2021-07-12T18:40:06,798 Created temporary directory: /tmp/pip-ephem-wheel-cache-32i4w64a
2021-07-12T18:40:06,801 Created temporary directory: /tmp/pip-req-tracker-mf31z5mx
2021-07-12T18:40:06,802 Initialized build tracking at /tmp/pip-req-tracker-mf31z5mx
2021-07-12T18:40:06,802 Created build tracker: /tmp/pip-req-tracker-mf31z5mx
2021-07-12T18:40:06,802 Entered build tracker: /tmp/pip-req-tracker-mf31z5mx
2021-07-12T18:40:06,803 Created temporary directory: /tmp/pip-wheel-eu7fgzx8
2021-07-12T18:40:06,833 1 location(s) to search for versions of biocode:
2021-07-12T18:40:06,833 * https://pypi.org/simple/biocode/
2021-07-12T18:40:06,833 Fetching project page and analyzing links: https://pypi.org/simple/biocode/
2021-07-12T18:40:06,834 Getting page https://pypi.org/simple/biocode/
2021-07-12T18:40:06,835 Found index url https://pypi.org/simple
2021-07-12T18:40:06,935   Found link https://files.pythonhosted.org/packages/e1/6d/8b417c8c08f02c960801f360bc8b38927a4c14dfee8cb1418978bdfc4946/biocode-0.1.0.tar.gz#sha256=98fb4d531f0a3d940f3f30a71c0c9a59e89063c30eefcbaa3032ed4c8e8eb7ad (from https://pypi.org/simple/biocode/), version: 0.1.0
2021-07-12T18:40:06,936   Found link https://files.pythonhosted.org/packages/96/e5/314879e7d54bee7e0ed6db1fc358d193ae2d118e4825a99d14f3269a9322/biocode-0.1.1.tar.gz#sha256=76bdb70852fc5e7a83f19de8e66074de97bace873dea6a3014b49f4305736fb0 (from https://pypi.org/simple/biocode/), version: 0.1.1
2021-07-12T18:40:06,936   Found link https://files.pythonhosted.org/packages/4e/94/c999970e61e13f3082eae7989bc32d745ef7d846824252dd9a3c09cfd19c/biocode-0.1.2.tar.gz#sha256=d72e37b2f0cefc2081b0888b603d39cf572382b5d966586390e02cb09b708cc9 (from https://pypi.org/simple/biocode/), version: 0.1.2
2021-07-12T18:40:06,936   Found link https://files.pythonhosted.org/packages/a5/2c/85a52abaf0192795d5fbc56842c58c349bc6b58c568b4b913b8fdf591617/biocode-0.1.3.tar.gz#sha256=ec904f8ddd1458821e75e8d2fffa08b2a7dee98c02bec8e5463f55997dda2fb1 (from https://pypi.org/simple/biocode/), version: 0.1.3
2021-07-12T18:40:06,937   Found link https://files.pythonhosted.org/packages/a5/06/562772ff9d04bcfcde87ed1ce76026eaf8f6b15cf7336fc6334bad04db00/biocode-0.1.4.tar.gz#sha256=603bf7f95b963b13a70cddb848e41953897e6ec38bbd9afed918667881190745 (from https://pypi.org/simple/biocode/), version: 0.1.4
2021-07-12T18:40:06,937   Found link https://files.pythonhosted.org/packages/27/c6/cdb7baa2821259f68c059a9e7385d613b817d90c00c8e727df7d3da23d2e/biocode-0.1.5.tar.gz#sha256=a9d3a7c9214b2625e44a0299c132e349279cd6b355c4ad30992aacdb27f123d6 (from https://pypi.org/simple/biocode/), version: 0.1.5
2021-07-12T18:40:06,937   Found link https://files.pythonhosted.org/packages/5d/ff/bda52fd80d3696809f96b27e1df816809c610a91587199fbb5611a82ff48/biocode-0.2.0.tar.gz#sha256=9b0e58ba93cb841d9f214c010d46e40c2c09a941a3f43874b58564abe357ccfd (from https://pypi.org/simple/biocode/), version: 0.2.0
2021-07-12T18:40:06,938   Found link https://files.pythonhosted.org/packages/4b/d4/61d22deda78a8fb9b998ac1a7e7fee95eb3e84adcb26ab1705fda8235d31/biocode-0.3.0.tar.gz#sha256=8d210b1a7ae16d60964df9a92d0e92eda846e7fca2c01f6add5105d6f26691d3 (from https://pypi.org/simple/biocode/), version: 0.3.0
2021-07-12T18:40:06,938   Found link https://files.pythonhosted.org/packages/9e/04/4a879cb84c7d4d8a11b9812e25668e5f1d4ef5e3cea429f7cc8202a0021b/biocode-0.3.1.tar.gz#sha256=aac38e473e1f4712d85db957f8b92caf980522c748d438ca3ef2597cab586f20 (from https://pypi.org/simple/biocode/), version: 0.3.1
2021-07-12T18:40:06,938   Found link https://files.pythonhosted.org/packages/72/af/9de76d7a8ae1cc6912488e33e53df8145aac259d36ddd42fc3dc803ea473/biocode-0.4.0.tar.gz#sha256=7e5c9d20368f8a7fdd8446e56b9d325a2e7d890cd5c76cc1f90740665a3886d8 (from https://pypi.org/simple/biocode/), version: 0.4.0
2021-07-12T18:40:06,938   Found link https://files.pythonhosted.org/packages/c7/93/31d3a353be167da9500e2bdff93451dba1a6a134e425767d426e297a0853/biocode-0.4.1.tar.gz#sha256=e5e17c522d8372246038b2d2b77ce112a38c9eb2770f3fba28bcfda4e2bfed10 (from https://pypi.org/simple/biocode/), version: 0.4.1
2021-07-12T18:40:06,939   Found link https://files.pythonhosted.org/packages/7a/24/cae23280630c49008e96590c77494485e47bbcf488f5c4b4e03ecc7b1e29/biocode-0.4.2.tar.gz#sha256=d49e59cc384507d62a7e379c6f21a6598262677ca9d50f98e47503e495a901ea (from https://pypi.org/simple/biocode/), version: 0.4.2
2021-07-12T18:40:06,939   Found link https://files.pythonhosted.org/packages/7f/5a/0d11038818cc78cee863d20da8a16a9907c20be8bfa8334ebabec4cb37e4/biocode-0.4.4.tar.gz#sha256=078dc61603ae5fe6944f271f8625f06779c884b9428154315c1cbc1dcd7c606f (from https://pypi.org/simple/biocode/), version: 0.4.4
2021-07-12T18:40:06,939   Found link https://files.pythonhosted.org/packages/43/8e/107a8d911b7af9db94a561f6740801f62b69a60cb8857fc6642268f0d99d/biocode-0.4.5.tar.gz#sha256=bca0bac61eb6ba3da8df7d2826edd314e3351df73b272df4db17e83b3881d5ea (from https://pypi.org/simple/biocode/), version: 0.4.5
2021-07-12T18:40:06,939   Found link https://files.pythonhosted.org/packages/02/e7/dc62a42fcfcb2288f397789f6bc83fd40a815d495edba4fa79e14759935c/biocode-0.4.7.tar.gz#sha256=8cfa6c8edbd1a65b03178d12f1941cb159d210a534447226846cc8ae4ad47148 (from https://pypi.org/simple/biocode/), version: 0.4.7
2021-07-12T18:40:06,940   Found link https://files.pythonhosted.org/packages/f2/fc/483f6dad337423c04dc8a1b2756c3e5326e9381648e5560eb602a4f83413/biocode-0.5.0.tar.gz#sha256=a96f0e2c3bde3e42f82590de9ce1be0e8782b50c9a58296bc3e872161fb3a3a3 (from https://pypi.org/simple/biocode/), version: 0.5.0
2021-07-12T18:40:06,940   Found link https://files.pythonhosted.org/packages/5c/b7/035e01334320dd66ac8c65be4baa910e8cb16215c563d7b65bfdfd5b56d6/biocode-0.5.1.tar.gz#sha256=ca80071c7e495380a875714ac7cf975dc20389ab8e36f72971a59f6e5a5ac83e (from https://pypi.org/simple/biocode/), version: 0.5.1
2021-07-12T18:40:06,940   Found link https://files.pythonhosted.org/packages/95/f7/e7ac262a9e90ac52d889c0a832aa8276b95fb6c23d0c65bf32fc2ccc1c7a/biocode-0.5.2.tar.gz#sha256=53cfdf987543f82bca9ccd37fa6aade4f257601f18d79b9ebd4dd924d55e5d01 (from https://pypi.org/simple/biocode/), version: 0.5.2
2021-07-12T18:40:06,941   Found link https://files.pythonhosted.org/packages/3b/2d/43287226a16b06ecdf7ed706752de718042382513bf2a3a5b0c9d2a41222/biocode-0.5.3.tar.gz#sha256=446811c773f4a93604591130ab64cdf30ddb26810a468b68588876985cc44003 (from https://pypi.org/simple/biocode/), version: 0.5.3
2021-07-12T18:40:06,941   Found link https://files.pythonhosted.org/packages/b3/e7/e8b3bd627d57954933c9c5a79bbdf28ad93073cc0792c61f71e3777f44d8/biocode-0.6.0.tar.gz#sha256=194619f6945592ac8795cebb80d2734b5e30ad85dc4cc5f5cf3365f9fc13491e (from https://pypi.org/simple/biocode/), version: 0.6.0
2021-07-12T18:40:06,941   Found link https://files.pythonhosted.org/packages/dd/d7/73e00082816c193207ea58420b38ac0a4041d345b8617f0d15501367c080/biocode-0.7.0.tar.gz#sha256=6f1f1ddb5e72687c18ae968414bb9c5b9003869b1bb5d8b69acb4f863bccffe8 (from https://pypi.org/simple/biocode/), version: 0.7.0
2021-07-12T18:40:06,941   Found link https://files.pythonhosted.org/packages/bb/7a/c073ca257a937286fec9e225190fa55c66a46132708e8dfa13569ef0cc37/biocode-0.7.1.tar.gz#sha256=98583da45aa2fb3258f676fd02cbd421b5dbf38ecac9f062a44157222671bb8b (from https://pypi.org/simple/biocode/), version: 0.7.1
2021-07-12T18:40:06,942   Found link https://files.pythonhosted.org/packages/a3/b5/0a5b44de28177113d5bbc0a8b510ea6e9acf82184b1e1ad5303357d1caa5/biocode-0.8.0.tar.gz#sha256=9ac96ea8d68d3770c815e91201080ef13485e550f42f2c955fb21df57384952b (from https://pypi.org/simple/biocode/), version: 0.8.0
2021-07-12T18:40:06,942   Found link https://files.pythonhosted.org/packages/ac/58/b16f07e13b99403a0069b7782dc963882f634b6863d6e4bba85d327bd634/biocode-0.9.0.tar.gz#sha256=3e8ef89dc0a699ed4f735563009a5e329c8101c60e23c21135ebb6ef9b44d3b8 (from https://pypi.org/simple/biocode/), version: 0.9.0
2021-07-12T18:40:06,942   Found link https://files.pythonhosted.org/packages/60/4d/1ede29387210a62ff0c6ccbb1c467e94890fb1a5802a2a3b3d37df3997cb/biocode-0.10.0.tar.gz#sha256=ab48e0ea92f52c7fe48c6c947d4d5aa43437f16cd42a804546c71ef0e5ba2265 (from https://pypi.org/simple/biocode/), version: 0.10.0
2021-07-12T18:40:06,942 Skipping link: not a file: https://pypi.org/simple/biocode/
2021-07-12T18:40:06,964 Given no hashes to check 1 links for project 'biocode': discarding no candidates
2021-07-12T18:40:06,985 Collecting biocode==0.4.4
2021-07-12T18:40:06,987   Created temporary directory: /tmp/pip-unpack-hdjx6dg2
2021-07-12T18:40:07,196   Downloading biocode-0.4.4.tar.gz (157 kB)
2021-07-12T18:40:07,515   Added biocode==0.4.4 from https://files.pythonhosted.org/packages/7f/5a/0d11038818cc78cee863d20da8a16a9907c20be8bfa8334ebabec4cb37e4/biocode-0.4.4.tar.gz#sha256=078dc61603ae5fe6944f271f8625f06779c884b9428154315c1cbc1dcd7c606f to build tracker '/tmp/pip-req-tracker-mf31z5mx'
2021-07-12T18:40:07,516     Running setup.py (path:/tmp/pip-wheel-eu7fgzx8/biocode_3a0aa3cac5964c85a8184a7dcccf8956/setup.py) egg_info for package biocode
2021-07-12T18:40:07,516     Created temporary directory: /tmp/pip-pip-egg-info-hctznfiz
2021-07-12T18:40:07,517     Running command python setup.py egg_info
2021-07-12T18:40:08,525     /tmp/pip-wheel-eu7fgzx8/biocode_3a0aa3cac5964c85a8184a7dcccf8956/setup.py:6: DeprecationWarning: Due to possible ambiguity, 'convert()' is deprecated. Use 'convert_file()'  or 'convert_text()'.
2021-07-12T18:40:08,525       read_md = lambda f: convert(f, 'rst', 'md')
2021-07-12T18:40:08,781     /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long'
2021-07-12T18:40:08,781       warnings.warn(msg)
2021-07-12T18:40:08,921     running egg_info
2021-07-12T18:40:08,923     creating /tmp/pip-pip-egg-info-hctznfiz/biocode.egg-info
2021-07-12T18:40:08,924     writing /tmp/pip-pip-egg-info-hctznfiz/biocode.egg-info/PKG-INFO
2021-07-12T18:40:08,927     writing dependency_links to /tmp/pip-pip-egg-info-hctznfiz/biocode.egg-info/dependency_links.txt
2021-07-12T18:40:08,930     writing requirements to /tmp/pip-pip-egg-info-hctznfiz/biocode.egg-info/requires.txt
2021-07-12T18:40:08,930     writing top-level names to /tmp/pip-pip-egg-info-hctznfiz/biocode.egg-info/top_level.txt
2021-07-12T18:40:08,932     writing manifest file '/tmp/pip-pip-egg-info-hctznfiz/biocode.egg-info/SOURCES.txt'
2021-07-12T18:40:09,125     reading manifest file '/tmp/pip-pip-egg-info-hctznfiz/biocode.egg-info/SOURCES.txt'
2021-07-12T18:40:09,127     reading manifest template 'MANIFEST.in'
2021-07-12T18:40:09,129     warning: no files found matching 'biocode/README.rst'
2021-07-12T18:40:09,130     adding license file 'LICENSE'
2021-07-12T18:40:09,137     writing manifest file '/tmp/pip-pip-egg-info-hctznfiz/biocode.egg-info/SOURCES.txt'
2021-07-12T18:40:09,221   Source in /tmp/pip-wheel-eu7fgzx8/biocode_3a0aa3cac5964c85a8184a7dcccf8956 has version 0.4.4, which satisfies requirement biocode==0.4.4 from https://files.pythonhosted.org/packages/7f/5a/0d11038818cc78cee863d20da8a16a9907c20be8bfa8334ebabec4cb37e4/biocode-0.4.4.tar.gz#sha256=078dc61603ae5fe6944f271f8625f06779c884b9428154315c1cbc1dcd7c606f
2021-07-12T18:40:09,222   Removed biocode==0.4.4 from https://files.pythonhosted.org/packages/7f/5a/0d11038818cc78cee863d20da8a16a9907c20be8bfa8334ebabec4cb37e4/biocode-0.4.4.tar.gz#sha256=078dc61603ae5fe6944f271f8625f06779c884b9428154315c1cbc1dcd7c606f from build tracker '/tmp/pip-req-tracker-mf31z5mx'
2021-07-12T18:40:09,226 Created temporary directory: /tmp/pip-unpack-f8z25e5u
2021-07-12T18:40:09,226 Building wheels for collected packages: biocode
2021-07-12T18:40:09,230   Created temporary directory: /tmp/pip-wheel-f6fgx5n6
2021-07-12T18:40:09,231   Building wheel for biocode (setup.py): started
2021-07-12T18:40:09,231   Destination directory: /tmp/pip-wheel-f6fgx5n6
2021-07-12T18:40:09,232   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-eu7fgzx8/biocode_3a0aa3cac5964c85a8184a7dcccf8956/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-eu7fgzx8/biocode_3a0aa3cac5964c85a8184a7dcccf8956/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-f6fgx5n6
2021-07-12T18:40:10,229   /tmp/pip-wheel-eu7fgzx8/biocode_3a0aa3cac5964c85a8184a7dcccf8956/setup.py:6: DeprecationWarning: Due to possible ambiguity, 'convert()' is deprecated. Use 'convert_file()'  or 'convert_text()'.
2021-07-12T18:40:10,229     read_md = lambda f: convert(f, 'rst', 'md')
2021-07-12T18:40:10,470   /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long'
2021-07-12T18:40:10,470     warnings.warn(msg)
2021-07-12T18:40:10,624   running bdist_wheel
2021-07-12T18:40:10,832   running build
2021-07-12T18:40:10,832   running build_py
2021-07-12T18:40:10,973   creating build
2021-07-12T18:40:10,973   creating build/lib
2021-07-12T18:40:10,974   creating build/lib/biocode
2021-07-12T18:40:10,975   copying biocode/utils.py -> build/lib/biocode
2021-07-12T18:40:10,978   copying biocode/__init__.py -> build/lib/biocode
2021-07-12T18:40:10,979   copying biocode/genbank.py -> build/lib/biocode
2021-07-12T18:40:10,981   copying biocode/things.py -> build/lib/biocode
2021-07-12T18:40:10,984   copying biocode/gff.py -> build/lib/biocode
2021-07-12T18:40:10,987   copying biocode/annotation.py -> build/lib/biocode
2021-07-12T18:40:10,990   copying biocode/tbl.py -> build/lib/biocode
2021-07-12T18:40:10,992   running egg_info
2021-07-12T18:40:11,008   writing biocode.egg-info/PKG-INFO
2021-07-12T18:40:11,011   writing dependency_links to biocode.egg-info/dependency_links.txt
2021-07-12T18:40:11,012   writing requirements to biocode.egg-info/requires.txt
2021-07-12T18:40:11,014   writing top-level names to biocode.egg-info/top_level.txt
2021-07-12T18:40:11,068   reading manifest file 'biocode.egg-info/SOURCES.txt'
2021-07-12T18:40:11,073   reading manifest template 'MANIFEST.in'
2021-07-12T18:40:11,074   warning: no files found matching 'biocode/README.rst'
2021-07-12T18:40:11,075   adding license file 'LICENSE'
2021-07-12T18:40:11,083   writing manifest file 'biocode.egg-info/SOURCES.txt'
2021-07-12T18:40:11,087   creating build/lib/biocode/data
2021-07-12T18:40:11,088   copying biocode/data/HMPslim.v2.1.obo -> build/lib/biocode/data
2021-07-12T18:40:11,093   copying biocode/data/__init__.py -> build/lib/biocode/data
2021-07-12T18:40:11,095   copying biocode/data/genbank_flat_file_header.template -> build/lib/biocode/data
2021-07-12T18:40:11,097   copying biocode/data/rsem_html_table.template -> build/lib/biocode/data
2021-07-12T18:40:11,101   running build_scripts
2021-07-12T18:40:11,102   creating build/scripts-3.9
2021-07-12T18:40:11,103   copying and adjusting bin/set_source_column.py -> build/scripts-3.9
2021-07-12T18:40:11,105   copying and adjusting bin/create_rsem_html_table.py -> build/scripts-3.9
2021-07-12T18:40:11,106   copying and adjusting bin/filter_uniref_by_repid.py -> build/scripts-3.9
2021-07-12T18:40:11,108   copying and adjusting bin/replace_gff_type_column_value.py -> build/scripts-3.9
2021-07-12T18:40:11,109   copying and adjusting bin/convert_blast_btab_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,111   copying and adjusting bin/report_or_replace_nonstandard_residues.py -> build/scripts-3.9
2021-07-12T18:40:11,113   copying and adjusting bin/calculate_query_coverage_by_blast.py -> build/scripts-3.9
2021-07-12T18:40:11,115   copying and adjusting bin/check_gff_for_internal_stops.py -> build/scripts-3.9
2021-07-12T18:40:11,116   copying and adjusting bin/extend_genes_to_stops.py -> build/scripts-3.9
2021-07-12T18:40:11,119   copying and adjusting bin/convert_cegma_gff_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,121   copying and adjusting bin/merge_bam_files.py -> build/scripts-3.9
2021-07-12T18:40:11,123   copying and adjusting bin/make_go_slim.py -> build/scripts-3.9
2021-07-12T18:40:11,125   copying and adjusting bin/convert_genbank_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,127   copying and adjusting bin/fasta_base_content.py -> build/scripts-3.9
2021-07-12T18:40:11,129   copying and adjusting bin/filter_fasta_by_header_regex.py -> build/scripts-3.9
2021-07-12T18:40:11,131   copying and adjusting bin/get_mpilup_from_id_list.py -> build/scripts-3.9
2021-07-12T18:40:11,133   copying and adjusting bin/hmmlib_to_sqlite3.py -> build/scripts-3.9
2021-07-12T18:40:11,135   copying and adjusting bin/uniref_to_sqlite3.py -> build/scripts-3.9
2021-07-12T18:40:11,137   copying and adjusting bin/validate_fasta.py -> build/scripts-3.9
2021-07-12T18:40:11,140   copying and adjusting bin/report_basic_gff_model_agreement.py -> build/scripts-3.9
2021-07-12T18:40:11,141   copying and adjusting bin/biothings_coordinate_comparisons.py -> build/scripts-3.9
2021-07-12T18:40:11,143   copying and adjusting bin/update_selected_column9_values.py -> build/scripts-3.9
2021-07-12T18:40:11,146   copying and adjusting bin/remove_duplicate_sequences.py -> build/scripts-3.9
2021-07-12T18:40:11,148   copying and adjusting bin/make_cufflinks_ids_unique.py -> build/scripts-3.9
2021-07-12T18:40:11,150   copying and adjusting bin/split_fasta_into_even_files.py -> build/scripts-3.9
2021-07-12T18:40:11,152   copying and adjusting bin/interleave_fastq.py -> build/scripts-3.9
2021-07-12T18:40:11,153   copying and adjusting bin/report_coverage_gaps.py -> build/scripts-3.9
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2021-07-12T18:40:11,157   copying and adjusting bin/report_gff3_statistics.py -> build/scripts-3.9
2021-07-12T18:40:11,160   copying and adjusting bin/convert_glimmerHMM_gff_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,162   copying and adjusting bin/correct_gff3_CDS_phase_column.py -> build/scripts-3.9
2021-07-12T18:40:11,164   copying and adjusting bin/check_for_embedded_fasta_headers.py -> build/scripts-3.9
2021-07-12T18:40:11,166   copying and adjusting bin/convert_metagenemark_gff_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,168   copying and adjusting bin/add_polypeptide_to_gff3_gene_models.py -> build/scripts-3.9
2021-07-12T18:40:11,171   copying and adjusting bin/report_gff_intron_and_intergenic_stats.py -> build/scripts-3.9
2021-07-12T18:40:11,173   copying and adjusting bin/filter_fasta_by_type.py -> build/scripts-3.9
2021-07-12T18:40:11,175   copying and adjusting bin/create_taxonomic_profile_from_blast.py -> build/scripts-3.9
2021-07-12T18:40:11,178   copying and adjusting bin/remove_orphaned_features.py -> build/scripts-3.9
2021-07-12T18:40:11,179   copying and adjusting bin/append_to_fastq_read_header.py -> build/scripts-3.9
2021-07-12T18:40:11,181   copying and adjusting bin/convert_gff3_to_gbk.py -> build/scripts-3.9
2021-07-12T18:40:11,184   copying and adjusting bin/mark_partial_genes.py -> build/scripts-3.9
2021-07-12T18:40:11,186   copying and adjusting bin/append_to_fasta_header.py -> build/scripts-3.9
2021-07-12T18:40:11,188   copying and adjusting bin/merge_masked_fasta_files.py -> build/scripts-3.9
2021-07-12T18:40:11,190   copying and adjusting bin/convert_cufflinks_gtf_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,192   copying and adjusting bin/filter_gff3_by_id_list.py -> build/scripts-3.9
2021-07-12T18:40:11,194   copying and adjusting bin/tigrfam_info_to_sqlite3.py -> build/scripts-3.9
2021-07-12T18:40:11,196   copying and adjusting bin/select_training_and_evaluation_transcripts.py -> build/scripts-3.9
2021-07-12T18:40:11,198   copying and adjusting bin/validate_feature_boundaries_on_molecules.py -> build/scripts-3.9
2021-07-12T18:40:11,200   copying and adjusting bin/filter_fastq_by_N_content.py -> build/scripts-3.9
2021-07-12T18:40:11,202   copying and adjusting bin/randomly_subsample_fastq.py -> build/scripts-3.9
2021-07-12T18:40:11,205   copying and adjusting bin/remove_masked_gene_models.py -> build/scripts-3.9
2021-07-12T18:40:11,206   copying and adjusting bin/detect_inverted_repeats.py -> build/scripts-3.9
2021-07-12T18:40:11,209   copying and adjusting bin/add_gff3_locus_tags.py -> build/scripts-3.9
2021-07-12T18:40:11,211   copying and adjusting bin/convert_gff3_to_ncbi_tbl.py -> build/scripts-3.9
2021-07-12T18:40:11,213   copying and adjusting bin/interleave_fasta.py -> build/scripts-3.9
2021-07-12T18:40:11,215   copying and adjusting bin/remove_duplicate_features.py -> build/scripts-3.9
2021-07-12T18:40:11,216   copying and adjusting bin/merge_fasta_files_and_uniquify_ids.py -> build/scripts-3.9
2021-07-12T18:40:11,218   copying and adjusting bin/extract_fasta_regions.py -> build/scripts-3.9
2021-07-12T18:40:11,220   copying and adjusting bin/convert_aat_btab_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,222   copying and adjusting bin/replace_homopolymeric_repeats_with_Ns.py -> build/scripts-3.9
2021-07-12T18:40:11,224   copying and adjusting bin/reverse_misordered_cds_coords.py -> build/scripts-3.9
2021-07-12T18:40:11,226   copying and adjusting bin/convert_fasta_contigs_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,228   copying and adjusting bin/append_to_column_9_value.py -> build/scripts-3.9
2021-07-12T18:40:11,230   copying and adjusting bin/write_fasta_from_gff.py -> build/scripts-3.9
2021-07-12T18:40:11,232   copying and adjusting bin/filter_uniref_by_taxonomy.py -> build/scripts-3.9
2021-07-12T18:40:11,234   copying and adjusting bin/convert_scipio_gff_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,236   copying and adjusting bin/split_molecules_on_gaps.py -> build/scripts-3.9
2021-07-12T18:40:11,238   copying and adjusting bin/split_interleaved_sequence_file.py -> build/scripts-3.9
2021-07-12T18:40:11,241   copying and adjusting bin/convert_prodigal_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,243   copying and adjusting bin/prepend_to_fasta_header.py -> build/scripts-3.9
2021-07-12T18:40:11,245   copying and adjusting bin/convert_gff3_to_gene_association_format.py -> build/scripts-3.9
2021-07-12T18:40:11,247   copying and adjusting bin/uniprot_sprot_to_sqlite3.py -> build/scripts-3.9
2021-07-12T18:40:11,250   copying and adjusting bin/convert_pasa_gff_to_models.py -> build/scripts-3.9
2021-07-12T18:40:11,253   copying and adjusting bin/reorient_sequences_by_id.py -> build/scripts-3.9
2021-07-12T18:40:11,255   copying and adjusting bin/make_go_slim_index.py -> build/scripts-3.9
2021-07-12T18:40:11,257   copying and adjusting bin/create_taxonomy_db.py -> build/scripts-3.9
2021-07-12T18:40:11,260   copying and adjusting bin/subsample_fasta.py -> build/scripts-3.9
2021-07-12T18:40:11,262   copying and adjusting bin/eggnog_to_sqlite3.py -> build/scripts-3.9
2021-07-12T18:40:11,264   copying and adjusting bin/compare_gene_structures.py -> build/scripts-3.9
2021-07-12T18:40:11,267   copying and adjusting bin/convert_fastq_to_fasta.py -> build/scripts-3.9
2021-07-12T18:40:11,269   copying and adjusting bin/fasta_size_distribution_plot.py -> build/scripts-3.9
2021-07-12T18:40:11,272   copying and adjusting bin/fastq_simple_stats.py -> build/scripts-3.9
2021-07-12T18:40:11,273   copying and adjusting bin/split_isoforms_into_individual_genes.py -> build/scripts-3.9
2021-07-12T18:40:11,275   copying and adjusting bin/convert_augustus_to_gff3.py -> build/scripts-3.9
2021-07-12T18:40:11,277   changing mode of build/scripts-3.9/set_source_column.py from 644 to 755
2021-07-12T18:40:11,277   changing mode of build/scripts-3.9/create_rsem_html_table.py from 644 to 755
2021-07-12T18:40:11,278   changing mode of build/scripts-3.9/filter_uniref_by_repid.py from 644 to 755
2021-07-12T18:40:11,278   changing mode of build/scripts-3.9/replace_gff_type_column_value.py from 644 to 755
2021-07-12T18:40:11,278   changing mode of build/scripts-3.9/convert_blast_btab_to_gff3.py from 644 to 755
2021-07-12T18:40:11,279   changing mode of build/scripts-3.9/report_or_replace_nonstandard_residues.py from 644 to 755
2021-07-12T18:40:11,279   changing mode of build/scripts-3.9/calculate_query_coverage_by_blast.py from 644 to 755
2021-07-12T18:40:11,279   changing mode of build/scripts-3.9/check_gff_for_internal_stops.py from 644 to 755
2021-07-12T18:40:11,279   changing mode of build/scripts-3.9/extend_genes_to_stops.py from 644 to 755
2021-07-12T18:40:11,280   changing mode of build/scripts-3.9/convert_cegma_gff_to_gff3.py from 644 to 755
2021-07-12T18:40:11,280   changing mode of build/scripts-3.9/merge_bam_files.py from 644 to 755
2021-07-12T18:40:11,280   changing mode of build/scripts-3.9/make_go_slim.py from 644 to 755
2021-07-12T18:40:11,281   changing mode of build/scripts-3.9/convert_genbank_to_gff3.py from 644 to 755
2021-07-12T18:40:11,281   changing mode of build/scripts-3.9/fasta_base_content.py from 644 to 755
2021-07-12T18:40:11,281   changing mode of build/scripts-3.9/filter_fasta_by_header_regex.py from 644 to 755
2021-07-12T18:40:11,282   changing mode of build/scripts-3.9/get_mpilup_from_id_list.py from 644 to 755
2021-07-12T18:40:11,282   changing mode of build/scripts-3.9/hmmlib_to_sqlite3.py from 644 to 755
2021-07-12T18:40:11,282   changing mode of build/scripts-3.9/uniref_to_sqlite3.py from 644 to 755
2021-07-12T18:40:11,282   changing mode of build/scripts-3.9/validate_fasta.py from 644 to 755
2021-07-12T18:40:11,283   changing mode of build/scripts-3.9/report_basic_gff_model_agreement.py from 644 to 755
2021-07-12T18:40:11,283   changing mode of build/scripts-3.9/biothings_coordinate_comparisons.py from 644 to 755
2021-07-12T18:40:11,283   changing mode of build/scripts-3.9/update_selected_column9_values.py from 644 to 755
2021-07-12T18:40:11,284   changing mode of build/scripts-3.9/remove_duplicate_sequences.py from 644 to 755
2021-07-12T18:40:11,284   changing mode of build/scripts-3.9/make_cufflinks_ids_unique.py from 644 to 755
2021-07-12T18:40:11,284   changing mode of build/scripts-3.9/split_fasta_into_even_files.py from 644 to 755
2021-07-12T18:40:11,285   changing mode of build/scripts-3.9/interleave_fastq.py from 644 to 755
2021-07-12T18:40:11,285   changing mode of build/scripts-3.9/report_coverage_gaps.py from 644 to 755
2021-07-12T18:40:11,285   changing mode of build/scripts-3.9/reformat_fasta_residue_lengths.py from 644 to 755
2021-07-12T18:40:11,286   changing mode of build/scripts-3.9/report_gff3_statistics.py from 644 to 755
2021-07-12T18:40:11,286   changing mode of build/scripts-3.9/convert_glimmerHMM_gff_to_gff3.py from 644 to 755
2021-07-12T18:40:11,286   changing mode of build/scripts-3.9/correct_gff3_CDS_phase_column.py from 644 to 755
2021-07-12T18:40:11,286   changing mode of build/scripts-3.9/check_for_embedded_fasta_headers.py from 644 to 755
2021-07-12T18:40:11,287   changing mode of build/scripts-3.9/convert_metagenemark_gff_to_gff3.py from 644 to 755
2021-07-12T18:40:11,287   changing mode of build/scripts-3.9/add_polypeptide_to_gff3_gene_models.py from 644 to 755
2021-07-12T18:40:11,287   changing mode of build/scripts-3.9/report_gff_intron_and_intergenic_stats.py from 644 to 755
2021-07-12T18:40:11,288   changing mode of build/scripts-3.9/filter_fasta_by_type.py from 644 to 755
2021-07-12T18:40:11,288   changing mode of build/scripts-3.9/create_taxonomic_profile_from_blast.py from 644 to 755
2021-07-12T18:40:11,288   changing mode of build/scripts-3.9/remove_orphaned_features.py from 644 to 755
2021-07-12T18:40:11,288   changing mode of build/scripts-3.9/append_to_fastq_read_header.py from 644 to 755
2021-07-12T18:40:11,289   changing mode of build/scripts-3.9/convert_gff3_to_gbk.py from 644 to 755
2021-07-12T18:40:11,289   changing mode of build/scripts-3.9/mark_partial_genes.py from 644 to 755
2021-07-12T18:40:11,289   changing mode of build/scripts-3.9/append_to_fasta_header.py from 644 to 755
2021-07-12T18:40:11,290   changing mode of build/scripts-3.9/merge_masked_fasta_files.py from 644 to 755
2021-07-12T18:40:11,290   changing mode of build/scripts-3.9/convert_cufflinks_gtf_to_gff3.py from 644 to 755
2021-07-12T18:40:11,290   changing mode of build/scripts-3.9/filter_gff3_by_id_list.py from 644 to 755
2021-07-12T18:40:11,291   changing mode of build/scripts-3.9/tigrfam_info_to_sqlite3.py from 644 to 755
2021-07-12T18:40:11,291   changing mode of build/scripts-3.9/select_training_and_evaluation_transcripts.py from 644 to 755
2021-07-12T18:40:11,291   changing mode of build/scripts-3.9/validate_feature_boundaries_on_molecules.py from 644 to 755
2021-07-12T18:40:11,291   changing mode of build/scripts-3.9/filter_fastq_by_N_content.py from 644 to 755
2021-07-12T18:40:11,292   changing mode of build/scripts-3.9/randomly_subsample_fastq.py from 644 to 755
2021-07-12T18:40:11,292   changing mode of build/scripts-3.9/remove_masked_gene_models.py from 644 to 755
2021-07-12T18:40:11,292   changing mode of build/scripts-3.9/detect_inverted_repeats.py from 644 to 755
2021-07-12T18:40:11,293   changing mode of build/scripts-3.9/add_gff3_locus_tags.py from 644 to 755
2021-07-12T18:40:11,293   changing mode of build/scripts-3.9/convert_gff3_to_ncbi_tbl.py from 644 to 755
2021-07-12T18:40:11,293   changing mode of build/scripts-3.9/interleave_fasta.py from 644 to 755
2021-07-12T18:40:11,294   changing mode of build/scripts-3.9/remove_duplicate_features.py from 644 to 755
2021-07-12T18:40:11,294   changing mode of build/scripts-3.9/merge_fasta_files_and_uniquify_ids.py from 644 to 755
2021-07-12T18:40:11,294   changing mode of build/scripts-3.9/extract_fasta_regions.py from 644 to 755
2021-07-12T18:40:11,294   changing mode of build/scripts-3.9/convert_aat_btab_to_gff3.py from 644 to 755
2021-07-12T18:40:11,295   changing mode of build/scripts-3.9/replace_homopolymeric_repeats_with_Ns.py from 644 to 755
2021-07-12T18:40:11,295   changing mode of build/scripts-3.9/reverse_misordered_cds_coords.py from 644 to 755
2021-07-12T18:40:11,295   changing mode of build/scripts-3.9/convert_fasta_contigs_to_gff3.py from 644 to 755
2021-07-12T18:40:11,296   changing mode of build/scripts-3.9/append_to_column_9_value.py from 644 to 755
2021-07-12T18:40:11,296   changing mode of build/scripts-3.9/write_fasta_from_gff.py from 644 to 755
2021-07-12T18:40:11,296   changing mode of build/scripts-3.9/filter_uniref_by_taxonomy.py from 644 to 755
2021-07-12T18:40:11,296   changing mode of build/scripts-3.9/convert_scipio_gff_to_gff3.py from 644 to 755
2021-07-12T18:40:11,296   changing mode of build/scripts-3.9/split_molecules_on_gaps.py from 644 to 755
2021-07-12T18:40:11,297   changing mode of build/scripts-3.9/split_interleaved_sequence_file.py from 644 to 755
2021-07-12T18:40:11,297   changing mode of build/scripts-3.9/convert_prodigal_to_gff3.py from 644 to 755
2021-07-12T18:40:11,297   changing mode of build/scripts-3.9/prepend_to_fasta_header.py from 644 to 755
2021-07-12T18:40:11,297   changing mode of build/scripts-3.9/convert_gff3_to_gene_association_format.py from 644 to 755
2021-07-12T18:40:11,298   changing mode of build/scripts-3.9/uniprot_sprot_to_sqlite3.py from 644 to 755
2021-07-12T18:40:11,298   changing mode of build/scripts-3.9/convert_pasa_gff_to_models.py from 644 to 755
2021-07-12T18:40:11,298   changing mode of build/scripts-3.9/reorient_sequences_by_id.py from 644 to 755
2021-07-12T18:40:11,298   changing mode of build/scripts-3.9/make_go_slim_index.py from 644 to 755
2021-07-12T18:40:11,299   changing mode of build/scripts-3.9/create_taxonomy_db.py from 644 to 755
2021-07-12T18:40:11,299   changing mode of build/scripts-3.9/subsample_fasta.py from 644 to 755
2021-07-12T18:40:11,299   changing mode of build/scripts-3.9/eggnog_to_sqlite3.py from 644 to 755
2021-07-12T18:40:11,299   changing mode of build/scripts-3.9/compare_gene_structures.py from 644 to 755
2021-07-12T18:40:11,300   changing mode of build/scripts-3.9/convert_fastq_to_fasta.py from 644 to 755
2021-07-12T18:40:11,300   changing mode of build/scripts-3.9/fasta_size_distribution_plot.py from 644 to 755
2021-07-12T18:40:11,300   changing mode of build/scripts-3.9/fastq_simple_stats.py from 644 to 755
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2021-07-12T18:40:11,301   changing mode of build/scripts-3.9/convert_augustus_to_gff3.py from 644 to 755
2021-07-12T18:40:11,308   installing to build/bdist.linux-armv7l/wheel
2021-07-12T18:40:11,308   running install
2021-07-12T18:40:11,309   running install_lib
2021-07-12T18:40:11,313   creating build/bdist.linux-armv7l
2021-07-12T18:40:11,314   creating build/bdist.linux-armv7l/wheel
2021-07-12T18:40:11,315   creating build/bdist.linux-armv7l/wheel/biocode
2021-07-12T18:40:11,316   copying build/lib/biocode/utils.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-12T18:40:11,319   copying build/lib/biocode/__init__.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-12T18:40:11,321   copying build/lib/biocode/genbank.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-12T18:40:11,323   copying build/lib/biocode/things.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-12T18:40:11,326   copying build/lib/biocode/gff.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-12T18:40:11,329   copying build/lib/biocode/annotation.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-12T18:40:11,333   creating build/bdist.linux-armv7l/wheel/biocode/data
2021-07-12T18:40:11,333   copying build/lib/biocode/data/HMPslim.v2.1.obo -> build/bdist.linux-armv7l/wheel/biocode/data
2021-07-12T18:40:11,337   copying build/lib/biocode/data/__init__.py -> build/bdist.linux-armv7l/wheel/biocode/data
2021-07-12T18:40:11,339   copying build/lib/biocode/data/rsem_html_table.template -> build/bdist.linux-armv7l/wheel/biocode/data
2021-07-12T18:40:11,343   copying build/lib/biocode/data/genbank_flat_file_header.template -> build/bdist.linux-armv7l/wheel/biocode/data
2021-07-12T18:40:11,345   copying build/lib/biocode/tbl.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-12T18:40:11,347   running install_egg_info
2021-07-12T18:40:11,353   Copying biocode.egg-info to build/bdist.linux-armv7l/wheel/biocode-0.4.4-py3.9.egg-info
2021-07-12T18:40:11,368   running install_scripts
2021-07-12T18:40:11,402   creating build/bdist.linux-armv7l/wheel/biocode-0.4.4.data
2021-07-12T18:40:11,402   creating build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,403   copying build/scripts-3.9/convert_scipio_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,406   copying build/scripts-3.9/report_gff_intron_and_intergenic_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,408   copying build/scripts-3.9/fasta_base_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,410   copying build/scripts-3.9/convert_gff3_to_ncbi_tbl.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,412   copying build/scripts-3.9/convert_gff3_to_gene_association_format.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,415   copying build/scripts-3.9/convert_fastq_to_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,417   copying build/scripts-3.9/get_mpilup_from_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,419   copying build/scripts-3.9/report_basic_gff_model_agreement.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,421   copying build/scripts-3.9/make_go_slim.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,424   copying build/scripts-3.9/remove_orphaned_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,426   copying build/scripts-3.9/convert_metagenemark_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,429   copying build/scripts-3.9/randomly_subsample_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,432   copying build/scripts-3.9/convert_blast_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,434   copying build/scripts-3.9/merge_masked_fasta_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,437   copying build/scripts-3.9/select_training_and_evaluation_transcripts.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,439   copying build/scripts-3.9/filter_fasta_by_header_regex.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,442   copying build/scripts-3.9/remove_duplicate_sequences.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,444   copying build/scripts-3.9/detect_inverted_repeats.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,446   copying build/scripts-3.9/hmmlib_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,449   copying build/scripts-3.9/interleave_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,451   copying build/scripts-3.9/filter_fasta_by_type.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,453   copying build/scripts-3.9/make_go_slim_index.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,455   copying build/scripts-3.9/split_isoforms_into_individual_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,457   copying build/scripts-3.9/append_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,459   copying build/scripts-3.9/convert_cufflinks_gtf_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,462   copying build/scripts-3.9/convert_augustus_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,464   copying build/scripts-3.9/update_selected_column9_values.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,467   copying build/scripts-3.9/prepend_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,469   copying build/scripts-3.9/split_interleaved_sequence_file.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,472   copying build/scripts-3.9/interleave_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,474   copying build/scripts-3.9/filter_gff3_by_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,476   copying build/scripts-3.9/create_taxonomic_profile_from_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,479   copying build/scripts-3.9/calculate_query_coverage_by_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,481   copying build/scripts-3.9/mark_partial_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,484   copying build/scripts-3.9/convert_genbank_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,486   copying build/scripts-3.9/reformat_fasta_residue_lengths.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,488   copying build/scripts-3.9/create_taxonomy_db.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,491   copying build/scripts-3.9/merge_fasta_files_and_uniquify_ids.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,493   copying build/scripts-3.9/convert_glimmerHMM_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,496   copying build/scripts-3.9/tigrfam_info_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,499   copying build/scripts-3.9/split_molecules_on_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,501   copying build/scripts-3.9/replace_gff_type_column_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,503   copying build/scripts-3.9/fastq_simple_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,506   copying build/scripts-3.9/replace_homopolymeric_repeats_with_Ns.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,508   copying build/scripts-3.9/merge_bam_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,510   copying build/scripts-3.9/uniprot_sprot_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,513   copying build/scripts-3.9/remove_masked_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,515   copying build/scripts-3.9/uniref_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,518   copying build/scripts-3.9/create_rsem_html_table.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,520   copying build/scripts-3.9/add_polypeptide_to_gff3_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,523   copying build/scripts-3.9/report_gff3_statistics.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,525   copying build/scripts-3.9/append_to_fastq_read_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,527   copying build/scripts-3.9/convert_aat_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,530   copying build/scripts-3.9/eggnog_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,533   copying build/scripts-3.9/set_source_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,535   copying build/scripts-3.9/report_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,537   copying build/scripts-3.9/split_fasta_into_even_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,539   copying build/scripts-3.9/filter_uniref_by_taxonomy.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,542   copying build/scripts-3.9/extend_genes_to_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,544   copying build/scripts-3.9/compare_gene_structures.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,547   copying build/scripts-3.9/report_or_replace_nonstandard_residues.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,550   copying build/scripts-3.9/make_cufflinks_ids_unique.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,552   copying build/scripts-3.9/remove_duplicate_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,554   copying build/scripts-3.9/convert_fasta_contigs_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,557   copying build/scripts-3.9/biothings_coordinate_comparisons.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,559   copying build/scripts-3.9/validate_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,562   copying build/scripts-3.9/filter_fastq_by_N_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,565   copying build/scripts-3.9/check_for_embedded_fasta_headers.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,567   copying build/scripts-3.9/correct_gff3_CDS_phase_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,570   copying build/scripts-3.9/check_gff_for_internal_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,572   copying build/scripts-3.9/add_gff3_locus_tags.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,575   copying build/scripts-3.9/filter_uniref_by_repid.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,577   copying build/scripts-3.9/write_fasta_from_gff.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,579   copying build/scripts-3.9/convert_cegma_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,582   copying build/scripts-3.9/append_to_column_9_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,585   copying build/scripts-3.9/reorient_sequences_by_id.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,587   copying build/scripts-3.9/convert_gff3_to_gbk.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,590   copying build/scripts-3.9/convert_pasa_gff_to_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,592   copying build/scripts-3.9/subsample_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,595   copying build/scripts-3.9/extract_fasta_regions.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,597   copying build/scripts-3.9/validate_feature_boundaries_on_molecules.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,600   copying build/scripts-3.9/convert_prodigal_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,603   copying build/scripts-3.9/fasta_size_distribution_plot.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,606   copying build/scripts-3.9/reverse_misordered_cds_coords.py -> build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts
2021-07-12T18:40:11,608   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_scipio_gff_to_gff3.py to 755
2021-07-12T18:40:11,608   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/report_gff_intron_and_intergenic_stats.py to 755
2021-07-12T18:40:11,609   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/fasta_base_content.py to 755
2021-07-12T18:40:11,609   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_gff3_to_ncbi_tbl.py to 755
2021-07-12T18:40:11,609   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_gff3_to_gene_association_format.py to 755
2021-07-12T18:40:11,609   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_fastq_to_fasta.py to 755
2021-07-12T18:40:11,610   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/get_mpilup_from_id_list.py to 755
2021-07-12T18:40:11,610   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/report_basic_gff_model_agreement.py to 755
2021-07-12T18:40:11,610   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/make_go_slim.py to 755
2021-07-12T18:40:11,611   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/remove_orphaned_features.py to 755
2021-07-12T18:40:11,611   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_metagenemark_gff_to_gff3.py to 755
2021-07-12T18:40:11,612   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/randomly_subsample_fastq.py to 755
2021-07-12T18:40:11,612   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_blast_btab_to_gff3.py to 755
2021-07-12T18:40:11,612   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/merge_masked_fasta_files.py to 755
2021-07-12T18:40:11,613   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/select_training_and_evaluation_transcripts.py to 755
2021-07-12T18:40:11,613   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/filter_fasta_by_header_regex.py to 755
2021-07-12T18:40:11,613   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/remove_duplicate_sequences.py to 755
2021-07-12T18:40:11,614   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/detect_inverted_repeats.py to 755
2021-07-12T18:40:11,614   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/hmmlib_to_sqlite3.py to 755
2021-07-12T18:40:11,614   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/interleave_fasta.py to 755
2021-07-12T18:40:11,615   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/filter_fasta_by_type.py to 755
2021-07-12T18:40:11,615   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/make_go_slim_index.py to 755
2021-07-12T18:40:11,615   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/split_isoforms_into_individual_genes.py to 755
2021-07-12T18:40:11,615   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/append_to_fasta_header.py to 755
2021-07-12T18:40:11,616   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_cufflinks_gtf_to_gff3.py to 755
2021-07-12T18:40:11,616   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_augustus_to_gff3.py to 755
2021-07-12T18:40:11,616   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/update_selected_column9_values.py to 755
2021-07-12T18:40:11,617   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/prepend_to_fasta_header.py to 755
2021-07-12T18:40:11,617   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/split_interleaved_sequence_file.py to 755
2021-07-12T18:40:11,617   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/interleave_fastq.py to 755
2021-07-12T18:40:11,618   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/filter_gff3_by_id_list.py to 755
2021-07-12T18:40:11,618   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/create_taxonomic_profile_from_blast.py to 755
2021-07-12T18:40:11,618   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/calculate_query_coverage_by_blast.py to 755
2021-07-12T18:40:11,619   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/mark_partial_genes.py to 755
2021-07-12T18:40:11,619   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_genbank_to_gff3.py to 755
2021-07-12T18:40:11,619   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/reformat_fasta_residue_lengths.py to 755
2021-07-12T18:40:11,620   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/create_taxonomy_db.py to 755
2021-07-12T18:40:11,620   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/merge_fasta_files_and_uniquify_ids.py to 755
2021-07-12T18:40:11,620   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_glimmerHMM_gff_to_gff3.py to 755
2021-07-12T18:40:11,621   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/tigrfam_info_to_sqlite3.py to 755
2021-07-12T18:40:11,621   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/split_molecules_on_gaps.py to 755
2021-07-12T18:40:11,621   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/replace_gff_type_column_value.py to 755
2021-07-12T18:40:11,622   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/fastq_simple_stats.py to 755
2021-07-12T18:40:11,622   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/replace_homopolymeric_repeats_with_Ns.py to 755
2021-07-12T18:40:11,622   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/merge_bam_files.py to 755
2021-07-12T18:40:11,623   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/uniprot_sprot_to_sqlite3.py to 755
2021-07-12T18:40:11,623   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/remove_masked_gene_models.py to 755
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2021-07-12T18:40:11,623   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/create_rsem_html_table.py to 755
2021-07-12T18:40:11,624   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/add_polypeptide_to_gff3_gene_models.py to 755
2021-07-12T18:40:11,624   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/report_gff3_statistics.py to 755
2021-07-12T18:40:11,625   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/append_to_fastq_read_header.py to 755
2021-07-12T18:40:11,625   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_aat_btab_to_gff3.py to 755
2021-07-12T18:40:11,625   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/eggnog_to_sqlite3.py to 755
2021-07-12T18:40:11,625   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/set_source_column.py to 755
2021-07-12T18:40:11,626   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/report_coverage_gaps.py to 755
2021-07-12T18:40:11,626   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/split_fasta_into_even_files.py to 755
2021-07-12T18:40:11,626   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/filter_uniref_by_taxonomy.py to 755
2021-07-12T18:40:11,627   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/extend_genes_to_stops.py to 755
2021-07-12T18:40:11,627   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/compare_gene_structures.py to 755
2021-07-12T18:40:11,627   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/report_or_replace_nonstandard_residues.py to 755
2021-07-12T18:40:11,627   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/make_cufflinks_ids_unique.py to 755
2021-07-12T18:40:11,628   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/remove_duplicate_features.py to 755
2021-07-12T18:40:11,628   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_fasta_contigs_to_gff3.py to 755
2021-07-12T18:40:11,628   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/biothings_coordinate_comparisons.py to 755
2021-07-12T18:40:11,629   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/validate_fasta.py to 755
2021-07-12T18:40:11,629   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/filter_fastq_by_N_content.py to 755
2021-07-12T18:40:11,629   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/check_for_embedded_fasta_headers.py to 755
2021-07-12T18:40:11,629   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/correct_gff3_CDS_phase_column.py to 755
2021-07-12T18:40:11,630   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/check_gff_for_internal_stops.py to 755
2021-07-12T18:40:11,630   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/add_gff3_locus_tags.py to 755
2021-07-12T18:40:11,630   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/filter_uniref_by_repid.py to 755
2021-07-12T18:40:11,631   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/write_fasta_from_gff.py to 755
2021-07-12T18:40:11,631   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_cegma_gff_to_gff3.py to 755
2021-07-12T18:40:11,631   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/append_to_column_9_value.py to 755
2021-07-12T18:40:11,631   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/reorient_sequences_by_id.py to 755
2021-07-12T18:40:11,632   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_gff3_to_gbk.py to 755
2021-07-12T18:40:11,632   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_pasa_gff_to_models.py to 755
2021-07-12T18:40:11,632   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/subsample_fasta.py to 755
2021-07-12T18:40:11,633   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/extract_fasta_regions.py to 755
2021-07-12T18:40:11,633   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/validate_feature_boundaries_on_molecules.py to 755
2021-07-12T18:40:11,633   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/convert_prodigal_to_gff3.py to 755
2021-07-12T18:40:11,633   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/fasta_size_distribution_plot.py to 755
2021-07-12T18:40:11,634   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.4.4.data/scripts/reverse_misordered_cds_coords.py to 755
2021-07-12T18:40:11,655   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2021-07-12T18:40:11,661   creating build/bdist.linux-armv7l/wheel/biocode-0.4.4.dist-info/WHEEL
2021-07-12T18:40:11,664   creating '/tmp/pip-wheel-f6fgx5n6/biocode-0.4.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-12T18:40:11,666   adding 'biocode/__init__.py'
2021-07-12T18:40:11,670   adding 'biocode/annotation.py'
2021-07-12T18:40:11,672   adding 'biocode/genbank.py'
2021-07-12T18:40:11,677   adding 'biocode/gff.py'
2021-07-12T18:40:11,680   adding 'biocode/tbl.py'
2021-07-12T18:40:11,688   adding 'biocode/things.py'
2021-07-12T18:40:11,691   adding 'biocode/utils.py'
2021-07-12T18:40:11,697   adding 'biocode/data/HMPslim.v2.1.obo'
2021-07-12T18:40:11,698   adding 'biocode/data/__init__.py'
2021-07-12T18:40:11,699   adding 'biocode/data/genbank_flat_file_header.template'
2021-07-12T18:40:11,702   adding 'biocode/data/rsem_html_table.template'
2021-07-12T18:40:11,706   adding 'biocode-0.4.4.data/scripts/add_gff3_locus_tags.py'
2021-07-12T18:40:11,708   adding 'biocode-0.4.4.data/scripts/add_polypeptide_to_gff3_gene_models.py'
2021-07-12T18:40:11,709   adding 'biocode-0.4.4.data/scripts/append_to_column_9_value.py'
2021-07-12T18:40:11,711   adding 'biocode-0.4.4.data/scripts/append_to_fasta_header.py'
2021-07-12T18:40:11,712   adding 'biocode-0.4.4.data/scripts/append_to_fastq_read_header.py'
2021-07-12T18:40:11,714   adding 'biocode-0.4.4.data/scripts/biothings_coordinate_comparisons.py'
2021-07-12T18:40:11,715   adding 'biocode-0.4.4.data/scripts/calculate_query_coverage_by_blast.py'
2021-07-12T18:40:11,717   adding 'biocode-0.4.4.data/scripts/check_for_embedded_fasta_headers.py'
2021-07-12T18:40:11,718   adding 'biocode-0.4.4.data/scripts/check_gff_for_internal_stops.py'
2021-07-12T18:40:11,721   adding 'biocode-0.4.4.data/scripts/compare_gene_structures.py'
2021-07-12T18:40:11,724   adding 'biocode-0.4.4.data/scripts/convert_aat_btab_to_gff3.py'
2021-07-12T18:40:11,726   adding 'biocode-0.4.4.data/scripts/convert_augustus_to_gff3.py'
2021-07-12T18:40:11,728   adding 'biocode-0.4.4.data/scripts/convert_blast_btab_to_gff3.py'
2021-07-12T18:40:11,729   adding 'biocode-0.4.4.data/scripts/convert_cegma_gff_to_gff3.py'
2021-07-12T18:40:11,731   adding 'biocode-0.4.4.data/scripts/convert_cufflinks_gtf_to_gff3.py'
2021-07-12T18:40:11,733   adding 'biocode-0.4.4.data/scripts/convert_fasta_contigs_to_gff3.py'
2021-07-12T18:40:11,734   adding 'biocode-0.4.4.data/scripts/convert_fastq_to_fasta.py'
2021-07-12T18:40:11,736   adding 'biocode-0.4.4.data/scripts/convert_genbank_to_gff3.py'
2021-07-12T18:40:11,738   adding 'biocode-0.4.4.data/scripts/convert_gff3_to_gbk.py'
2021-07-12T18:40:11,739   adding 'biocode-0.4.4.data/scripts/convert_gff3_to_gene_association_format.py'
2021-07-12T18:40:11,741   adding 'biocode-0.4.4.data/scripts/convert_gff3_to_ncbi_tbl.py'
2021-07-12T18:40:11,742   adding 'biocode-0.4.4.data/scripts/convert_glimmerHMM_gff_to_gff3.py'
2021-07-12T18:40:11,744   adding 'biocode-0.4.4.data/scripts/convert_metagenemark_gff_to_gff3.py'
2021-07-12T18:40:11,745   adding 'biocode-0.4.4.data/scripts/convert_pasa_gff_to_models.py'
2021-07-12T18:40:11,746   adding 'biocode-0.4.4.data/scripts/convert_prodigal_to_gff3.py'
2021-07-12T18:40:11,748   adding 'biocode-0.4.4.data/scripts/convert_scipio_gff_to_gff3.py'
2021-07-12T18:40:11,750   adding 'biocode-0.4.4.data/scripts/correct_gff3_CDS_phase_column.py'
2021-07-12T18:40:11,751   adding 'biocode-0.4.4.data/scripts/create_rsem_html_table.py'
2021-07-12T18:40:11,753   adding 'biocode-0.4.4.data/scripts/create_taxonomic_profile_from_blast.py'
2021-07-12T18:40:11,755   adding 'biocode-0.4.4.data/scripts/create_taxonomy_db.py'
2021-07-12T18:40:11,757   adding 'biocode-0.4.4.data/scripts/detect_inverted_repeats.py'
2021-07-12T18:40:11,758   adding 'biocode-0.4.4.data/scripts/eggnog_to_sqlite3.py'
2021-07-12T18:40:11,760   adding 'biocode-0.4.4.data/scripts/extend_genes_to_stops.py'
2021-07-12T18:40:11,761   adding 'biocode-0.4.4.data/scripts/extract_fasta_regions.py'
2021-07-12T18:40:11,762   adding 'biocode-0.4.4.data/scripts/fasta_base_content.py'
2021-07-12T18:40:11,764   adding 'biocode-0.4.4.data/scripts/fasta_size_distribution_plot.py'
2021-07-12T18:40:11,765   adding 'biocode-0.4.4.data/scripts/fastq_simple_stats.py'
2021-07-12T18:40:11,766   adding 'biocode-0.4.4.data/scripts/filter_fasta_by_header_regex.py'
2021-07-12T18:40:11,768   adding 'biocode-0.4.4.data/scripts/filter_fasta_by_type.py'
2021-07-12T18:40:11,769   adding 'biocode-0.4.4.data/scripts/filter_fastq_by_N_content.py'
2021-07-12T18:40:11,771   adding 'biocode-0.4.4.data/scripts/filter_gff3_by_id_list.py'
2021-07-12T18:40:11,772   adding 'biocode-0.4.4.data/scripts/filter_uniref_by_repid.py'
2021-07-12T18:40:11,774   adding 'biocode-0.4.4.data/scripts/filter_uniref_by_taxonomy.py'
2021-07-12T18:40:11,775   adding 'biocode-0.4.4.data/scripts/get_mpilup_from_id_list.py'
2021-07-12T18:40:11,777   adding 'biocode-0.4.4.data/scripts/hmmlib_to_sqlite3.py'
2021-07-12T18:40:11,778   adding 'biocode-0.4.4.data/scripts/interleave_fasta.py'
2021-07-12T18:40:11,779   adding 'biocode-0.4.4.data/scripts/interleave_fastq.py'
2021-07-12T18:40:11,781   adding 'biocode-0.4.4.data/scripts/make_cufflinks_ids_unique.py'
2021-07-12T18:40:11,783   adding 'biocode-0.4.4.data/scripts/make_go_slim.py'
2021-07-12T18:40:11,784   adding 'biocode-0.4.4.data/scripts/make_go_slim_index.py'
2021-07-12T18:40:11,786   adding 'biocode-0.4.4.data/scripts/mark_partial_genes.py'
2021-07-12T18:40:11,787   adding 'biocode-0.4.4.data/scripts/merge_bam_files.py'
2021-07-12T18:40:11,789   adding 'biocode-0.4.4.data/scripts/merge_fasta_files_and_uniquify_ids.py'
2021-07-12T18:40:11,790   adding 'biocode-0.4.4.data/scripts/merge_masked_fasta_files.py'
2021-07-12T18:40:11,791   adding 'biocode-0.4.4.data/scripts/prepend_to_fasta_header.py'
2021-07-12T18:40:11,793   adding 'biocode-0.4.4.data/scripts/randomly_subsample_fastq.py'
2021-07-12T18:40:11,795   adding 'biocode-0.4.4.data/scripts/reformat_fasta_residue_lengths.py'
2021-07-12T18:40:11,796   adding 'biocode-0.4.4.data/scripts/remove_duplicate_features.py'
2021-07-12T18:40:11,797   adding 'biocode-0.4.4.data/scripts/remove_duplicate_sequences.py'
2021-07-12T18:40:11,799   adding 'biocode-0.4.4.data/scripts/remove_masked_gene_models.py'
2021-07-12T18:40:11,800   adding 'biocode-0.4.4.data/scripts/remove_orphaned_features.py'
2021-07-12T18:40:11,801   adding 'biocode-0.4.4.data/scripts/reorient_sequences_by_id.py'
2021-07-12T18:40:11,802   adding 'biocode-0.4.4.data/scripts/replace_gff_type_column_value.py'
2021-07-12T18:40:11,804   adding 'biocode-0.4.4.data/scripts/replace_homopolymeric_repeats_with_Ns.py'
2021-07-12T18:40:11,805   adding 'biocode-0.4.4.data/scripts/report_basic_gff_model_agreement.py'
2021-07-12T18:40:11,807   adding 'biocode-0.4.4.data/scripts/report_coverage_gaps.py'
2021-07-12T18:40:11,808   adding 'biocode-0.4.4.data/scripts/report_gff3_statistics.py'
2021-07-12T18:40:11,810   adding 'biocode-0.4.4.data/scripts/report_gff_intron_and_intergenic_stats.py'
2021-07-12T18:40:11,812   adding 'biocode-0.4.4.data/scripts/report_or_replace_nonstandard_residues.py'
2021-07-12T18:40:11,814   adding 'biocode-0.4.4.data/scripts/reverse_misordered_cds_coords.py'
2021-07-12T18:40:11,815   adding 'biocode-0.4.4.data/scripts/select_training_and_evaluation_transcripts.py'
2021-07-12T18:40:11,816   adding 'biocode-0.4.4.data/scripts/set_source_column.py'
2021-07-12T18:40:11,818   adding 'biocode-0.4.4.data/scripts/split_fasta_into_even_files.py'
2021-07-12T18:40:11,819   adding 'biocode-0.4.4.data/scripts/split_interleaved_sequence_file.py'
2021-07-12T18:40:11,821   adding 'biocode-0.4.4.data/scripts/split_isoforms_into_individual_genes.py'
2021-07-12T18:40:11,822   adding 'biocode-0.4.4.data/scripts/split_molecules_on_gaps.py'
2021-07-12T18:40:11,824   adding 'biocode-0.4.4.data/scripts/subsample_fasta.py'
2021-07-12T18:40:11,825   adding 'biocode-0.4.4.data/scripts/tigrfam_info_to_sqlite3.py'
2021-07-12T18:40:11,827   adding 'biocode-0.4.4.data/scripts/uniprot_sprot_to_sqlite3.py'
2021-07-12T18:40:11,829   adding 'biocode-0.4.4.data/scripts/uniref_to_sqlite3.py'
2021-07-12T18:40:11,831   adding 'biocode-0.4.4.data/scripts/update_selected_column9_values.py'
2021-07-12T18:40:11,832   adding 'biocode-0.4.4.data/scripts/validate_fasta.py'
2021-07-12T18:40:11,834   adding 'biocode-0.4.4.data/scripts/validate_feature_boundaries_on_molecules.py'
2021-07-12T18:40:11,835   adding 'biocode-0.4.4.data/scripts/write_fasta_from_gff.py'
2021-07-12T18:40:11,838   adding 'biocode-0.4.4.dist-info/LICENSE'
2021-07-12T18:40:11,839   adding 'biocode-0.4.4.dist-info/METADATA'
2021-07-12T18:40:11,840   adding 'biocode-0.4.4.dist-info/WHEEL'
2021-07-12T18:40:11,840   adding 'biocode-0.4.4.dist-info/top_level.txt'
2021-07-12T18:40:11,843   adding 'biocode-0.4.4.dist-info/RECORD'
2021-07-12T18:40:11,848   removing build/bdist.linux-armv7l/wheel
2021-07-12T18:40:11,975   Building wheel for biocode (setup.py): finished with status 'done'
2021-07-12T18:40:11,980   Created wheel for biocode: filename=biocode-0.4.4-py3-none-any.whl size=212640 sha256=b61ad63c7d700f55cd2db1a75a68d247d54f08fcd6ec9308b547a5f1ea0ce0fe
2021-07-12T18:40:11,980   Stored in directory: /tmp/pip-ephem-wheel-cache-32i4w64a/wheels/a0/21/e1/1f2649487d79acdca2d7d941fb1196e6189a5a21317cc2fd90
2021-07-12T18:40:11,994 Successfully built biocode
2021-07-12T18:40:12,009 Removed build tracker: '/tmp/pip-req-tracker-mf31z5mx'