2021-07-12T20:22:39,557 Created temporary directory: /tmp/pip-ephem-wheel-cache-o4se4tse 2021-07-12T20:22:39,560 Created temporary directory: /tmp/pip-req-tracker-cotnvfq3 2021-07-12T20:22:39,561 Initialized build tracking at /tmp/pip-req-tracker-cotnvfq3 2021-07-12T20:22:39,561 Created build tracker: /tmp/pip-req-tracker-cotnvfq3 2021-07-12T20:22:39,561 Entered build tracker: /tmp/pip-req-tracker-cotnvfq3 2021-07-12T20:22:39,562 Created temporary directory: /tmp/pip-wheel-jnx4jyc6 2021-07-12T20:22:39,591 1 location(s) to search for versions of biocode: 2021-07-12T20:22:39,591 * https://pypi.org/simple/biocode/ 2021-07-12T20:22:39,592 Fetching project page and analyzing links: https://pypi.org/simple/biocode/ 2021-07-12T20:22:39,592 Getting page https://pypi.org/simple/biocode/ 2021-07-12T20:22:39,594 Found index url https://pypi.org/simple 2021-07-12T20:22:39,721 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 2021-07-12T20:22:39,721 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 2021-07-12T20:22:39,722 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 2021-07-12T20:22:39,722 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 2021-07-12T20:22:39,722 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 2021-07-12T20:22:39,723 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 2021-07-12T20:22:39,723 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 2021-07-12T20:22:39,723 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 2021-07-12T20:22:39,723 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 2021-07-12T20:22:39,724 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 2021-07-12T20:22:39,724 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 2021-07-12T20:22:39,724 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 2021-07-12T20:22:39,724 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 2021-07-12T20:22:39,725 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 2021-07-12T20:22:39,725 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 2021-07-12T20:22:39,725 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 2021-07-12T20:22:39,726 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 2021-07-12T20:22:39,726 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 2021-07-12T20:22:39,726 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 2021-07-12T20:22:39,726 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 2021-07-12T20:22:39,727 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 2021-07-12T20:22:39,727 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 2021-07-12T20:22:39,727 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 2021-07-12T20:22:39,728 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 2021-07-12T20:22:39,728 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 2021-07-12T20:22:39,728 Skipping link: not a file: https://pypi.org/simple/biocode/ 2021-07-12T20:22:39,749 Given no hashes to check 1 links for project 'biocode': discarding no candidates 2021-07-12T20:22:39,768 Collecting biocode==0.5.0 2021-07-12T20:22:39,770 Created temporary directory: /tmp/pip-unpack-xd1xrkxp 2021-07-12T20:22:40,000 Downloading biocode-0.5.0.tar.gz (161 kB) 2021-07-12T20:22:40,291 Added biocode==0.5.0 from https://files.pythonhosted.org/packages/f2/fc/483f6dad337423c04dc8a1b2756c3e5326e9381648e5560eb602a4f83413/biocode-0.5.0.tar.gz#sha256=a96f0e2c3bde3e42f82590de9ce1be0e8782b50c9a58296bc3e872161fb3a3a3 to build tracker '/tmp/pip-req-tracker-cotnvfq3' 2021-07-12T20:22:40,292 Running setup.py (path:/tmp/pip-wheel-jnx4jyc6/biocode_674dbad1ee994c25876e89fefc9ce56a/setup.py) egg_info for package biocode 2021-07-12T20:22:40,292 Created temporary directory: /tmp/pip-pip-egg-info-i311w83i 2021-07-12T20:22:40,293 Running command python setup.py egg_info 2021-07-12T20:22:41,104 /tmp/pip-wheel-jnx4jyc6/biocode_674dbad1ee994c25876e89fefc9ce56a/setup.py:6: DeprecationWarning: Due to possible ambiguity, 'convert()' is deprecated. Use 'convert_file()' or 'convert_text()'. 2021-07-12T20:22:41,104 read_md = lambda f: convert(f, 'rst', 'md') 2021-07-12T20:22:41,327 /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long' 2021-07-12T20:22:41,328 warnings.warn(msg) 2021-07-12T20:22:41,436 running egg_info 2021-07-12T20:22:41,438 creating /tmp/pip-pip-egg-info-i311w83i/biocode.egg-info 2021-07-12T20:22:41,439 writing /tmp/pip-pip-egg-info-i311w83i/biocode.egg-info/PKG-INFO 2021-07-12T20:22:41,442 writing dependency_links to /tmp/pip-pip-egg-info-i311w83i/biocode.egg-info/dependency_links.txt 2021-07-12T20:22:41,444 writing requirements to /tmp/pip-pip-egg-info-i311w83i/biocode.egg-info/requires.txt 2021-07-12T20:22:41,445 writing top-level names to /tmp/pip-pip-egg-info-i311w83i/biocode.egg-info/top_level.txt 2021-07-12T20:22:41,447 writing manifest file '/tmp/pip-pip-egg-info-i311w83i/biocode.egg-info/SOURCES.txt' 2021-07-12T20:22:41,603 reading manifest file '/tmp/pip-pip-egg-info-i311w83i/biocode.egg-info/SOURCES.txt' 2021-07-12T20:22:41,605 reading manifest template 'MANIFEST.in' 2021-07-12T20:22:41,606 warning: no files found matching 'biocode/README.rst' 2021-07-12T20:22:41,607 adding license file 'LICENSE' 2021-07-12T20:22:41,612 writing manifest file '/tmp/pip-pip-egg-info-i311w83i/biocode.egg-info/SOURCES.txt' 2021-07-12T20:22:41,685 Source in /tmp/pip-wheel-jnx4jyc6/biocode_674dbad1ee994c25876e89fefc9ce56a has version 0.5.0, which satisfies requirement biocode==0.5.0 from https://files.pythonhosted.org/packages/f2/fc/483f6dad337423c04dc8a1b2756c3e5326e9381648e5560eb602a4f83413/biocode-0.5.0.tar.gz#sha256=a96f0e2c3bde3e42f82590de9ce1be0e8782b50c9a58296bc3e872161fb3a3a3 2021-07-12T20:22:41,686 Removed biocode==0.5.0 from https://files.pythonhosted.org/packages/f2/fc/483f6dad337423c04dc8a1b2756c3e5326e9381648e5560eb602a4f83413/biocode-0.5.0.tar.gz#sha256=a96f0e2c3bde3e42f82590de9ce1be0e8782b50c9a58296bc3e872161fb3a3a3 from build tracker '/tmp/pip-req-tracker-cotnvfq3' 2021-07-12T20:22:41,690 Created temporary directory: /tmp/pip-unpack-yu6hspgc 2021-07-12T20:22:41,690 Building wheels for collected packages: biocode 2021-07-12T20:22:41,694 Created temporary directory: /tmp/pip-wheel-xtar7vo9 2021-07-12T20:22:41,694 Building wheel for biocode (setup.py): started 2021-07-12T20:22:41,695 Destination directory: /tmp/pip-wheel-xtar7vo9 2021-07-12T20:22:41,695 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-jnx4jyc6/biocode_674dbad1ee994c25876e89fefc9ce56a/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-jnx4jyc6/biocode_674dbad1ee994c25876e89fefc9ce56a/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-xtar7vo9 2021-07-12T20:22:42,503 /tmp/pip-wheel-jnx4jyc6/biocode_674dbad1ee994c25876e89fefc9ce56a/setup.py:6: DeprecationWarning: Due to possible ambiguity, 'convert()' is deprecated. Use 'convert_file()' or 'convert_text()'. 2021-07-12T20:22:42,504 read_md = lambda f: convert(f, 'rst', 'md') 2021-07-12T20:22:42,724 /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long' 2021-07-12T20:22:42,724 warnings.warn(msg) 2021-07-12T20:22:42,851 running bdist_wheel 2021-07-12T20:22:43,022 running build 2021-07-12T20:22:43,022 running build_py 2021-07-12T20:22:43,162 creating build 2021-07-12T20:22:43,162 creating build/lib 2021-07-12T20:22:43,163 creating build/lib/biocode 2021-07-12T20:22:43,164 copying biocode/annotation.py -> build/lib/biocode 2021-07-12T20:22:43,167 copying biocode/tbl.py -> build/lib/biocode 2021-07-12T20:22:43,169 copying biocode/utils.py -> build/lib/biocode 2021-07-12T20:22:43,171 copying biocode/gff.py -> build/lib/biocode 2021-07-12T20:22:43,174 copying biocode/__init__.py -> build/lib/biocode 2021-07-12T20:22:43,175 copying biocode/genbank.py -> build/lib/biocode 2021-07-12T20:22:43,177 copying biocode/things.py -> build/lib/biocode 2021-07-12T20:22:43,180 running egg_info 2021-07-12T20:22:43,195 writing biocode.egg-info/PKG-INFO 2021-07-12T20:22:43,196 writing dependency_links to biocode.egg-info/dependency_links.txt 2021-07-12T20:22:43,198 writing requirements to biocode.egg-info/requires.txt 2021-07-12T20:22:43,199 writing top-level names to biocode.egg-info/top_level.txt 2021-07-12T20:22:43,214 reading manifest file 'biocode.egg-info/SOURCES.txt' 2021-07-12T20:22:43,218 reading manifest template 'MANIFEST.in' 2021-07-12T20:22:43,219 warning: no files found matching 'biocode/README.rst' 2021-07-12T20:22:43,220 adding license file 'LICENSE' 2021-07-12T20:22:43,228 writing manifest file 'biocode.egg-info/SOURCES.txt' 2021-07-12T20:22:43,232 creating build/lib/biocode/data 2021-07-12T20:22:43,233 copying biocode/data/HMPslim.v2.1.obo -> build/lib/biocode/data 2021-07-12T20:22:43,237 copying biocode/data/__init__.py -> build/lib/biocode/data 2021-07-12T20:22:43,239 copying biocode/data/genbank_flat_file_header.template -> build/lib/biocode/data 2021-07-12T20:22:43,242 copying biocode/data/rsem_html_table.template -> build/lib/biocode/data 2021-07-12T20:22:43,245 running build_scripts 2021-07-12T20:22:43,245 creating build/scripts-3.9 2021-07-12T20:22:43,246 copying and adjusting bin/filter_fastq_by_N_content.py -> build/scripts-3.9 2021-07-12T20:22:43,249 copying and adjusting bin/convert_fastq_to_fasta.py -> build/scripts-3.9 2021-07-12T20:22:43,250 copying and adjusting bin/validate_fasta.py -> build/scripts-3.9 2021-07-12T20:22:43,252 copying and adjusting bin/filter_fasta_by_header_regex.py -> build/scripts-3.9 2021-07-12T20:22:43,253 copying and adjusting bin/add_gff3_locus_tags.py -> build/scripts-3.9 2021-07-12T20:22:43,256 copying and adjusting bin/split_molecules_on_gaps.py -> build/scripts-3.9 2021-07-12T20:22:43,257 copying and adjusting bin/convert_gff3_to_gene_association_format.py -> build/scripts-3.9 2021-07-12T20:22:43,259 copying and adjusting bin/extract_fasta_regions.py -> build/scripts-3.9 2021-07-12T20:22:43,261 copying and adjusting bin/hmmlib_to_sqlite3.py -> build/scripts-3.9 2021-07-12T20:22:43,263 copying and adjusting bin/convert_scipio_gff_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,265 copying and adjusting bin/report_coverage_gaps.py -> build/scripts-3.9 2021-07-12T20:22:43,267 copying and adjusting bin/remove_masked_gene_models.py -> build/scripts-3.9 2021-07-12T20:22:43,269 copying and adjusting bin/remove_duplicate_sequences.py -> build/scripts-3.9 2021-07-12T20:22:43,270 copying and adjusting bin/create_taxonomy_db.py -> build/scripts-3.9 2021-07-12T20:22:43,273 copying and adjusting bin/merge_predicted_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,275 copying and adjusting bin/report_or_replace_nonstandard_residues.py -> build/scripts-3.9 2021-07-12T20:22:43,276 copying and adjusting bin/convert_aat_btab_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,279 copying and adjusting bin/make_go_slim.py -> build/scripts-3.9 2021-07-12T20:22:43,281 copying and adjusting bin/validate_feature_boundaries_on_molecules.py -> build/scripts-3.9 2021-07-12T20:22:43,283 copying and adjusting bin/report_basic_gff_model_agreement.py -> build/scripts-3.9 2021-07-12T20:22:43,284 copying and adjusting bin/make_cufflinks_ids_unique.py -> build/scripts-3.9 2021-07-12T20:22:43,286 copying and adjusting bin/split_fasta_into_even_files.py -> build/scripts-3.9 2021-07-12T20:22:43,287 copying and adjusting bin/remove_duplicate_features.py -> build/scripts-3.9 2021-07-12T20:22:43,289 copying and adjusting bin/filter_gff3_by_id_list.py -> build/scripts-3.9 2021-07-12T20:22:43,291 copying and adjusting bin/randomly_subsample_fastq.py -> build/scripts-3.9 2021-07-12T20:22:43,293 copying and adjusting bin/convert_blast_btab_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,294 copying and adjusting bin/write_fasta_from_gff.py -> build/scripts-3.9 2021-07-12T20:22:43,296 copying and adjusting bin/replace_gff_type_column_value.py -> build/scripts-3.9 2021-07-12T20:22:43,298 copying and adjusting bin/convert_genbank_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,300 copying and adjusting bin/get_mpilup_from_id_list.py -> build/scripts-3.9 2021-07-12T20:22:43,302 copying and adjusting bin/uniprot_sprot_to_sqlite3.py -> build/scripts-3.9 2021-07-12T20:22:43,304 copying and adjusting bin/add_polypeptide_to_gff3_gene_models.py -> build/scripts-3.9 2021-07-12T20:22:43,306 copying and adjusting bin/split_interleaved_sequence_file.py -> build/scripts-3.9 2021-07-12T20:22:43,308 copying and adjusting bin/uniref_to_sqlite3.py -> build/scripts-3.9 2021-07-12T20:22:43,310 copying and adjusting bin/compare_gene_structures.py -> build/scripts-3.9 2021-07-12T20:22:43,313 copying and adjusting bin/convert_augustus_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,316 copying and adjusting bin/reorient_sequences_by_id.py -> build/scripts-3.9 2021-07-12T20:22:43,317 copying and adjusting bin/convert_gff3_to_gbk.py -> build/scripts-3.9 2021-07-12T20:22:43,320 copying and adjusting bin/reverse_misordered_cds_coords.py -> build/scripts-3.9 2021-07-12T20:22:43,322 copying and adjusting bin/convert_prodigal_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,323 copying and adjusting bin/interleave_fastq.py -> build/scripts-3.9 2021-07-12T20:22:43,325 copying and adjusting bin/tigrfam_info_to_sqlite3.py -> build/scripts-3.9 2021-07-12T20:22:43,327 copying and adjusting bin/mark_partial_genes.py -> build/scripts-3.9 2021-07-12T20:22:43,329 copying and adjusting bin/convert_pasa_gff_to_models.py -> build/scripts-3.9 2021-07-12T20:22:43,331 copying and adjusting bin/eggnog_to_sqlite3.py -> build/scripts-3.9 2021-07-12T20:22:43,333 copying and adjusting bin/filter_uniref_by_repid.py -> build/scripts-3.9 2021-07-12T20:22:43,334 copying and adjusting bin/merge_masked_fasta_files.py -> build/scripts-3.9 2021-07-12T20:22:43,336 copying and adjusting bin/convert_glimmerHMM_gff_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,338 copying and adjusting bin/update_selected_column9_values.py -> build/scripts-3.9 2021-07-12T20:22:43,340 copying and adjusting bin/interleave_fasta.py -> build/scripts-3.9 2021-07-12T20:22:43,341 copying and adjusting bin/make_go_slim_index.py -> build/scripts-3.9 2021-07-12T20:22:43,343 copying and adjusting bin/convert_cufflinks_gtf_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,346 copying and adjusting bin/check_gff_for_internal_stops.py -> build/scripts-3.9 2021-07-12T20:22:43,347 copying and adjusting bin/replace_homopolymeric_repeats_with_Ns.py -> build/scripts-3.9 2021-07-12T20:22:43,350 copying and adjusting bin/extend_genes_to_stops.py -> build/scripts-3.9 2021-07-12T20:22:43,352 copying and adjusting bin/append_to_fastq_read_header.py -> build/scripts-3.9 2021-07-12T20:22:43,353 copying and adjusting bin/convert_metagenemark_gff_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,355 copying and adjusting bin/report_gff3_statistics.py -> build/scripts-3.9 2021-07-12T20:22:43,357 copying and adjusting bin/convert_fasta_contigs_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,359 copying and adjusting bin/fasta_size_distribution_plot.py -> build/scripts-3.9 2021-07-12T20:22:43,361 copying and adjusting bin/merge_bam_files.py -> build/scripts-3.9 2021-07-12T20:22:43,362 copying and adjusting bin/correct_gff3_CDS_phase_column.py -> build/scripts-3.9 2021-07-12T20:22:43,364 copying and adjusting bin/biothings_coordinate_comparisons.py -> build/scripts-3.9 2021-07-12T20:22:43,366 copying and adjusting bin/prepend_to_fasta_header.py -> build/scripts-3.9 2021-07-12T20:22:43,367 copying and adjusting bin/split_isoforms_into_individual_genes.py -> build/scripts-3.9 2021-07-12T20:22:43,369 copying and adjusting bin/report_gff_intron_and_intergenic_stats.py -> build/scripts-3.9 2021-07-12T20:22:43,372 copying and adjusting bin/merge_fasta_files_and_uniquify_ids.py -> build/scripts-3.9 2021-07-12T20:22:43,373 copying and adjusting bin/subsample_fasta.py -> build/scripts-3.9 2021-07-12T20:22:43,375 copying and adjusting bin/convert_cegma_gff_to_gff3.py -> build/scripts-3.9 2021-07-12T20:22:43,377 copying and adjusting bin/detect_inverted_repeats.py -> build/scripts-3.9 2021-07-12T20:22:43,379 copying and adjusting bin/create_taxonomic_profile_from_blast.py -> build/scripts-3.9 2021-07-12T20:22:43,381 copying and adjusting bin/reformat_fasta_residue_lengths.py -> build/scripts-3.9 2021-07-12T20:22:43,383 copying and adjusting bin/select_training_and_evaluation_transcripts.py -> build/scripts-3.9 2021-07-12T20:22:43,385 copying and adjusting bin/append_to_fasta_header.py -> build/scripts-3.9 2021-07-12T20:22:43,386 copying and adjusting bin/calculate_query_coverage_by_blast.py -> build/scripts-3.9 2021-07-12T20:22:43,389 copying and adjusting bin/validate_uniref_member_characterization.py -> build/scripts-3.9 2021-07-12T20:22:43,391 copying and adjusting bin/convert_gff3_to_ncbi_tbl.py -> build/scripts-3.9 2021-07-12T20:22:43,393 copying and adjusting bin/filter_fasta_by_type.py -> build/scripts-3.9 2021-07-12T20:22:43,394 copying and adjusting bin/remove_orphaned_features.py -> build/scripts-3.9 2021-07-12T20:22:43,396 copying and adjusting bin/create_rsem_html_table.py -> build/scripts-3.9 2021-07-12T20:22:43,397 copying and adjusting bin/filter_uniref_by_taxonomy.py -> build/scripts-3.9 2021-07-12T20:22:43,399 copying and adjusting bin/set_source_column.py -> build/scripts-3.9 2021-07-12T20:22:43,401 copying and adjusting bin/fasta_base_content.py -> build/scripts-3.9 2021-07-12T20:22:43,403 copying and adjusting bin/check_for_embedded_fasta_headers.py -> build/scripts-3.9 2021-07-12T20:22:43,404 copying and adjusting bin/fastq_simple_stats.py -> build/scripts-3.9 2021-07-12T20:22:43,406 copying and adjusting bin/append_to_column_9_value.py -> build/scripts-3.9 2021-07-12T20:22:43,407 changing mode of build/scripts-3.9/filter_fastq_by_N_content.py from 644 to 755 2021-07-12T20:22:43,408 changing mode of build/scripts-3.9/convert_fastq_to_fasta.py from 644 to 755 2021-07-12T20:22:43,408 changing mode of build/scripts-3.9/validate_fasta.py from 644 to 755 2021-07-12T20:22:43,408 changing mode of build/scripts-3.9/filter_fasta_by_header_regex.py from 644 to 755 2021-07-12T20:22:43,409 changing mode of build/scripts-3.9/add_gff3_locus_tags.py from 644 to 755 2021-07-12T20:22:43,409 changing mode of build/scripts-3.9/split_molecules_on_gaps.py from 644 to 755 2021-07-12T20:22:43,409 changing mode of build/scripts-3.9/convert_gff3_to_gene_association_format.py from 644 to 755 2021-07-12T20:22:43,409 changing mode of build/scripts-3.9/extract_fasta_regions.py from 644 to 755 2021-07-12T20:22:43,410 changing mode of build/scripts-3.9/hmmlib_to_sqlite3.py from 644 to 755 2021-07-12T20:22:43,410 changing mode of build/scripts-3.9/convert_scipio_gff_to_gff3.py from 644 to 755 2021-07-12T20:22:43,410 changing mode of build/scripts-3.9/report_coverage_gaps.py from 644 to 755 2021-07-12T20:22:43,411 changing mode of build/scripts-3.9/remove_masked_gene_models.py from 644 to 755 2021-07-12T20:22:43,411 changing mode of build/scripts-3.9/remove_duplicate_sequences.py from 644 to 755 2021-07-12T20:22:43,411 changing mode of build/scripts-3.9/create_taxonomy_db.py from 644 to 755 2021-07-12T20:22:43,412 changing mode of build/scripts-3.9/merge_predicted_gff3.py from 644 to 755 2021-07-12T20:22:43,412 changing mode of build/scripts-3.9/report_or_replace_nonstandard_residues.py from 644 to 755 2021-07-12T20:22:43,412 changing mode of build/scripts-3.9/convert_aat_btab_to_gff3.py from 644 to 755 2021-07-12T20:22:43,412 changing mode of build/scripts-3.9/make_go_slim.py from 644 to 755 2021-07-12T20:22:43,413 changing mode of build/scripts-3.9/validate_feature_boundaries_on_molecules.py from 644 to 755 2021-07-12T20:22:43,413 changing mode of build/scripts-3.9/report_basic_gff_model_agreement.py from 644 to 755 2021-07-12T20:22:43,413 changing mode of build/scripts-3.9/make_cufflinks_ids_unique.py from 644 to 755 2021-07-12T20:22:43,413 changing mode of build/scripts-3.9/split_fasta_into_even_files.py from 644 to 755 2021-07-12T20:22:43,414 changing mode of build/scripts-3.9/remove_duplicate_features.py from 644 to 755 2021-07-12T20:22:43,414 changing mode of build/scripts-3.9/filter_gff3_by_id_list.py from 644 to 755 2021-07-12T20:22:43,414 changing mode of build/scripts-3.9/randomly_subsample_fastq.py from 644 to 755 2021-07-12T20:22:43,415 changing mode of build/scripts-3.9/convert_blast_btab_to_gff3.py from 644 to 755 2021-07-12T20:22:43,415 changing mode of build/scripts-3.9/write_fasta_from_gff.py from 644 to 755 2021-07-12T20:22:43,415 changing mode of build/scripts-3.9/replace_gff_type_column_value.py from 644 to 755 2021-07-12T20:22:43,415 changing mode of build/scripts-3.9/convert_genbank_to_gff3.py from 644 to 755 2021-07-12T20:22:43,416 changing mode of build/scripts-3.9/get_mpilup_from_id_list.py from 644 to 755 2021-07-12T20:22:43,416 changing mode of build/scripts-3.9/uniprot_sprot_to_sqlite3.py from 644 to 755 2021-07-12T20:22:43,416 changing mode of build/scripts-3.9/add_polypeptide_to_gff3_gene_models.py from 644 to 755 2021-07-12T20:22:43,417 changing mode of build/scripts-3.9/split_interleaved_sequence_file.py from 644 to 755 2021-07-12T20:22:43,417 changing mode of build/scripts-3.9/uniref_to_sqlite3.py from 644 to 755 2021-07-12T20:22:43,417 changing mode of build/scripts-3.9/compare_gene_structures.py from 644 to 755 2021-07-12T20:22:43,417 changing mode of build/scripts-3.9/convert_augustus_to_gff3.py from 644 to 755 2021-07-12T20:22:43,418 changing mode of build/scripts-3.9/reorient_sequences_by_id.py from 644 to 755 2021-07-12T20:22:43,419 changing mode of build/scripts-3.9/convert_gff3_to_gbk.py from 644 to 755 2021-07-12T20:22:43,419 changing mode of build/scripts-3.9/reverse_misordered_cds_coords.py from 644 to 755 2021-07-12T20:22:43,419 changing mode of build/scripts-3.9/convert_prodigal_to_gff3.py from 644 to 755 2021-07-12T20:22:43,419 changing mode of build/scripts-3.9/interleave_fastq.py from 644 to 755 2021-07-12T20:22:43,420 changing mode of build/scripts-3.9/tigrfam_info_to_sqlite3.py from 644 to 755 2021-07-12T20:22:43,420 changing mode of build/scripts-3.9/mark_partial_genes.py from 644 to 755 2021-07-12T20:22:43,420 changing mode of build/scripts-3.9/convert_pasa_gff_to_models.py from 644 to 755 2021-07-12T20:22:43,420 changing mode of build/scripts-3.9/eggnog_to_sqlite3.py from 644 to 755 2021-07-12T20:22:43,421 changing mode of build/scripts-3.9/filter_uniref_by_repid.py from 644 to 755 2021-07-12T20:22:43,421 changing mode of build/scripts-3.9/merge_masked_fasta_files.py from 644 to 755 2021-07-12T20:22:43,421 changing mode of build/scripts-3.9/convert_glimmerHMM_gff_to_gff3.py from 644 to 755 2021-07-12T20:22:43,422 changing mode of build/scripts-3.9/update_selected_column9_values.py from 644 to 755 2021-07-12T20:22:43,422 changing mode of build/scripts-3.9/interleave_fasta.py from 644 to 755 2021-07-12T20:22:43,422 changing mode of build/scripts-3.9/make_go_slim_index.py from 644 to 755 2021-07-12T20:22:43,422 changing mode of build/scripts-3.9/convert_cufflinks_gtf_to_gff3.py from 644 to 755 2021-07-12T20:22:43,423 changing mode of build/scripts-3.9/check_gff_for_internal_stops.py from 644 to 755 2021-07-12T20:22:43,423 changing mode of build/scripts-3.9/replace_homopolymeric_repeats_with_Ns.py from 644 to 755 2021-07-12T20:22:43,423 changing mode of build/scripts-3.9/extend_genes_to_stops.py from 644 to 755 2021-07-12T20:22:43,424 changing mode of build/scripts-3.9/append_to_fastq_read_header.py from 644 to 755 2021-07-12T20:22:43,424 changing mode of build/scripts-3.9/convert_metagenemark_gff_to_gff3.py from 644 to 755 2021-07-12T20:22:43,424 changing mode of build/scripts-3.9/report_gff3_statistics.py from 644 to 755 2021-07-12T20:22:43,424 changing mode of build/scripts-3.9/convert_fasta_contigs_to_gff3.py from 644 to 755 2021-07-12T20:22:43,425 changing mode of build/scripts-3.9/fasta_size_distribution_plot.py from 644 to 755 2021-07-12T20:22:43,425 changing mode of build/scripts-3.9/merge_bam_files.py from 644 to 755 2021-07-12T20:22:43,425 changing mode of build/scripts-3.9/correct_gff3_CDS_phase_column.py from 644 to 755 2021-07-12T20:22:43,425 changing mode of build/scripts-3.9/biothings_coordinate_comparisons.py from 644 to 755 2021-07-12T20:22:43,426 changing mode of build/scripts-3.9/prepend_to_fasta_header.py from 644 to 755 2021-07-12T20:22:43,426 changing mode of build/scripts-3.9/split_isoforms_into_individual_genes.py from 644 to 755 2021-07-12T20:22:43,426 changing mode of build/scripts-3.9/report_gff_intron_and_intergenic_stats.py from 644 to 755 2021-07-12T20:22:43,426 changing mode of build/scripts-3.9/merge_fasta_files_and_uniquify_ids.py from 644 to 755 2021-07-12T20:22:43,426 changing mode of build/scripts-3.9/subsample_fasta.py from 644 to 755 2021-07-12T20:22:43,427 changing mode of build/scripts-3.9/convert_cegma_gff_to_gff3.py from 644 to 755 2021-07-12T20:22:43,427 changing mode of build/scripts-3.9/detect_inverted_repeats.py from 644 to 755 2021-07-12T20:22:43,427 changing mode of build/scripts-3.9/create_taxonomic_profile_from_blast.py from 644 to 755 2021-07-12T20:22:43,427 changing mode of build/scripts-3.9/reformat_fasta_residue_lengths.py from 644 to 755 2021-07-12T20:22:43,428 changing mode of build/scripts-3.9/select_training_and_evaluation_transcripts.py from 644 to 755 2021-07-12T20:22:43,428 changing mode of build/scripts-3.9/append_to_fasta_header.py from 644 to 755 2021-07-12T20:22:43,428 changing mode of build/scripts-3.9/calculate_query_coverage_by_blast.py from 644 to 755 2021-07-12T20:22:43,428 changing mode of build/scripts-3.9/validate_uniref_member_characterization.py from 644 to 755 2021-07-12T20:22:43,428 changing mode of build/scripts-3.9/convert_gff3_to_ncbi_tbl.py from 644 to 755 2021-07-12T20:22:43,429 changing mode of build/scripts-3.9/filter_fasta_by_type.py from 644 to 755 2021-07-12T20:22:43,429 changing mode of build/scripts-3.9/remove_orphaned_features.py from 644 to 755 2021-07-12T20:22:43,429 changing mode of build/scripts-3.9/create_rsem_html_table.py from 644 to 755 2021-07-12T20:22:43,429 changing mode of build/scripts-3.9/filter_uniref_by_taxonomy.py from 644 to 755 2021-07-12T20:22:43,430 changing mode of build/scripts-3.9/set_source_column.py from 644 to 755 2021-07-12T20:22:43,430 changing mode of build/scripts-3.9/fasta_base_content.py from 644 to 755 2021-07-12T20:22:43,430 changing mode of build/scripts-3.9/check_for_embedded_fasta_headers.py from 644 to 755 2021-07-12T20:22:43,430 changing mode of build/scripts-3.9/fastq_simple_stats.py from 644 to 755 2021-07-12T20:22:43,431 changing mode of build/scripts-3.9/append_to_column_9_value.py from 644 to 755 2021-07-12T20:22:43,437 installing to build/bdist.linux-armv7l/wheel 2021-07-12T20:22:43,437 running install 2021-07-12T20:22:43,438 running install_lib 2021-07-12T20:22:43,442 creating build/bdist.linux-armv7l 2021-07-12T20:22:43,442 creating build/bdist.linux-armv7l/wheel 2021-07-12T20:22:43,444 creating build/bdist.linux-armv7l/wheel/biocode 2021-07-12T20:22:43,445 copying build/lib/biocode/annotation.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T20:22:43,448 copying build/lib/biocode/tbl.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T20:22:43,451 creating build/bdist.linux-armv7l/wheel/biocode/data 2021-07-12T20:22:43,452 copying build/lib/biocode/data/genbank_flat_file_header.template -> build/bdist.linux-armv7l/wheel/biocode/data 2021-07-12T20:22:43,454 copying build/lib/biocode/data/HMPslim.v2.1.obo -> build/bdist.linux-armv7l/wheel/biocode/data 2021-07-12T20:22:43,458 copying build/lib/biocode/data/rsem_html_table.template -> build/bdist.linux-armv7l/wheel/biocode/data 2021-07-12T20:22:43,461 copying build/lib/biocode/data/__init__.py -> build/bdist.linux-armv7l/wheel/biocode/data 2021-07-12T20:22:43,462 copying build/lib/biocode/utils.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T20:22:43,465 copying build/lib/biocode/gff.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T20:22:43,468 copying build/lib/biocode/__init__.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T20:22:43,470 copying build/lib/biocode/genbank.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T20:22:43,472 copying build/lib/biocode/things.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T20:22:43,476 running install_egg_info 2021-07-12T20:22:43,485 Copying biocode.egg-info to build/bdist.linux-armv7l/wheel/biocode-0.5.0-py3.9.egg-info 2021-07-12T20:22:43,498 running install_scripts 2021-07-12T20:22:43,530 creating build/bdist.linux-armv7l/wheel/biocode-0.5.0.data 2021-07-12T20:22:43,530 creating build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,531 copying build/scripts-3.9/make_go_slim_index.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,533 copying build/scripts-3.9/prepend_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,535 copying build/scripts-3.9/filter_fasta_by_type.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,537 copying build/scripts-3.9/write_fasta_from_gff.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,539 copying build/scripts-3.9/make_cufflinks_ids_unique.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,541 copying build/scripts-3.9/randomly_subsample_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,543 copying build/scripts-3.9/interleave_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,546 copying build/scripts-3.9/convert_augustus_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,548 copying build/scripts-3.9/filter_uniref_by_repid.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,550 copying build/scripts-3.9/update_selected_column9_values.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,552 copying build/scripts-3.9/replace_gff_type_column_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,554 copying build/scripts-3.9/tigrfam_info_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,557 copying build/scripts-3.9/create_taxonomic_profile_from_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,560 copying build/scripts-3.9/remove_duplicate_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,562 copying build/scripts-3.9/convert_glimmerHMM_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,564 copying build/scripts-3.9/reorient_sequences_by_id.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,566 copying build/scripts-3.9/convert_fastq_to_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,568 copying build/scripts-3.9/remove_masked_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,570 copying build/scripts-3.9/convert_cufflinks_gtf_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,573 copying build/scripts-3.9/convert_scipio_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,576 copying build/scripts-3.9/append_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,578 copying build/scripts-3.9/add_gff3_locus_tags.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,581 copying build/scripts-3.9/filter_fasta_by_header_regex.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,583 copying build/scripts-3.9/calculate_query_coverage_by_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,586 copying build/scripts-3.9/set_source_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,587 copying build/scripts-3.9/select_training_and_evaluation_transcripts.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,590 copying build/scripts-3.9/convert_blast_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,593 copying build/scripts-3.9/hmmlib_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,595 copying build/scripts-3.9/filter_fastq_by_N_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,598 copying build/scripts-3.9/merge_predicted_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,601 copying build/scripts-3.9/convert_genbank_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,604 copying build/scripts-3.9/convert_fasta_contigs_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,606 copying build/scripts-3.9/eggnog_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,608 copying build/scripts-3.9/mark_partial_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,611 copying build/scripts-3.9/report_basic_gff_model_agreement.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,613 copying build/scripts-3.9/append_to_column_9_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,614 copying build/scripts-3.9/report_gff_intron_and_intergenic_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,617 copying build/scripts-3.9/reformat_fasta_residue_lengths.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,619 copying build/scripts-3.9/check_for_embedded_fasta_headers.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,621 copying build/scripts-3.9/report_or_replace_nonstandard_residues.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,623 copying build/scripts-3.9/create_taxonomy_db.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,626 copying build/scripts-3.9/filter_uniref_by_taxonomy.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,628 copying build/scripts-3.9/convert_metagenemark_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,631 copying build/scripts-3.9/compare_gene_structures.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,634 copying build/scripts-3.9/replace_homopolymeric_repeats_with_Ns.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,636 copying build/scripts-3.9/extract_fasta_regions.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,638 copying build/scripts-3.9/validate_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,640 copying build/scripts-3.9/split_isoforms_into_individual_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,642 copying build/scripts-3.9/uniprot_sprot_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,644 copying build/scripts-3.9/check_gff_for_internal_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,646 copying build/scripts-3.9/report_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,649 copying build/scripts-3.9/convert_pasa_gff_to_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,651 copying build/scripts-3.9/validate_uniref_member_characterization.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,653 copying build/scripts-3.9/merge_masked_fasta_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,655 copying build/scripts-3.9/convert_aat_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,658 copying build/scripts-3.9/extend_genes_to_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,660 copying build/scripts-3.9/create_rsem_html_table.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,662 copying build/scripts-3.9/split_interleaved_sequence_file.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,664 copying build/scripts-3.9/split_molecules_on_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,666 copying build/scripts-3.9/append_to_fastq_read_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,669 copying build/scripts-3.9/convert_gff3_to_gbk.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,671 copying build/scripts-3.9/detect_inverted_repeats.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,673 copying build/scripts-3.9/biothings_coordinate_comparisons.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,675 copying build/scripts-3.9/convert_cegma_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,677 copying build/scripts-3.9/get_mpilup_from_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,679 copying build/scripts-3.9/interleave_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,681 copying build/scripts-3.9/remove_duplicate_sequences.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,683 copying build/scripts-3.9/split_fasta_into_even_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,685 copying build/scripts-3.9/correct_gff3_CDS_phase_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,687 copying build/scripts-3.9/merge_bam_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,689 copying build/scripts-3.9/fastq_simple_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,691 copying build/scripts-3.9/merge_fasta_files_and_uniquify_ids.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,693 copying build/scripts-3.9/convert_gff3_to_gene_association_format.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,696 copying build/scripts-3.9/convert_gff3_to_ncbi_tbl.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,698 copying build/scripts-3.9/reverse_misordered_cds_coords.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,700 copying build/scripts-3.9/remove_orphaned_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,702 copying build/scripts-3.9/fasta_base_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,704 copying build/scripts-3.9/make_go_slim.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,707 copying build/scripts-3.9/fasta_size_distribution_plot.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,709 copying build/scripts-3.9/report_gff3_statistics.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,711 copying build/scripts-3.9/uniref_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,714 copying build/scripts-3.9/validate_feature_boundaries_on_molecules.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,716 copying build/scripts-3.9/filter_gff3_by_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,719 copying build/scripts-3.9/subsample_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,721 copying build/scripts-3.9/add_polypeptide_to_gff3_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,723 copying build/scripts-3.9/convert_prodigal_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts 2021-07-12T20:22:43,725 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/make_go_slim_index.py to 755 2021-07-12T20:22:43,725 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/prepend_to_fasta_header.py to 755 2021-07-12T20:22:43,725 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/filter_fasta_by_type.py to 755 2021-07-12T20:22:43,726 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/write_fasta_from_gff.py to 755 2021-07-12T20:22:43,726 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/make_cufflinks_ids_unique.py to 755 2021-07-12T20:22:43,726 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/randomly_subsample_fastq.py to 755 2021-07-12T20:22:43,727 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/interleave_fastq.py to 755 2021-07-12T20:22:43,727 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_augustus_to_gff3.py to 755 2021-07-12T20:22:43,727 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/filter_uniref_by_repid.py to 755 2021-07-12T20:22:43,727 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/update_selected_column9_values.py to 755 2021-07-12T20:22:43,728 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/replace_gff_type_column_value.py to 755 2021-07-12T20:22:43,728 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/tigrfam_info_to_sqlite3.py to 755 2021-07-12T20:22:43,728 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/create_taxonomic_profile_from_blast.py to 755 2021-07-12T20:22:43,729 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/remove_duplicate_features.py to 755 2021-07-12T20:22:43,729 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_glimmerHMM_gff_to_gff3.py to 755 2021-07-12T20:22:43,729 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/reorient_sequences_by_id.py to 755 2021-07-12T20:22:43,729 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_fastq_to_fasta.py to 755 2021-07-12T20:22:43,730 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/remove_masked_gene_models.py to 755 2021-07-12T20:22:43,730 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_cufflinks_gtf_to_gff3.py to 755 2021-07-12T20:22:43,730 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_scipio_gff_to_gff3.py to 755 2021-07-12T20:22:43,731 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/append_to_fasta_header.py to 755 2021-07-12T20:22:43,731 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/add_gff3_locus_tags.py to 755 2021-07-12T20:22:43,731 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/filter_fasta_by_header_regex.py to 755 2021-07-12T20:22:43,731 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/calculate_query_coverage_by_blast.py to 755 2021-07-12T20:22:43,732 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/set_source_column.py to 755 2021-07-12T20:22:43,732 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/select_training_and_evaluation_transcripts.py to 755 2021-07-12T20:22:43,732 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_blast_btab_to_gff3.py to 755 2021-07-12T20:22:43,732 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/hmmlib_to_sqlite3.py to 755 2021-07-12T20:22:43,733 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/filter_fastq_by_N_content.py to 755 2021-07-12T20:22:43,733 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/merge_predicted_gff3.py to 755 2021-07-12T20:22:43,733 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_genbank_to_gff3.py to 755 2021-07-12T20:22:43,733 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_fasta_contigs_to_gff3.py to 755 2021-07-12T20:22:43,734 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/eggnog_to_sqlite3.py to 755 2021-07-12T20:22:43,734 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/mark_partial_genes.py to 755 2021-07-12T20:22:43,734 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/report_basic_gff_model_agreement.py to 755 2021-07-12T20:22:43,735 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/append_to_column_9_value.py to 755 2021-07-12T20:22:43,735 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/report_gff_intron_and_intergenic_stats.py to 755 2021-07-12T20:22:43,735 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/reformat_fasta_residue_lengths.py to 755 2021-07-12T20:22:43,735 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/check_for_embedded_fasta_headers.py to 755 2021-07-12T20:22:43,736 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/report_or_replace_nonstandard_residues.py to 755 2021-07-12T20:22:43,736 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/create_taxonomy_db.py to 755 2021-07-12T20:22:43,736 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/filter_uniref_by_taxonomy.py to 755 2021-07-12T20:22:43,736 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_metagenemark_gff_to_gff3.py to 755 2021-07-12T20:22:43,737 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/compare_gene_structures.py to 755 2021-07-12T20:22:43,737 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/replace_homopolymeric_repeats_with_Ns.py to 755 2021-07-12T20:22:43,737 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/extract_fasta_regions.py to 755 2021-07-12T20:22:43,738 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/validate_fasta.py to 755 2021-07-12T20:22:43,738 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/split_isoforms_into_individual_genes.py to 755 2021-07-12T20:22:43,738 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/uniprot_sprot_to_sqlite3.py to 755 2021-07-12T20:22:43,738 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/check_gff_for_internal_stops.py to 755 2021-07-12T20:22:43,739 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/report_coverage_gaps.py to 755 2021-07-12T20:22:43,739 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_pasa_gff_to_models.py to 755 2021-07-12T20:22:43,739 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/validate_uniref_member_characterization.py to 755 2021-07-12T20:22:43,740 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/merge_masked_fasta_files.py to 755 2021-07-12T20:22:43,740 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_aat_btab_to_gff3.py to 755 2021-07-12T20:22:43,740 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/extend_genes_to_stops.py to 755 2021-07-12T20:22:43,740 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/create_rsem_html_table.py to 755 2021-07-12T20:22:43,741 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/split_interleaved_sequence_file.py to 755 2021-07-12T20:22:43,741 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/split_molecules_on_gaps.py to 755 2021-07-12T20:22:43,741 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/append_to_fastq_read_header.py to 755 2021-07-12T20:22:43,741 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_gff3_to_gbk.py to 755 2021-07-12T20:22:43,742 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/detect_inverted_repeats.py to 755 2021-07-12T20:22:43,742 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/biothings_coordinate_comparisons.py to 755 2021-07-12T20:22:43,742 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_cegma_gff_to_gff3.py to 755 2021-07-12T20:22:43,743 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/get_mpilup_from_id_list.py to 755 2021-07-12T20:22:43,743 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/interleave_fasta.py to 755 2021-07-12T20:22:43,743 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/remove_duplicate_sequences.py to 755 2021-07-12T20:22:43,743 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/split_fasta_into_even_files.py to 755 2021-07-12T20:22:43,744 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/correct_gff3_CDS_phase_column.py to 755 2021-07-12T20:22:43,744 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/merge_bam_files.py to 755 2021-07-12T20:22:43,744 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/fastq_simple_stats.py to 755 2021-07-12T20:22:43,745 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/merge_fasta_files_and_uniquify_ids.py to 755 2021-07-12T20:22:43,745 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_gff3_to_gene_association_format.py to 755 2021-07-12T20:22:43,745 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_gff3_to_ncbi_tbl.py to 755 2021-07-12T20:22:43,745 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/reverse_misordered_cds_coords.py to 755 2021-07-12T20:22:43,746 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/remove_orphaned_features.py to 755 2021-07-12T20:22:43,746 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/fasta_base_content.py to 755 2021-07-12T20:22:43,746 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/make_go_slim.py to 755 2021-07-12T20:22:43,746 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/fasta_size_distribution_plot.py to 755 2021-07-12T20:22:43,747 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/report_gff3_statistics.py to 755 2021-07-12T20:22:43,747 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/uniref_to_sqlite3.py to 755 2021-07-12T20:22:43,747 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/validate_feature_boundaries_on_molecules.py to 755 2021-07-12T20:22:43,748 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/filter_gff3_by_id_list.py to 755 2021-07-12T20:22:43,748 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/subsample_fasta.py to 755 2021-07-12T20:22:43,748 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/add_polypeptide_to_gff3_gene_models.py to 755 2021-07-12T20:22:43,749 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.0.data/scripts/convert_prodigal_to_gff3.py to 755 2021-07-12T20:22:43,766 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-12T20:22:43,770 creating build/bdist.linux-armv7l/wheel/biocode-0.5.0.dist-info/WHEEL 2021-07-12T20:22:43,772 creating '/tmp/pip-wheel-xtar7vo9/biocode-0.5.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-12T20:22:43,775 adding 'biocode/__init__.py' 2021-07-12T20:22:43,778 adding 'biocode/annotation.py' 2021-07-12T20:22:43,780 adding 'biocode/genbank.py' 2021-07-12T20:22:43,784 adding 'biocode/gff.py' 2021-07-12T20:22:43,786 adding 'biocode/tbl.py' 2021-07-12T20:22:43,794 adding 'biocode/things.py' 2021-07-12T20:22:43,796 adding 'biocode/utils.py' 2021-07-12T20:22:43,802 adding 'biocode/data/HMPslim.v2.1.obo' 2021-07-12T20:22:43,803 adding 'biocode/data/__init__.py' 2021-07-12T20:22:43,804 adding 'biocode/data/genbank_flat_file_header.template' 2021-07-12T20:22:43,806 adding 'biocode/data/rsem_html_table.template' 2021-07-12T20:22:43,811 adding 'biocode-0.5.0.data/scripts/add_gff3_locus_tags.py' 2021-07-12T20:22:43,813 adding 'biocode-0.5.0.data/scripts/add_polypeptide_to_gff3_gene_models.py' 2021-07-12T20:22:43,814 adding 'biocode-0.5.0.data/scripts/append_to_column_9_value.py' 2021-07-12T20:22:43,815 adding 'biocode-0.5.0.data/scripts/append_to_fasta_header.py' 2021-07-12T20:22:43,817 adding 'biocode-0.5.0.data/scripts/append_to_fastq_read_header.py' 2021-07-12T20:22:43,818 adding 'biocode-0.5.0.data/scripts/biothings_coordinate_comparisons.py' 2021-07-12T20:22:43,819 adding 'biocode-0.5.0.data/scripts/calculate_query_coverage_by_blast.py' 2021-07-12T20:22:43,821 adding 'biocode-0.5.0.data/scripts/check_for_embedded_fasta_headers.py' 2021-07-12T20:22:43,822 adding 'biocode-0.5.0.data/scripts/check_gff_for_internal_stops.py' 2021-07-12T20:22:43,825 adding 'biocode-0.5.0.data/scripts/compare_gene_structures.py' 2021-07-12T20:22:43,827 adding 'biocode-0.5.0.data/scripts/convert_aat_btab_to_gff3.py' 2021-07-12T20:22:43,829 adding 'biocode-0.5.0.data/scripts/convert_augustus_to_gff3.py' 2021-07-12T20:22:43,831 adding 'biocode-0.5.0.data/scripts/convert_blast_btab_to_gff3.py' 2021-07-12T20:22:43,833 adding 'biocode-0.5.0.data/scripts/convert_cegma_gff_to_gff3.py' 2021-07-12T20:22:43,834 adding 'biocode-0.5.0.data/scripts/convert_cufflinks_gtf_to_gff3.py' 2021-07-12T20:22:43,836 adding 'biocode-0.5.0.data/scripts/convert_fasta_contigs_to_gff3.py' 2021-07-12T20:22:43,837 adding 'biocode-0.5.0.data/scripts/convert_fastq_to_fasta.py' 2021-07-12T20:22:43,839 adding 'biocode-0.5.0.data/scripts/convert_genbank_to_gff3.py' 2021-07-12T20:22:43,840 adding 'biocode-0.5.0.data/scripts/convert_gff3_to_gbk.py' 2021-07-12T20:22:43,842 adding 'biocode-0.5.0.data/scripts/convert_gff3_to_gene_association_format.py' 2021-07-12T20:22:43,843 adding 'biocode-0.5.0.data/scripts/convert_gff3_to_ncbi_tbl.py' 2021-07-12T20:22:43,845 adding 'biocode-0.5.0.data/scripts/convert_glimmerHMM_gff_to_gff3.py' 2021-07-12T20:22:43,846 adding 'biocode-0.5.0.data/scripts/convert_metagenemark_gff_to_gff3.py' 2021-07-12T20:22:43,848 adding 'biocode-0.5.0.data/scripts/convert_pasa_gff_to_models.py' 2021-07-12T20:22:43,849 adding 'biocode-0.5.0.data/scripts/convert_prodigal_to_gff3.py' 2021-07-12T20:22:43,851 adding 'biocode-0.5.0.data/scripts/convert_scipio_gff_to_gff3.py' 2021-07-12T20:22:43,852 adding 'biocode-0.5.0.data/scripts/correct_gff3_CDS_phase_column.py' 2021-07-12T20:22:43,853 adding 'biocode-0.5.0.data/scripts/create_rsem_html_table.py' 2021-07-12T20:22:43,855 adding 'biocode-0.5.0.data/scripts/create_taxonomic_profile_from_blast.py' 2021-07-12T20:22:43,857 adding 'biocode-0.5.0.data/scripts/create_taxonomy_db.py' 2021-07-12T20:22:43,859 adding 'biocode-0.5.0.data/scripts/detect_inverted_repeats.py' 2021-07-12T20:22:43,860 adding 'biocode-0.5.0.data/scripts/eggnog_to_sqlite3.py' 2021-07-12T20:22:43,862 adding 'biocode-0.5.0.data/scripts/extend_genes_to_stops.py' 2021-07-12T20:22:43,863 adding 'biocode-0.5.0.data/scripts/extract_fasta_regions.py' 2021-07-12T20:22:43,865 adding 'biocode-0.5.0.data/scripts/fasta_base_content.py' 2021-07-12T20:22:43,866 adding 'biocode-0.5.0.data/scripts/fasta_size_distribution_plot.py' 2021-07-12T20:22:43,867 adding 'biocode-0.5.0.data/scripts/fastq_simple_stats.py' 2021-07-12T20:22:43,869 adding 'biocode-0.5.0.data/scripts/filter_fasta_by_header_regex.py' 2021-07-12T20:22:43,870 adding 'biocode-0.5.0.data/scripts/filter_fasta_by_type.py' 2021-07-12T20:22:43,872 adding 'biocode-0.5.0.data/scripts/filter_fastq_by_N_content.py' 2021-07-12T20:22:43,873 adding 'biocode-0.5.0.data/scripts/filter_gff3_by_id_list.py' 2021-07-12T20:22:43,874 adding 'biocode-0.5.0.data/scripts/filter_uniref_by_repid.py' 2021-07-12T20:22:43,876 adding 'biocode-0.5.0.data/scripts/filter_uniref_by_taxonomy.py' 2021-07-12T20:22:43,877 adding 'biocode-0.5.0.data/scripts/get_mpilup_from_id_list.py' 2021-07-12T20:22:43,879 adding 'biocode-0.5.0.data/scripts/hmmlib_to_sqlite3.py' 2021-07-12T20:22:43,880 adding 'biocode-0.5.0.data/scripts/interleave_fasta.py' 2021-07-12T20:22:43,882 adding 'biocode-0.5.0.data/scripts/interleave_fastq.py' 2021-07-12T20:22:43,883 adding 'biocode-0.5.0.data/scripts/make_cufflinks_ids_unique.py' 2021-07-12T20:22:43,884 adding 'biocode-0.5.0.data/scripts/make_go_slim.py' 2021-07-12T20:22:43,886 adding 'biocode-0.5.0.data/scripts/make_go_slim_index.py' 2021-07-12T20:22:43,888 adding 'biocode-0.5.0.data/scripts/mark_partial_genes.py' 2021-07-12T20:22:43,889 adding 'biocode-0.5.0.data/scripts/merge_bam_files.py' 2021-07-12T20:22:43,891 adding 'biocode-0.5.0.data/scripts/merge_fasta_files_and_uniquify_ids.py' 2021-07-12T20:22:43,892 adding 'biocode-0.5.0.data/scripts/merge_masked_fasta_files.py' 2021-07-12T20:22:43,893 adding 'biocode-0.5.0.data/scripts/merge_predicted_gff3.py' 2021-07-12T20:22:43,895 adding 'biocode-0.5.0.data/scripts/prepend_to_fasta_header.py' 2021-07-12T20:22:43,896 adding 'biocode-0.5.0.data/scripts/randomly_subsample_fastq.py' 2021-07-12T20:22:43,898 adding 'biocode-0.5.0.data/scripts/reformat_fasta_residue_lengths.py' 2021-07-12T20:22:43,899 adding 'biocode-0.5.0.data/scripts/remove_duplicate_features.py' 2021-07-12T20:22:43,900 adding 'biocode-0.5.0.data/scripts/remove_duplicate_sequences.py' 2021-07-12T20:22:43,901 adding 'biocode-0.5.0.data/scripts/remove_masked_gene_models.py' 2021-07-12T20:22:43,903 adding 'biocode-0.5.0.data/scripts/remove_orphaned_features.py' 2021-07-12T20:22:43,904 adding 'biocode-0.5.0.data/scripts/reorient_sequences_by_id.py' 2021-07-12T20:22:43,905 adding 'biocode-0.5.0.data/scripts/replace_gff_type_column_value.py' 2021-07-12T20:22:43,907 adding 'biocode-0.5.0.data/scripts/replace_homopolymeric_repeats_with_Ns.py' 2021-07-12T20:22:43,908 adding 'biocode-0.5.0.data/scripts/report_basic_gff_model_agreement.py' 2021-07-12T20:22:43,909 adding 'biocode-0.5.0.data/scripts/report_coverage_gaps.py' 2021-07-12T20:22:43,911 adding 'biocode-0.5.0.data/scripts/report_gff3_statistics.py' 2021-07-12T20:22:43,913 adding 'biocode-0.5.0.data/scripts/report_gff_intron_and_intergenic_stats.py' 2021-07-12T20:22:43,914 adding 'biocode-0.5.0.data/scripts/report_or_replace_nonstandard_residues.py' 2021-07-12T20:22:43,915 adding 'biocode-0.5.0.data/scripts/reverse_misordered_cds_coords.py' 2021-07-12T20:22:43,917 adding 'biocode-0.5.0.data/scripts/select_training_and_evaluation_transcripts.py' 2021-07-12T20:22:43,918 adding 'biocode-0.5.0.data/scripts/set_source_column.py' 2021-07-12T20:22:43,920 adding 'biocode-0.5.0.data/scripts/split_fasta_into_even_files.py' 2021-07-12T20:22:43,921 adding 'biocode-0.5.0.data/scripts/split_interleaved_sequence_file.py' 2021-07-12T20:22:43,922 adding 'biocode-0.5.0.data/scripts/split_isoforms_into_individual_genes.py' 2021-07-12T20:22:43,924 adding 'biocode-0.5.0.data/scripts/split_molecules_on_gaps.py' 2021-07-12T20:22:43,925 adding 'biocode-0.5.0.data/scripts/subsample_fasta.py' 2021-07-12T20:22:43,927 adding 'biocode-0.5.0.data/scripts/tigrfam_info_to_sqlite3.py' 2021-07-12T20:22:43,928 adding 'biocode-0.5.0.data/scripts/uniprot_sprot_to_sqlite3.py' 2021-07-12T20:22:43,930 adding 'biocode-0.5.0.data/scripts/uniref_to_sqlite3.py' 2021-07-12T20:22:43,931 adding 'biocode-0.5.0.data/scripts/update_selected_column9_values.py' 2021-07-12T20:22:43,933 adding 'biocode-0.5.0.data/scripts/validate_fasta.py' 2021-07-12T20:22:43,934 adding 'biocode-0.5.0.data/scripts/validate_feature_boundaries_on_molecules.py' 2021-07-12T20:22:43,936 adding 'biocode-0.5.0.data/scripts/validate_uniref_member_characterization.py' 2021-07-12T20:22:43,937 adding 'biocode-0.5.0.data/scripts/write_fasta_from_gff.py' 2021-07-12T20:22:43,940 adding 'biocode-0.5.0.dist-info/LICENSE' 2021-07-12T20:22:43,941 adding 'biocode-0.5.0.dist-info/METADATA' 2021-07-12T20:22:43,941 adding 'biocode-0.5.0.dist-info/WHEEL' 2021-07-12T20:22:43,942 adding 'biocode-0.5.0.dist-info/top_level.txt' 2021-07-12T20:22:43,944 adding 'biocode-0.5.0.dist-info/RECORD' 2021-07-12T20:22:43,951 removing build/bdist.linux-armv7l/wheel 2021-07-12T20:22:44,067 Building wheel for biocode (setup.py): finished with status 'done' 2021-07-12T20:22:44,072 Created wheel for biocode: filename=biocode-0.5.0-py3-none-any.whl size=218338 sha256=6ce7d47e815c46602fb4ba8a8764d62c5f26910a6c168c63956baf4983f90a45 2021-07-12T20:22:44,073 Stored in directory: /tmp/pip-ephem-wheel-cache-o4se4tse/wheels/d8/df/30/75fa9b1dcb1f2ecfccdfb0aae7735666a2cfa3ca2075341b53 2021-07-12T20:22:44,085 Successfully built biocode 2021-07-12T20:22:44,095 Removed build tracker: '/tmp/pip-req-tracker-cotnvfq3'