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https://files.pythonhosted.org/packages/92/2e/b4dd15951f023be983d8d4fefc2d7df1afe7f4745370646e4c8211e24150/dark-matter-3.0.61.tar.gz#sha256=d1954a4a444e1d25fff20ee03e355ecd2424de9da95ec1a7d3f68247f47a2086 (from https://pypi.org/simple/dark-matter/), version: 3.0.61 Found link https://files.pythonhosted.org/packages/d2/fc/074a7854b33bb14b8a7aefcf61a9b3e0459ebc44018d16eafd3f66797144/dark-matter-3.0.62.tar.gz#sha256=31dceb8c4b36d4acfaee9cbb14f7d36b752a3fe2d889fa0e14825374372fca08 (from https://pypi.org/simple/dark-matter/), version: 3.0.62 Found link https://files.pythonhosted.org/packages/ff/08/0d32772dce2bd7ce4d54692f420e5065b2916f39b8f9a3d67bd8dc2830d3/dark-matter-3.0.63.tar.gz#sha256=2b4fe4e02e8092166ccfd7166a0376e505674a68f029efae95671bc142f45c78 (from https://pypi.org/simple/dark-matter/), version: 3.0.63 Using version 3.0.63 (newest of versions: 3.0.63) Created temporary directory: /tmp/pip-unpack-tmbddd2p Downloading https://files.pythonhosted.org/packages/ff/08/0d32772dce2bd7ce4d54692f420e5065b2916f39b8f9a3d67bd8dc2830d3/dark-matter-3.0.63.tar.gz (228kB) Downloading from URL https://files.pythonhosted.org/packages/ff/08/0d32772dce2bd7ce4d54692f420e5065b2916f39b8f9a3d67bd8dc2830d3/dark-matter-3.0.63.tar.gz#sha256=2b4fe4e02e8092166ccfd7166a0376e505674a68f029efae95671bc142f45c78 (from https://pypi.org/simple/dark-matter/) Added dark-matter==3.0.63 from https://files.pythonhosted.org/packages/ff/08/0d32772dce2bd7ce4d54692f420e5065b2916f39b8f9a3d67bd8dc2830d3/dark-matter-3.0.63.tar.gz#sha256=2b4fe4e02e8092166ccfd7166a0376e505674a68f029efae95671bc142f45c78 to build tracker '/tmp/pip-req-tracker-uasg26b0' Running setup.py (path:/tmp/pip-wheel-wr17t98e/dark-matter/setup.py) egg_info for package dark-matter Running command python setup.py egg_info running egg_info creating pip-egg-info/dark_matter.egg-info writing pip-egg-info/dark_matter.egg-info/PKG-INFO writing dependency_links to pip-egg-info/dark_matter.egg-info/dependency_links.txt writing requirements to pip-egg-info/dark_matter.egg-info/requires.txt writing top-level names to pip-egg-info/dark_matter.egg-info/top_level.txt writing manifest file 'pip-egg-info/dark_matter.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/dark_matter.egg-info/SOURCES.txt' writing manifest file 'pip-egg-info/dark_matter.egg-info/SOURCES.txt' Source in /tmp/pip-wheel-wr17t98e/dark-matter has version 3.0.63, which satisfies requirement dark-matter==3.0.63 from https://files.pythonhosted.org/packages/ff/08/0d32772dce2bd7ce4d54692f420e5065b2916f39b8f9a3d67bd8dc2830d3/dark-matter-3.0.63.tar.gz#sha256=2b4fe4e02e8092166ccfd7166a0376e505674a68f029efae95671bc142f45c78 Removed dark-matter==3.0.63 from https://files.pythonhosted.org/packages/ff/08/0d32772dce2bd7ce4d54692f420e5065b2916f39b8f9a3d67bd8dc2830d3/dark-matter-3.0.63.tar.gz#sha256=2b4fe4e02e8092166ccfd7166a0376e505674a68f029efae95671bc142f45c78 from build tracker '/tmp/pip-req-tracker-uasg26b0' Building wheels for collected packages: dark-matter Created temporary directory: /tmp/pip-wheel-0x2k764o Running setup.py bdist_wheel for dark-matter: started Destination directory: /tmp/pip-wheel-0x2k764o Running command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-wheel-wr17t98e/dark-matter/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-0x2k764o running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/dark copying dark/alignments.py -> build/lib/dark copying dark/fasta.py -> build/lib/dark copying dark/mutations.py -> build/lib/dark copying dark/graphics.py -> build/lib/dark copying dark/distance.py -> build/lib/dark copying dark/reads.py -> build/lib/dark copying dark/baseimage.py -> build/lib/dark copying dark/process.py -> build/lib/dark copying dark/btop.py -> build/lib/dark copying dark/intervals.py -> build/lib/dark copying dark/ipynb.py -> build/lib/dark copying dark/fasta_ss.py -> build/lib/dark copying dark/ncbidb.py -> build/lib/dark copying dark/local_align.py -> build/lib/dark copying dark/sam.py -> build/lib/dark copying dark/taxonomy.py -> build/lib/dark copying dark/sequence.py -> build/lib/dark copying dark/simplify.py -> build/lib/dark copying dark/fastq.py -> build/lib/dark copying dark/html.py -> build/lib/dark copying dark/orfs.py -> build/lib/dark copying dark/proteins.py -> build/lib/dark copying dark/titles.py -> build/lib/dark copying dark/__init__.py -> build/lib/dark copying dark/score.py -> build/lib/dark copying dark/filter.py -> build/lib/dark copying dark/analyze_reads.py -> build/lib/dark copying dark/codonDistance.py -> build/lib/dark copying dark/summarize.py -> build/lib/dark copying dark/consensus.py -> build/lib/dark copying dark/entrez.py -> build/lib/dark copying dark/hsp.py -> build/lib/dark copying dark/utils.py -> build/lib/dark copying dark/dimension.py -> build/lib/dark copying dark/dna.py -> build/lib/dark copying dark/features.py -> build/lib/dark copying dark/aa.py -> build/lib/dark copying dark/database.py -> build/lib/dark creating build/lib/dark/blast copying dark/blast/alignments.py -> build/lib/dark/blast copying dark/blast/params.py -> build/lib/dark/blast copying dark/blast/conversion.py -> build/lib/dark/blast copying dark/blast/__init__.py -> build/lib/dark/blast copying dark/blast/score.py -> build/lib/dark/blast copying dark/blast/hacks.py -> build/lib/dark/blast copying dark/blast/hsp.py -> build/lib/dark/blast copying dark/blast/records.py -> build/lib/dark/blast creating build/lib/dark/diamond copying dark/diamond/alignments.py -> build/lib/dark/diamond copying dark/diamond/conversion.py -> build/lib/dark/diamond copying dark/diamond/__init__.py -> build/lib/dark/diamond copying dark/diamond/hsp.py -> build/lib/dark/diamond running build_scripts creating build/scripts-3.4 copying and adjusting bin/aa-info.py -> build/scripts-3.4 copying and adjusting bin/aa-to-properties.py -> build/scripts-3.4 copying and adjusting bin/adaptor-distances.py -> build/scripts-3.4 copying and adjusting bin/alignments-per-read.py -> build/scripts-3.4 copying and adjusting bin/bit-score-to-e-value.py -> build/scripts-3.4 copying and adjusting bin/cat-json-blast-records.py -> build/scripts-3.4 copying and adjusting bin/check-fasta-json-blast-consistency.py -> build/scripts-3.4 copying and adjusting bin/codon-distance.py -> build/scripts-3.4 copying and adjusting bin/compare-consensuses.py -> build/scripts-3.4 copying and adjusting bin/compare-sequences.py -> build/scripts-3.4 copying and adjusting bin/convert-blast-xml-to-json.py -> build/scripts-3.4 copying and adjusting bin/convert-diamond-to-json.py -> build/scripts-3.4 copying and adjusting bin/convert-diamond-to-sam.py -> build/scripts-3.4 copying bin/convert-sam-to-fastq.sh -> build/scripts-3.4 copying and adjusting bin/dark-matter-version.py -> build/scripts-3.4 copying and adjusting bin/dna-to-aa.py -> build/scripts-3.4 copying and adjusting bin/e-value-to-bit-score.py -> build/scripts-3.4 copying and adjusting bin/extract-ORFs.py -> build/scripts-3.4 copying and adjusting bin/fasta-base-indices.py -> build/scripts-3.4 copying and adjusting bin/fasta-count.py -> build/scripts-3.4 copying bin/fasta-diff.sh -> build/scripts-3.4 copying and adjusting bin/fasta-identity-table.py -> build/scripts-3.4 copying and adjusting bin/fasta-ids.py -> build/scripts-3.4 copying and adjusting bin/fasta-join.py -> build/scripts-3.4 copying and adjusting bin/fasta-lengths.py -> build/scripts-3.4 copying and adjusting bin/fasta-sequences.py -> build/scripts-3.4 copying and adjusting bin/fasta-sort.py -> build/scripts-3.4 copying and adjusting bin/fasta-split-by-id.py -> build/scripts-3.4 copying and adjusting bin/fasta-subset.py -> build/scripts-3.4 copying and adjusting bin/fasta-subtraction.py -> build/scripts-3.4 copying and adjusting bin/fasta-to-phylip.py -> build/scripts-3.4 copying and adjusting bin/filter-fasta-by-complexity.py -> build/scripts-3.4 copying and adjusting bin/filter-fasta-by-taxonomy.py -> build/scripts-3.4 copying and adjusting bin/filter-fasta.py -> build/scripts-3.4 copying and adjusting bin/filter-hits-to-fasta.py -> build/scripts-3.4 copying and adjusting bin/filter-reads-alignments.py -> build/scripts-3.4 copying and adjusting bin/filter-sam.py -> build/scripts-3.4 copying and adjusting bin/find-hits.py -> build/scripts-3.4 copying and adjusting bin/get-features.py -> build/scripts-3.4 copying and adjusting bin/get-reads.py -> build/scripts-3.4 copying and adjusting bin/graph-evalues.py -> build/scripts-3.4 copying and adjusting bin/local-align.py -> build/scripts-3.4 copying and adjusting bin/make-fasta-database.py -> build/scripts-3.4 copying and adjusting bin/ncbi-fetch-id.py -> build/scripts-3.4 copying and adjusting bin/newick-to-ascii.py -> build/scripts-3.4 copying and adjusting bin/noninteractive-alignment-panel.py -> build/scripts-3.4 copying and adjusting bin/position-summary.py -> build/scripts-3.4 copying bin/pre-commit.sh -> build/scripts-3.4 copying and adjusting bin/print-blast-xml-for-derek.py -> build/scripts-3.4 copying and adjusting bin/print-blast-xml.py -> build/scripts-3.4 copying and adjusting bin/print-read-lengths.py -> build/scripts-3.4 copying and adjusting bin/proteins-to-pathogens.py -> build/scripts-3.4 copying and adjusting bin/randomize-fasta.py -> build/scripts-3.4 copying and adjusting bin/read-blast-json.py -> build/scripts-3.4 copying and adjusting bin/read-blast-xml.py -> build/scripts-3.4 copying and adjusting bin/sam-to-fasta-alignment.py -> build/scripts-3.4 copying and adjusting bin/sam-reference-read-counts.py -> build/scripts-3.4 copying and adjusting bin/sam-references.py -> build/scripts-3.4 copying and adjusting bin/sff-to-fastq.py -> build/scripts-3.4 copying and adjusting bin/split-fasta-by-adaptors.py -> build/scripts-3.4 copying and adjusting bin/summarize-fasta-bases.py -> build/scripts-3.4 copying and adjusting bin/summarize-reads.py -> build/scripts-3.4 copying and adjusting bin/trim-primers.py -> build/scripts-3.4 copying and adjusting bin/trim-reads.py -> build/scripts-3.4 copying and adjusting bin/write-htcondor-job-spec.py -> build/scripts-3.4 changing mode of build/scripts-3.4/aa-info.py from 644 to 755 changing mode of build/scripts-3.4/aa-to-properties.py from 644 to 755 changing mode of build/scripts-3.4/adaptor-distances.py from 644 to 755 changing mode of build/scripts-3.4/alignments-per-read.py from 644 to 755 changing mode of build/scripts-3.4/bit-score-to-e-value.py from 644 to 755 changing mode of build/scripts-3.4/cat-json-blast-records.py from 644 to 755 changing mode of build/scripts-3.4/check-fasta-json-blast-consistency.py from 644 to 755 changing mode of build/scripts-3.4/codon-distance.py from 644 to 755 changing mode of build/scripts-3.4/compare-consensuses.py from 644 to 755 changing mode of build/scripts-3.4/compare-sequences.py from 644 to 755 changing mode of build/scripts-3.4/convert-blast-xml-to-json.py from 644 to 755 changing mode of build/scripts-3.4/convert-diamond-to-json.py from 644 to 755 changing mode of build/scripts-3.4/convert-diamond-to-sam.py from 644 to 755 changing mode of build/scripts-3.4/dark-matter-version.py from 644 to 755 changing mode of build/scripts-3.4/dna-to-aa.py from 644 to 755 changing mode of build/scripts-3.4/e-value-to-bit-score.py from 644 to 755 changing mode of build/scripts-3.4/extract-ORFs.py from 644 to 755 changing mode of build/scripts-3.4/fasta-base-indices.py from 644 to 755 changing mode of build/scripts-3.4/fasta-count.py from 644 to 755 changing mode of build/scripts-3.4/fasta-identity-table.py from 644 to 755 changing mode of build/scripts-3.4/fasta-ids.py from 644 to 755 changing mode of build/scripts-3.4/fasta-join.py from 644 to 755 changing mode of build/scripts-3.4/fasta-lengths.py from 644 to 755 changing mode of build/scripts-3.4/fasta-sequences.py from 644 to 755 changing mode of build/scripts-3.4/fasta-sort.py from 644 to 755 changing mode of build/scripts-3.4/fasta-split-by-id.py from 644 to 755 changing mode of build/scripts-3.4/fasta-subset.py from 644 to 755 changing mode of build/scripts-3.4/fasta-subtraction.py from 644 to 755 changing mode of build/scripts-3.4/fasta-to-phylip.py from 644 to 755 changing mode of build/scripts-3.4/filter-fasta-by-complexity.py from 644 to 755 changing mode of build/scripts-3.4/filter-fasta-by-taxonomy.py from 644 to 755 changing mode of build/scripts-3.4/filter-fasta.py from 644 to 755 changing mode of build/scripts-3.4/filter-hits-to-fasta.py from 644 to 755 changing mode of build/scripts-3.4/filter-reads-alignments.py from 644 to 755 changing mode of build/scripts-3.4/filter-sam.py from 644 to 755 changing mode of build/scripts-3.4/find-hits.py from 644 to 755 changing mode of build/scripts-3.4/get-features.py from 644 to 755 changing mode of build/scripts-3.4/get-reads.py from 644 to 755 changing mode of build/scripts-3.4/graph-evalues.py from 644 to 755 changing mode of build/scripts-3.4/local-align.py from 644 to 755 changing mode of build/scripts-3.4/make-fasta-database.py from 644 to 755 changing mode of build/scripts-3.4/ncbi-fetch-id.py from 644 to 755 changing mode of build/scripts-3.4/newick-to-ascii.py from 644 to 755 changing mode of build/scripts-3.4/noninteractive-alignment-panel.py from 644 to 755 changing mode of build/scripts-3.4/position-summary.py from 644 to 755 changing mode of build/scripts-3.4/print-blast-xml-for-derek.py from 644 to 755 changing mode of build/scripts-3.4/print-blast-xml.py from 644 to 755 changing mode of build/scripts-3.4/print-read-lengths.py from 644 to 755 changing mode of build/scripts-3.4/proteins-to-pathogens.py from 644 to 755 changing mode of build/scripts-3.4/randomize-fasta.py from 644 to 755 changing mode of build/scripts-3.4/read-blast-json.py from 644 to 755 changing mode of build/scripts-3.4/read-blast-xml.py from 644 to 755 changing mode of build/scripts-3.4/sam-to-fasta-alignment.py from 644 to 755 changing mode of build/scripts-3.4/sam-reference-read-counts.py from 644 to 755 changing mode of build/scripts-3.4/sam-references.py from 644 to 755 changing mode of build/scripts-3.4/sff-to-fastq.py from 644 to 755 changing mode of build/scripts-3.4/split-fasta-by-adaptors.py from 644 to 755 changing mode of build/scripts-3.4/summarize-fasta-bases.py from 644 to 755 changing mode of build/scripts-3.4/summarize-reads.py from 644 to 755 changing mode of build/scripts-3.4/trim-primers.py from 644 to 755 changing mode of build/scripts-3.4/trim-reads.py from 644 to 755 changing mode of build/scripts-3.4/write-htcondor-job-spec.py from 644 to 755 installing to build/bdist.linux-armv7l/wheel running install running install_lib creating build/bdist.linux-armv7l creating build/bdist.linux-armv7l/wheel creating build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/alignments.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/fasta.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/mutations.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/graphics.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/distance.py -> build/bdist.linux-armv7l/wheel/dark creating build/bdist.linux-armv7l/wheel/dark/blast copying build/lib/dark/blast/alignments.py -> build/bdist.linux-armv7l/wheel/dark/blast copying build/lib/dark/blast/params.py -> build/bdist.linux-armv7l/wheel/dark/blast copying build/lib/dark/blast/conversion.py -> build/bdist.linux-armv7l/wheel/dark/blast copying build/lib/dark/blast/__init__.py -> build/bdist.linux-armv7l/wheel/dark/blast copying build/lib/dark/blast/score.py -> build/bdist.linux-armv7l/wheel/dark/blast copying build/lib/dark/blast/hacks.py -> build/bdist.linux-armv7l/wheel/dark/blast copying build/lib/dark/blast/hsp.py -> build/bdist.linux-armv7l/wheel/dark/blast copying build/lib/dark/blast/records.py -> build/bdist.linux-armv7l/wheel/dark/blast copying build/lib/dark/reads.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/baseimage.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/process.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/btop.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/intervals.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/ipynb.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/fasta_ss.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/ncbidb.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/local_align.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/sam.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/taxonomy.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/sequence.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/simplify.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/fastq.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/html.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/orfs.py -> build/bdist.linux-armv7l/wheel/dark creating build/bdist.linux-armv7l/wheel/dark/diamond copying build/lib/dark/diamond/alignments.py -> build/bdist.linux-armv7l/wheel/dark/diamond copying build/lib/dark/diamond/conversion.py -> build/bdist.linux-armv7l/wheel/dark/diamond copying build/lib/dark/diamond/__init__.py -> build/bdist.linux-armv7l/wheel/dark/diamond copying build/lib/dark/diamond/hsp.py -> build/bdist.linux-armv7l/wheel/dark/diamond copying build/lib/dark/proteins.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/titles.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/__init__.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/score.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/filter.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/analyze_reads.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/codonDistance.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/summarize.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/consensus.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/entrez.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/hsp.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/utils.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/dimension.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/dna.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/features.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/aa.py -> build/bdist.linux-armv7l/wheel/dark copying build/lib/dark/database.py -> build/bdist.linux-armv7l/wheel/dark running install_egg_info running egg_info writing dark_matter.egg-info/PKG-INFO writing dependency_links to dark_matter.egg-info/dependency_links.txt writing requirements to dark_matter.egg-info/requires.txt writing top-level names to dark_matter.egg-info/top_level.txt reading manifest file 'dark_matter.egg-info/SOURCES.txt' writing manifest file 'dark_matter.egg-info/SOURCES.txt' Copying dark_matter.egg-info to build/bdist.linux-armv7l/wheel/dark_matter-3.0.63-py3.4.egg-info running install_scripts creating build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data creating build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/sam-to-fasta-alignment.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/ncbi-fetch-id.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/print-blast-xml-for-derek.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-count.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/aa-to-properties.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/read-blast-json.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/check-fasta-json-blast-consistency.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/sff-to-fastq.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-sort.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-diff.sh -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/convert-diamond-to-sam.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-subset.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/write-htcondor-job-spec.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/find-hits.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/read-blast-xml.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/newick-to-ascii.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/get-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/convert-diamond-to-json.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-join.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-base-indices.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-ids.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/local-align.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/make-fasta-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/summarize-fasta-bases.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-identity-table.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/proteins-to-pathogens.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/randomize-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/filter-reads-alignments.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-sequences.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/get-features.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-lengths.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/compare-sequences.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/compare-consensuses.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/codon-distance.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/position-summary.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-split-by-id.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-to-phylip.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/summarize-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/convert-blast-xml-to-json.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/e-value-to-bit-score.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/aa-info.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/noninteractive-alignment-panel.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/sam-references.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/cat-json-blast-records.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/print-read-lengths.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/filter-fasta-by-taxonomy.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/split-fasta-by-adaptors.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/dna-to-aa.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/extract-ORFs.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/dark-matter-version.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/adaptor-distances.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/alignments-per-read.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/sam-reference-read-counts.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/convert-sam-to-fastq.sh -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/trim-primers.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/pre-commit.sh -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/bit-score-to-e-value.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/filter-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/filter-hits-to-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/fasta-subtraction.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/print-blast-xml.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/filter-fasta-by-complexity.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/trim-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/filter-sam.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts copying build/scripts-3.4/graph-evalues.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/sam-to-fasta-alignment.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/ncbi-fetch-id.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/print-blast-xml-for-derek.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-count.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/aa-to-properties.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/read-blast-json.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/check-fasta-json-blast-consistency.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/sff-to-fastq.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-sort.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-diff.sh to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/convert-diamond-to-sam.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-subset.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/write-htcondor-job-spec.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/find-hits.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/read-blast-xml.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/newick-to-ascii.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/get-reads.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/convert-diamond-to-json.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-join.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-base-indices.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-ids.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/local-align.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/make-fasta-database.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/summarize-fasta-bases.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-identity-table.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/proteins-to-pathogens.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/randomize-fasta.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/filter-reads-alignments.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-sequences.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/get-features.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-lengths.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/compare-sequences.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/compare-consensuses.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/codon-distance.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/position-summary.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-split-by-id.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-to-phylip.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/summarize-reads.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/convert-blast-xml-to-json.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/e-value-to-bit-score.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/aa-info.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/noninteractive-alignment-panel.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/sam-references.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/cat-json-blast-records.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/print-read-lengths.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/filter-fasta-by-taxonomy.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/split-fasta-by-adaptors.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/dna-to-aa.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/extract-ORFs.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/dark-matter-version.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/adaptor-distances.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/alignments-per-read.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/sam-reference-read-counts.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/convert-sam-to-fastq.sh to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/trim-primers.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/pre-commit.sh to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/bit-score-to-e-value.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/filter-fasta.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/filter-hits-to-fasta.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/fasta-subtraction.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/print-blast-xml.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/filter-fasta-by-complexity.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/trim-reads.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/filter-sam.py to 755 changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.data/scripts/graph-evalues.py to 755 creating build/bdist.linux-armv7l/wheel/dark_matter-3.0.63.dist-info/WHEEL creating '/tmp/pip-wheel-0x2k764o/dark_matter-3.0.63-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it adding 'dark/__init__.py' adding 'dark/aa.py' adding 'dark/alignments.py' adding 'dark/analyze_reads.py' adding 'dark/baseimage.py' adding 'dark/btop.py' adding 'dark/codonDistance.py' adding 'dark/consensus.py' adding 'dark/database.py' adding 'dark/dimension.py' adding 'dark/distance.py' adding 'dark/dna.py' adding 'dark/entrez.py' adding 'dark/fasta.py' adding 'dark/fasta_ss.py' adding 'dark/fastq.py' adding 'dark/features.py' adding 'dark/filter.py' adding 'dark/graphics.py' adding 'dark/hsp.py' adding 'dark/html.py' adding 'dark/intervals.py' adding 'dark/ipynb.py' adding 'dark/local_align.py' adding 'dark/mutations.py' adding 'dark/ncbidb.py' adding 'dark/orfs.py' adding 'dark/process.py' adding 'dark/proteins.py' adding 'dark/reads.py' adding 'dark/sam.py' adding 'dark/score.py' adding 'dark/sequence.py' adding 'dark/simplify.py' adding 'dark/summarize.py' adding 'dark/taxonomy.py' adding 'dark/titles.py' adding 'dark/utils.py' adding 'dark/blast/__init__.py' adding 'dark/blast/alignments.py' adding 'dark/blast/conversion.py' adding 'dark/blast/hacks.py' adding 'dark/blast/hsp.py' adding 'dark/blast/params.py' adding 'dark/blast/records.py' adding 'dark/blast/score.py' adding 'dark/diamond/__init__.py' adding 'dark/diamond/alignments.py' adding 'dark/diamond/conversion.py' adding 'dark/diamond/hsp.py' adding 'dark_matter-3.0.63.data/scripts/aa-info.py' adding 'dark_matter-3.0.63.data/scripts/aa-to-properties.py' adding 'dark_matter-3.0.63.data/scripts/adaptor-distances.py' adding 'dark_matter-3.0.63.data/scripts/alignments-per-read.py' adding 'dark_matter-3.0.63.data/scripts/bit-score-to-e-value.py' adding 'dark_matter-3.0.63.data/scripts/cat-json-blast-records.py' adding 'dark_matter-3.0.63.data/scripts/check-fasta-json-blast-consistency.py' adding 'dark_matter-3.0.63.data/scripts/codon-distance.py' adding 'dark_matter-3.0.63.data/scripts/compare-consensuses.py' adding 'dark_matter-3.0.63.data/scripts/compare-sequences.py' adding 'dark_matter-3.0.63.data/scripts/convert-blast-xml-to-json.py' adding 'dark_matter-3.0.63.data/scripts/convert-diamond-to-json.py' adding 'dark_matter-3.0.63.data/scripts/convert-diamond-to-sam.py' adding 'dark_matter-3.0.63.data/scripts/convert-sam-to-fastq.sh' adding 'dark_matter-3.0.63.data/scripts/dark-matter-version.py' adding 'dark_matter-3.0.63.data/scripts/dna-to-aa.py' adding 'dark_matter-3.0.63.data/scripts/e-value-to-bit-score.py' adding 'dark_matter-3.0.63.data/scripts/extract-ORFs.py' adding 'dark_matter-3.0.63.data/scripts/fasta-base-indices.py' adding 'dark_matter-3.0.63.data/scripts/fasta-count.py' adding 'dark_matter-3.0.63.data/scripts/fasta-diff.sh' adding 'dark_matter-3.0.63.data/scripts/fasta-identity-table.py' adding 'dark_matter-3.0.63.data/scripts/fasta-ids.py' adding 'dark_matter-3.0.63.data/scripts/fasta-join.py' adding 'dark_matter-3.0.63.data/scripts/fasta-lengths.py' adding 'dark_matter-3.0.63.data/scripts/fasta-sequences.py' adding 'dark_matter-3.0.63.data/scripts/fasta-sort.py' adding 'dark_matter-3.0.63.data/scripts/fasta-split-by-id.py' adding 'dark_matter-3.0.63.data/scripts/fasta-subset.py' adding 'dark_matter-3.0.63.data/scripts/fasta-subtraction.py' adding 'dark_matter-3.0.63.data/scripts/fasta-to-phylip.py' adding 'dark_matter-3.0.63.data/scripts/filter-fasta-by-complexity.py' adding 'dark_matter-3.0.63.data/scripts/filter-fasta-by-taxonomy.py' adding 'dark_matter-3.0.63.data/scripts/filter-fasta.py' adding 'dark_matter-3.0.63.data/scripts/filter-hits-to-fasta.py' adding 'dark_matter-3.0.63.data/scripts/filter-reads-alignments.py' adding 'dark_matter-3.0.63.data/scripts/filter-sam.py' adding 'dark_matter-3.0.63.data/scripts/find-hits.py' adding 'dark_matter-3.0.63.data/scripts/get-features.py' adding 'dark_matter-3.0.63.data/scripts/get-reads.py' adding 'dark_matter-3.0.63.data/scripts/graph-evalues.py' adding 'dark_matter-3.0.63.data/scripts/local-align.py' adding 'dark_matter-3.0.63.data/scripts/make-fasta-database.py' adding 'dark_matter-3.0.63.data/scripts/ncbi-fetch-id.py' adding 'dark_matter-3.0.63.data/scripts/newick-to-ascii.py' adding 'dark_matter-3.0.63.data/scripts/noninteractive-alignment-panel.py' adding 'dark_matter-3.0.63.data/scripts/position-summary.py' adding 'dark_matter-3.0.63.data/scripts/pre-commit.sh' adding 'dark_matter-3.0.63.data/scripts/print-blast-xml-for-derek.py' adding 'dark_matter-3.0.63.data/scripts/print-blast-xml.py' adding 'dark_matter-3.0.63.data/scripts/print-read-lengths.py' adding 'dark_matter-3.0.63.data/scripts/proteins-to-pathogens.py' adding 'dark_matter-3.0.63.data/scripts/randomize-fasta.py' adding 'dark_matter-3.0.63.data/scripts/read-blast-json.py' adding 'dark_matter-3.0.63.data/scripts/read-blast-xml.py' adding 'dark_matter-3.0.63.data/scripts/sam-reference-read-counts.py' adding 'dark_matter-3.0.63.data/scripts/sam-references.py' adding 'dark_matter-3.0.63.data/scripts/sam-to-fasta-alignment.py' adding 'dark_matter-3.0.63.data/scripts/sff-to-fastq.py' adding 'dark_matter-3.0.63.data/scripts/split-fasta-by-adaptors.py' adding 'dark_matter-3.0.63.data/scripts/summarize-fasta-bases.py' adding 'dark_matter-3.0.63.data/scripts/summarize-reads.py' adding 'dark_matter-3.0.63.data/scripts/trim-primers.py' adding 'dark_matter-3.0.63.data/scripts/trim-reads.py' adding 'dark_matter-3.0.63.data/scripts/write-htcondor-job-spec.py' adding 'dark_matter-3.0.63.dist-info/METADATA' adding 'dark_matter-3.0.63.dist-info/WHEEL' adding 'dark_matter-3.0.63.dist-info/top_level.txt' adding 'dark_matter-3.0.63.dist-info/RECORD' removing build/bdist.linux-armv7l/wheel Running setup.py bdist_wheel for dark-matter: finished with status 'done' Stored in directory: /tmp/tmpwbicwvgx Successfully built dark-matter Cleaning up... Removing source in /tmp/pip-wheel-wr17t98e/dark-matter Removed build tracker '/tmp/pip-req-tracker-uasg26b0'