2021-07-12T21:23:50,832 Created temporary directory: /tmp/pip-ephem-wheel-cache-mtzsifla 2021-07-12T21:23:50,836 Created temporary directory: /tmp/pip-req-tracker-y37bifh6 2021-07-12T21:23:50,836 Initialized build tracking at /tmp/pip-req-tracker-y37bifh6 2021-07-12T21:23:50,836 Created build tracker: /tmp/pip-req-tracker-y37bifh6 2021-07-12T21:23:50,836 Entered build tracker: /tmp/pip-req-tracker-y37bifh6 2021-07-12T21:23:50,837 Created temporary directory: /tmp/pip-wheel-c2eqo9kj 2021-07-12T21:23:50,868 1 location(s) to search for versions of biocode: 2021-07-12T21:23:50,868 * https://pypi.org/simple/biocode/ 2021-07-12T21:23:50,869 Fetching project page and analyzing links: https://pypi.org/simple/biocode/ 2021-07-12T21:23:50,869 Getting page https://pypi.org/simple/biocode/ 2021-07-12T21:23:50,871 Found index url https://pypi.org/simple 2021-07-12T21:23:50,972 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 2021-07-12T21:23:50,972 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 2021-07-12T21:23:50,972 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 2021-07-12T21:23:50,973 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 2021-07-12T21:23:50,973 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 2021-07-12T21:23:50,973 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 2021-07-12T21:23:50,974 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 2021-07-12T21:23:50,974 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 2021-07-12T21:23:50,974 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 2021-07-12T21:23:50,974 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 2021-07-12T21:23:50,975 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 2021-07-12T21:23:50,975 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 2021-07-12T21:23:50,975 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 2021-07-12T21:23:50,975 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 2021-07-12T21:23:50,976 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 2021-07-12T21:23:50,976 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 2021-07-12T21:23:50,976 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 2021-07-12T21:23:50,977 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 2021-07-12T21:23:50,977 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 2021-07-12T21:23:50,977 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 2021-07-12T21:23:50,977 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 2021-07-12T21:23:50,978 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 2021-07-12T21:23:50,978 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 2021-07-12T21:23:50,978 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 2021-07-12T21:23:50,978 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 2021-07-12T21:23:50,979 Skipping link: not a file: https://pypi.org/simple/biocode/ 2021-07-12T21:23:51,000 Given no hashes to check 1 links for project 'biocode': discarding no candidates 2021-07-12T21:23:51,022 Collecting biocode==0.5.1 2021-07-12T21:23:51,023 Created temporary directory: /tmp/pip-unpack-aoakkoge 2021-07-12T21:23:51,428 Downloading biocode-0.5.1.tar.gz (163 kB) 2021-07-12T21:23:51,745 Added biocode==0.5.1 from https://files.pythonhosted.org/packages/5c/b7/035e01334320dd66ac8c65be4baa910e8cb16215c563d7b65bfdfd5b56d6/biocode-0.5.1.tar.gz#sha256=ca80071c7e495380a875714ac7cf975dc20389ab8e36f72971a59f6e5a5ac83e to build tracker '/tmp/pip-req-tracker-y37bifh6' 2021-07-12T21:23:51,746 Running setup.py (path:/tmp/pip-wheel-c2eqo9kj/biocode_3738f8db16c946c6b277d81ae4ea4537/setup.py) egg_info for package biocode 2021-07-12T21:23:51,747 Created temporary directory: /tmp/pip-pip-egg-info-0esunsbz 2021-07-12T21:23:51,748 Running command python setup.py egg_info 2021-07-12T21:23:52,795 /tmp/pip-wheel-c2eqo9kj/biocode_3738f8db16c946c6b277d81ae4ea4537/setup.py:6: DeprecationWarning: Due to possible ambiguity, 'convert()' is deprecated. Use 'convert_file()' or 'convert_text()'. 2021-07-12T21:23:52,795 read_md = lambda f: convert(f, 'rst', 'md') 2021-07-12T21:23:53,067 /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long' 2021-07-12T21:23:53,067 warnings.warn(msg) 2021-07-12T21:23:53,206 running egg_info 2021-07-12T21:23:53,210 creating /tmp/pip-pip-egg-info-0esunsbz/biocode.egg-info 2021-07-12T21:23:53,211 writing /tmp/pip-pip-egg-info-0esunsbz/biocode.egg-info/PKG-INFO 2021-07-12T21:23:53,214 writing dependency_links to /tmp/pip-pip-egg-info-0esunsbz/biocode.egg-info/dependency_links.txt 2021-07-12T21:23:53,216 writing requirements to /tmp/pip-pip-egg-info-0esunsbz/biocode.egg-info/requires.txt 2021-07-12T21:23:53,217 writing top-level names to /tmp/pip-pip-egg-info-0esunsbz/biocode.egg-info/top_level.txt 2021-07-12T21:23:53,219 writing manifest file '/tmp/pip-pip-egg-info-0esunsbz/biocode.egg-info/SOURCES.txt' 2021-07-12T21:23:53,417 reading manifest file '/tmp/pip-pip-egg-info-0esunsbz/biocode.egg-info/SOURCES.txt' 2021-07-12T21:23:53,420 reading manifest template 'MANIFEST.in' 2021-07-12T21:23:53,421 warning: no files found matching 'biocode/README.rst' 2021-07-12T21:23:53,423 adding license file 'LICENSE' 2021-07-12T21:23:53,429 writing manifest file '/tmp/pip-pip-egg-info-0esunsbz/biocode.egg-info/SOURCES.txt' 2021-07-12T21:23:53,511 Source in /tmp/pip-wheel-c2eqo9kj/biocode_3738f8db16c946c6b277d81ae4ea4537 has version 0.5.1, which satisfies requirement biocode==0.5.1 from https://files.pythonhosted.org/packages/5c/b7/035e01334320dd66ac8c65be4baa910e8cb16215c563d7b65bfdfd5b56d6/biocode-0.5.1.tar.gz#sha256=ca80071c7e495380a875714ac7cf975dc20389ab8e36f72971a59f6e5a5ac83e 2021-07-12T21:23:53,512 Removed biocode==0.5.1 from https://files.pythonhosted.org/packages/5c/b7/035e01334320dd66ac8c65be4baa910e8cb16215c563d7b65bfdfd5b56d6/biocode-0.5.1.tar.gz#sha256=ca80071c7e495380a875714ac7cf975dc20389ab8e36f72971a59f6e5a5ac83e from build tracker '/tmp/pip-req-tracker-y37bifh6' 2021-07-12T21:23:53,516 Created temporary directory: /tmp/pip-unpack-da7sxl3v 2021-07-12T21:23:53,517 Building wheels for collected packages: biocode 2021-07-12T21:23:53,521 Created temporary directory: /tmp/pip-wheel-hs5d02g9 2021-07-12T21:23:53,522 Building wheel for biocode (setup.py): started 2021-07-12T21:23:53,522 Destination directory: /tmp/pip-wheel-hs5d02g9 2021-07-12T21:23:53,522 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-c2eqo9kj/biocode_3738f8db16c946c6b277d81ae4ea4537/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-c2eqo9kj/biocode_3738f8db16c946c6b277d81ae4ea4537/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-hs5d02g9 2021-07-12T21:23:54,547 /tmp/pip-wheel-c2eqo9kj/biocode_3738f8db16c946c6b277d81ae4ea4537/setup.py:6: DeprecationWarning: Due to possible ambiguity, 'convert()' is deprecated. Use 'convert_file()' or 'convert_text()'. 2021-07-12T21:23:54,548 read_md = lambda f: convert(f, 'rst', 'md') 2021-07-12T21:23:54,799 /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long' 2021-07-12T21:23:54,799 warnings.warn(msg) 2021-07-12T21:23:54,960 running bdist_wheel 2021-07-12T21:23:55,144 running build 2021-07-12T21:23:55,145 running build_py 2021-07-12T21:23:55,285 creating build 2021-07-12T21:23:55,286 creating build/lib 2021-07-12T21:23:55,287 creating build/lib/biocode 2021-07-12T21:23:55,288 copying biocode/annotation.py -> build/lib/biocode 2021-07-12T21:23:55,291 copying biocode/genbank.py -> build/lib/biocode 2021-07-12T21:23:55,294 copying biocode/utils.py -> build/lib/biocode 2021-07-12T21:23:55,297 copying biocode/__init__.py -> build/lib/biocode 2021-07-12T21:23:55,298 copying biocode/gff.py -> build/lib/biocode 2021-07-12T21:23:55,302 copying biocode/things.py -> build/lib/biocode 2021-07-12T21:23:55,305 copying biocode/tbl.py -> build/lib/biocode 2021-07-12T21:23:55,307 running egg_info 2021-07-12T21:23:55,323 writing biocode.egg-info/PKG-INFO 2021-07-12T21:23:55,325 writing dependency_links to biocode.egg-info/dependency_links.txt 2021-07-12T21:23:55,327 writing requirements to biocode.egg-info/requires.txt 2021-07-12T21:23:55,328 writing top-level names to biocode.egg-info/top_level.txt 2021-07-12T21:23:55,388 reading manifest file 'biocode.egg-info/SOURCES.txt' 2021-07-12T21:23:55,394 reading manifest template 'MANIFEST.in' 2021-07-12T21:23:55,395 warning: no files found matching 'biocode/README.rst' 2021-07-12T21:23:55,396 adding license file 'LICENSE' 2021-07-12T21:23:55,403 writing manifest file 'biocode.egg-info/SOURCES.txt' 2021-07-12T21:23:55,407 creating build/lib/biocode/data 2021-07-12T21:23:55,408 copying biocode/data/HMPslim.v2.1.obo -> build/lib/biocode/data 2021-07-12T21:23:55,412 copying biocode/data/__init__.py -> build/lib/biocode/data 2021-07-12T21:23:55,414 copying biocode/data/genbank_flat_file_header.template -> build/lib/biocode/data 2021-07-12T21:23:55,416 copying biocode/data/rsem_html_table.template -> build/lib/biocode/data 2021-07-12T21:23:55,420 running build_scripts 2021-07-12T21:23:55,421 creating build/scripts-3.9 2021-07-12T21:23:55,421 copying and adjusting bin/convert_blast_btab_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,424 copying and adjusting bin/fasta_base_content.py -> build/scripts-3.9 2021-07-12T21:23:55,426 copying and adjusting bin/subsample_fasta.py -> build/scripts-3.9 2021-07-12T21:23:55,427 copying and adjusting bin/convert_glimmerHMM_gff_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,429 copying and adjusting bin/merge_predicted_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,431 copying and adjusting bin/add_gff3_locus_tags.py -> build/scripts-3.9 2021-07-12T21:23:55,433 copying and adjusting bin/convert_gff3_to_gene_association_format.py -> build/scripts-3.9 2021-07-12T21:23:55,435 copying and adjusting bin/detect_inverted_repeats.py -> build/scripts-3.9 2021-07-12T21:23:55,437 copying and adjusting bin/correct_gff3_CDS_phase_column.py -> build/scripts-3.9 2021-07-12T21:23:55,439 copying and adjusting bin/remove_duplicate_features.py -> build/scripts-3.9 2021-07-12T21:23:55,441 copying and adjusting bin/merge_masked_fasta_files.py -> build/scripts-3.9 2021-07-12T21:23:55,443 copying and adjusting bin/create_taxonomic_profile_from_blast.py -> build/scripts-3.9 2021-07-12T21:23:55,446 copying and adjusting bin/check_for_embedded_fasta_headers.py -> build/scripts-3.9 2021-07-12T21:23:55,448 copying and adjusting bin/split_isoforms_into_individual_genes.py -> build/scripts-3.9 2021-07-12T21:23:55,450 copying and adjusting bin/filter_fastq_by_N_content.py -> build/scripts-3.9 2021-07-12T21:23:55,452 copying and adjusting bin/select_training_and_evaluation_transcripts.py -> build/scripts-3.9 2021-07-12T21:23:55,454 copying and adjusting bin/convert_cegma_gff_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,457 copying and adjusting bin/biothings_coordinate_comparisons.py -> build/scripts-3.9 2021-07-12T21:23:55,459 copying and adjusting bin/validate_fasta.py -> build/scripts-3.9 2021-07-12T21:23:55,461 copying and adjusting bin/validate_feature_boundaries_on_molecules.py -> build/scripts-3.9 2021-07-12T21:23:55,463 copying and adjusting bin/report_coverage_gaps.py -> build/scripts-3.9 2021-07-12T21:23:55,465 copying and adjusting bin/mark_partial_genes.py -> build/scripts-3.9 2021-07-12T21:23:55,467 copying and adjusting bin/convert_aat_btab_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,470 copying and adjusting bin/filter_uniref_by_repid.py -> build/scripts-3.9 2021-07-12T21:23:55,473 copying and adjusting bin/calculate_query_coverage_by_blast.py -> build/scripts-3.9 2021-07-12T21:23:55,475 copying and adjusting bin/convert_gff3_to_ncbi_tbl.py -> build/scripts-3.9 2021-07-12T21:23:55,477 copying and adjusting bin/filter_gff3_by_id_list.py -> build/scripts-3.9 2021-07-12T21:23:55,479 copying and adjusting bin/split_fasta_into_even_files.py -> build/scripts-3.9 2021-07-12T21:23:55,482 copying and adjusting bin/replace_gff_type_column_value.py -> build/scripts-3.9 2021-07-12T21:23:55,483 copying and adjusting bin/merge_bam_files.py -> build/scripts-3.9 2021-07-12T21:23:55,485 copying and adjusting bin/prepend_to_fasta_header.py -> build/scripts-3.9 2021-07-12T21:23:55,487 copying and adjusting bin/add_polypeptide_to_gff3_gene_models.py -> build/scripts-3.9 2021-07-12T21:23:55,490 copying and adjusting bin/check_gff_for_internal_stops.py -> build/scripts-3.9 2021-07-12T21:23:55,492 copying and adjusting bin/remove_orphaned_features.py -> build/scripts-3.9 2021-07-12T21:23:55,494 copying and adjusting bin/convert_gff3_to_gbk.py -> build/scripts-3.9 2021-07-12T21:23:55,497 copying and adjusting bin/report_or_replace_nonstandard_residues.py -> build/scripts-3.9 2021-07-12T21:23:55,499 copying and adjusting bin/make_go_slim_index.py -> build/scripts-3.9 2021-07-12T21:23:55,502 copying and adjusting bin/extend_genes_to_stops.py -> build/scripts-3.9 2021-07-12T21:23:55,504 copying and adjusting bin/remove_masked_gene_models.py -> build/scripts-3.9 2021-07-12T21:23:55,506 copying and adjusting bin/randomly_subsample_fastq.py -> build/scripts-3.9 2021-07-12T21:23:55,509 copying and adjusting bin/fasta_size_distribution_plot.py -> build/scripts-3.9 2021-07-12T21:23:55,511 copying and adjusting bin/remove_duplicate_sequences.py -> build/scripts-3.9 2021-07-12T21:23:55,513 copying and adjusting bin/convert_metagenemark_gff_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,515 copying and adjusting bin/filter_fasta_by_header_regex.py -> build/scripts-3.9 2021-07-12T21:23:55,517 copying and adjusting bin/split_molecules_on_gaps.py -> build/scripts-3.9 2021-07-12T21:23:55,518 copying and adjusting bin/convert_fasta_contigs_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,520 copying and adjusting bin/report_gff_intron_and_intergenic_stats.py -> build/scripts-3.9 2021-07-12T21:23:55,522 copying and adjusting bin/append_to_column_9_value.py -> build/scripts-3.9 2021-07-12T21:23:55,524 copying and adjusting bin/split_interleaved_sequence_file.py -> build/scripts-3.9 2021-07-12T21:23:55,526 copying and adjusting bin/filter_fasta_by_type.py -> build/scripts-3.9 2021-07-12T21:23:55,527 copying and adjusting bin/convert_augustus_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,530 copying and adjusting bin/uniprot_sprot_to_sqlite3.py -> build/scripts-3.9 2021-07-12T21:23:55,532 copying and adjusting bin/hmmlib_to_sqlite3.py -> build/scripts-3.9 2021-07-12T21:23:55,535 copying and adjusting bin/update_selected_column9_values.py -> build/scripts-3.9 2021-07-12T21:23:55,537 copying and adjusting bin/get_mpilup_from_id_list.py -> build/scripts-3.9 2021-07-12T21:23:55,539 copying and adjusting bin/convert_prodigal_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,540 copying and adjusting bin/append_to_fastq_read_header.py -> build/scripts-3.9 2021-07-12T21:23:55,542 copying and adjusting bin/convert_genbank_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,544 copying and adjusting bin/validate_uniref_member_characterization.py -> build/scripts-3.9 2021-07-12T21:23:55,546 copying and adjusting bin/compare_gene_structures.py -> build/scripts-3.9 2021-07-12T21:23:55,550 copying and adjusting bin/uniref_to_sqlite3.py -> build/scripts-3.9 2021-07-12T21:23:55,552 copying and adjusting bin/extract_fasta_regions.py -> build/scripts-3.9 2021-07-12T21:23:55,554 copying and adjusting bin/reverse_misordered_cds_coords.py -> build/scripts-3.9 2021-07-12T21:23:55,555 copying and adjusting bin/convert_scipio_gff_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,558 copying and adjusting bin/interleave_fasta.py -> build/scripts-3.9 2021-07-12T21:23:55,559 copying and adjusting bin/make_go_slim.py -> build/scripts-3.9 2021-07-12T21:23:55,561 copying and adjusting bin/report_basic_gff_model_agreement.py -> build/scripts-3.9 2021-07-12T21:23:55,563 copying and adjusting bin/make_cufflinks_ids_unique.py -> build/scripts-3.9 2021-07-12T21:23:55,564 copying and adjusting bin/fastq_simple_stats.py -> build/scripts-3.9 2021-07-12T21:23:55,566 copying and adjusting bin/eggnog_to_sqlite3.py -> build/scripts-3.9 2021-07-12T21:23:55,568 copying and adjusting bin/create_taxonomy_db.py -> build/scripts-3.9 2021-07-12T21:23:55,571 copying and adjusting bin/append_to_fasta_header.py -> build/scripts-3.9 2021-07-12T21:23:55,573 copying and adjusting bin/tigrfam_info_to_sqlite3.py -> build/scripts-3.9 2021-07-12T21:23:55,575 copying and adjusting bin/filter_uniref_by_taxonomy.py -> build/scripts-3.9 2021-07-12T21:23:55,577 copying and adjusting bin/reformat_fasta_residue_lengths.py -> build/scripts-3.9 2021-07-12T21:23:55,579 copying and adjusting bin/replace_homopolymeric_repeats_with_Ns.py -> build/scripts-3.9 2021-07-12T21:23:55,581 copying and adjusting bin/create_rsem_html_table.py -> build/scripts-3.9 2021-07-12T21:23:55,583 copying and adjusting bin/convert_cufflinks_gtf_to_gff3.py -> build/scripts-3.9 2021-07-12T21:23:55,585 copying and adjusting bin/reorient_sequences_by_id.py -> build/scripts-3.9 2021-07-12T21:23:55,587 copying and adjusting bin/convert_fastq_to_fasta.py -> build/scripts-3.9 2021-07-12T21:23:55,589 copying and adjusting bin/write_fasta_from_gff.py -> build/scripts-3.9 2021-07-12T21:23:55,591 copying and adjusting bin/convert_pasa_gff_to_models.py -> build/scripts-3.9 2021-07-12T21:23:55,593 copying and adjusting bin/set_source_column.py -> build/scripts-3.9 2021-07-12T21:23:55,595 copying and adjusting bin/interleave_fastq.py -> build/scripts-3.9 2021-07-12T21:23:55,596 copying and adjusting bin/report_gff3_statistics.py -> build/scripts-3.9 2021-07-12T21:23:55,598 copying and adjusting bin/merge_fasta_files_and_uniquify_ids.py -> build/scripts-3.9 2021-07-12T21:23:55,600 changing mode of build/scripts-3.9/convert_blast_btab_to_gff3.py from 644 to 755 2021-07-12T21:23:55,600 changing mode of build/scripts-3.9/fasta_base_content.py from 644 to 755 2021-07-12T21:23:55,600 changing mode of build/scripts-3.9/subsample_fasta.py from 644 to 755 2021-07-12T21:23:55,601 changing mode of build/scripts-3.9/convert_glimmerHMM_gff_to_gff3.py from 644 to 755 2021-07-12T21:23:55,601 changing mode of build/scripts-3.9/merge_predicted_gff3.py from 644 to 755 2021-07-12T21:23:55,601 changing mode of build/scripts-3.9/add_gff3_locus_tags.py from 644 to 755 2021-07-12T21:23:55,602 changing mode of build/scripts-3.9/convert_gff3_to_gene_association_format.py from 644 to 755 2021-07-12T21:23:55,602 changing mode of build/scripts-3.9/detect_inverted_repeats.py from 644 to 755 2021-07-12T21:23:55,603 changing mode of build/scripts-3.9/correct_gff3_CDS_phase_column.py from 644 to 755 2021-07-12T21:23:55,603 changing mode of build/scripts-3.9/remove_duplicate_features.py from 644 to 755 2021-07-12T21:23:55,603 changing mode of build/scripts-3.9/merge_masked_fasta_files.py from 644 to 755 2021-07-12T21:23:55,604 changing mode of build/scripts-3.9/create_taxonomic_profile_from_blast.py from 644 to 755 2021-07-12T21:23:55,604 changing mode of build/scripts-3.9/check_for_embedded_fasta_headers.py from 644 to 755 2021-07-12T21:23:55,604 changing mode of build/scripts-3.9/split_isoforms_into_individual_genes.py from 644 to 755 2021-07-12T21:23:55,604 changing mode of build/scripts-3.9/filter_fastq_by_N_content.py from 644 to 755 2021-07-12T21:23:55,605 changing mode of build/scripts-3.9/select_training_and_evaluation_transcripts.py from 644 to 755 2021-07-12T21:23:55,605 changing mode of build/scripts-3.9/convert_cegma_gff_to_gff3.py from 644 to 755 2021-07-12T21:23:55,605 changing mode of build/scripts-3.9/biothings_coordinate_comparisons.py from 644 to 755 2021-07-12T21:23:55,606 changing mode of build/scripts-3.9/validate_fasta.py from 644 to 755 2021-07-12T21:23:55,606 changing mode of build/scripts-3.9/validate_feature_boundaries_on_molecules.py from 644 to 755 2021-07-12T21:23:55,606 changing mode of build/scripts-3.9/report_coverage_gaps.py from 644 to 755 2021-07-12T21:23:55,607 changing mode of build/scripts-3.9/mark_partial_genes.py from 644 to 755 2021-07-12T21:23:55,607 changing mode of build/scripts-3.9/convert_aat_btab_to_gff3.py from 644 to 755 2021-07-12T21:23:55,607 changing mode of build/scripts-3.9/filter_uniref_by_repid.py from 644 to 755 2021-07-12T21:23:55,608 changing mode of build/scripts-3.9/calculate_query_coverage_by_blast.py from 644 to 755 2021-07-12T21:23:55,608 changing mode of build/scripts-3.9/convert_gff3_to_ncbi_tbl.py from 644 to 755 2021-07-12T21:23:55,608 changing mode of build/scripts-3.9/filter_gff3_by_id_list.py from 644 to 755 2021-07-12T21:23:55,608 changing mode of build/scripts-3.9/split_fasta_into_even_files.py from 644 to 755 2021-07-12T21:23:55,609 changing mode of build/scripts-3.9/replace_gff_type_column_value.py from 644 to 755 2021-07-12T21:23:55,609 changing mode of build/scripts-3.9/merge_bam_files.py from 644 to 755 2021-07-12T21:23:55,609 changing mode of build/scripts-3.9/prepend_to_fasta_header.py from 644 to 755 2021-07-12T21:23:55,610 changing mode of build/scripts-3.9/add_polypeptide_to_gff3_gene_models.py from 644 to 755 2021-07-12T21:23:55,610 changing mode of build/scripts-3.9/check_gff_for_internal_stops.py from 644 to 755 2021-07-12T21:23:55,610 changing mode of build/scripts-3.9/remove_orphaned_features.py from 644 to 755 2021-07-12T21:23:55,611 changing mode of build/scripts-3.9/convert_gff3_to_gbk.py from 644 to 755 2021-07-12T21:23:55,611 changing mode of build/scripts-3.9/report_or_replace_nonstandard_residues.py from 644 to 755 2021-07-12T21:23:55,611 changing mode of build/scripts-3.9/make_go_slim_index.py from 644 to 755 2021-07-12T21:23:55,611 changing mode of build/scripts-3.9/extend_genes_to_stops.py from 644 to 755 2021-07-12T21:23:55,612 changing mode of build/scripts-3.9/remove_masked_gene_models.py from 644 to 755 2021-07-12T21:23:55,612 changing mode of build/scripts-3.9/randomly_subsample_fastq.py from 644 to 755 2021-07-12T21:23:55,612 changing mode of build/scripts-3.9/fasta_size_distribution_plot.py from 644 to 755 2021-07-12T21:23:55,613 changing mode of build/scripts-3.9/remove_duplicate_sequences.py from 644 to 755 2021-07-12T21:23:55,613 changing mode of build/scripts-3.9/convert_metagenemark_gff_to_gff3.py from 644 to 755 2021-07-12T21:23:55,613 changing mode of build/scripts-3.9/filter_fasta_by_header_regex.py from 644 to 755 2021-07-12T21:23:55,614 changing mode of build/scripts-3.9/split_molecules_on_gaps.py from 644 to 755 2021-07-12T21:23:55,614 changing mode of build/scripts-3.9/convert_fasta_contigs_to_gff3.py from 644 to 755 2021-07-12T21:23:55,614 changing mode of build/scripts-3.9/report_gff_intron_and_intergenic_stats.py from 644 to 755 2021-07-12T21:23:55,615 changing mode of build/scripts-3.9/append_to_column_9_value.py from 644 to 755 2021-07-12T21:23:55,615 changing mode of build/scripts-3.9/split_interleaved_sequence_file.py from 644 to 755 2021-07-12T21:23:55,615 changing mode of build/scripts-3.9/filter_fasta_by_type.py from 644 to 755 2021-07-12T21:23:55,615 changing mode of build/scripts-3.9/convert_augustus_to_gff3.py from 644 to 755 2021-07-12T21:23:55,616 changing mode of build/scripts-3.9/uniprot_sprot_to_sqlite3.py from 644 to 755 2021-07-12T21:23:55,616 changing mode of build/scripts-3.9/hmmlib_to_sqlite3.py from 644 to 755 2021-07-12T21:23:55,616 changing mode of build/scripts-3.9/update_selected_column9_values.py from 644 to 755 2021-07-12T21:23:55,616 changing mode of build/scripts-3.9/get_mpilup_from_id_list.py from 644 to 755 2021-07-12T21:23:55,617 changing mode of build/scripts-3.9/convert_prodigal_to_gff3.py from 644 to 755 2021-07-12T21:23:55,617 changing mode of build/scripts-3.9/append_to_fastq_read_header.py from 644 to 755 2021-07-12T21:23:55,617 changing mode of build/scripts-3.9/convert_genbank_to_gff3.py from 644 to 755 2021-07-12T21:23:55,618 changing mode of build/scripts-3.9/validate_uniref_member_characterization.py from 644 to 755 2021-07-12T21:23:55,618 changing mode of build/scripts-3.9/compare_gene_structures.py from 644 to 755 2021-07-12T21:23:55,618 changing mode of build/scripts-3.9/uniref_to_sqlite3.py from 644 to 755 2021-07-12T21:23:55,619 changing mode of build/scripts-3.9/extract_fasta_regions.py from 644 to 755 2021-07-12T21:23:55,619 changing mode of build/scripts-3.9/reverse_misordered_cds_coords.py from 644 to 755 2021-07-12T21:23:55,619 changing mode of build/scripts-3.9/convert_scipio_gff_to_gff3.py from 644 to 755 2021-07-12T21:23:55,620 changing mode of build/scripts-3.9/interleave_fasta.py from 644 to 755 2021-07-12T21:23:55,620 changing mode of build/scripts-3.9/make_go_slim.py from 644 to 755 2021-07-12T21:23:55,620 changing mode of build/scripts-3.9/report_basic_gff_model_agreement.py from 644 to 755 2021-07-12T21:23:55,621 changing mode of build/scripts-3.9/make_cufflinks_ids_unique.py from 644 to 755 2021-07-12T21:23:55,621 changing mode of build/scripts-3.9/fastq_simple_stats.py from 644 to 755 2021-07-12T21:23:55,621 changing mode of build/scripts-3.9/eggnog_to_sqlite3.py from 644 to 755 2021-07-12T21:23:55,622 changing mode of build/scripts-3.9/create_taxonomy_db.py from 644 to 755 2021-07-12T21:23:55,622 changing mode of build/scripts-3.9/append_to_fasta_header.py from 644 to 755 2021-07-12T21:23:55,622 changing mode of build/scripts-3.9/tigrfam_info_to_sqlite3.py from 644 to 755 2021-07-12T21:23:55,623 changing mode of build/scripts-3.9/filter_uniref_by_taxonomy.py from 644 to 755 2021-07-12T21:23:55,623 changing mode of build/scripts-3.9/reformat_fasta_residue_lengths.py from 644 to 755 2021-07-12T21:23:55,623 changing mode of build/scripts-3.9/replace_homopolymeric_repeats_with_Ns.py from 644 to 755 2021-07-12T21:23:55,623 changing mode of build/scripts-3.9/create_rsem_html_table.py from 644 to 755 2021-07-12T21:23:55,624 changing mode of build/scripts-3.9/convert_cufflinks_gtf_to_gff3.py from 644 to 755 2021-07-12T21:23:55,624 changing mode of build/scripts-3.9/reorient_sequences_by_id.py from 644 to 755 2021-07-12T21:23:55,624 changing mode of build/scripts-3.9/convert_fastq_to_fasta.py from 644 to 755 2021-07-12T21:23:55,625 changing mode of build/scripts-3.9/write_fasta_from_gff.py from 644 to 755 2021-07-12T21:23:55,625 changing mode of build/scripts-3.9/convert_pasa_gff_to_models.py from 644 to 755 2021-07-12T21:23:55,625 changing mode of build/scripts-3.9/set_source_column.py from 644 to 755 2021-07-12T21:23:55,625 changing mode of build/scripts-3.9/interleave_fastq.py from 644 to 755 2021-07-12T21:23:55,626 changing mode of build/scripts-3.9/report_gff3_statistics.py from 644 to 755 2021-07-12T21:23:55,626 changing mode of build/scripts-3.9/merge_fasta_files_and_uniquify_ids.py from 644 to 755 2021-07-12T21:23:55,634 installing to build/bdist.linux-armv7l/wheel 2021-07-12T21:23:55,634 running install 2021-07-12T21:23:55,635 running install_lib 2021-07-12T21:23:55,640 creating build/bdist.linux-armv7l 2021-07-12T21:23:55,640 creating build/bdist.linux-armv7l/wheel 2021-07-12T21:23:55,642 creating build/bdist.linux-armv7l/wheel/biocode 2021-07-12T21:23:55,643 copying build/lib/biocode/annotation.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T21:23:55,646 copying build/lib/biocode/genbank.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T21:23:55,649 copying build/lib/biocode/utils.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T21:23:55,653 creating build/bdist.linux-armv7l/wheel/biocode/data 2021-07-12T21:23:55,654 copying build/lib/biocode/data/genbank_flat_file_header.template -> build/bdist.linux-armv7l/wheel/biocode/data 2021-07-12T21:23:55,656 copying build/lib/biocode/data/rsem_html_table.template -> build/bdist.linux-armv7l/wheel/biocode/data 2021-07-12T21:23:55,659 copying build/lib/biocode/data/__init__.py -> build/bdist.linux-armv7l/wheel/biocode/data 2021-07-12T21:23:55,661 copying build/lib/biocode/data/HMPslim.v2.1.obo -> build/bdist.linux-armv7l/wheel/biocode/data 2021-07-12T21:23:55,665 copying build/lib/biocode/__init__.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T21:23:55,666 copying build/lib/biocode/gff.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T21:23:55,670 copying build/lib/biocode/things.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T21:23:55,674 copying build/lib/biocode/tbl.py -> build/bdist.linux-armv7l/wheel/biocode 2021-07-12T21:23:55,677 running install_egg_info 2021-07-12T21:23:55,683 Copying biocode.egg-info to build/bdist.linux-armv7l/wheel/biocode-0.5.1-py3.9.egg-info 2021-07-12T21:23:55,697 running install_scripts 2021-07-12T21:23:55,728 creating build/bdist.linux-armv7l/wheel/biocode-0.5.1.data 2021-07-12T21:23:55,729 creating build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,730 copying build/scripts-3.9/check_for_embedded_fasta_headers.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,732 copying build/scripts-3.9/calculate_query_coverage_by_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,734 copying build/scripts-3.9/convert_cegma_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,737 copying build/scripts-3.9/detect_inverted_repeats.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,739 copying build/scripts-3.9/fastq_simple_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,741 copying build/scripts-3.9/eggnog_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,744 copying build/scripts-3.9/remove_masked_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,746 copying build/scripts-3.9/report_basic_gff_model_agreement.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,748 copying build/scripts-3.9/convert_blast_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,751 copying build/scripts-3.9/report_gff3_statistics.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,754 copying build/scripts-3.9/convert_aat_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,756 copying build/scripts-3.9/randomly_subsample_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,759 copying build/scripts-3.9/interleave_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,761 copying build/scripts-3.9/filter_fastq_by_N_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,764 copying build/scripts-3.9/convert_cufflinks_gtf_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,767 copying build/scripts-3.9/replace_homopolymeric_repeats_with_Ns.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,770 copying build/scripts-3.9/split_molecules_on_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,772 copying build/scripts-3.9/set_source_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,774 copying build/scripts-3.9/merge_fasta_files_and_uniquify_ids.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,777 copying build/scripts-3.9/make_cufflinks_ids_unique.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,779 copying build/scripts-3.9/convert_gff3_to_gbk.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,781 copying build/scripts-3.9/make_go_slim.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,784 copying build/scripts-3.9/filter_uniref_by_repid.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,786 copying build/scripts-3.9/correct_gff3_CDS_phase_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,789 copying build/scripts-3.9/extract_fasta_regions.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,791 copying build/scripts-3.9/filter_gff3_by_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,793 copying build/scripts-3.9/filter_fasta_by_header_regex.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,795 copying build/scripts-3.9/fasta_base_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,798 copying build/scripts-3.9/reorient_sequences_by_id.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,800 copying build/scripts-3.9/create_taxonomic_profile_from_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,803 copying build/scripts-3.9/report_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,806 copying build/scripts-3.9/add_gff3_locus_tags.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,809 copying build/scripts-3.9/validate_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,812 copying build/scripts-3.9/merge_bam_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,814 copying build/scripts-3.9/check_gff_for_internal_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,817 copying build/scripts-3.9/interleave_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,819 copying build/scripts-3.9/append_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,822 copying build/scripts-3.9/convert_fasta_contigs_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,824 copying build/scripts-3.9/convert_scipio_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,827 copying build/scripts-3.9/make_go_slim_index.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,830 copying build/scripts-3.9/biothings_coordinate_comparisons.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,833 copying build/scripts-3.9/replace_gff_type_column_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,835 copying build/scripts-3.9/extend_genes_to_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,837 copying build/scripts-3.9/remove_duplicate_sequences.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,840 copying build/scripts-3.9/append_to_fastq_read_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,842 copying build/scripts-3.9/uniprot_sprot_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,845 copying build/scripts-3.9/filter_uniref_by_taxonomy.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,848 copying build/scripts-3.9/get_mpilup_from_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,850 copying build/scripts-3.9/uniref_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,853 copying build/scripts-3.9/write_fasta_from_gff.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,855 copying build/scripts-3.9/convert_pasa_gff_to_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,858 copying build/scripts-3.9/prepend_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,860 copying build/scripts-3.9/reverse_misordered_cds_coords.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,863 copying build/scripts-3.9/fasta_size_distribution_plot.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,865 copying build/scripts-3.9/mark_partial_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,868 copying build/scripts-3.9/convert_glimmerHMM_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,871 copying build/scripts-3.9/filter_fasta_by_type.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,873 copying build/scripts-3.9/add_polypeptide_to_gff3_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,876 copying build/scripts-3.9/update_selected_column9_values.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,879 copying build/scripts-3.9/report_gff_intron_and_intergenic_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,882 copying build/scripts-3.9/create_rsem_html_table.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,884 copying build/scripts-3.9/create_taxonomy_db.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,887 copying build/scripts-3.9/subsample_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,890 copying build/scripts-3.9/append_to_column_9_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,892 copying build/scripts-3.9/convert_genbank_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,895 copying build/scripts-3.9/remove_orphaned_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,898 copying build/scripts-3.9/convert_gff3_to_gene_association_format.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,901 copying build/scripts-3.9/split_fasta_into_even_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,903 copying build/scripts-3.9/compare_gene_structures.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,907 copying build/scripts-3.9/merge_predicted_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,910 copying build/scripts-3.9/convert_metagenemark_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,913 copying build/scripts-3.9/select_training_and_evaluation_transcripts.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,916 copying build/scripts-3.9/hmmlib_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,919 copying build/scripts-3.9/convert_gff3_to_ncbi_tbl.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,921 copying build/scripts-3.9/split_interleaved_sequence_file.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,924 copying build/scripts-3.9/reformat_fasta_residue_lengths.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,926 copying build/scripts-3.9/merge_masked_fasta_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,929 copying build/scripts-3.9/validate_feature_boundaries_on_molecules.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,931 copying build/scripts-3.9/tigrfam_info_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,934 copying build/scripts-3.9/remove_duplicate_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,936 copying build/scripts-3.9/report_or_replace_nonstandard_residues.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,939 copying build/scripts-3.9/convert_augustus_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,942 copying build/scripts-3.9/split_isoforms_into_individual_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,944 copying build/scripts-3.9/convert_prodigal_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,947 copying build/scripts-3.9/validate_uniref_member_characterization.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,949 copying build/scripts-3.9/convert_fastq_to_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts 2021-07-12T21:23:55,951 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/check_for_embedded_fasta_headers.py to 755 2021-07-12T21:23:55,952 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/calculate_query_coverage_by_blast.py to 755 2021-07-12T21:23:55,952 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_cegma_gff_to_gff3.py to 755 2021-07-12T21:23:55,952 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/detect_inverted_repeats.py to 755 2021-07-12T21:23:55,953 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/fastq_simple_stats.py to 755 2021-07-12T21:23:55,953 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/eggnog_to_sqlite3.py to 755 2021-07-12T21:23:55,953 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/remove_masked_gene_models.py to 755 2021-07-12T21:23:55,953 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/report_basic_gff_model_agreement.py to 755 2021-07-12T21:23:55,954 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_blast_btab_to_gff3.py to 755 2021-07-12T21:23:55,954 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/report_gff3_statistics.py to 755 2021-07-12T21:23:55,954 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_aat_btab_to_gff3.py to 755 2021-07-12T21:23:55,955 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/randomly_subsample_fastq.py to 755 2021-07-12T21:23:55,955 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/interleave_fastq.py to 755 2021-07-12T21:23:55,956 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/filter_fastq_by_N_content.py to 755 2021-07-12T21:23:55,956 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_cufflinks_gtf_to_gff3.py to 755 2021-07-12T21:23:55,956 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/replace_homopolymeric_repeats_with_Ns.py to 755 2021-07-12T21:23:55,957 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/split_molecules_on_gaps.py to 755 2021-07-12T21:23:55,957 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/set_source_column.py to 755 2021-07-12T21:23:55,957 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/merge_fasta_files_and_uniquify_ids.py to 755 2021-07-12T21:23:55,957 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/make_cufflinks_ids_unique.py to 755 2021-07-12T21:23:55,958 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_gff3_to_gbk.py to 755 2021-07-12T21:23:55,958 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/make_go_slim.py to 755 2021-07-12T21:23:55,958 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/filter_uniref_by_repid.py to 755 2021-07-12T21:23:55,958 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/correct_gff3_CDS_phase_column.py to 755 2021-07-12T21:23:55,959 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/extract_fasta_regions.py to 755 2021-07-12T21:23:55,959 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/filter_gff3_by_id_list.py to 755 2021-07-12T21:23:55,959 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/filter_fasta_by_header_regex.py to 755 2021-07-12T21:23:55,960 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/fasta_base_content.py to 755 2021-07-12T21:23:55,960 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/reorient_sequences_by_id.py to 755 2021-07-12T21:23:55,960 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/create_taxonomic_profile_from_blast.py to 755 2021-07-12T21:23:55,961 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/report_coverage_gaps.py to 755 2021-07-12T21:23:55,961 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/add_gff3_locus_tags.py to 755 2021-07-12T21:23:55,962 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/validate_fasta.py to 755 2021-07-12T21:23:55,962 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/merge_bam_files.py to 755 2021-07-12T21:23:55,962 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/check_gff_for_internal_stops.py to 755 2021-07-12T21:23:55,962 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/interleave_fasta.py to 755 2021-07-12T21:23:55,963 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/append_to_fasta_header.py to 755 2021-07-12T21:23:55,963 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_fasta_contigs_to_gff3.py to 755 2021-07-12T21:23:55,963 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_scipio_gff_to_gff3.py to 755 2021-07-12T21:23:55,964 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/make_go_slim_index.py to 755 2021-07-12T21:23:55,964 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/biothings_coordinate_comparisons.py to 755 2021-07-12T21:23:55,965 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/replace_gff_type_column_value.py to 755 2021-07-12T21:23:55,965 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/extend_genes_to_stops.py to 755 2021-07-12T21:23:55,965 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/remove_duplicate_sequences.py to 755 2021-07-12T21:23:55,966 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/append_to_fastq_read_header.py to 755 2021-07-12T21:23:55,966 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/uniprot_sprot_to_sqlite3.py to 755 2021-07-12T21:23:55,966 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/filter_uniref_by_taxonomy.py to 755 2021-07-12T21:23:55,967 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/get_mpilup_from_id_list.py to 755 2021-07-12T21:23:55,967 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/uniref_to_sqlite3.py to 755 2021-07-12T21:23:55,967 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/write_fasta_from_gff.py to 755 2021-07-12T21:23:55,968 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_pasa_gff_to_models.py to 755 2021-07-12T21:23:55,968 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/prepend_to_fasta_header.py to 755 2021-07-12T21:23:55,968 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/reverse_misordered_cds_coords.py to 755 2021-07-12T21:23:55,969 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/fasta_size_distribution_plot.py to 755 2021-07-12T21:23:55,969 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/mark_partial_genes.py to 755 2021-07-12T21:23:55,969 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_glimmerHMM_gff_to_gff3.py to 755 2021-07-12T21:23:55,970 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/filter_fasta_by_type.py to 755 2021-07-12T21:23:55,970 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/add_polypeptide_to_gff3_gene_models.py to 755 2021-07-12T21:23:55,970 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/update_selected_column9_values.py to 755 2021-07-12T21:23:55,971 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/report_gff_intron_and_intergenic_stats.py to 755 2021-07-12T21:23:55,971 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/create_rsem_html_table.py to 755 2021-07-12T21:23:55,972 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/create_taxonomy_db.py to 755 2021-07-12T21:23:55,972 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/subsample_fasta.py to 755 2021-07-12T21:23:55,972 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/append_to_column_9_value.py to 755 2021-07-12T21:23:55,972 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_genbank_to_gff3.py to 755 2021-07-12T21:23:55,973 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/remove_orphaned_features.py to 755 2021-07-12T21:23:55,973 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_gff3_to_gene_association_format.py to 755 2021-07-12T21:23:55,973 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/split_fasta_into_even_files.py to 755 2021-07-12T21:23:55,974 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/compare_gene_structures.py to 755 2021-07-12T21:23:55,974 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/merge_predicted_gff3.py to 755 2021-07-12T21:23:55,974 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_metagenemark_gff_to_gff3.py to 755 2021-07-12T21:23:55,974 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/select_training_and_evaluation_transcripts.py to 755 2021-07-12T21:23:55,975 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/hmmlib_to_sqlite3.py to 755 2021-07-12T21:23:55,975 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_gff3_to_ncbi_tbl.py to 755 2021-07-12T21:23:55,975 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/split_interleaved_sequence_file.py to 755 2021-07-12T21:23:55,976 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/reformat_fasta_residue_lengths.py to 755 2021-07-12T21:23:55,976 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/merge_masked_fasta_files.py to 755 2021-07-12T21:23:55,976 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/validate_feature_boundaries_on_molecules.py to 755 2021-07-12T21:23:55,977 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/tigrfam_info_to_sqlite3.py to 755 2021-07-12T21:23:55,977 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/remove_duplicate_features.py to 755 2021-07-12T21:23:55,977 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/report_or_replace_nonstandard_residues.py to 755 2021-07-12T21:23:55,978 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_augustus_to_gff3.py to 755 2021-07-12T21:23:55,978 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/split_isoforms_into_individual_genes.py to 755 2021-07-12T21:23:55,978 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_prodigal_to_gff3.py to 755 2021-07-12T21:23:55,979 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/validate_uniref_member_characterization.py to 755 2021-07-12T21:23:55,979 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.5.1.data/scripts/convert_fastq_to_fasta.py to 755 2021-07-12T21:23:56,001 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-12T21:23:56,006 creating build/bdist.linux-armv7l/wheel/biocode-0.5.1.dist-info/WHEEL 2021-07-12T21:23:56,009 creating '/tmp/pip-wheel-hs5d02g9/biocode-0.5.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-12T21:23:56,013 adding 'biocode/__init__.py' 2021-07-12T21:23:56,016 adding 'biocode/annotation.py' 2021-07-12T21:23:56,018 adding 'biocode/genbank.py' 2021-07-12T21:23:56,023 adding 'biocode/gff.py' 2021-07-12T21:23:56,026 adding 'biocode/tbl.py' 2021-07-12T21:23:56,034 adding 'biocode/things.py' 2021-07-12T21:23:56,037 adding 'biocode/utils.py' 2021-07-12T21:23:56,042 adding 'biocode/data/HMPslim.v2.1.obo' 2021-07-12T21:23:56,044 adding 'biocode/data/__init__.py' 2021-07-12T21:23:56,045 adding 'biocode/data/genbank_flat_file_header.template' 2021-07-12T21:23:56,048 adding 'biocode/data/rsem_html_table.template' 2021-07-12T21:23:56,053 adding 'biocode-0.5.1.data/scripts/add_gff3_locus_tags.py' 2021-07-12T21:23:56,055 adding 'biocode-0.5.1.data/scripts/add_polypeptide_to_gff3_gene_models.py' 2021-07-12T21:23:56,057 adding 'biocode-0.5.1.data/scripts/append_to_column_9_value.py' 2021-07-12T21:23:56,058 adding 'biocode-0.5.1.data/scripts/append_to_fasta_header.py' 2021-07-12T21:23:56,060 adding 'biocode-0.5.1.data/scripts/append_to_fastq_read_header.py' 2021-07-12T21:23:56,061 adding 'biocode-0.5.1.data/scripts/biothings_coordinate_comparisons.py' 2021-07-12T21:23:56,063 adding 'biocode-0.5.1.data/scripts/calculate_query_coverage_by_blast.py' 2021-07-12T21:23:56,064 adding 'biocode-0.5.1.data/scripts/check_for_embedded_fasta_headers.py' 2021-07-12T21:23:56,066 adding 'biocode-0.5.1.data/scripts/check_gff_for_internal_stops.py' 2021-07-12T21:23:56,069 adding 'biocode-0.5.1.data/scripts/compare_gene_structures.py' 2021-07-12T21:23:56,072 adding 'biocode-0.5.1.data/scripts/convert_aat_btab_to_gff3.py' 2021-07-12T21:23:56,074 adding 'biocode-0.5.1.data/scripts/convert_augustus_to_gff3.py' 2021-07-12T21:23:56,076 adding 'biocode-0.5.1.data/scripts/convert_blast_btab_to_gff3.py' 2021-07-12T21:23:56,078 adding 'biocode-0.5.1.data/scripts/convert_cegma_gff_to_gff3.py' 2021-07-12T21:23:56,080 adding 'biocode-0.5.1.data/scripts/convert_cufflinks_gtf_to_gff3.py' 2021-07-12T21:23:56,081 adding 'biocode-0.5.1.data/scripts/convert_fasta_contigs_to_gff3.py' 2021-07-12T21:23:56,083 adding 'biocode-0.5.1.data/scripts/convert_fastq_to_fasta.py' 2021-07-12T21:23:56,085 adding 'biocode-0.5.1.data/scripts/convert_genbank_to_gff3.py' 2021-07-12T21:23:56,086 adding 'biocode-0.5.1.data/scripts/convert_gff3_to_gbk.py' 2021-07-12T21:23:56,088 adding 'biocode-0.5.1.data/scripts/convert_gff3_to_gene_association_format.py' 2021-07-12T21:23:56,090 adding 'biocode-0.5.1.data/scripts/convert_gff3_to_ncbi_tbl.py' 2021-07-12T21:23:56,092 adding 'biocode-0.5.1.data/scripts/convert_glimmerHMM_gff_to_gff3.py' 2021-07-12T21:23:56,094 adding 'biocode-0.5.1.data/scripts/convert_metagenemark_gff_to_gff3.py' 2021-07-12T21:23:56,095 adding 'biocode-0.5.1.data/scripts/convert_pasa_gff_to_models.py' 2021-07-12T21:23:56,097 adding 'biocode-0.5.1.data/scripts/convert_prodigal_to_gff3.py' 2021-07-12T21:23:56,098 adding 'biocode-0.5.1.data/scripts/convert_scipio_gff_to_gff3.py' 2021-07-12T21:23:56,100 adding 'biocode-0.5.1.data/scripts/correct_gff3_CDS_phase_column.py' 2021-07-12T21:23:56,101 adding 'biocode-0.5.1.data/scripts/create_rsem_html_table.py' 2021-07-12T21:23:56,103 adding 'biocode-0.5.1.data/scripts/create_taxonomic_profile_from_blast.py' 2021-07-12T21:23:56,105 adding 'biocode-0.5.1.data/scripts/create_taxonomy_db.py' 2021-07-12T21:23:56,106 adding 'biocode-0.5.1.data/scripts/detect_inverted_repeats.py' 2021-07-12T21:23:56,108 adding 'biocode-0.5.1.data/scripts/eggnog_to_sqlite3.py' 2021-07-12T21:23:56,110 adding 'biocode-0.5.1.data/scripts/extend_genes_to_stops.py' 2021-07-12T21:23:56,111 adding 'biocode-0.5.1.data/scripts/extract_fasta_regions.py' 2021-07-12T21:23:56,113 adding 'biocode-0.5.1.data/scripts/fasta_base_content.py' 2021-07-12T21:23:56,114 adding 'biocode-0.5.1.data/scripts/fasta_size_distribution_plot.py' 2021-07-12T21:23:56,115 adding 'biocode-0.5.1.data/scripts/fastq_simple_stats.py' 2021-07-12T21:23:56,117 adding 'biocode-0.5.1.data/scripts/filter_fasta_by_header_regex.py' 2021-07-12T21:23:56,118 adding 'biocode-0.5.1.data/scripts/filter_fasta_by_type.py' 2021-07-12T21:23:56,120 adding 'biocode-0.5.1.data/scripts/filter_fastq_by_N_content.py' 2021-07-12T21:23:56,121 adding 'biocode-0.5.1.data/scripts/filter_gff3_by_id_list.py' 2021-07-12T21:23:56,123 adding 'biocode-0.5.1.data/scripts/filter_uniref_by_repid.py' 2021-07-12T21:23:56,124 adding 'biocode-0.5.1.data/scripts/filter_uniref_by_taxonomy.py' 2021-07-12T21:23:56,125 adding 'biocode-0.5.1.data/scripts/get_mpilup_from_id_list.py' 2021-07-12T21:23:56,128 adding 'biocode-0.5.1.data/scripts/hmmlib_to_sqlite3.py' 2021-07-12T21:23:56,129 adding 'biocode-0.5.1.data/scripts/interleave_fasta.py' 2021-07-12T21:23:56,130 adding 'biocode-0.5.1.data/scripts/interleave_fastq.py' 2021-07-12T21:23:56,132 adding 'biocode-0.5.1.data/scripts/make_cufflinks_ids_unique.py' 2021-07-12T21:23:56,134 adding 'biocode-0.5.1.data/scripts/make_go_slim.py' 2021-07-12T21:23:56,135 adding 'biocode-0.5.1.data/scripts/make_go_slim_index.py' 2021-07-12T21:23:56,137 adding 'biocode-0.5.1.data/scripts/mark_partial_genes.py' 2021-07-12T21:23:56,139 adding 'biocode-0.5.1.data/scripts/merge_bam_files.py' 2021-07-12T21:23:56,140 adding 'biocode-0.5.1.data/scripts/merge_fasta_files_and_uniquify_ids.py' 2021-07-12T21:23:56,142 adding 'biocode-0.5.1.data/scripts/merge_masked_fasta_files.py' 2021-07-12T21:23:56,144 adding 'biocode-0.5.1.data/scripts/merge_predicted_gff3.py' 2021-07-12T21:23:56,145 adding 'biocode-0.5.1.data/scripts/prepend_to_fasta_header.py' 2021-07-12T21:23:56,147 adding 'biocode-0.5.1.data/scripts/randomly_subsample_fastq.py' 2021-07-12T21:23:56,149 adding 'biocode-0.5.1.data/scripts/reformat_fasta_residue_lengths.py' 2021-07-12T21:23:56,150 adding 'biocode-0.5.1.data/scripts/remove_duplicate_features.py' 2021-07-12T21:23:56,152 adding 'biocode-0.5.1.data/scripts/remove_duplicate_sequences.py' 2021-07-12T21:23:56,153 adding 'biocode-0.5.1.data/scripts/remove_masked_gene_models.py' 2021-07-12T21:23:56,155 adding 'biocode-0.5.1.data/scripts/remove_orphaned_features.py' 2021-07-12T21:23:56,156 adding 'biocode-0.5.1.data/scripts/reorient_sequences_by_id.py' 2021-07-12T21:23:56,158 adding 'biocode-0.5.1.data/scripts/replace_gff_type_column_value.py' 2021-07-12T21:23:56,159 adding 'biocode-0.5.1.data/scripts/replace_homopolymeric_repeats_with_Ns.py' 2021-07-12T21:23:56,161 adding 'biocode-0.5.1.data/scripts/report_basic_gff_model_agreement.py' 2021-07-12T21:23:56,162 adding 'biocode-0.5.1.data/scripts/report_coverage_gaps.py' 2021-07-12T21:23:56,164 adding 'biocode-0.5.1.data/scripts/report_gff3_statistics.py' 2021-07-12T21:23:56,166 adding 'biocode-0.5.1.data/scripts/report_gff_intron_and_intergenic_stats.py' 2021-07-12T21:23:56,168 adding 'biocode-0.5.1.data/scripts/report_or_replace_nonstandard_residues.py' 2021-07-12T21:23:56,170 adding 'biocode-0.5.1.data/scripts/reverse_misordered_cds_coords.py' 2021-07-12T21:23:56,171 adding 'biocode-0.5.1.data/scripts/select_training_and_evaluation_transcripts.py' 2021-07-12T21:23:56,173 adding 'biocode-0.5.1.data/scripts/set_source_column.py' 2021-07-12T21:23:56,174 adding 'biocode-0.5.1.data/scripts/split_fasta_into_even_files.py' 2021-07-12T21:23:56,176 adding 'biocode-0.5.1.data/scripts/split_interleaved_sequence_file.py' 2021-07-12T21:23:56,177 adding 'biocode-0.5.1.data/scripts/split_isoforms_into_individual_genes.py' 2021-07-12T21:23:56,179 adding 'biocode-0.5.1.data/scripts/split_molecules_on_gaps.py' 2021-07-12T21:23:56,180 adding 'biocode-0.5.1.data/scripts/subsample_fasta.py' 2021-07-12T21:23:56,182 adding 'biocode-0.5.1.data/scripts/tigrfam_info_to_sqlite3.py' 2021-07-12T21:23:56,184 adding 'biocode-0.5.1.data/scripts/uniprot_sprot_to_sqlite3.py' 2021-07-12T21:23:56,186 adding 'biocode-0.5.1.data/scripts/uniref_to_sqlite3.py' 2021-07-12T21:23:56,187 adding 'biocode-0.5.1.data/scripts/update_selected_column9_values.py' 2021-07-12T21:23:56,189 adding 'biocode-0.5.1.data/scripts/validate_fasta.py' 2021-07-12T21:23:56,191 adding 'biocode-0.5.1.data/scripts/validate_feature_boundaries_on_molecules.py' 2021-07-12T21:23:56,192 adding 'biocode-0.5.1.data/scripts/validate_uniref_member_characterization.py' 2021-07-12T21:23:56,194 adding 'biocode-0.5.1.data/scripts/write_fasta_from_gff.py' 2021-07-12T21:23:56,197 adding 'biocode-0.5.1.dist-info/LICENSE' 2021-07-12T21:23:56,198 adding 'biocode-0.5.1.dist-info/METADATA' 2021-07-12T21:23:56,199 adding 'biocode-0.5.1.dist-info/WHEEL' 2021-07-12T21:23:56,199 adding 'biocode-0.5.1.dist-info/top_level.txt' 2021-07-12T21:23:56,202 adding 'biocode-0.5.1.dist-info/RECORD' 2021-07-12T21:23:56,208 removing build/bdist.linux-armv7l/wheel 2021-07-12T21:23:56,330 Building wheel for biocode (setup.py): finished with status 'done' 2021-07-12T21:23:56,335 Created wheel for biocode: filename=biocode-0.5.1-py3-none-any.whl size=218359 sha256=bf9a0479e6b373349ff4d030deed21980a2b0adab49430c21616bd78cdf290b1 2021-07-12T21:23:56,335 Stored in directory: /tmp/pip-ephem-wheel-cache-mtzsifla/wheels/ce/12/72/def9717dec46f38e684c58324a9f352fa309d460c4ca6f8f68 2021-07-12T21:23:56,348 Successfully built biocode 2021-07-12T21:23:56,358 Removed build tracker: '/tmp/pip-req-tracker-y37bifh6'