/lib/cap2/capalyzer
2021-09-18T12:32:31,390   copying cap2/capalyzer/cli.py -> build/lib/cap2/capalyzer
2021-09-18T12:32:31,395   copying cap2/capalyzer/__init__.py -> build/lib/cap2/capalyzer
2021-09-18T12:32:31,399   copying cap2/capalyzer/exceptions.py -> build/lib/cap2/capalyzer
2021-09-18T12:32:31,402   copying cap2/capalyzer/parsers.py -> build/lib/cap2/capalyzer
2021-09-18T12:32:31,408   creating build/lib/cap2/pangea
2021-09-18T12:32:31,410   copying cap2/pangea/cli.py -> build/lib/cap2/pangea
2021-09-18T12:32:31,416   copying cap2/pangea/constants.py -> build/lib/cap2/pangea
2021-09-18T12:32:31,422   copying cap2/pangea/api.py -> build/lib/cap2/pangea
2021-09-18T12:32:31,428   copying cap2/pangea/__init__.py -> build/lib/cap2/pangea
2021-09-18T12:32:31,433   copying cap2/pangea/download_reads.py -> build/lib/cap2/pangea
2021-09-18T12:32:31,437   copying cap2/pangea/load_task.py -> build/lib/cap2/pangea
2021-09-18T12:32:31,445   copying cap2/pangea/cli_utils.py -> build/lib/cap2/pangea
2021-09-18T12:32:31,452   copying cap2/pangea/pangea_sample.py -> build/lib/cap2/pangea
2021-09-18T12:32:31,459   copying cap2/pangea/sra_utils.py -> build/lib/cap2/pangea
2021-09-18T12:32:31,466   creating build/lib/cap2/pipeline
2021-09-18T12:32:31,469   copying cap2/pipeline/constants.py -> build/lib/cap2/pipeline
2021-09-18T12:32:31,474   copying cap2/pipeline/__init__.py -> build/lib/cap2/pipeline
2021-09-18T12:32:31,478   copying cap2/pipeline/config.py -> build/lib/cap2/pipeline
2021-09-18T12:32:31,482   copying cap2/pipeline/full_pipeline.py -> build/lib/cap2/pipeline
2021-09-18T12:32:31,487   creating build/lib/cap2/extensions
2021-09-18T12:32:31,489   copying cap2/extensions/cli.py -> build/lib/cap2/extensions
2021-09-18T12:32:31,492   copying cap2/extensions/__init__.py -> build/lib/cap2/extensions
2021-09-18T12:32:31,498   creating build/lib/cap2/capalyzer/table_builder
2021-09-18T12:32:31,501   copying cap2/capalyzer/table_builder/base_module.py -> build/lib/cap2/capalyzer/table_builder
2021-09-18T12:32:31,506   copying cap2/capalyzer/table_builder/__init__.py -> build/lib/cap2/capalyzer/table_builder
2021-09-18T12:32:31,512   copying cap2/capalyzer/table_builder/cap_table_builder.py -> build/lib/cap2/capalyzer/table_builder
2021-09-18T12:32:31,518   copying cap2/capalyzer/table_builder/parsers.py -> build/lib/cap2/capalyzer/table_builder
2021-09-18T12:32:31,523   creating build/lib/cap2/capalyzer/pangea
2021-09-18T12:32:31,525   copying cap2/capalyzer/pangea/pangea_file_source.py -> build/lib/cap2/capalyzer/pangea
2021-09-18T12:32:31,530   copying cap2/capalyzer/pangea/utils.py -> build/lib/cap2/capalyzer/pangea
2021-09-18T12:32:31,534   copying cap2/capalyzer/pangea/cli.py -> build/lib/cap2/capalyzer/pangea
2021-09-18T12:32:31,539   copying cap2/capalyzer/pangea/api.py -> build/lib/cap2/capalyzer/pangea
2021-09-18T12:32:31,544   copying cap2/capalyzer/pangea/__init__.py -> build/lib/cap2/capalyzer/pangea
2021-09-18T12:32:31,550   copying cap2/capalyzer/pangea/pangea_file_uploader.py -> build/lib/cap2/capalyzer/pangea
2021-09-18T12:32:31,555   copying cap2/capalyzer/pangea/parsers.py -> build/lib/cap2/capalyzer/pangea
2021-09-18T12:32:31,561   creating build/lib/cap2/capalyzer/table_parser
2021-09-18T12:32:31,563   copying cap2/capalyzer/table_parser/analysis_utils.py -> build/lib/cap2/capalyzer/table_parser
2021-09-18T12:32:31,569   copying cap2/capalyzer/table_parser/__init__.py -> build/lib/cap2/capalyzer/table_parser
2021-09-18T12:32:31,573   copying cap2/capalyzer/table_parser/cap_table_parser.py -> build/lib/cap2/capalyzer/table_parser
2021-09-18T12:32:31,580   creating build/lib/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:31,582   copying cap2/capalyzer/table_builder/modules/basic_stats_summary.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:31,588   copying cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:31,594   copying cap2/capalyzer/table_builder/modules/__init__.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:31,599   copying cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:31,603   copying cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:31,607   copying cap2/capalyzer/table_builder/modules/covid_variant_table.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:31,611   copying cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py -> build/lib/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:31,617   creating build/lib/cap2/pipeline/assembly
2021-09-18T12:32:31,619   copying cap2/pipeline/assembly/metabat2.py -> build/lib/cap2/pipeline/assembly
2021-09-18T12:32:31,625   copying cap2/pipeline/assembly/__init__.py -> build/lib/cap2/pipeline/assembly
2021-09-18T12:32:31,630   copying cap2/pipeline/assembly/clean_contigs.py -> build/lib/cap2/pipeline/assembly
2021-09-18T12:32:31,636   copying cap2/pipeline/assembly/metaspades.py -> build/lib/cap2/pipeline/assembly
2021-09-18T12:32:31,644   creating build/lib/cap2/pipeline/contigs
2021-09-18T12:32:31,646   copying cap2/pipeline/contigs/__init__.py -> build/lib/cap2/pipeline/contigs
2021-09-18T12:32:31,652   copying cap2/pipeline/contigs/amr_identification.py -> build/lib/cap2/pipeline/contigs
2021-09-18T12:32:31,658   copying cap2/pipeline/contigs/prodigal.py -> build/lib/cap2/pipeline/contigs
2021-09-18T12:32:31,665   creating build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,667   copying cap2/pipeline/short_read/humann2.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,672   copying cap2/pipeline/short_read/jellyfish.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,676   copying cap2/pipeline/short_read/microbe_census.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,680   copying cap2/pipeline/short_read/processed_reads.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,686   copying cap2/pipeline/short_read/read_stats.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,692   copying cap2/pipeline/short_read/kraken2.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,698   copying cap2/pipeline/short_read/__init__.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,703   copying cap2/pipeline/short_read/hmp_comparison.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,709   copying cap2/pipeline/short_read/krakenuniq.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,715   copying cap2/pipeline/short_read/sakeima.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,720   copying cap2/pipeline/short_read/amrs.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,726   copying cap2/pipeline/short_read/mash.py -> build/lib/cap2/pipeline/short_read
2021-09-18T12:32:31,732   creating build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,734   copying cap2/pipeline/preprocessing/basic_sample_stats.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,739   copying cap2/pipeline/preprocessing/fastqc.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,744   copying cap2/pipeline/preprocessing/count_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,749   copying cap2/pipeline/preprocessing/fast_taxa.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,755   copying cap2/pipeline/preprocessing/multiqc.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,761   copying cap2/pipeline/preprocessing/map_to_human.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,767   copying cap2/pipeline/preprocessing/__init__.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,772   copying cap2/pipeline/preprocessing/control_sample_abundances.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,779   copying cap2/pipeline/preprocessing/error_correct_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,785   copying cap2/pipeline/preprocessing/remove_adapters.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,791   copying cap2/pipeline/preprocessing/map_to_mouse.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,796   copying cap2/pipeline/preprocessing/base_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,802   copying cap2/pipeline/preprocessing/clean_reads.py -> build/lib/cap2/pipeline/preprocessing
2021-09-18T12:32:31,810   creating build/lib/cap2/pipeline/utils
2021-09-18T12:32:31,812   copying cap2/pipeline/utils/utils.py -> build/lib/cap2/pipeline/utils
2021-09-18T12:32:31,818   copying cap2/pipeline/utils/__init__.py -> build/lib/cap2/pipeline/utils
2021-09-18T12:32:31,824   copying cap2/pipeline/utils/cap_task.py -> build/lib/cap2/pipeline/utils
2021-09-18T12:32:31,830   copying cap2/pipeline/utils/conda.py -> build/lib/cap2/pipeline/utils
2021-09-18T12:32:31,837   creating build/lib/cap2/pipeline/databases
2021-09-18T12:32:31,839   copying cap2/pipeline/databases/amr_db.py -> build/lib/cap2/pipeline/databases
2021-09-18T12:32:31,843   copying cap2/pipeline/databases/taxonomic_db.py -> build/lib/cap2/pipeline/databases
2021-09-18T12:32:31,849   copying cap2/pipeline/databases/mouse_removal_db.py -> build/lib/cap2/pipeline/databases
2021-09-18T12:32:31,854   copying cap2/pipeline/databases/uniref.py -> build/lib/cap2/pipeline/databases
2021-09-18T12:32:31,861   copying cap2/pipeline/databases/__init__.py -> build/lib/cap2/pipeline/databases
2021-09-18T12:32:31,866   copying cap2/pipeline/databases/kraken2_db.py -> build/lib/cap2/pipeline/databases
2021-09-18T12:32:31,871   copying cap2/pipeline/databases/human_removal_db.py -> build/lib/cap2/pipeline/databases
2021-09-18T12:32:31,875   copying cap2/pipeline/databases/hmp_db.py -> build/lib/cap2/pipeline/databases
2021-09-18T12:32:31,879   copying cap2/pipeline/databases/fast_kraken2_db.py -> build/lib/cap2/pipeline/databases
2021-09-18T12:32:31,885   creating build/lib/cap2/extensions/experimental
2021-09-18T12:32:31,887   copying cap2/extensions/experimental/cli.py -> build/lib/cap2/extensions/experimental
2021-09-18T12:32:31,893   copying cap2/extensions/experimental/__init__.py -> build/lib/cap2/extensions/experimental
2021-09-18T12:32:31,900   creating build/lib/cap2/extensions/experimental/tcems
2021-09-18T12:32:31,903   copying cap2/extensions/experimental/tcems/cli.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-18T12:32:31,909   copying cap2/extensions/experimental/tcems/__init__.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-18T12:32:31,913   copying cap2/extensions/experimental/tcems/tcem_aa_db.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-18T12:32:31,918   copying cap2/extensions/experimental/tcems/tcem_repertoire.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-18T12:32:31,923   copying cap2/extensions/experimental/tcems/mixcr.py -> build/lib/cap2/extensions/experimental/tcems
2021-09-18T12:32:31,931   creating build/lib/cap2/extensions/experimental/covid
2021-09-18T12:32:31,934   copying cap2/extensions/experimental/covid/make_pileup.py -> build/lib/cap2/extensions/experimental/covid
2021-09-18T12:32:31,940   copying cap2/extensions/experimental/covid/cli.py -> build/lib/cap2/extensions/experimental/covid
2021-09-18T12:32:31,946   copying cap2/extensions/experimental/covid/__init__.py -> build/lib/cap2/extensions/experimental/covid
2021-09-18T12:32:31,951   copying cap2/extensions/experimental/covid/make_covid_consensus_seq.py -> build/lib/cap2/extensions/experimental/covid
2021-09-18T12:32:31,955   copying cap2/extensions/experimental/covid/align_to_covid_genome.py -> build/lib/cap2/extensions/experimental/covid
2021-09-18T12:32:31,960   copying cap2/extensions/experimental/covid/fast_detect.py -> build/lib/cap2/extensions/experimental/covid
2021-09-18T12:32:31,964   copying cap2/extensions/experimental/covid/covid_genome_db.py -> build/lib/cap2/extensions/experimental/covid
2021-09-18T12:32:31,969   copying cap2/extensions/experimental/covid/genome_coverage.py -> build/lib/cap2/extensions/experimental/covid
2021-09-18T12:32:31,974   copying cap2/extensions/experimental/covid/call_covid_variants.py -> build/lib/cap2/extensions/experimental/covid
2021-09-18T12:32:31,984   creating build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:31,987   copying cap2/extensions/experimental/strains/make_pileup.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:31,992   copying cap2/extensions/experimental/strains/utils.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:31,996   copying cap2/extensions/experimental/strains/make_snp_graph.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,001   copying cap2/extensions/experimental/strains/make_snp_table.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,005   copying cap2/extensions/experimental/strains/cli.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,011   copying cap2/extensions/experimental/strains/bacterial_genome_getter.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,016   copying cap2/extensions/experimental/strains/merge_snp_clusters.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,022   copying cap2/extensions/experimental/strains/merge_snp_graph.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,027   copying cap2/extensions/experimental/strains/__init__.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,032   copying cap2/extensions/experimental/strains/align_to_genome.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,037   copying cap2/extensions/experimental/strains/make_snp_clusters.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,041   copying cap2/extensions/experimental/strains/tasks.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,045   copying cap2/extensions/experimental/strains/align_to_genome_db.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,050   copying cap2/extensions/experimental/strains/get_microbial_genome.py -> build/lib/cap2/extensions/experimental/strains
2021-09-18T12:32:32,058   creating build/lib/cap2/extensions/experimental/preclassify
2021-09-18T12:32:32,061   copying cap2/extensions/experimental/preclassify/dynamic_pipeline.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-18T12:32:32,068   copying cap2/extensions/experimental/preclassify/cli.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-18T12:32:32,073   copying cap2/extensions/experimental/preclassify/__init__.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-18T12:32:32,076   copying cap2/extensions/experimental/preclassify/preclassify_db.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-18T12:32:32,081   copying cap2/extensions/experimental/preclassify/preclassify.py -> build/lib/cap2/extensions/experimental/preclassify
2021-09-18T12:32:32,087   creating build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:32,089   copying cap2/extensions/experimental/strains/strainotyping/cli.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:32,095   copying cap2/extensions/experimental/strains/strainotyping/api.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:32,101   copying cap2/extensions/experimental/strains/strainotyping/clustering.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:32,106   copying cap2/extensions/experimental/strains/strainotyping/__init__.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:32,112   copying cap2/extensions/experimental/strains/strainotyping/graphs.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:32,116   copying cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:32,121   copying cap2/extensions/experimental/strains/strainotyping/io.py -> build/lib/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:32,169   installing to build/bdist.linux-armv7l/wheel
2021-09-18T12:32:32,170   running install
2021-09-18T12:32:32,173   running install_lib
2021-09-18T12:32:32,180   creating build/bdist.linux-armv7l
2021-09-18T12:32:32,181   creating build/bdist.linux-armv7l/wheel
2021-09-18T12:32:32,185   creating build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,187   copying build/lib/tests/test_pangea.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,193   copying build/lib/tests/test_experimental_covid.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,199   copying build/lib/tests/test_tcems.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,205   copying build/lib/tests/test_short_read.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,211   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,215   copying build/lib/tests/test_assembly.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,221   copying build/lib/tests/test_versions.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,227   copying build/lib/tests/test_experimental_strain.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,233   copying build/lib/tests/test_api.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,239   copying build/lib/tests/test_databases.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,245   copying build/lib/tests/test_strainotyping.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,251   copying build/lib/tests/test_pipeline_preprocessing.py -> build/bdist.linux-armv7l/wheel/tests
2021-09-18T12:32:32,259   creating build/bdist.linux-armv7l/wheel/cap2
2021-09-18T12:32:32,262   copying build/lib/cap2/utils.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-18T12:32:32,267   copying build/lib/cap2/cli.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-18T12:32:32,273   copying build/lib/cap2/constants.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-18T12:32:32,278   copying build/lib/cap2/api.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-18T12:32:32,283   copying build/lib/cap2/__init__.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-18T12:32:32,288   copying build/lib/cap2/sample.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-18T12:32:32,295   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-18T12:32:32,297   copying build/lib/cap2/capalyzer/version.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-18T12:32:32,303   copying build/lib/cap2/capalyzer/cli.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-18T12:32:32,308   copying build/lib/cap2/capalyzer/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-18T12:32:32,315   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-18T12:32:32,319   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:32,322   copying build/lib/cap2/capalyzer/table_builder/modules/basic_stats_summary.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:32,327   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_taxa_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:32,333   copying build/lib/cap2/capalyzer/table_builder/modules/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:32,338   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_fast_taxa.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:32,344   copying build/lib/cap2/capalyzer/table_builder/modules/tcem_repertoire_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:32,349   copying build/lib/cap2/capalyzer/table_builder/modules/covid_variant_table.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:32,354   copying build/lib/cap2/capalyzer/table_builder/modules/kraken2_covid_fast_detect.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder/modules
2021-09-18T12:32:32,360   copying build/lib/cap2/capalyzer/table_builder/base_module.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-18T12:32:32,365   copying build/lib/cap2/capalyzer/table_builder/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-18T12:32:32,370   copying build/lib/cap2/capalyzer/table_builder/cap_table_builder.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-18T12:32:32,376   copying build/lib/cap2/capalyzer/table_builder/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_builder
2021-09-18T12:32:32,382   copying build/lib/cap2/capalyzer/exceptions.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-18T12:32:32,389   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-18T12:32:32,391   copying build/lib/cap2/capalyzer/pangea/pangea_file_source.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-18T12:32:32,397   copying build/lib/cap2/capalyzer/pangea/utils.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-18T12:32:32,403   copying build/lib/cap2/capalyzer/pangea/cli.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-18T12:32:32,408   copying build/lib/cap2/capalyzer/pangea/api.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-18T12:32:32,413   copying build/lib/cap2/capalyzer/pangea/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-18T12:32:32,419   copying build/lib/cap2/capalyzer/pangea/pangea_file_uploader.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-18T12:32:32,424   copying build/lib/cap2/capalyzer/pangea/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/pangea
2021-09-18T12:32:32,430   copying build/lib/cap2/capalyzer/parsers.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer
2021-09-18T12:32:32,436   creating build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-18T12:32:32,439   copying build/lib/cap2/capalyzer/table_parser/analysis_utils.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-18T12:32:32,446   copying build/lib/cap2/capalyzer/table_parser/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-18T12:32:32,451   copying build/lib/cap2/capalyzer/table_parser/cap_table_parser.py -> build/bdist.linux-armv7l/wheel/cap2/capalyzer/table_parser
2021-09-18T12:32:32,457   copying build/lib/cap2/exceptions.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-18T12:32:32,464   creating build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-18T12:32:32,466   copying build/lib/cap2/pangea/cli.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-18T12:32:32,473   copying build/lib/cap2/pangea/constants.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-18T12:32:32,478   copying build/lib/cap2/pangea/api.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-18T12:32:32,484   copying build/lib/cap2/pangea/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-18T12:32:32,489   copying build/lib/cap2/pangea/download_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-18T12:32:32,493   copying build/lib/cap2/pangea/load_task.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-18T12:32:32,501   copying build/lib/cap2/pangea/cli_utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-18T12:32:32,507   copying build/lib/cap2/pangea/pangea_sample.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-18T12:32:32,514   copying build/lib/cap2/pangea/sra_utils.py -> build/bdist.linux-armv7l/wheel/cap2/pangea
2021-09-18T12:32:32,519   copying build/lib/cap2/setup_logging.py -> build/bdist.linux-armv7l/wheel/cap2
2021-09-18T12:32:32,526   creating build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-18T12:32:32,529   copying build/lib/cap2/pipeline/constants.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-18T12:32:32,536   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-18T12:32:32,538   copying build/lib/cap2/pipeline/assembly/metabat2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-18T12:32:32,544   copying build/lib/cap2/pipeline/assembly/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-18T12:32:32,550   copying build/lib/cap2/pipeline/assembly/clean_contigs.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-18T12:32:32,555   copying build/lib/cap2/pipeline/assembly/metaspades.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/assembly
2021-09-18T12:32:32,562   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-18T12:32:32,564   copying build/lib/cap2/pipeline/contigs/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-18T12:32:32,570   copying build/lib/cap2/pipeline/contigs/amr_identification.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-18T12:32:32,575   copying build/lib/cap2/pipeline/contigs/prodigal.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/contigs
2021-09-18T12:32:32,581   copying build/lib/cap2/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-18T12:32:32,585   copying build/lib/cap2/pipeline/config.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-18T12:32:32,592   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,595   copying build/lib/cap2/pipeline/short_read/humann2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,602   copying build/lib/cap2/pipeline/short_read/jellyfish.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,607   copying build/lib/cap2/pipeline/short_read/microbe_census.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,613   copying build/lib/cap2/pipeline/short_read/processed_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,619   copying build/lib/cap2/pipeline/short_read/read_stats.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,624   copying build/lib/cap2/pipeline/short_read/kraken2.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,630   copying build/lib/cap2/pipeline/short_read/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,636   copying build/lib/cap2/pipeline/short_read/hmp_comparison.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,641   copying build/lib/cap2/pipeline/short_read/krakenuniq.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,646   copying build/lib/cap2/pipeline/short_read/sakeima.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,652   copying build/lib/cap2/pipeline/short_read/amrs.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,658   copying build/lib/cap2/pipeline/short_read/mash.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/short_read
2021-09-18T12:32:32,665   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,668   copying build/lib/cap2/pipeline/preprocessing/basic_sample_stats.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,674   copying build/lib/cap2/pipeline/preprocessing/fastqc.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,679   copying build/lib/cap2/pipeline/preprocessing/count_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,685   copying build/lib/cap2/pipeline/preprocessing/fast_taxa.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,690   copying build/lib/cap2/pipeline/preprocessing/multiqc.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,696   copying build/lib/cap2/pipeline/preprocessing/map_to_human.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,701   copying build/lib/cap2/pipeline/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,706   copying build/lib/cap2/pipeline/preprocessing/control_sample_abundances.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,713   copying build/lib/cap2/pipeline/preprocessing/error_correct_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,719   copying build/lib/cap2/pipeline/preprocessing/remove_adapters.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,724   copying build/lib/cap2/pipeline/preprocessing/map_to_mouse.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,730   copying build/lib/cap2/pipeline/preprocessing/base_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,735   copying build/lib/cap2/pipeline/preprocessing/clean_reads.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/preprocessing
2021-09-18T12:32:32,742   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-18T12:32:32,744   copying build/lib/cap2/pipeline/utils/utils.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-18T12:32:32,750   copying build/lib/cap2/pipeline/utils/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-18T12:32:32,755   copying build/lib/cap2/pipeline/utils/cap_task.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-18T12:32:32,763   copying build/lib/cap2/pipeline/utils/conda.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/utils
2021-09-18T12:32:32,769   copying build/lib/cap2/pipeline/full_pipeline.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline
2021-09-18T12:32:32,776   creating build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-18T12:32:32,778   copying build/lib/cap2/pipeline/databases/amr_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-18T12:32:32,784   copying build/lib/cap2/pipeline/databases/taxonomic_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-18T12:32:32,790   copying build/lib/cap2/pipeline/databases/mouse_removal_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-18T12:32:32,795   copying build/lib/cap2/pipeline/databases/uniref.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-18T12:32:32,802   copying build/lib/cap2/pipeline/databases/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-18T12:32:32,807   copying build/lib/cap2/pipeline/databases/kraken2_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-18T12:32:32,814   copying build/lib/cap2/pipeline/databases/human_removal_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-18T12:32:32,820   copying build/lib/cap2/pipeline/databases/hmp_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-18T12:32:32,825   copying build/lib/cap2/pipeline/databases/fast_kraken2_db.py -> build/bdist.linux-armv7l/wheel/cap2/pipeline/databases
2021-09-18T12:32:32,832   creating build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-18T12:32:32,834   copying build/lib/cap2/extensions/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-18T12:32:32,839   copying build/lib/cap2/extensions/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions
2021-09-18T12:32:32,845   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-18T12:32:32,849   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-18T12:32:32,852   copying build/lib/cap2/extensions/experimental/tcems/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-18T12:32:32,857   copying build/lib/cap2/extensions/experimental/tcems/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-18T12:32:32,860   copying build/lib/cap2/extensions/experimental/tcems/tcem_aa_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-18T12:32:32,865   copying build/lib/cap2/extensions/experimental/tcems/tcem_repertoire.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-18T12:32:32,870   copying build/lib/cap2/extensions/experimental/tcems/mixcr.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/tcems
2021-09-18T12:32:32,876   copying build/lib/cap2/extensions/experimental/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-18T12:32:32,881   copying build/lib/cap2/extensions/experimental/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental
2021-09-18T12:32:32,887   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-18T12:32:32,890   copying build/lib/cap2/extensions/experimental/covid/make_pileup.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-18T12:32:32,895   copying build/lib/cap2/extensions/experimental/covid/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-18T12:32:32,900   copying build/lib/cap2/extensions/experimental/covid/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-18T12:32:32,903   copying build/lib/cap2/extensions/experimental/covid/make_covid_consensus_seq.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-18T12:32:32,907   copying build/lib/cap2/extensions/experimental/covid/align_to_covid_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-18T12:32:32,912   copying build/lib/cap2/extensions/experimental/covid/fast_detect.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-18T12:32:32,918   copying build/lib/cap2/extensions/experimental/covid/covid_genome_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-18T12:32:32,924   copying build/lib/cap2/extensions/experimental/covid/genome_coverage.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-18T12:32:32,929   copying build/lib/cap2/extensions/experimental/covid/call_covid_variants.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/covid
2021-09-18T12:32:32,936   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,937   copying build/lib/cap2/extensions/experimental/strains/make_pileup.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,942   copying build/lib/cap2/extensions/experimental/strains/utils.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,946   copying build/lib/cap2/extensions/experimental/strains/make_snp_graph.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,950   copying build/lib/cap2/extensions/experimental/strains/make_snp_table.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,954   copying build/lib/cap2/extensions/experimental/strains/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,961   copying build/lib/cap2/extensions/experimental/strains/bacterial_genome_getter.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,967   copying build/lib/cap2/extensions/experimental/strains/merge_snp_clusters.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,972   copying build/lib/cap2/extensions/experimental/strains/merge_snp_graph.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,976   copying build/lib/cap2/extensions/experimental/strains/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,980   copying build/lib/cap2/extensions/experimental/strains/align_to_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,985   copying build/lib/cap2/extensions/experimental/strains/make_snp_clusters.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,989   copying build/lib/cap2/extensions/experimental/strains/tasks.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,993   copying build/lib/cap2/extensions/experimental/strains/align_to_genome_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:32,998   copying build/lib/cap2/extensions/experimental/strains/get_microbial_genome.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains
2021-09-18T12:32:33,005   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:33,013   copying build/lib/cap2/extensions/experimental/strains/strainotyping/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:33,019   copying build/lib/cap2/extensions/experimental/strains/strainotyping/api.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:33,025   copying build/lib/cap2/extensions/experimental/strains/strainotyping/clustering.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:33,030   copying build/lib/cap2/extensions/experimental/strains/strainotyping/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:33,035   copying build/lib/cap2/extensions/experimental/strains/strainotyping/graphs.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:33,041   copying build/lib/cap2/extensions/experimental/strains/strainotyping/snp_barcodes.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:33,047   copying build/lib/cap2/extensions/experimental/strains/strainotyping/io.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/strains/strainotyping
2021-09-18T12:32:33,054   creating build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-18T12:32:33,056   copying build/lib/cap2/extensions/experimental/preclassify/dynamic_pipeline.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-18T12:32:33,062   copying build/lib/cap2/extensions/experimental/preclassify/cli.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-18T12:32:33,068   copying build/lib/cap2/extensions/experimental/preclassify/__init__.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-18T12:32:33,073   copying build/lib/cap2/extensions/experimental/preclassify/preclassify_db.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-18T12:32:33,078   copying build/lib/cap2/extensions/experimental/preclassify/preclassify.py -> build/bdist.linux-armv7l/wheel/cap2/extensions/experimental/preclassify
2021-09-18T12:32:33,084   running install_egg_info
2021-09-18T12:32:33,134   running egg_info
2021-09-18T12:32:33,136   writing top-level names to cap2.egg-info/top_level.txt
2021-09-18T12:32:33,139   writing requirements to cap2.egg-info/requires.txt
2021-09-18T12:32:33,141   writing dependency_links to cap2.egg-info/dependency_links.txt
2021-09-18T12:32:33,144   writing entry points to cap2.egg-info/entry_points.txt
2021-09-18T12:32:33,146   writing cap2.egg-info/PKG-INFO
2021-09-18T12:32:33,190   reading manifest file 'cap2.egg-info/SOURCES.txt'
2021-09-18T12:32:33,226   writing manifest file 'cap2.egg-info/SOURCES.txt'
2021-09-18T12:32:33,230   Copying cap2.egg-info to build/bdist.linux-armv7l/wheel/cap2-0.4.1-py3.5.egg-info
2021-09-18T12:32:33,260   running install_scripts
2021-09-18T12:32:33,481   creating build/bdist.linux-armv7l/wheel/cap2-0.4.1.dist-info/WHEEL
2021-09-18T12:32:34,320   Building wheel for cap2 (setup.py): finished with status 'done'
2021-09-18T12:32:34,326   Created wheel for cap2: filename=cap2-0.4.1-py3-none-any.whl size=142746 sha256=2c3f9a43fc7583e80720736ac32c3bd96d3ee5c9a77b0d6a957c5da1d02b797a
2021-09-18T12:32:34,327   Stored in directory: /tmp/pip-ephem-wheel-cache-v2yiuycj/wheels/e4/eb/63/6dfc26f28df6f1c5fb4b377630fe5d9ff5686ba133cd8086f6
2021-09-18T12:32:34,359 Successfully built cap2
2021-09-18T12:32:34,387 Removed build tracker: '/tmp/pip-req-tracker-vvj9cj8y'