2021-02-16T14:54:17,765 DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality. 2021-02-16T14:54:18,430 Created temporary directory: /tmp/pip-ephem-wheel-cache-2satr6nk 2021-02-16T14:54:18,435 Created temporary directory: /tmp/pip-req-tracker-aog9fkxv 2021-02-16T14:54:18,436 Initialized build tracking at /tmp/pip-req-tracker-aog9fkxv 2021-02-16T14:54:18,436 Created build tracker: /tmp/pip-req-tracker-aog9fkxv 2021-02-16T14:54:18,437 Entered build tracker: /tmp/pip-req-tracker-aog9fkxv 2021-02-16T14:54:18,438 Created temporary directory: /tmp/pip-wheel-i6jkg1me 2021-02-16T14:54:18,502 1 location(s) to search for versions of dark-matter: 2021-02-16T14:54:18,502 * https://pypi.org/simple/dark-matter/ 2021-02-16T14:54:18,503 Fetching project page and analyzing links: https://pypi.org/simple/dark-matter/ 2021-02-16T14:54:18,505 Getting page https://pypi.org/simple/dark-matter/ 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https://files.pythonhosted.org/packages/e3/99/4ede5f73adb9a626398f1c60828357875bb15ce6a089f1f5d7cccdc23727/dark-matter-3.1.73.tar.gz#sha256=91427c52968f8db1c8ad6985ad39286155f6f1918e6d4c330942655ef61e3905 (from https://pypi.org/simple/dark-matter/), version: 3.1.73 2021-02-16T14:54:19,445 Found link https://files.pythonhosted.org/packages/63/f5/c113abaa137fabb548cbce7de51585a391ccbef68fdb50bac8b113c7881e/dark-matter-3.1.74.tar.gz#sha256=68d96ddda46298d92677dd83f4be92cf0f4d7bff45017ec362d4a7b954281bc0 (from https://pypi.org/simple/dark-matter/), version: 3.1.74 2021-02-16T14:54:19,446 Found link https://files.pythonhosted.org/packages/98/08/0cb8bda914063ba75079777c29571d3ef387047b097842dd5ed1790422d6/dark-matter-3.1.75.tar.gz#sha256=d69aa004b92d0683e421274f18add6a26e0d0c864c56c078bc7c6e67ca827f77 (from https://pypi.org/simple/dark-matter/), version: 3.1.75 2021-02-16T14:54:19,454 Found link https://files.pythonhosted.org/packages/cb/7f/75d266c4266f1b9179b22bb1edb7d38f5a6083b094c5e6fc53ef6c8a2995/dark-matter-3.1.76.tar.gz#sha256=a0bb511247a7ec82ceb8cf8eabfa045aa569e75d9f59def183f0c6158bdd7f17 (from https://pypi.org/simple/dark-matter/), version: 3.1.76 2021-02-16T14:54:19,455 Found link https://files.pythonhosted.org/packages/b2/c0/c5db9094660aae28d21252b24d6d21619149da37833da5164f407c9ea128/dark-matter-3.1.79.tar.gz#sha256=cc14e1021624cb50886b2e5b70b94259e004c975f0480ff35d9a3381e352f07e (from https://pypi.org/simple/dark-matter/), version: 3.1.79 2021-02-16T14:54:19,456 Found link https://files.pythonhosted.org/packages/bb/91/b9cb62df81f871bb56fb78d6038753845d4d4e90d1737ae6f410160ff31f/dark-matter-3.1.81.tar.gz#sha256=3d20c804033e2c2a2e453bb96b58fcde16e8ddca3057696e77330aa6e8df00d5 (from https://pypi.org/simple/dark-matter/), version: 3.1.81 2021-02-16T14:54:19,457 Found link https://files.pythonhosted.org/packages/fc/7c/182ac5794f96f41e378916d74a2f61883be0fc04f51e9fc88856cf55ff99/dark-matter-3.1.82.tar.gz#sha256=ab9cdf88400e98a49d5233b4deac87c60d1394f1a66bb1d770e24a7542b061dd (from https://pypi.org/simple/dark-matter/), version: 3.1.82 2021-02-16T14:54:19,458 Found link https://files.pythonhosted.org/packages/d1/29/20a1d35035fece08efda70f18f4fea4913d179edd497a811516589b6f6c0/dark-matter-3.1.84.tar.gz#sha256=8202263762607e3312781054ed326f82c0b8348bae1b9b803f21b07ea1ce15fd (from https://pypi.org/simple/dark-matter/), version: 3.1.84 2021-02-16T14:54:19,459 Found link https://files.pythonhosted.org/packages/13/d4/262226886768170d06cdc7b41b143e9151aaf6651725b48a949f9920305f/dark-matter-3.1.85.tar.gz#sha256=ef2ba3420eec01ff6aa91d30ac7a7e19e3abc53b270fb66c060540b4fbdb703a (from https://pypi.org/simple/dark-matter/), version: 3.1.85 2021-02-16T14:54:19,460 Found link https://files.pythonhosted.org/packages/b1/83/5f937593c1325857d5820729d1571331c1384af1b2c750848f0ddf25f32c/dark-matter-3.1.86.tar.gz#sha256=0c94c6ee0b76e1aa9e2d2820ba54ae865cd72fc99d32c89ac0cffb85b66dee90 (from https://pypi.org/simple/dark-matter/), version: 3.1.86 2021-02-16T14:54:19,461 Found link https://files.pythonhosted.org/packages/da/f4/36e03445ef41eab619e83e9b305085541a1fe3afe4080c7bbfd910538b73/dark-matter-3.1.87.tar.gz#sha256=fdc7c53b959e42dbc15e8be69e686459637121e160f922afc4f6ea724dce2e6a (from https://pypi.org/simple/dark-matter/), version: 3.1.87 2021-02-16T14:54:19,462 Found link https://files.pythonhosted.org/packages/c0/00/7fae5de4b38e001949cf2f5604456f361a4e4b16dccac360cad9c618774e/dark-matter-3.1.88.tar.gz#sha256=ee3972366f54ac8e8a8e6d82bb5eb3c8858e6991b839180cec0cd3726e2d2764 (from https://pypi.org/simple/dark-matter/), version: 3.1.88 2021-02-16T14:54:19,463 Found link https://files.pythonhosted.org/packages/a2/29/f9efce08d7da120118a4d3d554207a40ec0fe7f640338dcce34459ed65de/dark-matter-3.2.2.tar.gz#sha256=a774c902f7c8c61d0a03b485283767d52a414e8835a2286295f2fbe94f982d6c (from https://pypi.org/simple/dark-matter/), version: 3.2.2 2021-02-16T14:54:19,613 Given no hashes to check 1 links for project 'dark-matter': discarding no candidates 2021-02-16T14:54:19,654 Collecting dark-matter==3.2.2 2021-02-16T14:54:19,657 Created temporary directory: /tmp/pip-unpack-toxleoge 2021-02-16T14:54:19,909 Downloading dark-matter-3.2.2.tar.gz (331 kB) 2021-02-16T14:54:21,328 Added dark-matter==3.2.2 from https://files.pythonhosted.org/packages/a2/29/f9efce08d7da120118a4d3d554207a40ec0fe7f640338dcce34459ed65de/dark-matter-3.2.2.tar.gz#sha256=a774c902f7c8c61d0a03b485283767d52a414e8835a2286295f2fbe94f982d6c to build tracker '/tmp/pip-req-tracker-aog9fkxv' 2021-02-16T14:54:21,330 Running setup.py (path:/tmp/pip-wheel-i6jkg1me/dark-matter_f5be93794bb84e959f65943a1f330368/setup.py) egg_info for package dark-matter 2021-02-16T14:54:21,332 Created temporary directory: /tmp/pip-pip-egg-info-zz4mhu9v 2021-02-16T14:54:21,332 Running command python setup.py egg_info 2021-02-16T14:54:23,660 running egg_info 2021-02-16T14:54:23,667 creating /tmp/pip-pip-egg-info-zz4mhu9v/dark_matter.egg-info 2021-02-16T14:54:23,670 writing top-level names to /tmp/pip-pip-egg-info-zz4mhu9v/dark_matter.egg-info/top_level.txt 2021-02-16T14:54:23,673 writing requirements to /tmp/pip-pip-egg-info-zz4mhu9v/dark_matter.egg-info/requires.txt 2021-02-16T14:54:23,675 writing /tmp/pip-pip-egg-info-zz4mhu9v/dark_matter.egg-info/PKG-INFO 2021-02-16T14:54:23,679 writing dependency_links to /tmp/pip-pip-egg-info-zz4mhu9v/dark_matter.egg-info/dependency_links.txt 2021-02-16T14:54:23,685 writing manifest file '/tmp/pip-pip-egg-info-zz4mhu9v/dark_matter.egg-info/SOURCES.txt' 2021-02-16T14:54:24,120 reading manifest file '/tmp/pip-pip-egg-info-zz4mhu9v/dark_matter.egg-info/SOURCES.txt' 2021-02-16T14:54:24,142 writing manifest file '/tmp/pip-pip-egg-info-zz4mhu9v/dark_matter.egg-info/SOURCES.txt' 2021-02-16T14:54:24,279 Source in /tmp/pip-wheel-i6jkg1me/dark-matter_f5be93794bb84e959f65943a1f330368 has version 3.2.2, which satisfies requirement dark-matter==3.2.2 from https://files.pythonhosted.org/packages/a2/29/f9efce08d7da120118a4d3d554207a40ec0fe7f640338dcce34459ed65de/dark-matter-3.2.2.tar.gz#sha256=a774c902f7c8c61d0a03b485283767d52a414e8835a2286295f2fbe94f982d6c 2021-02-16T14:54:24,281 Removed dark-matter==3.2.2 from https://files.pythonhosted.org/packages/a2/29/f9efce08d7da120118a4d3d554207a40ec0fe7f640338dcce34459ed65de/dark-matter-3.2.2.tar.gz#sha256=a774c902f7c8c61d0a03b485283767d52a414e8835a2286295f2fbe94f982d6c from build tracker '/tmp/pip-req-tracker-aog9fkxv' 2021-02-16T14:54:24,289 Created temporary directory: /tmp/pip-unpack-_80d0m2j 2021-02-16T14:54:24,290 Building wheels for collected packages: dark-matter 2021-02-16T14:54:24,299 Created temporary directory: /tmp/pip-wheel-3x8w_fhs 2021-02-16T14:54:24,300 Building wheel for dark-matter (setup.py): started 2021-02-16T14:54:24,300 Destination directory: /tmp/pip-wheel-3x8w_fhs 2021-02-16T14:54:24,301 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-i6jkg1me/dark-matter_f5be93794bb84e959f65943a1f330368/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-i6jkg1me/dark-matter_f5be93794bb84e959f65943a1f330368/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-3x8w_fhs 2021-02-16T14:54:26,613 running bdist_wheel 2021-02-16T14:54:26,629 running build 2021-02-16T14:54:26,629 running build_py 2021-02-16T14:54:26,972 creating build 2021-02-16T14:54:26,973 creating build/lib 2021-02-16T14:54:26,975 creating build/lib/dark 2021-02-16T14:54:26,977 copying dark/intervals.py -> build/lib/dark 2021-02-16T14:54:26,982 copying dark/sam.py -> build/lib/dark 2021-02-16T14:54:26,990 copying dark/taxonomy.py -> build/lib/dark 2021-02-16T14:54:26,998 copying dark/process.py -> build/lib/dark 2021-02-16T14:54:27,004 copying dark/cigar.py -> build/lib/dark 2021-02-16T14:54:27,010 copying dark/entrez.py -> build/lib/dark 2021-02-16T14:54:27,015 copying dark/dna.py -> build/lib/dark 2021-02-16T14:54:27,023 copying dark/reads.py -> build/lib/dark 2021-02-16T14:54:27,034 copying dark/summarize.py -> build/lib/dark 2021-02-16T14:54:27,038 copying dark/aa.py -> build/lib/dark 2021-02-16T14:54:27,046 copying dark/alignments.py -> build/lib/dark 2021-02-16T14:54:27,053 copying dark/proteins.py -> build/lib/dark 2021-02-16T14:54:27,063 copying dark/html.py -> build/lib/dark 2021-02-16T14:54:27,070 copying dark/baseimage.py -> build/lib/dark 2021-02-16T14:54:27,076 copying dark/fasta.py -> build/lib/dark 2021-02-16T14:54:27,083 copying dark/ncbidb.py -> build/lib/dark 2021-02-16T14:54:27,089 copying dark/consensus.py -> build/lib/dark 2021-02-16T14:54:27,095 copying dark/utils.py -> build/lib/dark 2021-02-16T14:54:27,102 copying dark/fasta_ss.py -> build/lib/dark 2021-02-16T14:54:27,108 copying dark/analyze_reads.py -> build/lib/dark 2021-02-16T14:54:27,114 copying dark/features.py -> build/lib/dark 2021-02-16T14:54:27,121 copying dark/genomes.py -> build/lib/dark 2021-02-16T14:54:27,127 copying dark/dimension.py -> build/lib/dark 2021-02-16T14:54:27,133 copying dark/local_align.py -> build/lib/dark 2021-02-16T14:54:27,140 copying dark/bowtie2.py -> build/lib/dark 2021-02-16T14:54:27,147 copying dark/titles.py -> build/lib/dark 2021-02-16T14:54:27,155 copying dark/database.py -> build/lib/dark 2021-02-16T14:54:27,160 copying dark/colors.py -> build/lib/dark 2021-02-16T14:54:27,166 copying dark/genbank.py -> build/lib/dark 2021-02-16T14:54:27,173 copying dark/graphics.py -> build/lib/dark 2021-02-16T14:54:27,182 copying dark/codonDistance.py -> build/lib/dark 2021-02-16T14:54:27,188 copying dark/fastq.py -> build/lib/dark 2021-02-16T14:54:27,195 copying dark/filter.py -> build/lib/dark 2021-02-16T14:54:27,203 copying dark/hsp.py -> build/lib/dark 2021-02-16T14:54:27,209 copying dark/mutations.py -> build/lib/dark 2021-02-16T14:54:27,216 copying dark/sequence.py -> build/lib/dark 2021-02-16T14:54:27,220 copying dark/ipynb.py -> build/lib/dark 2021-02-16T14:54:27,224 copying dark/simplify.py -> build/lib/dark 2021-02-16T14:54:27,228 copying dark/distance.py -> build/lib/dark 2021-02-16T14:54:27,232 copying dark/orfs.py -> build/lib/dark 2021-02-16T14:54:27,237 copying dark/score.py -> build/lib/dark 2021-02-16T14:54:27,242 copying dark/errors.py -> build/lib/dark 2021-02-16T14:54:27,248 copying dark/fpcache.py -> build/lib/dark 2021-02-16T14:54:27,253 copying dark/btop.py -> build/lib/dark 2021-02-16T14:54:27,271 copying dark/aligners.py -> build/lib/dark 2021-02-16T14:54:27,277 copying dark/__init__.py -> build/lib/dark 2021-02-16T14:54:27,285 creating build/lib/dark/blast 2021-02-16T14:54:27,287 copying dark/blast/alignments.py -> build/lib/dark/blast 2021-02-16T14:54:27,295 copying dark/blast/params.py -> build/lib/dark/blast 2021-02-16T14:54:27,299 copying dark/blast/conversion.py -> build/lib/dark/blast 2021-02-16T14:54:27,305 copying dark/blast/records.py -> build/lib/dark/blast 2021-02-16T14:54:27,309 copying dark/blast/hacks.py -> build/lib/dark/blast 2021-02-16T14:54:27,312 copying dark/blast/hsp.py -> build/lib/dark/blast 2021-02-16T14:54:27,318 copying dark/blast/score.py -> build/lib/dark/blast 2021-02-16T14:54:27,324 copying dark/blast/__init__.py -> build/lib/dark/blast 2021-02-16T14:54:27,331 creating build/lib/dark/diamond 2021-02-16T14:54:27,333 copying dark/diamond/sam.py -> build/lib/dark/diamond 2021-02-16T14:54:27,340 copying dark/diamond/alignments.py -> build/lib/dark/diamond 2021-02-16T14:54:27,345 copying dark/diamond/conversion.py -> build/lib/dark/diamond 2021-02-16T14:54:27,351 copying dark/diamond/run.py -> build/lib/dark/diamond 2021-02-16T14:54:27,355 copying dark/diamond/hsp.py -> build/lib/dark/diamond 2021-02-16T14:54:27,361 copying dark/diamond/__init__.py -> build/lib/dark/diamond 2021-02-16T14:54:27,367 creating build/lib/dark/civ 2021-02-16T14:54:27,370 copying dark/civ/proteins.py -> build/lib/dark/civ 2021-02-16T14:54:27,385 copying dark/civ/html.py -> build/lib/dark/civ 2021-02-16T14:54:27,390 copying dark/civ/graphics.py -> build/lib/dark/civ 2021-02-16T14:54:27,396 copying dark/civ/__init__.py -> build/lib/dark/civ 2021-02-16T14:54:27,421 running build_scripts 2021-02-16T14:54:27,422 creating build/scripts-3.5 2021-02-16T14:54:27,425 copying and adjusting bin/aa-info.py -> build/scripts-3.5 2021-02-16T14:54:27,428 copying and adjusting bin/aa-to-dna.py -> build/scripts-3.5 2021-02-16T14:54:27,432 copying and adjusting bin/aa-to-properties.py -> build/scripts-3.5 2021-02-16T14:54:27,435 copying and adjusting bin/adaptor-distances.py -> build/scripts-3.5 2021-02-16T14:54:27,438 copying and adjusting bin/alignment-panel-civ.py -> build/scripts-3.5 2021-02-16T14:54:27,444 copying and adjusting bin/alignments-per-read.py -> build/scripts-3.5 2021-02-16T14:54:27,447 copying and adjusting bin/bit-score-to-e-value.py -> build/scripts-3.5 2021-02-16T14:54:27,451 copying and adjusting bin/cat-json-blast-records.py -> build/scripts-3.5 2021-02-16T14:54:27,454 copying and adjusting bin/check-fasta-json-blast-consistency.py -> build/scripts-3.5 2021-02-16T14:54:27,458 copying and adjusting bin/codon-distance.py -> build/scripts-3.5 2021-02-16T14:54:27,462 copying and adjusting bin/compare-consensuses.py -> build/scripts-3.5 2021-02-16T14:54:27,468 copying and adjusting bin/compare-sequences.py -> build/scripts-3.5 2021-02-16T14:54:27,474 copying and adjusting bin/convert-blast-xml-to-json.py -> build/scripts-3.5 2021-02-16T14:54:27,479 copying and adjusting bin/convert-diamond-to-json.py -> build/scripts-3.5 2021-02-16T14:54:27,483 copying and adjusting bin/convert-diamond-to-sam.py -> build/scripts-3.5 2021-02-16T14:54:27,488 copying bin/convert-sam-to-fastq.sh -> build/scripts-3.5 2021-02-16T14:54:27,493 copying and adjusting bin/create-newick-relabeling-output.py -> build/scripts-3.5 2021-02-16T14:54:27,496 copying and adjusting bin/dark-matter-version.py -> build/scripts-3.5 2021-02-16T14:54:27,499 copying and adjusting bin/describe-protein-database.py -> build/scripts-3.5 2021-02-16T14:54:27,503 copying and adjusting bin/dna-to-aa.py -> build/scripts-3.5 2021-02-16T14:54:27,509 copying bin/download-genbank.sh -> build/scripts-3.5 2021-02-16T14:54:27,517 copying and adjusting bin/e-value-to-bit-score.py -> build/scripts-3.5 2021-02-16T14:54:27,523 copying and adjusting bin/extract-ORFs.py -> build/scripts-3.5 2021-02-16T14:54:27,528 copying and adjusting bin/fasta-base-indices.py -> build/scripts-3.5 2021-02-16T14:54:27,532 copying and adjusting bin/fasta-count.py -> build/scripts-3.5 2021-02-16T14:54:27,537 copying bin/fasta-diff.sh -> build/scripts-3.5 2021-02-16T14:54:27,542 copying and adjusting bin/fasta-identity-table.py -> build/scripts-3.5 2021-02-16T14:54:27,550 copying and adjusting bin/fasta-ids.py -> build/scripts-3.5 2021-02-16T14:54:27,554 copying and adjusting bin/fasta-join.py -> build/scripts-3.5 2021-02-16T14:54:27,558 copying and adjusting bin/fasta-lengths.py -> build/scripts-3.5 2021-02-16T14:54:27,562 copying and adjusting bin/fasta-sequences.py -> build/scripts-3.5 2021-02-16T14:54:27,567 copying and adjusting bin/fasta-sort.py -> build/scripts-3.5 2021-02-16T14:54:27,571 copying and adjusting bin/fasta-split-by-id.py -> build/scripts-3.5 2021-02-16T14:54:27,575 copying and adjusting bin/fasta-subset.py -> build/scripts-3.5 2021-02-16T14:54:27,580 copying and adjusting bin/fasta-subtraction.py -> build/scripts-3.5 2021-02-16T14:54:27,584 copying and adjusting bin/fasta-to-phylip.py -> build/scripts-3.5 2021-02-16T14:54:27,588 copying and adjusting bin/fasta-variable-sites.py -> build/scripts-3.5 2021-02-16T14:54:27,594 copying and adjusting bin/filter-fasta-by-complexity.py -> build/scripts-3.5 2021-02-16T14:54:27,598 copying and adjusting bin/filter-fasta-by-taxonomy.py -> build/scripts-3.5 2021-02-16T14:54:27,604 copying and adjusting bin/filter-fasta.py -> build/scripts-3.5 2021-02-16T14:54:27,607 copying and adjusting bin/filter-hits-to-fasta.py -> build/scripts-3.5 2021-02-16T14:54:27,612 copying and adjusting bin/filter-reads-alignments.py -> build/scripts-3.5 2021-02-16T14:54:27,618 copying and adjusting bin/filter-sam.py -> build/scripts-3.5 2021-02-16T14:54:27,624 copying and adjusting bin/find-hits.py -> build/scripts-3.5 2021-02-16T14:54:27,630 copying and adjusting bin/format-fasta.py -> build/scripts-3.5 2021-02-16T14:54:27,636 copying and adjusting bin/genome-protein-summary.py -> build/scripts-3.5 2021-02-16T14:54:27,644 copying and adjusting bin/get-features.py -> build/scripts-3.5 2021-02-16T14:54:27,649 copying and adjusting bin/get-hosts.py -> build/scripts-3.5 2021-02-16T14:54:27,654 copying and adjusting bin/get-reads.py -> build/scripts-3.5 2021-02-16T14:54:27,659 copying and adjusting bin/get-taxonomy.py -> build/scripts-3.5 2021-02-16T14:54:27,664 copying and adjusting bin/graph-evalues.py -> build/scripts-3.5 2021-02-16T14:54:27,669 copying and adjusting bin/local-align.py -> build/scripts-3.5 2021-02-16T14:54:27,673 copying and adjusting bin/make-consensus.py -> build/scripts-3.5 2021-02-16T14:54:27,679 copying and adjusting bin/make-fasta-database.py -> build/scripts-3.5 2021-02-16T14:54:27,683 copying and adjusting bin/make-protein-database.py -> build/scripts-3.5 2021-02-16T14:54:27,689 copying and adjusting bin/ncbi-fetch-id.py -> build/scripts-3.5 2021-02-16T14:54:27,693 copying and adjusting bin/newick-to-ascii.py -> build/scripts-3.5 2021-02-16T14:54:27,698 copying and adjusting bin/noninteractive-alignment-panel.py -> build/scripts-3.5 2021-02-16T14:54:27,705 copying and adjusting bin/parse-genbank-flat-file.py -> build/scripts-3.5 2021-02-16T14:54:27,711 copying and adjusting bin/position-summary.py -> build/scripts-3.5 2021-02-16T14:54:27,717 copying bin/pre-commit.sh -> build/scripts-3.5 2021-02-16T14:54:27,725 copying and adjusting bin/print-blast-xml-for-derek.py -> build/scripts-3.5 2021-02-16T14:54:27,730 copying and adjusting bin/print-blast-xml.py -> build/scripts-3.5 2021-02-16T14:54:27,734 copying and adjusting bin/print-read-lengths.py -> build/scripts-3.5 2021-02-16T14:54:27,739 copying and adjusting bin/proteins-to-pathogens.py -> build/scripts-3.5 2021-02-16T14:54:27,745 copying and adjusting bin/proteins-to-pathogens-civ.py -> build/scripts-3.5 2021-02-16T14:54:27,751 copying and adjusting bin/randomize-fasta.py -> build/scripts-3.5 2021-02-16T14:54:27,756 copying and adjusting bin/read-blast-json.py -> build/scripts-3.5 2021-02-16T14:54:27,760 copying and adjusting bin/read-blast-xml.py -> build/scripts-3.5 2021-02-16T14:54:27,764 copying and adjusting bin/relabel-newick-tree.py -> build/scripts-3.5 2021-02-16T14:54:27,769 copying and adjusting bin/run-bwa.py -> build/scripts-3.5 2021-02-16T14:54:27,776 copying and adjusting bin/run-bowtie2.py -> build/scripts-3.5 2021-02-16T14:54:27,786 copying and adjusting bin/sam-coverage.py -> build/scripts-3.5 2021-02-16T14:54:27,791 copying and adjusting bin/sam-coverage-depth.py -> build/scripts-3.5 2021-02-16T14:54:27,797 copying and adjusting bin/sam-to-fasta-alignment.py -> build/scripts-3.5 2021-02-16T14:54:27,801 copying and adjusting bin/sam-reference-read-counts.py -> build/scripts-3.5 2021-02-16T14:54:27,806 copying and adjusting bin/sam-references.py -> build/scripts-3.5 2021-02-16T14:54:27,810 copying and adjusting bin/sff-to-fastq.py -> build/scripts-3.5 2021-02-16T14:54:27,814 copying and adjusting bin/split-fasta-by-adaptors.py -> build/scripts-3.5 2021-02-16T14:54:27,820 copying and adjusting bin/subset-protein-database.py -> build/scripts-3.5 2021-02-16T14:54:27,824 copying and adjusting bin/summarize-fasta-bases.py -> build/scripts-3.5 2021-02-16T14:54:27,829 copying and adjusting bin/summarize-reads.py -> build/scripts-3.5 2021-02-16T14:54:27,833 copying and adjusting bin/translate.py -> build/scripts-3.5 2021-02-16T14:54:27,836 copying and adjusting bin/trim-primers.py -> build/scripts-3.5 2021-02-16T14:54:27,840 copying and adjusting bin/trim-reads.py -> build/scripts-3.5 2021-02-16T14:54:27,843 copying and adjusting bin/write-htcondor-job-spec.py -> build/scripts-3.5 2021-02-16T14:54:27,847 changing mode of build/scripts-3.5/aa-info.py from 644 to 755 2021-02-16T14:54:27,847 changing mode of build/scripts-3.5/aa-to-dna.py from 644 to 755 2021-02-16T14:54:27,848 changing mode of build/scripts-3.5/aa-to-properties.py from 644 to 755 2021-02-16T14:54:27,850 changing mode of build/scripts-3.5/adaptor-distances.py from 644 to 755 2021-02-16T14:54:27,851 changing mode of build/scripts-3.5/alignment-panel-civ.py from 644 to 755 2021-02-16T14:54:27,852 changing mode of build/scripts-3.5/alignments-per-read.py from 644 to 755 2021-02-16T14:54:27,853 changing mode of build/scripts-3.5/bit-score-to-e-value.py from 644 to 755 2021-02-16T14:54:27,854 changing mode of build/scripts-3.5/cat-json-blast-records.py from 644 to 755 2021-02-16T14:54:27,855 changing mode of build/scripts-3.5/check-fasta-json-blast-consistency.py from 644 to 755 2021-02-16T14:54:27,856 changing mode of build/scripts-3.5/codon-distance.py from 644 to 755 2021-02-16T14:54:27,858 changing mode of build/scripts-3.5/compare-consensuses.py from 644 to 755 2021-02-16T14:54:27,859 changing mode of build/scripts-3.5/compare-sequences.py from 644 to 755 2021-02-16T14:54:27,860 changing mode of build/scripts-3.5/convert-blast-xml-to-json.py from 644 to 755 2021-02-16T14:54:27,861 changing mode of build/scripts-3.5/convert-diamond-to-json.py from 644 to 755 2021-02-16T14:54:27,863 changing mode of build/scripts-3.5/convert-diamond-to-sam.py from 644 to 755 2021-02-16T14:54:27,864 changing mode of build/scripts-3.5/create-newick-relabeling-output.py from 644 to 755 2021-02-16T14:54:27,865 changing mode of build/scripts-3.5/dark-matter-version.py from 644 to 755 2021-02-16T14:54:27,866 changing mode of build/scripts-3.5/describe-protein-database.py from 644 to 755 2021-02-16T14:54:27,867 changing mode of build/scripts-3.5/dna-to-aa.py from 644 to 755 2021-02-16T14:54:27,868 changing mode of build/scripts-3.5/e-value-to-bit-score.py from 644 to 755 2021-02-16T14:54:27,869 changing mode of build/scripts-3.5/extract-ORFs.py from 644 to 755 2021-02-16T14:54:27,870 changing mode of build/scripts-3.5/fasta-base-indices.py from 644 to 755 2021-02-16T14:54:27,871 changing mode of build/scripts-3.5/fasta-count.py from 644 to 755 2021-02-16T14:54:27,871 changing mode of build/scripts-3.5/fasta-identity-table.py from 644 to 755 2021-02-16T14:54:27,872 changing mode of build/scripts-3.5/fasta-ids.py from 644 to 755 2021-02-16T14:54:27,872 changing mode of build/scripts-3.5/fasta-join.py from 644 to 755 2021-02-16T14:54:27,873 changing mode of build/scripts-3.5/fasta-lengths.py from 644 to 755 2021-02-16T14:54:27,874 changing mode of build/scripts-3.5/fasta-sequences.py from 644 to 755 2021-02-16T14:54:27,874 changing mode of build/scripts-3.5/fasta-sort.py from 644 to 755 2021-02-16T14:54:27,875 changing mode of build/scripts-3.5/fasta-split-by-id.py from 644 to 755 2021-02-16T14:54:27,876 changing mode of build/scripts-3.5/fasta-subset.py from 644 to 755 2021-02-16T14:54:27,876 changing mode of build/scripts-3.5/fasta-subtraction.py from 644 to 755 2021-02-16T14:54:27,877 changing mode of build/scripts-3.5/fasta-to-phylip.py from 644 to 755 2021-02-16T14:54:27,877 changing mode of build/scripts-3.5/fasta-variable-sites.py from 644 to 755 2021-02-16T14:54:27,878 changing mode of build/scripts-3.5/filter-fasta-by-complexity.py from 644 to 755 2021-02-16T14:54:27,879 changing mode of build/scripts-3.5/filter-fasta-by-taxonomy.py from 644 to 755 2021-02-16T14:54:27,879 changing mode of build/scripts-3.5/filter-fasta.py from 644 to 755 2021-02-16T14:54:27,880 changing mode of build/scripts-3.5/filter-hits-to-fasta.py from 644 to 755 2021-02-16T14:54:27,881 changing mode of build/scripts-3.5/filter-reads-alignments.py from 644 to 755 2021-02-16T14:54:27,881 changing mode of build/scripts-3.5/filter-sam.py from 644 to 755 2021-02-16T14:54:27,882 changing mode of build/scripts-3.5/find-hits.py from 644 to 755 2021-02-16T14:54:27,883 changing mode of build/scripts-3.5/format-fasta.py from 644 to 755 2021-02-16T14:54:27,883 changing mode of build/scripts-3.5/genome-protein-summary.py from 644 to 755 2021-02-16T14:54:27,884 changing mode of build/scripts-3.5/get-features.py from 644 to 755 2021-02-16T14:54:27,884 changing mode of build/scripts-3.5/get-hosts.py from 644 to 755 2021-02-16T14:54:27,885 changing mode of build/scripts-3.5/get-reads.py from 644 to 755 2021-02-16T14:54:27,886 changing mode of build/scripts-3.5/get-taxonomy.py from 644 to 755 2021-02-16T14:54:27,886 changing mode of build/scripts-3.5/graph-evalues.py from 644 to 755 2021-02-16T14:54:27,887 changing mode of build/scripts-3.5/local-align.py from 644 to 755 2021-02-16T14:54:27,887 changing mode of build/scripts-3.5/make-consensus.py from 644 to 755 2021-02-16T14:54:27,888 changing mode of build/scripts-3.5/make-fasta-database.py from 644 to 755 2021-02-16T14:54:27,889 changing mode of build/scripts-3.5/make-protein-database.py from 644 to 755 2021-02-16T14:54:27,890 changing mode of build/scripts-3.5/ncbi-fetch-id.py from 644 to 755 2021-02-16T14:54:27,890 changing mode of build/scripts-3.5/newick-to-ascii.py from 644 to 755 2021-02-16T14:54:27,891 changing mode of build/scripts-3.5/noninteractive-alignment-panel.py from 644 to 755 2021-02-16T14:54:27,892 changing mode of build/scripts-3.5/parse-genbank-flat-file.py from 644 to 755 2021-02-16T14:54:27,892 changing mode of build/scripts-3.5/position-summary.py from 644 to 755 2021-02-16T14:54:27,893 changing mode of build/scripts-3.5/print-blast-xml-for-derek.py from 644 to 755 2021-02-16T14:54:27,894 changing mode of build/scripts-3.5/print-blast-xml.py from 644 to 755 2021-02-16T14:54:27,894 changing mode of build/scripts-3.5/print-read-lengths.py from 644 to 755 2021-02-16T14:54:27,895 changing mode of build/scripts-3.5/proteins-to-pathogens.py from 644 to 755 2021-02-16T14:54:27,895 changing mode of build/scripts-3.5/proteins-to-pathogens-civ.py from 644 to 755 2021-02-16T14:54:27,896 changing mode of build/scripts-3.5/randomize-fasta.py from 644 to 755 2021-02-16T14:54:27,897 changing mode of build/scripts-3.5/read-blast-json.py from 644 to 755 2021-02-16T14:54:27,897 changing mode of build/scripts-3.5/read-blast-xml.py from 644 to 755 2021-02-16T14:54:27,898 changing mode of build/scripts-3.5/relabel-newick-tree.py from 644 to 755 2021-02-16T14:54:27,899 changing mode of build/scripts-3.5/run-bwa.py from 644 to 755 2021-02-16T14:54:27,899 changing mode of build/scripts-3.5/run-bowtie2.py from 644 to 755 2021-02-16T14:54:27,900 changing mode of build/scripts-3.5/sam-coverage.py from 644 to 755 2021-02-16T14:54:27,901 changing mode of build/scripts-3.5/sam-coverage-depth.py from 644 to 755 2021-02-16T14:54:27,901 changing mode of build/scripts-3.5/sam-to-fasta-alignment.py from 644 to 755 2021-02-16T14:54:27,902 changing mode of build/scripts-3.5/sam-reference-read-counts.py from 644 to 755 2021-02-16T14:54:27,902 changing mode of build/scripts-3.5/sam-references.py from 644 to 755 2021-02-16T14:54:27,903 changing mode of build/scripts-3.5/sff-to-fastq.py from 644 to 755 2021-02-16T14:54:27,904 changing mode of build/scripts-3.5/split-fasta-by-adaptors.py from 644 to 755 2021-02-16T14:54:27,904 changing mode of build/scripts-3.5/subset-protein-database.py from 644 to 755 2021-02-16T14:54:27,905 changing mode of build/scripts-3.5/summarize-fasta-bases.py from 644 to 755 2021-02-16T14:54:27,906 changing mode of build/scripts-3.5/summarize-reads.py from 644 to 755 2021-02-16T14:54:27,906 changing mode of build/scripts-3.5/translate.py from 644 to 755 2021-02-16T14:54:27,907 changing mode of build/scripts-3.5/trim-primers.py from 644 to 755 2021-02-16T14:54:27,908 changing mode of build/scripts-3.5/trim-reads.py from 644 to 755 2021-02-16T14:54:27,908 changing mode of build/scripts-3.5/write-htcondor-job-spec.py from 644 to 755 2021-02-16T14:54:27,915 installing to build/bdist.linux-armv7l/wheel 2021-02-16T14:54:27,916 running install 2021-02-16T14:54:27,917 running install_lib 2021-02-16T14:54:27,925 creating build/bdist.linux-armv7l 2021-02-16T14:54:27,926 creating build/bdist.linux-armv7l/wheel 2021-02-16T14:54:27,932 creating build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:27,934 copying build/lib/dark/intervals.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:27,941 copying build/lib/dark/sam.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:27,949 copying build/lib/dark/taxonomy.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:27,957 copying build/lib/dark/process.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:27,963 copying build/lib/dark/cigar.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:27,969 copying build/lib/dark/entrez.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:27,975 copying build/lib/dark/dna.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:27,985 creating build/bdist.linux-armv7l/wheel/dark/diamond 2021-02-16T14:54:27,987 copying build/lib/dark/diamond/sam.py -> build/bdist.linux-armv7l/wheel/dark/diamond 2021-02-16T14:54:27,995 copying build/lib/dark/diamond/alignments.py -> build/bdist.linux-armv7l/wheel/dark/diamond 2021-02-16T14:54:28,000 copying build/lib/dark/diamond/conversion.py -> build/bdist.linux-armv7l/wheel/dark/diamond 2021-02-16T14:54:28,007 copying build/lib/dark/diamond/run.py -> build/bdist.linux-armv7l/wheel/dark/diamond 2021-02-16T14:54:28,012 copying build/lib/dark/diamond/hsp.py -> build/bdist.linux-armv7l/wheel/dark/diamond 2021-02-16T14:54:28,019 copying build/lib/dark/diamond/__init__.py -> build/bdist.linux-armv7l/wheel/dark/diamond 2021-02-16T14:54:28,024 copying build/lib/dark/reads.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,035 copying build/lib/dark/summarize.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,040 copying build/lib/dark/aa.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,048 copying build/lib/dark/alignments.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,058 creating build/bdist.linux-armv7l/wheel/dark/civ 2021-02-16T14:54:28,060 copying build/lib/dark/civ/proteins.py -> build/bdist.linux-armv7l/wheel/dark/civ 2021-02-16T14:54:28,077 copying build/lib/dark/civ/html.py -> build/bdist.linux-armv7l/wheel/dark/civ 2021-02-16T14:54:28,084 copying build/lib/dark/civ/graphics.py -> build/bdist.linux-armv7l/wheel/dark/civ 2021-02-16T14:54:28,092 copying build/lib/dark/civ/__init__.py -> build/bdist.linux-armv7l/wheel/dark/civ 2021-02-16T14:54:28,096 copying build/lib/dark/proteins.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,109 creating build/bdist.linux-armv7l/wheel/dark/blast 2021-02-16T14:54:28,111 copying build/lib/dark/blast/alignments.py -> build/bdist.linux-armv7l/wheel/dark/blast 2021-02-16T14:54:28,117 copying build/lib/dark/blast/params.py -> build/bdist.linux-armv7l/wheel/dark/blast 2021-02-16T14:54:28,122 copying build/lib/dark/blast/conversion.py -> build/bdist.linux-armv7l/wheel/dark/blast 2021-02-16T14:54:28,127 copying build/lib/dark/blast/records.py -> build/bdist.linux-armv7l/wheel/dark/blast 2021-02-16T14:54:28,132 copying build/lib/dark/blast/hacks.py -> build/bdist.linux-armv7l/wheel/dark/blast 2021-02-16T14:54:28,137 copying build/lib/dark/blast/hsp.py -> build/bdist.linux-armv7l/wheel/dark/blast 2021-02-16T14:54:28,144 copying build/lib/dark/blast/score.py -> build/bdist.linux-armv7l/wheel/dark/blast 2021-02-16T14:54:28,150 copying build/lib/dark/blast/__init__.py -> build/bdist.linux-armv7l/wheel/dark/blast 2021-02-16T14:54:28,155 copying build/lib/dark/html.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,162 copying build/lib/dark/baseimage.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,167 copying build/lib/dark/fasta.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,175 copying build/lib/dark/ncbidb.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,181 copying build/lib/dark/consensus.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,187 copying build/lib/dark/utils.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,194 copying build/lib/dark/fasta_ss.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,200 copying build/lib/dark/analyze_reads.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,206 copying build/lib/dark/features.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,213 copying build/lib/dark/genomes.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,220 copying build/lib/dark/dimension.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,225 copying build/lib/dark/local_align.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,233 copying build/lib/dark/bowtie2.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,240 copying build/lib/dark/titles.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,248 copying build/lib/dark/database.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,254 copying build/lib/dark/colors.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,260 copying build/lib/dark/genbank.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,266 copying build/lib/dark/graphics.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,276 copying build/lib/dark/codonDistance.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,282 copying build/lib/dark/fastq.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,288 copying build/lib/dark/filter.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,296 copying build/lib/dark/hsp.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,303 copying build/lib/dark/mutations.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,310 copying build/lib/dark/sequence.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,316 copying build/lib/dark/ipynb.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,322 copying build/lib/dark/simplify.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,327 copying build/lib/dark/distance.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,333 copying build/lib/dark/orfs.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,339 copying build/lib/dark/score.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,344 copying build/lib/dark/errors.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,350 copying build/lib/dark/fpcache.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,355 copying build/lib/dark/btop.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,362 copying build/lib/dark/aligners.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,367 copying build/lib/dark/__init__.py -> build/bdist.linux-armv7l/wheel/dark 2021-02-16T14:54:28,372 running install_egg_info 2021-02-16T14:54:28,421 running egg_info 2021-02-16T14:54:28,422 writing top-level names to dark_matter.egg-info/top_level.txt 2021-02-16T14:54:28,424 writing requirements to dark_matter.egg-info/requires.txt 2021-02-16T14:54:28,427 writing dark_matter.egg-info/PKG-INFO 2021-02-16T14:54:28,432 writing dependency_links to dark_matter.egg-info/dependency_links.txt 2021-02-16T14:54:28,481 reading manifest file 'dark_matter.egg-info/SOURCES.txt' 2021-02-16T14:54:28,522 writing manifest file 'dark_matter.egg-info/SOURCES.txt' 2021-02-16T14:54:28,526 Copying dark_matter.egg-info to build/bdist.linux-armv7l/wheel/dark_matter-3.2.2-py3.5.egg-info 2021-02-16T14:54:28,551 running install_scripts 2021-02-16T14:54:28,696 creating build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data 2021-02-16T14:54:28,696 creating build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,699 copying build/scripts-3.5/compare-sequences.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,705 copying build/scripts-3.5/convert-diamond-to-sam.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,710 copying build/scripts-3.5/bit-score-to-e-value.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,716 copying build/scripts-3.5/aa-to-dna.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,721 copying build/scripts-3.5/filter-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,727 copying build/scripts-3.5/run-bowtie2.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,734 copying build/scripts-3.5/sff-to-fastq.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,740 copying build/scripts-3.5/parse-genbank-flat-file.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,745 copying build/scripts-3.5/get-features.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,751 copying build/scripts-3.5/e-value-to-bit-score.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,756 copying build/scripts-3.5/genome-protein-summary.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,763 copying build/scripts-3.5/fasta-base-indices.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,769 copying build/scripts-3.5/sam-to-fasta-alignment.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,775 copying build/scripts-3.5/fasta-variable-sites.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,781 copying build/scripts-3.5/summarize-fasta-bases.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,787 copying build/scripts-3.5/ncbi-fetch-id.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,793 copying build/scripts-3.5/sam-coverage.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,799 copying build/scripts-3.5/codon-distance.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,804 copying build/scripts-3.5/cat-json-blast-records.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,810 copying build/scripts-3.5/sam-coverage-depth.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,816 copying build/scripts-3.5/extract-ORFs.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,824 copying build/scripts-3.5/print-read-lengths.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,831 copying build/scripts-3.5/read-blast-xml.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,837 copying build/scripts-3.5/filter-sam.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,843 copying build/scripts-3.5/adaptor-distances.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,848 copying build/scripts-3.5/filter-hits-to-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,854 copying build/scripts-3.5/noninteractive-alignment-panel.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,864 copying build/scripts-3.5/randomize-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,871 copying build/scripts-3.5/make-consensus.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,879 copying build/scripts-3.5/fasta-count.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,884 copying build/scripts-3.5/run-bwa.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,889 copying build/scripts-3.5/describe-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,894 copying build/scripts-3.5/summarize-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,901 copying build/scripts-3.5/trim-primers.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,908 copying build/scripts-3.5/filter-fasta-by-complexity.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,915 copying build/scripts-3.5/get-hosts.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,921 copying build/scripts-3.5/fasta-identity-table.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,929 copying build/scripts-3.5/format-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,935 copying build/scripts-3.5/alignments-per-read.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,940 copying build/scripts-3.5/print-blast-xml.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,944 copying build/scripts-3.5/sam-references.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,949 copying build/scripts-3.5/proteins-to-pathogens.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,954 copying build/scripts-3.5/alignment-panel-civ.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,962 copying build/scripts-3.5/fasta-subtraction.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,967 copying build/scripts-3.5/convert-blast-xml-to-json.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,973 copying build/scripts-3.5/fasta-diff.sh -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,979 copying build/scripts-3.5/fasta-subset.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,984 copying build/scripts-3.5/trim-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,988 copying build/scripts-3.5/find-hits.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,992 copying build/scripts-3.5/fasta-split-by-id.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:28,997 copying build/scripts-3.5/get-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,003 copying build/scripts-3.5/print-blast-xml-for-derek.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,009 copying build/scripts-3.5/position-summary.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,015 copying build/scripts-3.5/graph-evalues.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,020 copying build/scripts-3.5/fasta-join.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,025 copying build/scripts-3.5/compare-consensuses.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,031 copying build/scripts-3.5/split-fasta-by-adaptors.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,036 copying build/scripts-3.5/newick-to-ascii.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,042 copying build/scripts-3.5/dark-matter-version.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,047 copying build/scripts-3.5/fasta-ids.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,053 copying build/scripts-3.5/convert-sam-to-fastq.sh -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,059 copying build/scripts-3.5/sam-reference-read-counts.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,064 copying build/scripts-3.5/fasta-sort.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,068 copying build/scripts-3.5/fasta-sequences.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,072 copying build/scripts-3.5/pre-commit.sh -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,077 copying build/scripts-3.5/download-genbank.sh -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,083 copying build/scripts-3.5/make-fasta-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,089 copying build/scripts-3.5/read-blast-json.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,095 copying build/scripts-3.5/local-align.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,101 copying build/scripts-3.5/fasta-to-phylip.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,105 copying build/scripts-3.5/relabel-newick-tree.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,110 copying build/scripts-3.5/translate.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,114 copying build/scripts-3.5/subset-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,119 copying build/scripts-3.5/convert-diamond-to-json.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,124 copying build/scripts-3.5/aa-to-properties.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,130 copying build/scripts-3.5/filter-fasta-by-taxonomy.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,137 copying build/scripts-3.5/write-htcondor-job-spec.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,143 copying build/scripts-3.5/check-fasta-json-blast-consistency.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,148 copying build/scripts-3.5/create-newick-relabeling-output.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,152 copying build/scripts-3.5/proteins-to-pathogens-civ.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,158 copying build/scripts-3.5/fasta-lengths.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,163 copying build/scripts-3.5/filter-reads-alignments.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,170 copying build/scripts-3.5/make-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,177 copying build/scripts-3.5/dna-to-aa.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,183 copying build/scripts-3.5/get-taxonomy.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,187 copying build/scripts-3.5/aa-info.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts 2021-02-16T14:54:29,191 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/compare-sequences.py to 755 2021-02-16T14:54:29,192 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/convert-diamond-to-sam.py to 755 2021-02-16T14:54:29,193 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/bit-score-to-e-value.py to 755 2021-02-16T14:54:29,194 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/aa-to-dna.py to 755 2021-02-16T14:54:29,194 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/filter-fasta.py to 755 2021-02-16T14:54:29,195 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/run-bowtie2.py to 755 2021-02-16T14:54:29,196 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/sff-to-fastq.py to 755 2021-02-16T14:54:29,197 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/parse-genbank-flat-file.py to 755 2021-02-16T14:54:29,197 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/get-features.py to 755 2021-02-16T14:54:29,198 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/e-value-to-bit-score.py to 755 2021-02-16T14:54:29,199 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/genome-protein-summary.py to 755 2021-02-16T14:54:29,200 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/fasta-base-indices.py to 755 2021-02-16T14:54:29,200 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/sam-to-fasta-alignment.py to 755 2021-02-16T14:54:29,201 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/fasta-variable-sites.py to 755 2021-02-16T14:54:29,202 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/summarize-fasta-bases.py to 755 2021-02-16T14:54:29,203 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/ncbi-fetch-id.py to 755 2021-02-16T14:54:29,203 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/sam-coverage.py to 755 2021-02-16T14:54:29,204 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/codon-distance.py to 755 2021-02-16T14:54:29,205 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/cat-json-blast-records.py to 755 2021-02-16T14:54:29,206 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/sam-coverage-depth.py to 755 2021-02-16T14:54:29,206 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/extract-ORFs.py to 755 2021-02-16T14:54:29,207 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/print-read-lengths.py to 755 2021-02-16T14:54:29,208 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/read-blast-xml.py to 755 2021-02-16T14:54:29,208 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/filter-sam.py to 755 2021-02-16T14:54:29,209 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/adaptor-distances.py to 755 2021-02-16T14:54:29,210 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/filter-hits-to-fasta.py to 755 2021-02-16T14:54:29,211 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/noninteractive-alignment-panel.py to 755 2021-02-16T14:54:29,211 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/randomize-fasta.py to 755 2021-02-16T14:54:29,212 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/make-consensus.py to 755 2021-02-16T14:54:29,213 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/fasta-count.py to 755 2021-02-16T14:54:29,214 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/run-bwa.py to 755 2021-02-16T14:54:29,214 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/describe-protein-database.py to 755 2021-02-16T14:54:29,215 changing mode of 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build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/get-taxonomy.py to 755 2021-02-16T14:54:29,254 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.data/scripts/aa-info.py to 755 2021-02-16T14:54:29,348 creating build/bdist.linux-armv7l/wheel/dark_matter-3.2.2.dist-info/WHEEL 2021-02-16T14:54:30,314 Building wheel for dark-matter (setup.py): finished with status 'done' 2021-02-16T14:54:30,324 Created wheel for dark-matter: filename=dark_matter-3.2.2-py3-none-any.whl size=316036 sha256=3461d746139590bb40eb41d16db11e4d63761d3164af08f1feed17066819c58e 2021-02-16T14:54:30,325 Stored in directory: /tmp/pip-ephem-wheel-cache-2satr6nk/wheels/cd/5d/55/d494590af47c9695b444ce27e21a27df2741f21a4535556f3e 2021-02-16T14:54:30,357 Successfully built dark-matter 2021-02-16T14:54:30,416 Removed build tracker: '/tmp/pip-req-tracker-aog9fkxv'