Created temporary directory: /tmp/pip-ephem-wheel-cache-fzatk0lu Created temporary directory: /tmp/pip-wheel-h7qmb1qa Looking in indexes: https://pypi.python.org/simple Collecting pathogenseq==0.1.dev0 1 location(s) to search for versions of pathogenseq: * https://pypi.python.org/simple/pathogenseq/ Getting page https://pypi.python.org/simple/pathogenseq/ Analyzing links from page https://pypi.org/simple/pathogenseq/ Skipping link https://files.pythonhosted.org/packages/40/f2/397affe187eb66a94e277d8315266c7cded74735387ced5d14c6bdb92868/pathogenseq-0.1.dev0-py2-none-any.whl#sha256=bd2f0e7aec556842e425cc39a42744c60106da918710bd61508915479d73fecd (from https://pypi.org/simple/pathogenseq/); it is not compatible with this Python Skipping link https://files.pythonhosted.org/packages/e1/8f/a85ea7e8307ff10c11702301f91d372278f7c94a7a89af00cfe5404e2a03/pathogenseq-0.1.dev0-py2.7.egg#sha256=912e1f479573b1f355869888d1d73162b4db89ffbac30dff1f2a9af4f250272f (from https://pypi.org/simple/pathogenseq/); unsupported archive format: .egg Found link https://files.pythonhosted.org/packages/65/76/30674dfd57b0d2fa76d5ed71ac3674f96ef81285436fe517d7b8361423bc/pathogenseq-0.1.dev0.tar.gz#sha256=9ebf43d229bcfb7e9e530e55b6ea91cd00614894b4c3dcca844a7b2a80fdea12 (from https://pypi.org/simple/pathogenseq/), version: 0.1.dev0 Using version 0.1.dev0 (newest of versions: 0.1.dev0) Created temporary directory: /tmp/pip-unpack-neapv28f Downloading https://files.pythonhosted.org/packages/65/76/30674dfd57b0d2fa76d5ed71ac3674f96ef81285436fe517d7b8361423bc/pathogenseq-0.1.dev0.tar.gz (43kB) Downloading from URL https://files.pythonhosted.org/packages/65/76/30674dfd57b0d2fa76d5ed71ac3674f96ef81285436fe517d7b8361423bc/pathogenseq-0.1.dev0.tar.gz#sha256=9ebf43d229bcfb7e9e530e55b6ea91cd00614894b4c3dcca844a7b2a80fdea12 (from https://pypi.org/simple/pathogenseq/) Running setup.py (path:/tmp/pip-wheel-h7qmb1qa/pathogenseq/setup.py) egg_info for package pathogenseq Running command python setup.py egg_info running egg_info creating pip-egg-info/pathogenseq.egg-info writing dependency_links to pip-egg-info/pathogenseq.egg-info/dependency_links.txt writing pip-egg-info/pathogenseq.egg-info/PKG-INFO writing top-level names to pip-egg-info/pathogenseq.egg-info/top_level.txt writing manifest file 'pip-egg-info/pathogenseq.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/pathogenseq.egg-info/SOURCES.txt' writing manifest file 'pip-egg-info/pathogenseq.egg-info/SOURCES.txt' /home/piwheels/.local/lib/python3.4/site-packages/setuptools/dist.py:398: UserWarning: Normalizing '0.1dev' to '0.1.dev0' normalized_version, Source in /tmp/pip-wheel-h7qmb1qa/pathogenseq has version 0.1.dev0, which satisfies requirement pathogenseq==0.1.dev0 from https://files.pythonhosted.org/packages/65/76/30674dfd57b0d2fa76d5ed71ac3674f96ef81285436fe517d7b8361423bc/pathogenseq-0.1.dev0.tar.gz#sha256=9ebf43d229bcfb7e9e530e55b6ea91cd00614894b4c3dcca844a7b2a80fdea12 Building wheels for collected packages: pathogenseq Created temporary directory: /tmp/pip-wheel-quqajv3k Running setup.py bdist_wheel for pathogenseq: started Destination directory: /tmp/pip-wheel-quqajv3k Running command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-wheel-h7qmb1qa/pathogenseq/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-quqajv3k /home/piwheels/.local/lib/python3.4/site-packages/setuptools/dist.py:398: UserWarning: Normalizing '0.1dev' to '0.1.dev0' normalized_version, running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/pathogenseq copying pathogenseq/fasta.py -> build/lib/pathogenseq copying pathogenseq/mvcf.py -> build/lib/pathogenseq copying pathogenseq/mt_functions.py -> build/lib/pathogenseq copying pathogenseq/bam.py -> build/lib/pathogenseq copying pathogenseq/logger.py -> build/lib/pathogenseq copying pathogenseq/fastq.py -> build/lib/pathogenseq copying pathogenseq/mutation_db.py -> build/lib/pathogenseq copying pathogenseq/files.py -> build/lib/pathogenseq copying pathogenseq/mfa.py -> build/lib/pathogenseq copying pathogenseq/__init__.py -> build/lib/pathogenseq copying pathogenseq/vcf_merge.py -> build/lib/pathogenseq copying pathogenseq/utils.py -> build/lib/pathogenseq copying pathogenseq/phylo.py -> build/lib/pathogenseq copying pathogenseq/qc.py -> build/lib/pathogenseq running build_scripts creating build/scripts-3.4 copying and adjusting scripts/bcf2consensus.py -> build/scripts-3.4 copying and adjusting scripts/bam_report.py -> build/scripts-3.4 copying and adjusting scripts/bcf2fasta.py -> build/scripts-3.4 copying and adjusting scripts/bam2vcf.py -> build/scripts-3.4 copying and adjusting scripts/collate_json.py -> build/scripts-3.4 copying and adjusting scripts/cov_plt.py -> build/scripts-3.4 copying and adjusting scripts/examl.py -> build/scripts-3.4 copying and adjusting scripts/fastq_report.py -> build/scripts-3.4 copying and adjusting scripts/mapping.py -> build/scripts-3.4 copying and adjusting scripts/merge_vcfs.py -> build/scripts-3.4 copying and adjusting scripts/minION_pipeline.py -> build/scripts-3.4 copying and adjusting scripts/Mtb_pipeline.py -> build/scripts-3.4 copying and adjusting scripts/Mtb_pipeline_no_filt.py -> build/scripts-3.4 copying and adjusting scripts/sambamba_depth.py -> build/scripts-3.4 copying and adjusting scripts/splitchr.py -> build/scripts-3.4 copying and adjusting scripts/venn_diagram.py -> build/scripts-3.4 copying and adjusting scripts/fasta2vcf.py -> build/scripts-3.4 copying and adjusting scripts/pathogen-profiler.py -> build/scripts-3.4 copying and adjusting scripts/combine_dict_list.py -> build/scripts-3.4 copying and adjusting scripts/illumina_pipeline.py -> build/scripts-3.4 copying and adjusting scripts/generate_run_file.py -> build/scripts-3.4 copying and adjusting scripts/vcf2itol.py -> build/scripts-3.4 copying and adjusting scripts/csv2fasta.py -> build/scripts-3.4 copying and adjusting scripts/rename_fq.py -> build/scripts-3.4 copying and adjusting scripts/profiler2tbprofiler.py -> build/scripts-3.4 copying and adjusting scripts/select_reference.py -> build/scripts-3.4 copying and adjusting scripts/bcf2dist.py -> build/scripts-3.4 copying and adjusting scripts/bcf_sample_stats.py -> build/scripts-3.4 copying and adjusting scripts/extract_dosage.py -> build/scripts-3.4 changing mode of build/scripts-3.4/bcf2consensus.py from 644 to 755 changing mode of build/scripts-3.4/bam_report.py from 644 to 755 changing mode of build/scripts-3.4/bcf2fasta.py from 644 to 755 changing mode of build/scripts-3.4/bam2vcf.py from 644 to 755 changing mode of build/scripts-3.4/collate_json.py from 644 to 755 changing mode of build/scripts-3.4/cov_plt.py from 644 to 755 changing mode of build/scripts-3.4/examl.py from 644 to 755 changing mode of build/scripts-3.4/fastq_report.py from 644 to 755 changing mode of build/scripts-3.4/mapping.py from 644 to 755 changing mode of build/scripts-3.4/merge_vcfs.py from 644 to 755 changing mode of build/scripts-3.4/minION_pipeline.py from 644 to 755 changing mode of build/scripts-3.4/Mtb_pipeline.py from 644 to 755 changing mode of build/scripts-3.4/Mtb_pipeline_no_filt.py from 644 to 755 changing mode of build/scripts-3.4/sambamba_depth.py from 644 to 755 changing mode of build/scripts-3.4/splitchr.py from 644 to 755 changing mode of build/scripts-3.4/venn_diagram.py from 644 to 755 changing mode of build/scripts-3.4/fasta2vcf.py from 644 to 755 changing mode of build/scripts-3.4/pathogen-profiler.py from 644 to 755 changing mode of build/scripts-3.4/combine_dict_list.py from 644 to 755 changing mode of build/scripts-3.4/illumina_pipeline.py from 644 to 755 changing mode of build/scripts-3.4/generate_run_file.py from 644 to 755 changing mode of build/scripts-3.4/vcf2itol.py from 644 to 755 changing mode of build/scripts-3.4/csv2fasta.py from 644 to 755 changing mode of build/scripts-3.4/rename_fq.py from 644 to 755 changing mode of build/scripts-3.4/profiler2tbprofiler.py from 644 to 755 changing mode of build/scripts-3.4/select_reference.py from 644 to 755 changing mode of build/scripts-3.4/bcf2dist.py from 644 to 755 changing mode of build/scripts-3.4/bcf_sample_stats.py from 644 to 755 changing mode of build/scripts-3.4/extract_dosage.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/pathogenseq copying build/lib/pathogenseq/fasta.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/mvcf.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/mt_functions.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/bam.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/logger.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/fastq.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/mutation_db.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/files.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/mfa.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/__init__.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/vcf_merge.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/utils.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/phylo.py -> build/bdist.linux-armv7l/wheel/pathogenseq copying build/lib/pathogenseq/qc.py -> build/bdist.linux-armv7l/wheel/pathogenseq running install_egg_info running egg_info writing dependency_links to pathogenseq.egg-info/dependency_links.txt writing top-level names to pathogenseq.egg-info/top_level.txt writing pathogenseq.egg-info/PKG-INFO reading manifest file 'pathogenseq.egg-info/SOURCES.txt' writing manifest file 'pathogenseq.egg-info/SOURCES.txt' Copying pathogenseq.egg-info to build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0-py3.4.egg-info running install_scripts creating build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data creating build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/venn_diagram.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/sambamba_depth.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/mapping.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/combine_dict_list.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/Mtb_pipeline.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/generate_run_file.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/bcf2fasta.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/illumina_pipeline.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/examl.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/extract_dosage.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/merge_vcfs.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/csv2fasta.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/bcf2consensus.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/collate_json.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/bam_report.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/Mtb_pipeline_no_filt.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/rename_fq.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/bam2vcf.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/splitchr.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/bcf2dist.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/bcf_sample_stats.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/fastq_report.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/profiler2tbprofiler.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/cov_plt.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/fasta2vcf.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/select_reference.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/vcf2itol.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/pathogen-profiler.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts copying build/scripts-3.4/minION_pipeline.py -> build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/venn_diagram.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/sambamba_depth.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/mapping.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/combine_dict_list.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/Mtb_pipeline.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/generate_run_file.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/bcf2fasta.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/illumina_pipeline.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/examl.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/extract_dosage.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/merge_vcfs.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/csv2fasta.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/bcf2consensus.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/collate_json.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/bam_report.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/Mtb_pipeline_no_filt.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/rename_fq.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/bam2vcf.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/splitchr.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/bcf2dist.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/bcf_sample_stats.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/fastq_report.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/profiler2tbprofiler.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/cov_plt.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/fasta2vcf.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/select_reference.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/vcf2itol.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/pathogen-profiler.py to 755 changing mode of build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.data/scripts/minION_pipeline.py to 755 creating build/bdist.linux-armv7l/wheel/pathogenseq-0.1.dev0.dist-info/WHEEL creating '/tmp/pip-wheel-quqajv3k/pathogenseq-0.1.dev0-py3-none-any.whl' and adding '.' to it adding 'pathogenseq/__init__.py' adding 'pathogenseq/bam.py' adding 'pathogenseq/fasta.py' adding 'pathogenseq/fastq.py' adding 'pathogenseq/files.py' adding 'pathogenseq/logger.py' adding 'pathogenseq/mfa.py' adding 'pathogenseq/mt_functions.py' adding 'pathogenseq/mutation_db.py' adding 'pathogenseq/mvcf.py' adding 'pathogenseq/phylo.py' adding 'pathogenseq/qc.py' adding 'pathogenseq/utils.py' adding 'pathogenseq/vcf_merge.py' adding 'pathogenseq-0.1.dev0.data/scripts/Mtb_pipeline.py' adding 'pathogenseq-0.1.dev0.data/scripts/Mtb_pipeline_no_filt.py' adding 'pathogenseq-0.1.dev0.data/scripts/bam2vcf.py' adding 'pathogenseq-0.1.dev0.data/scripts/bam_report.py' adding 'pathogenseq-0.1.dev0.data/scripts/bcf2consensus.py' adding 'pathogenseq-0.1.dev0.data/scripts/bcf2dist.py' adding 'pathogenseq-0.1.dev0.data/scripts/bcf2fasta.py' adding 'pathogenseq-0.1.dev0.data/scripts/bcf_sample_stats.py' adding 'pathogenseq-0.1.dev0.data/scripts/collate_json.py' adding 'pathogenseq-0.1.dev0.data/scripts/combine_dict_list.py' adding 'pathogenseq-0.1.dev0.data/scripts/cov_plt.py' adding 'pathogenseq-0.1.dev0.data/scripts/csv2fasta.py' adding 'pathogenseq-0.1.dev0.data/scripts/examl.py' adding 'pathogenseq-0.1.dev0.data/scripts/extract_dosage.py' adding 'pathogenseq-0.1.dev0.data/scripts/fasta2vcf.py' adding 'pathogenseq-0.1.dev0.data/scripts/fastq_report.py' adding 'pathogenseq-0.1.dev0.data/scripts/generate_run_file.py' adding 'pathogenseq-0.1.dev0.data/scripts/illumina_pipeline.py' adding 'pathogenseq-0.1.dev0.data/scripts/mapping.py' adding 'pathogenseq-0.1.dev0.data/scripts/merge_vcfs.py' adding 'pathogenseq-0.1.dev0.data/scripts/minION_pipeline.py' adding 'pathogenseq-0.1.dev0.data/scripts/pathogen-profiler.py' adding 'pathogenseq-0.1.dev0.data/scripts/profiler2tbprofiler.py' adding 'pathogenseq-0.1.dev0.data/scripts/rename_fq.py' adding 'pathogenseq-0.1.dev0.data/scripts/sambamba_depth.py' adding 'pathogenseq-0.1.dev0.data/scripts/select_reference.py' adding 'pathogenseq-0.1.dev0.data/scripts/splitchr.py' adding 'pathogenseq-0.1.dev0.data/scripts/vcf2itol.py' adding 'pathogenseq-0.1.dev0.data/scripts/venn_diagram.py' adding 'pathogenseq-0.1.dev0.dist-info/top_level.txt' adding 'pathogenseq-0.1.dev0.dist-info/WHEEL' adding 'pathogenseq-0.1.dev0.dist-info/METADATA' adding 'pathogenseq-0.1.dev0.dist-info/RECORD' removing build/bdist.linux-armv7l/wheel Running setup.py bdist_wheel for pathogenseq: finished with status 'done' Stored in directory: /tmp/tmpwjxtr511 Successfully built pathogenseq Cleaning up... Removing source in /tmp/pip-wheel-h7qmb1qa/pathogenseq