2021-07-11T23:53:33,855 Created temporary directory: /tmp/pip-ephem-wheel-cache-qtqp3h8e
2021-07-11T23:53:33,858 Created temporary directory: /tmp/pip-req-tracker-0sivxrew
2021-07-11T23:53:33,858 Initialized build tracking at /tmp/pip-req-tracker-0sivxrew
2021-07-11T23:53:33,858 Created build tracker: /tmp/pip-req-tracker-0sivxrew
2021-07-11T23:53:33,858 Entered build tracker: /tmp/pip-req-tracker-0sivxrew
2021-07-11T23:53:33,859 Created temporary directory: /tmp/pip-wheel-jbis_6lv
2021-07-11T23:53:33,889 1 location(s) to search for versions of biocode:
2021-07-11T23:53:33,889 * https://pypi.org/simple/biocode/
2021-07-11T23:53:33,889 Fetching project page and analyzing links: https://pypi.org/simple/biocode/
2021-07-11T23:53:33,890 Getting page https://pypi.org/simple/biocode/
2021-07-11T23:53:33,891 Found index url https://pypi.org/simple
2021-07-11T23:53:34,037   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
2021-07-11T23:53:34,038   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
2021-07-11T23:53:34,038   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
2021-07-11T23:53:34,038   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
2021-07-11T23:53:34,039   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
2021-07-11T23:53:34,039   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
2021-07-11T23:53:34,039   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
2021-07-11T23:53:34,039   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
2021-07-11T23:53:34,040   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
2021-07-11T23:53:34,040   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
2021-07-11T23:53:34,040   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
2021-07-11T23:53:34,041   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
2021-07-11T23:53:34,041   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
2021-07-11T23:53:34,041   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
2021-07-11T23:53:34,042   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
2021-07-11T23:53:34,042   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
2021-07-11T23:53:34,042   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
2021-07-11T23:53:34,042   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
2021-07-11T23:53:34,043   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
2021-07-11T23:53:34,043   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
2021-07-11T23:53:34,043   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
2021-07-11T23:53:34,043   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
2021-07-11T23:53:34,044   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
2021-07-11T23:53:34,044   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
2021-07-11T23:53:34,044   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
2021-07-11T23:53:34,045 Skipping link: not a file: https://pypi.org/simple/biocode/
2021-07-11T23:53:34,065 Given no hashes to check 1 links for project 'biocode': discarding no candidates
2021-07-11T23:53:34,085 Collecting biocode==0.1.2
2021-07-11T23:53:34,086   Created temporary directory: /tmp/pip-unpack-fzo_a1j8
2021-07-11T23:53:34,315   Downloading biocode-0.1.2.tar.gz (131 kB)
2021-07-11T23:53:34,581   Added biocode==0.1.2 from https://files.pythonhosted.org/packages/4e/94/c999970e61e13f3082eae7989bc32d745ef7d846824252dd9a3c09cfd19c/biocode-0.1.2.tar.gz#sha256=d72e37b2f0cefc2081b0888b603d39cf572382b5d966586390e02cb09b708cc9 to build tracker '/tmp/pip-req-tracker-0sivxrew'
2021-07-11T23:53:34,582     Running setup.py (path:/tmp/pip-wheel-jbis_6lv/biocode_7cea6d1f179a4d0081a21ab417175f40/setup.py) egg_info for package biocode
2021-07-11T23:53:34,583     Created temporary directory: /tmp/pip-pip-egg-info-yye6vgw2
2021-07-11T23:53:34,583     Running command python setup.py egg_info
2021-07-11T23:53:35,710     /tmp/pip-wheel-jbis_6lv/biocode_7cea6d1f179a4d0081a21ab417175f40/setup.py:6: DeprecationWarning: Due to possible ambiguity, 'convert()' is deprecated. Use 'convert_file()'  or 'convert_text()'.
2021-07-11T23:53:35,710       read_md = lambda f: convert(f, 'rst', 'md')
2021-07-11T23:53:35,953     /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long'
2021-07-11T23:53:35,953       warnings.warn(msg)
2021-07-11T23:53:36,083     running egg_info
2021-07-11T23:53:36,085     creating /tmp/pip-pip-egg-info-yye6vgw2/biocode.egg-info
2021-07-11T23:53:36,086     writing /tmp/pip-pip-egg-info-yye6vgw2/biocode.egg-info/PKG-INFO
2021-07-11T23:53:36,089     writing dependency_links to /tmp/pip-pip-egg-info-yye6vgw2/biocode.egg-info/dependency_links.txt
2021-07-11T23:53:36,091     writing requirements to /tmp/pip-pip-egg-info-yye6vgw2/biocode.egg-info/requires.txt
2021-07-11T23:53:36,092     writing top-level names to /tmp/pip-pip-egg-info-yye6vgw2/biocode.egg-info/top_level.txt
2021-07-11T23:53:36,093     writing manifest file '/tmp/pip-pip-egg-info-yye6vgw2/biocode.egg-info/SOURCES.txt'
2021-07-11T23:53:36,272     reading manifest file '/tmp/pip-pip-egg-info-yye6vgw2/biocode.egg-info/SOURCES.txt'
2021-07-11T23:53:36,274     reading manifest template 'MANIFEST.in'
2021-07-11T23:53:36,276     warning: no files found matching 'README.rstinclude'
2021-07-11T23:53:36,276     adding license file 'LICENSE'
2021-07-11T23:53:36,283     writing manifest file '/tmp/pip-pip-egg-info-yye6vgw2/biocode.egg-info/SOURCES.txt'
2021-07-11T23:53:36,364   Source in /tmp/pip-wheel-jbis_6lv/biocode_7cea6d1f179a4d0081a21ab417175f40 has version 0.1.2, which satisfies requirement biocode==0.1.2 from https://files.pythonhosted.org/packages/4e/94/c999970e61e13f3082eae7989bc32d745ef7d846824252dd9a3c09cfd19c/biocode-0.1.2.tar.gz#sha256=d72e37b2f0cefc2081b0888b603d39cf572382b5d966586390e02cb09b708cc9
2021-07-11T23:53:36,365   Removed biocode==0.1.2 from https://files.pythonhosted.org/packages/4e/94/c999970e61e13f3082eae7989bc32d745ef7d846824252dd9a3c09cfd19c/biocode-0.1.2.tar.gz#sha256=d72e37b2f0cefc2081b0888b603d39cf572382b5d966586390e02cb09b708cc9 from build tracker '/tmp/pip-req-tracker-0sivxrew'
2021-07-11T23:53:36,369 Created temporary directory: /tmp/pip-unpack-yv0_ewl5
2021-07-11T23:53:36,370 Building wheels for collected packages: biocode
2021-07-11T23:53:36,374   Created temporary directory: /tmp/pip-wheel-sf7tg8do
2021-07-11T23:53:36,375   Building wheel for biocode (setup.py): started
2021-07-11T23:53:36,375   Destination directory: /tmp/pip-wheel-sf7tg8do
2021-07-11T23:53:36,375   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-jbis_6lv/biocode_7cea6d1f179a4d0081a21ab417175f40/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-jbis_6lv/biocode_7cea6d1f179a4d0081a21ab417175f40/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-sf7tg8do
2021-07-11T23:53:37,339   /tmp/pip-wheel-jbis_6lv/biocode_7cea6d1f179a4d0081a21ab417175f40/setup.py:6: DeprecationWarning: Due to possible ambiguity, 'convert()' is deprecated. Use 'convert_file()'  or 'convert_text()'.
2021-07-11T23:53:37,340     read_md = lambda f: convert(f, 'rst', 'md')
2021-07-11T23:53:37,579   /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long'
2021-07-11T23:53:37,579     warnings.warn(msg)
2021-07-11T23:53:37,727   running bdist_wheel
2021-07-11T23:53:37,888   running build
2021-07-11T23:53:37,889   running build_py
2021-07-11T23:53:38,029   creating build
2021-07-11T23:53:38,030   creating build/lib
2021-07-11T23:53:38,030   creating build/lib/biocode
2021-07-11T23:53:38,031   copying biocode/annotation.py -> build/lib/biocode
2021-07-11T23:53:38,034   copying biocode/genbank.py -> build/lib/biocode
2021-07-11T23:53:38,036   copying biocode/utils.py -> build/lib/biocode
2021-07-11T23:53:38,038   copying biocode/__init__.py -> build/lib/biocode
2021-07-11T23:53:38,040   copying biocode/gff.py -> build/lib/biocode
2021-07-11T23:53:38,043   copying biocode/things.py -> build/lib/biocode
2021-07-11T23:53:38,046   copying biocode/tbl.py -> build/lib/biocode
2021-07-11T23:53:38,049   running egg_info
2021-07-11T23:53:38,064   writing biocode.egg-info/PKG-INFO
2021-07-11T23:53:38,065   writing dependency_links to biocode.egg-info/dependency_links.txt
2021-07-11T23:53:38,067   writing requirements to biocode.egg-info/requires.txt
2021-07-11T23:53:38,068   writing top-level names to biocode.egg-info/top_level.txt
2021-07-11T23:53:38,121   reading manifest file 'biocode.egg-info/SOURCES.txt'
2021-07-11T23:53:38,126   reading manifest template 'MANIFEST.in'
2021-07-11T23:53:38,126   warning: no files found matching 'README.rstinclude'
2021-07-11T23:53:38,127   adding license file 'LICENSE'
2021-07-11T23:53:38,135   writing manifest file 'biocode.egg-info/SOURCES.txt'
2021-07-11T23:53:38,140   running build_scripts
2021-07-11T23:53:38,141   creating build/scripts-3.9
2021-07-11T23:53:38,142   copying and adjusting bin/filter_fastq_by_N_content.py -> build/scripts-3.9
2021-07-11T23:53:38,145   copying and adjusting bin/convert_fastq_to_fasta.py -> build/scripts-3.9
2021-07-11T23:53:38,146   copying and adjusting bin/validate_fasta.py -> build/scripts-3.9
2021-07-11T23:53:38,148   copying and adjusting bin/filter_fasta_by_header_regex.py -> build/scripts-3.9
2021-07-11T23:53:38,150   copying and adjusting bin/add_gff3_locus_tags.py -> build/scripts-3.9
2021-07-11T23:53:38,152   copying and adjusting bin/split_molecules_on_gaps.py -> build/scripts-3.9
2021-07-11T23:53:38,153   copying and adjusting bin/convert_gff3_to_gene_association_format.py -> build/scripts-3.9
2021-07-11T23:53:38,155   copying and adjusting bin/extract_fasta_regions.py -> build/scripts-3.9
2021-07-11T23:53:38,156   copying and adjusting bin/hmmlib_to_sqlite3.py -> build/scripts-3.9
2021-07-11T23:53:38,158   copying and adjusting bin/convert_scipio_gff_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,160   copying and adjusting bin/report_coverage_gaps.py -> build/scripts-3.9
2021-07-11T23:53:38,162   copying and adjusting bin/remove_masked_gene_models.py -> build/scripts-3.9
2021-07-11T23:53:38,164   copying and adjusting bin/remove_duplicate_sequences.py -> build/scripts-3.9
2021-07-11T23:53:38,166   copying and adjusting bin/create_taxonomy_db.py -> build/scripts-3.9
2021-07-11T23:53:38,168   copying and adjusting bin/report_or_replace_nonstandard_residues.py -> build/scripts-3.9
2021-07-11T23:53:38,170   copying and adjusting bin/convert_aat_btab_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,173   copying and adjusting bin/make_go_slim.py -> build/scripts-3.9
2021-07-11T23:53:38,176   copying and adjusting bin/validate_feature_boundaries_on_molecules.py -> build/scripts-3.9
2021-07-11T23:53:38,178   copying and adjusting bin/report_basic_gff_model_agreement.py -> build/scripts-3.9
2021-07-11T23:53:38,180   copying and adjusting bin/make_cufflinks_ids_unique.py -> build/scripts-3.9
2021-07-11T23:53:38,181   copying and adjusting bin/split_fasta_into_even_files.py -> build/scripts-3.9
2021-07-11T23:53:38,183   copying and adjusting bin/remove_duplicate_features.py -> build/scripts-3.9
2021-07-11T23:53:38,185   copying and adjusting bin/filter_gff3_by_id_list.py -> build/scripts-3.9
2021-07-11T23:53:38,187   copying and adjusting bin/randomly_subsample_fastq.py -> build/scripts-3.9
2021-07-11T23:53:38,189   copying and adjusting bin/convert_blast_btab_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,192   copying and adjusting bin/write_fasta_from_gff.py -> build/scripts-3.9
2021-07-11T23:53:38,194   copying and adjusting bin/replace_gff_type_column_value.py -> build/scripts-3.9
2021-07-11T23:53:38,196   copying and adjusting bin/convert_genbank_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,198   copying and adjusting bin/get_mpilup_from_id_list.py -> build/scripts-3.9
2021-07-11T23:53:38,200   copying and adjusting bin/uniprot_sprot_to_sqlite3.py -> build/scripts-3.9
2021-07-11T23:53:38,202   copying and adjusting bin/split_interleaved_sequence_file.py -> build/scripts-3.9
2021-07-11T23:53:38,204   copying and adjusting bin/uniref_to_sqlite3.py -> build/scripts-3.9
2021-07-11T23:53:38,207   copying and adjusting bin/compare_gene_structures.py -> build/scripts-3.9
2021-07-11T23:53:38,210   copying and adjusting bin/convert_augustus_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,212   copying and adjusting bin/reorient_sequences_by_id.py -> build/scripts-3.9
2021-07-11T23:53:38,214   copying and adjusting bin/convert_gff3_to_gbk.py -> build/scripts-3.9
2021-07-11T23:53:38,216   copying and adjusting bin/reverse_misordered_cds_coords.py -> build/scripts-3.9
2021-07-11T23:53:38,218   copying and adjusting bin/convert_prodigal_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,220   copying and adjusting bin/interleave_fastq.py -> build/scripts-3.9
2021-07-11T23:53:38,221   copying and adjusting bin/tigrfam_info_to_sqlite3.py -> build/scripts-3.9
2021-07-11T23:53:38,224   copying and adjusting bin/convert_pasa_gff_to_models.py -> build/scripts-3.9
2021-07-11T23:53:38,226   copying and adjusting bin/eggnog_to_sqlite3.py -> build/scripts-3.9
2021-07-11T23:53:38,228   copying and adjusting bin/merge_masked_fasta_files.py -> build/scripts-3.9
2021-07-11T23:53:38,229   copying and adjusting bin/convert_glimmerHMM_gff_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,232   copying and adjusting bin/update_selected_column9_values.py -> build/scripts-3.9
2021-07-11T23:53:38,233   copying and adjusting bin/interleave_fasta.py -> build/scripts-3.9
2021-07-11T23:53:38,235   copying and adjusting bin/convert_cufflinks_gtf_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,237   copying and adjusting bin/check_gff_for_internal_stops.py -> build/scripts-3.9
2021-07-11T23:53:38,239   copying and adjusting bin/replace_homopolymeric_repeats_with_Ns.py -> build/scripts-3.9
2021-07-11T23:53:38,241   copying and adjusting bin/append_to_fastq_read_header.py -> build/scripts-3.9
2021-07-11T23:53:38,243   copying and adjusting bin/convert_metagenemark_gff_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,246   copying and adjusting bin/report_gff3_statistics.py -> build/scripts-3.9
2021-07-11T23:53:38,248   copying and adjusting bin/convert_fasta_contigs_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,250   copying and adjusting bin/fasta_size_distribution_plot.py -> build/scripts-3.9
2021-07-11T23:53:38,252   copying and adjusting bin/merge_bam_files.py -> build/scripts-3.9
2021-07-11T23:53:38,254   copying and adjusting bin/correct_gff3_CDS_phase_column.py -> build/scripts-3.9
2021-07-11T23:53:38,256   copying and adjusting bin/biothings_coordinate_comparisons.py -> build/scripts-3.9
2021-07-11T23:53:38,258   copying and adjusting bin/prepend_to_fasta_header.py -> build/scripts-3.9
2021-07-11T23:53:38,260   copying and adjusting bin/split_isoforms_into_individual_genes.py -> build/scripts-3.9
2021-07-11T23:53:38,262   copying and adjusting bin/report_gff_intron_and_intergenic_stats.py -> build/scripts-3.9
2021-07-11T23:53:38,265   copying and adjusting bin/merge_fasta_files_and_uniquify_ids.py -> build/scripts-3.9
2021-07-11T23:53:38,267   copying and adjusting bin/subsample_fasta.py -> build/scripts-3.9
2021-07-11T23:53:38,269   copying and adjusting bin/convert_cegma_gff_to_gff3.py -> build/scripts-3.9
2021-07-11T23:53:38,273   copying and adjusting bin/detect_inverted_repeats.py -> build/scripts-3.9
2021-07-11T23:53:38,492   copying and adjusting bin/create_taxonomic_profile_from_blast.py -> build/scripts-3.9
2021-07-11T23:53:38,496   copying and adjusting bin/reformat_fasta_residue_lengths.py -> build/scripts-3.9
2021-07-11T23:53:38,498   copying and adjusting bin/select_training_and_evaluation_transcripts.py -> build/scripts-3.9
2021-07-11T23:53:38,501   copying and adjusting bin/append_to_fasta_header.py -> build/scripts-3.9
2021-07-11T23:53:38,504   copying and adjusting bin/calculate_query_coverage_by_blast.py -> build/scripts-3.9
2021-07-11T23:53:38,507   copying and adjusting bin/convert_gff3_to_ncbi_tbl.py -> build/scripts-3.9
2021-07-11T23:53:38,509   copying and adjusting bin/filter_fasta_by_type.py -> build/scripts-3.9
2021-07-11T23:53:38,512   copying and adjusting bin/remove_orphaned_features.py -> build/scripts-3.9
2021-07-11T23:53:38,514   copying and adjusting bin/create_rsem_html_table.py -> build/scripts-3.9
2021-07-11T23:53:38,516   copying and adjusting bin/set_source_column.py -> build/scripts-3.9
2021-07-11T23:53:38,518   copying and adjusting bin/fasta_base_content.py -> build/scripts-3.9
2021-07-11T23:53:38,520   copying and adjusting bin/check_for_embedded_fasta_headers.py -> build/scripts-3.9
2021-07-11T23:53:38,521   copying and adjusting bin/fastq_simple_stats.py -> build/scripts-3.9
2021-07-11T23:53:38,523   copying and adjusting bin/append_to_column_9_value.py -> build/scripts-3.9
2021-07-11T23:53:38,524   changing mode of build/scripts-3.9/filter_fastq_by_N_content.py from 644 to 755
2021-07-11T23:53:38,525   changing mode of build/scripts-3.9/convert_fastq_to_fasta.py from 644 to 755
2021-07-11T23:53:38,525   changing mode of build/scripts-3.9/validate_fasta.py from 644 to 755
2021-07-11T23:53:38,525   changing mode of build/scripts-3.9/filter_fasta_by_header_regex.py from 644 to 755
2021-07-11T23:53:38,526   changing mode of build/scripts-3.9/add_gff3_locus_tags.py from 644 to 755
2021-07-11T23:53:38,526   changing mode of build/scripts-3.9/split_molecules_on_gaps.py from 644 to 755
2021-07-11T23:53:38,526   changing mode of build/scripts-3.9/convert_gff3_to_gene_association_format.py from 644 to 755
2021-07-11T23:53:38,527   changing mode of build/scripts-3.9/extract_fasta_regions.py from 644 to 755
2021-07-11T23:53:38,527   changing mode of build/scripts-3.9/hmmlib_to_sqlite3.py from 644 to 755
2021-07-11T23:53:38,527   changing mode of build/scripts-3.9/convert_scipio_gff_to_gff3.py from 644 to 755
2021-07-11T23:53:38,528   changing mode of build/scripts-3.9/report_coverage_gaps.py from 644 to 755
2021-07-11T23:53:38,528   changing mode of build/scripts-3.9/remove_masked_gene_models.py from 644 to 755
2021-07-11T23:53:38,528   changing mode of build/scripts-3.9/remove_duplicate_sequences.py from 644 to 755
2021-07-11T23:53:38,529   changing mode of build/scripts-3.9/create_taxonomy_db.py from 644 to 755
2021-07-11T23:53:38,529   changing mode of build/scripts-3.9/report_or_replace_nonstandard_residues.py from 644 to 755
2021-07-11T23:53:38,529   changing mode of build/scripts-3.9/convert_aat_btab_to_gff3.py from 644 to 755
2021-07-11T23:53:38,529   changing mode of build/scripts-3.9/make_go_slim.py from 644 to 755
2021-07-11T23:53:38,530   changing mode of build/scripts-3.9/validate_feature_boundaries_on_molecules.py from 644 to 755
2021-07-11T23:53:38,530   changing mode of build/scripts-3.9/report_basic_gff_model_agreement.py from 644 to 755
2021-07-11T23:53:38,530   changing mode of build/scripts-3.9/make_cufflinks_ids_unique.py from 644 to 755
2021-07-11T23:53:38,531   changing mode of build/scripts-3.9/split_fasta_into_even_files.py from 644 to 755
2021-07-11T23:53:38,531   changing mode of build/scripts-3.9/remove_duplicate_features.py from 644 to 755
2021-07-11T23:53:38,531   changing mode of build/scripts-3.9/filter_gff3_by_id_list.py from 644 to 755
2021-07-11T23:53:38,532   changing mode of build/scripts-3.9/randomly_subsample_fastq.py from 644 to 755
2021-07-11T23:53:38,532   changing mode of build/scripts-3.9/convert_blast_btab_to_gff3.py from 644 to 755
2021-07-11T23:53:38,532   changing mode of build/scripts-3.9/write_fasta_from_gff.py from 644 to 755
2021-07-11T23:53:38,533   changing mode of build/scripts-3.9/replace_gff_type_column_value.py from 644 to 755
2021-07-11T23:53:38,533   changing mode of build/scripts-3.9/convert_genbank_to_gff3.py from 644 to 755
2021-07-11T23:53:38,533   changing mode of build/scripts-3.9/get_mpilup_from_id_list.py from 644 to 755
2021-07-11T23:53:38,533   changing mode of build/scripts-3.9/uniprot_sprot_to_sqlite3.py from 644 to 755
2021-07-11T23:53:38,534   changing mode of build/scripts-3.9/split_interleaved_sequence_file.py from 644 to 755
2021-07-11T23:53:38,534   changing mode of build/scripts-3.9/uniref_to_sqlite3.py from 644 to 755
2021-07-11T23:53:38,534   changing mode of build/scripts-3.9/compare_gene_structures.py from 644 to 755
2021-07-11T23:53:38,535   changing mode of build/scripts-3.9/convert_augustus_to_gff3.py from 644 to 755
2021-07-11T23:53:38,535   changing mode of build/scripts-3.9/reorient_sequences_by_id.py from 644 to 755
2021-07-11T23:53:38,535   changing mode of build/scripts-3.9/convert_gff3_to_gbk.py from 644 to 755
2021-07-11T23:53:38,535   changing mode of build/scripts-3.9/reverse_misordered_cds_coords.py from 644 to 755
2021-07-11T23:53:38,536   changing mode of build/scripts-3.9/convert_prodigal_to_gff3.py from 644 to 755
2021-07-11T23:53:38,536   changing mode of build/scripts-3.9/interleave_fastq.py from 644 to 755
2021-07-11T23:53:38,536   changing mode of build/scripts-3.9/tigrfam_info_to_sqlite3.py from 644 to 755
2021-07-11T23:53:38,536   changing mode of build/scripts-3.9/convert_pasa_gff_to_models.py from 644 to 755
2021-07-11T23:53:38,537   changing mode of build/scripts-3.9/eggnog_to_sqlite3.py from 644 to 755
2021-07-11T23:53:38,537   changing mode of build/scripts-3.9/merge_masked_fasta_files.py from 644 to 755
2021-07-11T23:53:38,537   changing mode of build/scripts-3.9/convert_glimmerHMM_gff_to_gff3.py from 644 to 755
2021-07-11T23:53:38,537   changing mode of build/scripts-3.9/update_selected_column9_values.py from 644 to 755
2021-07-11T23:53:38,538   changing mode of build/scripts-3.9/interleave_fasta.py from 644 to 755
2021-07-11T23:53:38,538   changing mode of build/scripts-3.9/convert_cufflinks_gtf_to_gff3.py from 644 to 755
2021-07-11T23:53:38,538   changing mode of build/scripts-3.9/check_gff_for_internal_stops.py from 644 to 755
2021-07-11T23:53:38,538   changing mode of build/scripts-3.9/replace_homopolymeric_repeats_with_Ns.py from 644 to 755
2021-07-11T23:53:38,539   changing mode of build/scripts-3.9/append_to_fastq_read_header.py from 644 to 755
2021-07-11T23:53:38,539   changing mode of build/scripts-3.9/convert_metagenemark_gff_to_gff3.py from 644 to 755
2021-07-11T23:53:38,539   changing mode of build/scripts-3.9/report_gff3_statistics.py from 644 to 755
2021-07-11T23:53:38,539   changing mode of build/scripts-3.9/convert_fasta_contigs_to_gff3.py from 644 to 755
2021-07-11T23:53:38,540   changing mode of build/scripts-3.9/fasta_size_distribution_plot.py from 644 to 755
2021-07-11T23:53:38,540   changing mode of build/scripts-3.9/merge_bam_files.py from 644 to 755
2021-07-11T23:53:38,540   changing mode of build/scripts-3.9/correct_gff3_CDS_phase_column.py from 644 to 755
2021-07-11T23:53:38,541   changing mode of build/scripts-3.9/biothings_coordinate_comparisons.py from 644 to 755
2021-07-11T23:53:38,541   changing mode of build/scripts-3.9/prepend_to_fasta_header.py from 644 to 755
2021-07-11T23:53:38,541   changing mode of build/scripts-3.9/split_isoforms_into_individual_genes.py from 644 to 755
2021-07-11T23:53:38,541   changing mode of build/scripts-3.9/report_gff_intron_and_intergenic_stats.py from 644 to 755
2021-07-11T23:53:38,542   changing mode of build/scripts-3.9/merge_fasta_files_and_uniquify_ids.py from 644 to 755
2021-07-11T23:53:38,542   changing mode of build/scripts-3.9/subsample_fasta.py from 644 to 755
2021-07-11T23:53:38,542   changing mode of build/scripts-3.9/convert_cegma_gff_to_gff3.py from 644 to 755
2021-07-11T23:53:38,543   changing mode of build/scripts-3.9/detect_inverted_repeats.py from 644 to 755
2021-07-11T23:53:38,543   changing mode of build/scripts-3.9/create_taxonomic_profile_from_blast.py from 644 to 755
2021-07-11T23:53:38,543   changing mode of build/scripts-3.9/reformat_fasta_residue_lengths.py from 644 to 755
2021-07-11T23:53:38,544   changing mode of build/scripts-3.9/select_training_and_evaluation_transcripts.py from 644 to 755
2021-07-11T23:53:38,544   changing mode of build/scripts-3.9/append_to_fasta_header.py from 644 to 755
2021-07-11T23:53:38,544   changing mode of build/scripts-3.9/calculate_query_coverage_by_blast.py from 644 to 755
2021-07-11T23:53:38,544   changing mode of build/scripts-3.9/convert_gff3_to_ncbi_tbl.py from 644 to 755
2021-07-11T23:53:38,545   changing mode of build/scripts-3.9/filter_fasta_by_type.py from 644 to 755
2021-07-11T23:53:38,545   changing mode of build/scripts-3.9/remove_orphaned_features.py from 644 to 755
2021-07-11T23:53:38,545   changing mode of build/scripts-3.9/create_rsem_html_table.py from 644 to 755
2021-07-11T23:53:38,545   changing mode of build/scripts-3.9/set_source_column.py from 644 to 755
2021-07-11T23:53:38,546   changing mode of build/scripts-3.9/fasta_base_content.py from 644 to 755
2021-07-11T23:53:38,546   changing mode of build/scripts-3.9/check_for_embedded_fasta_headers.py from 644 to 755
2021-07-11T23:53:38,546   changing mode of build/scripts-3.9/fastq_simple_stats.py from 644 to 755
2021-07-11T23:53:38,546   changing mode of build/scripts-3.9/append_to_column_9_value.py from 644 to 755
2021-07-11T23:53:38,553   installing to build/bdist.linux-armv7l/wheel
2021-07-11T23:53:38,553   running install
2021-07-11T23:53:38,554   running install_lib
2021-07-11T23:53:38,559   creating build/bdist.linux-armv7l
2021-07-11T23:53:38,559   creating build/bdist.linux-armv7l/wheel
2021-07-11T23:53:38,561   creating build/bdist.linux-armv7l/wheel/biocode
2021-07-11T23:53:38,562   copying build/lib/biocode/annotation.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-11T23:53:38,565   copying build/lib/biocode/genbank.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-11T23:53:38,567   copying build/lib/biocode/utils.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-11T23:53:38,570   copying build/lib/biocode/__init__.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-11T23:53:38,571   copying build/lib/biocode/gff.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-11T23:53:38,574   copying build/lib/biocode/things.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-11T23:53:38,577   copying build/lib/biocode/tbl.py -> build/bdist.linux-armv7l/wheel/biocode
2021-07-11T23:53:38,580   running install_egg_info
2021-07-11T23:53:38,585   Copying biocode.egg-info to build/bdist.linux-armv7l/wheel/biocode-0.1.2-py3.9.egg-info
2021-07-11T23:53:38,598   running install_scripts
2021-07-11T23:53:38,627   creating build/bdist.linux-armv7l/wheel/biocode-0.1.2.data
2021-07-11T23:53:38,628   creating build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,629   copying build/scripts-3.9/check_for_embedded_fasta_headers.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,631   copying build/scripts-3.9/calculate_query_coverage_by_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,633   copying build/scripts-3.9/convert_cegma_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,635   copying build/scripts-3.9/detect_inverted_repeats.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,637   copying build/scripts-3.9/fastq_simple_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,639   copying build/scripts-3.9/eggnog_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,642   copying build/scripts-3.9/remove_masked_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,644   copying build/scripts-3.9/report_basic_gff_model_agreement.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,646   copying build/scripts-3.9/convert_blast_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,648   copying build/scripts-3.9/report_gff3_statistics.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,650   copying build/scripts-3.9/convert_aat_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,653   copying build/scripts-3.9/randomly_subsample_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,656   copying build/scripts-3.9/interleave_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,658   copying build/scripts-3.9/filter_fastq_by_N_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,660   copying build/scripts-3.9/convert_cufflinks_gtf_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,663   copying build/scripts-3.9/replace_homopolymeric_repeats_with_Ns.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,666   copying build/scripts-3.9/split_molecules_on_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,668   copying build/scripts-3.9/set_source_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,670   copying build/scripts-3.9/merge_fasta_files_and_uniquify_ids.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,672   copying build/scripts-3.9/make_cufflinks_ids_unique.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,674   copying build/scripts-3.9/convert_gff3_to_gbk.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,677   copying build/scripts-3.9/make_go_slim.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,680   copying build/scripts-3.9/correct_gff3_CDS_phase_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,682   copying build/scripts-3.9/extract_fasta_regions.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,684   copying build/scripts-3.9/filter_gff3_by_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,686   copying build/scripts-3.9/filter_fasta_by_header_regex.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,689   copying build/scripts-3.9/fasta_base_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,691   copying build/scripts-3.9/reorient_sequences_by_id.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,693   copying build/scripts-3.9/create_taxonomic_profile_from_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,696   copying build/scripts-3.9/report_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,699   copying build/scripts-3.9/add_gff3_locus_tags.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,702   copying build/scripts-3.9/validate_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,704   copying build/scripts-3.9/merge_bam_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,707   copying build/scripts-3.9/check_gff_for_internal_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,709   copying build/scripts-3.9/interleave_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,711   copying build/scripts-3.9/append_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,713   copying build/scripts-3.9/convert_fasta_contigs_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,715   copying build/scripts-3.9/convert_scipio_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,718   copying build/scripts-3.9/biothings_coordinate_comparisons.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,720   copying build/scripts-3.9/replace_gff_type_column_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,722   copying build/scripts-3.9/remove_duplicate_sequences.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,724   copying build/scripts-3.9/append_to_fastq_read_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,726   copying build/scripts-3.9/uniprot_sprot_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,729   copying build/scripts-3.9/get_mpilup_from_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,731   copying build/scripts-3.9/uniref_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,734   copying build/scripts-3.9/write_fasta_from_gff.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,737   copying build/scripts-3.9/convert_pasa_gff_to_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,739   copying build/scripts-3.9/prepend_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,741   copying build/scripts-3.9/reverse_misordered_cds_coords.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,743   copying build/scripts-3.9/fasta_size_distribution_plot.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,746   copying build/scripts-3.9/convert_glimmerHMM_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,748   copying build/scripts-3.9/filter_fasta_by_type.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,750   copying build/scripts-3.9/update_selected_column9_values.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,753   copying build/scripts-3.9/report_gff_intron_and_intergenic_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,756   copying build/scripts-3.9/create_rsem_html_table.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,758   copying build/scripts-3.9/create_taxonomy_db.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,760   copying build/scripts-3.9/subsample_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,763   copying build/scripts-3.9/append_to_column_9_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,765   copying build/scripts-3.9/convert_genbank_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,767   copying build/scripts-3.9/remove_orphaned_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,769   copying build/scripts-3.9/convert_gff3_to_gene_association_format.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,772   copying build/scripts-3.9/split_fasta_into_even_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,774   copying build/scripts-3.9/compare_gene_structures.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,777   copying build/scripts-3.9/convert_metagenemark_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,780   copying build/scripts-3.9/select_training_and_evaluation_transcripts.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,783   copying build/scripts-3.9/hmmlib_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,786   copying build/scripts-3.9/convert_gff3_to_ncbi_tbl.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,788   copying build/scripts-3.9/split_interleaved_sequence_file.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,790   copying build/scripts-3.9/reformat_fasta_residue_lengths.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,792   copying build/scripts-3.9/merge_masked_fasta_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,795   copying build/scripts-3.9/validate_feature_boundaries_on_molecules.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,797   copying build/scripts-3.9/tigrfam_info_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,799   copying build/scripts-3.9/remove_duplicate_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,801   copying build/scripts-3.9/report_or_replace_nonstandard_residues.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,804   copying build/scripts-3.9/convert_augustus_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,807   copying build/scripts-3.9/split_isoforms_into_individual_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,809   copying build/scripts-3.9/convert_prodigal_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,811   copying build/scripts-3.9/convert_fastq_to_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts
2021-07-11T23:53:38,813   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/check_for_embedded_fasta_headers.py to 755
2021-07-11T23:53:38,813   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/calculate_query_coverage_by_blast.py to 755
2021-07-11T23:53:38,813   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/convert_cegma_gff_to_gff3.py to 755
2021-07-11T23:53:38,814   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/detect_inverted_repeats.py to 755
2021-07-11T23:53:38,814   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/fastq_simple_stats.py to 755
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2021-07-11T23:53:38,817   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/replace_homopolymeric_repeats_with_Ns.py to 755
2021-07-11T23:53:38,817   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/split_molecules_on_gaps.py to 755
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2021-07-11T23:53:38,818   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/merge_fasta_files_and_uniquify_ids.py to 755
2021-07-11T23:53:38,818   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/make_cufflinks_ids_unique.py to 755
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2021-07-11T23:53:38,819   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/extract_fasta_regions.py to 755
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2021-07-11T23:53:38,823   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/interleave_fasta.py to 755
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2021-07-11T23:53:38,823   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/convert_scipio_gff_to_gff3.py to 755
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2021-07-11T23:53:38,832   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/merge_masked_fasta_files.py to 755
2021-07-11T23:53:38,833   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/validate_feature_boundaries_on_molecules.py to 755
2021-07-11T23:53:38,833   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/tigrfam_info_to_sqlite3.py to 755
2021-07-11T23:53:38,833   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/remove_duplicate_features.py to 755
2021-07-11T23:53:38,833   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/report_or_replace_nonstandard_residues.py to 755
2021-07-11T23:53:38,834   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/convert_augustus_to_gff3.py to 755
2021-07-11T23:53:38,834   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/split_isoforms_into_individual_genes.py to 755
2021-07-11T23:53:38,834   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/convert_prodigal_to_gff3.py to 755
2021-07-11T23:53:38,835   changing mode of build/bdist.linux-armv7l/wheel/biocode-0.1.2.data/scripts/convert_fastq_to_fasta.py to 755
2021-07-11T23:53:38,854   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2021-07-11T23:53:38,859   creating build/bdist.linux-armv7l/wheel/biocode-0.1.2.dist-info/WHEEL
2021-07-11T23:53:38,862   creating '/tmp/pip-wheel-sf7tg8do/biocode-0.1.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-11T23:53:38,864   adding 'biocode/__init__.py'
2021-07-11T23:53:38,866   adding 'biocode/annotation.py'
2021-07-11T23:53:38,869   adding 'biocode/genbank.py'
2021-07-11T23:53:38,873   adding 'biocode/gff.py'
2021-07-11T23:53:38,875   adding 'biocode/tbl.py'
2021-07-11T23:53:38,883   adding 'biocode/things.py'
2021-07-11T23:53:38,885   adding 'biocode/utils.py'
2021-07-11T23:53:38,890   adding 'biocode-0.1.2.data/scripts/add_gff3_locus_tags.py'
2021-07-11T23:53:38,892   adding 'biocode-0.1.2.data/scripts/append_to_column_9_value.py'
2021-07-11T23:53:38,893   adding 'biocode-0.1.2.data/scripts/append_to_fasta_header.py'
2021-07-11T23:53:38,895   adding 'biocode-0.1.2.data/scripts/append_to_fastq_read_header.py'
2021-07-11T23:53:38,896   adding 'biocode-0.1.2.data/scripts/biothings_coordinate_comparisons.py'
2021-07-11T23:53:38,897   adding 'biocode-0.1.2.data/scripts/calculate_query_coverage_by_blast.py'
2021-07-11T23:53:38,899   adding 'biocode-0.1.2.data/scripts/check_for_embedded_fasta_headers.py'
2021-07-11T23:53:38,900   adding 'biocode-0.1.2.data/scripts/check_gff_for_internal_stops.py'
2021-07-11T23:53:38,904   adding 'biocode-0.1.2.data/scripts/compare_gene_structures.py'
2021-07-11T23:53:38,906   adding 'biocode-0.1.2.data/scripts/convert_aat_btab_to_gff3.py'
2021-07-11T23:53:38,908   adding 'biocode-0.1.2.data/scripts/convert_augustus_to_gff3.py'
2021-07-11T23:53:38,910   adding 'biocode-0.1.2.data/scripts/convert_blast_btab_to_gff3.py'
2021-07-11T23:53:38,912   adding 'biocode-0.1.2.data/scripts/convert_cegma_gff_to_gff3.py'
2021-07-11T23:53:38,914   adding 'biocode-0.1.2.data/scripts/convert_cufflinks_gtf_to_gff3.py'
2021-07-11T23:53:38,915   adding 'biocode-0.1.2.data/scripts/convert_fasta_contigs_to_gff3.py'
2021-07-11T23:53:38,917   adding 'biocode-0.1.2.data/scripts/convert_fastq_to_fasta.py'
2021-07-11T23:53:38,919   adding 'biocode-0.1.2.data/scripts/convert_genbank_to_gff3.py'
2021-07-11T23:53:38,920   adding 'biocode-0.1.2.data/scripts/convert_gff3_to_gbk.py'
2021-07-11T23:53:38,922   adding 'biocode-0.1.2.data/scripts/convert_gff3_to_gene_association_format.py'
2021-07-11T23:53:38,924   adding 'biocode-0.1.2.data/scripts/convert_gff3_to_ncbi_tbl.py'
2021-07-11T23:53:38,925   adding 'biocode-0.1.2.data/scripts/convert_glimmerHMM_gff_to_gff3.py'
2021-07-11T23:53:38,927   adding 'biocode-0.1.2.data/scripts/convert_metagenemark_gff_to_gff3.py'
2021-07-11T23:53:38,929   adding 'biocode-0.1.2.data/scripts/convert_pasa_gff_to_models.py'
2021-07-11T23:53:38,930   adding 'biocode-0.1.2.data/scripts/convert_prodigal_to_gff3.py'
2021-07-11T23:53:38,932   adding 'biocode-0.1.2.data/scripts/convert_scipio_gff_to_gff3.py'
2021-07-11T23:53:38,933   adding 'biocode-0.1.2.data/scripts/correct_gff3_CDS_phase_column.py'
2021-07-11T23:53:38,934   adding 'biocode-0.1.2.data/scripts/create_rsem_html_table.py'
2021-07-11T23:53:38,936   adding 'biocode-0.1.2.data/scripts/create_taxonomic_profile_from_blast.py'
2021-07-11T23:53:38,938   adding 'biocode-0.1.2.data/scripts/create_taxonomy_db.py'
2021-07-11T23:53:38,940   adding 'biocode-0.1.2.data/scripts/detect_inverted_repeats.py'
2021-07-11T23:53:38,942   adding 'biocode-0.1.2.data/scripts/eggnog_to_sqlite3.py'
2021-07-11T23:53:38,943   adding 'biocode-0.1.2.data/scripts/extract_fasta_regions.py'
2021-07-11T23:53:38,945   adding 'biocode-0.1.2.data/scripts/fasta_base_content.py'
2021-07-11T23:53:38,946   adding 'biocode-0.1.2.data/scripts/fasta_size_distribution_plot.py'
2021-07-11T23:53:38,948   adding 'biocode-0.1.2.data/scripts/fastq_simple_stats.py'
2021-07-11T23:53:38,949   adding 'biocode-0.1.2.data/scripts/filter_fasta_by_header_regex.py'
2021-07-11T23:53:38,950   adding 'biocode-0.1.2.data/scripts/filter_fasta_by_type.py'
2021-07-11T23:53:38,952   adding 'biocode-0.1.2.data/scripts/filter_fastq_by_N_content.py'
2021-07-11T23:53:38,953   adding 'biocode-0.1.2.data/scripts/filter_gff3_by_id_list.py'
2021-07-11T23:53:38,955   adding 'biocode-0.1.2.data/scripts/get_mpilup_from_id_list.py'
2021-07-11T23:53:38,957   adding 'biocode-0.1.2.data/scripts/hmmlib_to_sqlite3.py'
2021-07-11T23:53:38,958   adding 'biocode-0.1.2.data/scripts/interleave_fasta.py'
2021-07-11T23:53:38,959   adding 'biocode-0.1.2.data/scripts/interleave_fastq.py'
2021-07-11T23:53:38,961   adding 'biocode-0.1.2.data/scripts/make_cufflinks_ids_unique.py'
2021-07-11T23:53:38,962   adding 'biocode-0.1.2.data/scripts/make_go_slim.py'
2021-07-11T23:53:38,964   adding 'biocode-0.1.2.data/scripts/merge_bam_files.py'
2021-07-11T23:53:38,965   adding 'biocode-0.1.2.data/scripts/merge_fasta_files_and_uniquify_ids.py'
2021-07-11T23:53:38,967   adding 'biocode-0.1.2.data/scripts/merge_masked_fasta_files.py'
2021-07-11T23:53:38,968   adding 'biocode-0.1.2.data/scripts/prepend_to_fasta_header.py'
2021-07-11T23:53:38,970   adding 'biocode-0.1.2.data/scripts/randomly_subsample_fastq.py'
2021-07-11T23:53:38,971   adding 'biocode-0.1.2.data/scripts/reformat_fasta_residue_lengths.py'
2021-07-11T23:53:38,972   adding 'biocode-0.1.2.data/scripts/remove_duplicate_features.py'
2021-07-11T23:53:38,974   adding 'biocode-0.1.2.data/scripts/remove_duplicate_sequences.py'
2021-07-11T23:53:38,975   adding 'biocode-0.1.2.data/scripts/remove_masked_gene_models.py'
2021-07-11T23:53:38,976   adding 'biocode-0.1.2.data/scripts/remove_orphaned_features.py'
2021-07-11T23:53:38,978   adding 'biocode-0.1.2.data/scripts/reorient_sequences_by_id.py'
2021-07-11T23:53:38,979   adding 'biocode-0.1.2.data/scripts/replace_gff_type_column_value.py'
2021-07-11T23:53:38,980   adding 'biocode-0.1.2.data/scripts/replace_homopolymeric_repeats_with_Ns.py'
2021-07-11T23:53:38,982   adding 'biocode-0.1.2.data/scripts/report_basic_gff_model_agreement.py'
2021-07-11T23:53:38,983   adding 'biocode-0.1.2.data/scripts/report_coverage_gaps.py'
2021-07-11T23:53:38,985   adding 'biocode-0.1.2.data/scripts/report_gff3_statistics.py'
2021-07-11T23:53:38,987   adding 'biocode-0.1.2.data/scripts/report_gff_intron_and_intergenic_stats.py'
2021-07-11T23:53:38,989   adding 'biocode-0.1.2.data/scripts/report_or_replace_nonstandard_residues.py'
2021-07-11T23:53:38,990   adding 'biocode-0.1.2.data/scripts/reverse_misordered_cds_coords.py'
2021-07-11T23:53:38,992   adding 'biocode-0.1.2.data/scripts/select_training_and_evaluation_transcripts.py'
2021-07-11T23:53:38,993   adding 'biocode-0.1.2.data/scripts/set_source_column.py'
2021-07-11T23:53:38,994   adding 'biocode-0.1.2.data/scripts/split_fasta_into_even_files.py'
2021-07-11T23:53:38,996   adding 'biocode-0.1.2.data/scripts/split_interleaved_sequence_file.py'
2021-07-11T23:53:38,997   adding 'biocode-0.1.2.data/scripts/split_isoforms_into_individual_genes.py'
2021-07-11T23:53:38,999   adding 'biocode-0.1.2.data/scripts/split_molecules_on_gaps.py'
2021-07-11T23:53:39,000   adding 'biocode-0.1.2.data/scripts/subsample_fasta.py'
2021-07-11T23:53:39,002   adding 'biocode-0.1.2.data/scripts/tigrfam_info_to_sqlite3.py'
2021-07-11T23:53:39,004   adding 'biocode-0.1.2.data/scripts/uniprot_sprot_to_sqlite3.py'
2021-07-11T23:53:39,005   adding 'biocode-0.1.2.data/scripts/uniref_to_sqlite3.py'
2021-07-11T23:53:39,007   adding 'biocode-0.1.2.data/scripts/update_selected_column9_values.py'
2021-07-11T23:53:39,008   adding 'biocode-0.1.2.data/scripts/validate_fasta.py'
2021-07-11T23:53:39,010   adding 'biocode-0.1.2.data/scripts/validate_feature_boundaries_on_molecules.py'
2021-07-11T23:53:39,012   adding 'biocode-0.1.2.data/scripts/write_fasta_from_gff.py'
2021-07-11T23:53:39,014   adding 'biocode-0.1.2.dist-info/LICENSE'
2021-07-11T23:53:39,015   adding 'biocode-0.1.2.dist-info/METADATA'
2021-07-11T23:53:39,016   adding 'biocode-0.1.2.dist-info/WHEEL'
2021-07-11T23:53:39,017   adding 'biocode-0.1.2.dist-info/top_level.txt'
2021-07-11T23:53:39,019   adding 'biocode-0.1.2.dist-info/RECORD'
2021-07-11T23:53:39,024   removing build/bdist.linux-armv7l/wheel
2021-07-11T23:53:39,145   Building wheel for biocode (setup.py): finished with status 'done'
2021-07-11T23:53:39,149   Created wheel for biocode: filename=biocode-0.1.2-py3-none-any.whl size=182279 sha256=cccf2290fd0a5cfcf8edbf2ca2bb07a469ad361c612567cb949e326d52c77c39
2021-07-11T23:53:39,150   Stored in directory: /tmp/pip-ephem-wheel-cache-qtqp3h8e/wheels/9c/f7/a0/75eb20ea565e880bdd3fbc97ed148891a08c1701246aa87fe7
2021-07-11T23:53:39,162 Successfully built biocode
2021-07-11T23:53:39,176 Removed build tracker: '/tmp/pip-req-tracker-0sivxrew'