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bcbio_nextgen vep installation bug (terminal output)
2015-06-11 14:53:37 +0200
export FTP_PASSIVE=1 && /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl -a a -d /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib -c /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/share/data
Using non-default installation directory /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib - you will probably need to add /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib to your PERL5LIB
Setting up directories
Downloading required files
- fetching ensembl
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
^M 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0curl: (77) error setting certificate verify locations:
CAfile: /etc/pki/tls/certs/ca-bundle.crt
CApath: none
- unpacking /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip
format error: file is too short
at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 683.
Archive::Zip::Archive::_findEndOfCentralDirectory('Archive::Zip::Archive=HASH(0x281ee30)', 'IO::File=GLOB(0x281ed28)') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 597
Archive::Zip::Archive::readFromFileHandle('Archive::Zip::Archive=HASH(0x281ee30)', 'IO::File=GLOB(0x281ed28)', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 565
Archive::Zip::Archive::read('Archive::Zip::Archive=HASH(0x281ee30)', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Extract.pm line 1154
Archive::Extract::_unzip_az('Archive::Extract=HASH(0x1a6fa60)') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Extract.pm line 432
Archive::Extract::extract('Archive::Extract=HASH(0x1a6fa60)', 'to', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990
main::unpack_arch('/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 292
main::install_api() called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 133
main::api() called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 101
Unable to read '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip' at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990.
Unable to unzip '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip': [/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip]
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
zipinfo: cannot find zipfile directory in one of /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip or
/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.zip, and cannot find /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.ZIP, period.
at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990.
Extract failed due to errors at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990.
Unable to read '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip'
Unable to unzip '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip': [/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip]
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
zipinfo: cannot find zipfile directory in one of /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip or
/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.zip, and cannot find /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.ZIP, period.
Extract failed due to errors at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990.
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew.git
HEAD: d0844607d93192f6012cf19676c157cbfc31954d
Last commit: 20 hours ago
HOMEBREW_PREFIX: /home/mpschr/bin/bcbionextgen/tools
HOMEBREW_CELLAR: /home/mpschr/bin/bcbionextgen/tools/Cellar
CPU: 24-core 64-bit 6
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: N/A
System Ruby: 1.9.3-p484 => /usr/bin/ruby1.9.1
Perl: /usr/bin/perl
Python: /home/mpschr/anaconda3/bin/python => /home/mpschr/anaconda3/bin/python3.4
Ruby: /usr/bin/ruby => /usr/bin/ruby1.9.1
Java: 1.8.0_45
CC: /usr/bin/gcc => /usr/bin/gcc-4.8
CXX: /usr/bin/g++ => /usr/bin/g++-4.8
CFLAGS: -Os -w -pipe
CXXFLAGS: -Os -w -pipe
CPPFLAGS: -isystem/home/mpschr/bin/bcbionextgen/tools/include
LDFLAGS: -L/home/mpschr/bin/bcbionextgen/tools/lib -Wl,-rpath,/home/mpschr/bin/bcbionextgen/tools/lib
MAKEFLAGS: -j24
CMAKE_PREFIX_PATH: /home/mpschr/bin/bcbionextgen/tools
PKG_CONFIG_LIBDIR: /home/mpschr/bin/bcbionextgen/tools/lib/pkgconfig:/usr/lib/pkgconfig
PATH: /home/mpschr/bin/bcbionextgen/tools/bin:/home/mpschr/anaconda3/bin:/home/mpschr/bin/jdk/jdk1.8.0_45/bin:/home/mpschr/anaconda3/bin:/home/mpschr/bin:/home/mpschr/bin/jdk/jdk1.8.0_45/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/mpschr/bin:/home/mpschr/.local/bin:/home/mpschr/bin:/home/mpschr/.local/bin:/home/mpschr/bin/bcbionextgen/tools/Library/ENV/scm
==> Installing vep from chapmanb/homebrew-cbl
==> Downloading https://github.com/Ensembl/ensembl-tools/archive/4a86cbf.zip
Already downloaded: /home/mpschr/.cache/Homebrew/vep-79_2015-04-13.zip
==> Verifying vep-79_2015-04-13.zip checksum
unzip /home/mpschr/.cache/Homebrew/vep-79_2015-04-13.zip
Archive: /home/mpschr/.cache/Homebrew/vep-79_2015-04-13.zip
4a86cbf5b2229cef36dda20492f7678cdbd0f466
creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/.travis.yml
creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/
creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/assembly_converter/
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/assembly_converter/AssemblyMapper.pl
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/assembly_converter/README.txt
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/assembly_converter/assemblymapper.in
creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/id_history_converter/
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/id_history_converter/IDmapper.pl
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/id_history_converter/README.txt
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/id_history_converter/idmapper.in
creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/region_reporter/
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/region_reporter/README.txt
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/region_reporter/region_report.pl
creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/INSTALL.pl
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/README.txt
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/convert_cache.pl
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/example_GRCh37.vcf
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/example_GRCh38.vcf
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/filter_vep.pl
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/gtf2vep.pl
creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/convert_cache.t
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/filter_vep.t
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/test.conf
creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/TestPlugin.pm
extracting: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/filter.list
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/filter.txt
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/filter.vcf
extracting: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/testdata/test_vep_input.txt.gz
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/t/variant_effect_predictor.t
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/scripts/variant_effect_predictor/variant_effect_predictor.pl
creating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/travisci/
inflating: ensembl-tools-4a86cbf5b2229cef36dda20492f7678cdbd0f466/travisci/harness.sh
==> export FTP_PASSIVE=1 && /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl -a a -d /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib -c /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/share/data
Using non-default installation directory /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib - you will probably need to add /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib to your PERL5LIB
Setting up directories
Downloading required files
- fetching ensembl
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
^M 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0curl: (77) error setting certificate verify locations:
CAfile: /etc/pki/tls/certs/ca-bundle.crt
CApath: none
- unpacking /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip
format error: file is too short
at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 683.
Archive::Zip::Archive::_findEndOfCentralDirectory('Archive::Zip::Archive=HASH(0x281ee30)', 'IO::File=GLOB(0x281ed28)') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 597
Archive::Zip::Archive::readFromFileHandle('Archive::Zip::Archive=HASH(0x281ee30)', 'IO::File=GLOB(0x281ed28)', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Zip/Archive.pm line 565
Archive::Zip::Archive::read('Archive::Zip::Archive=HASH(0x281ee30)', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Extract.pm line 1154
Archive::Extract::_unzip_az('Archive::Extract=HASH(0x1a6fa60)') called at /home/mpschr/bin/bcbionextgen/tools/lib/perl5/Archive/Extract.pm line 432
Archive::Extract::extract('Archive::Extract=HASH(0x1a6fa60)', 'to', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990
main::unpack_arch('/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...', '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/...') called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 292
main::install_api() called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 133
main::api() called at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 101
Unable to read '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip' at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990.
Unable to unzip '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip': [/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip]
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
zipinfo: cannot find zipfile directory in one of /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip or
/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.zip, and cannot find /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.ZIP, period.
at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990.
Extract failed due to errors at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990.
Unable to read '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip'
Unable to unzip '/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip': [/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip]
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
zipinfo: cannot find zipfile directory in one of /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip or
/home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.zip, and cannot find /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib/Bio/tmp/ensembl.zip.ZIP, period.
Extract failed due to errors at /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl line 990.
==> Formula
Tap: chapmanb/homebrew-cbl
Path: /home/mpschr/bin/bcbionextgen/tools/Library/Taps/chapmanb/homebrew-cbl/vep.rb
==> Configuration
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew.git
HEAD: d0844607d93192f6012cf19676c157cbfc31954d
Last commit: 20 hours ago
HOMEBREW_PREFIX: /home/mpschr/bin/bcbionextgen/tools
HOMEBREW_CELLAR: /home/mpschr/bin/bcbionextgen/tools/Cellar
CPU: 24-core 64-bit 6
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: N/A
System Ruby: 1.9.3-p484 => /usr/bin/ruby1.9.1
Perl: /usr/bin/perl
Python: /home/mpschr/anaconda3/bin/python => /home/mpschr/anaconda3/bin/python3.4
Ruby: /usr/bin/ruby => /usr/bin/ruby1.9.1
Java: 1.8.0_45
==> ENV
CC: /usr/bin/gcc => /usr/bin/gcc-4.8
CXX: /usr/bin/g++ => /usr/bin/g++-4.8
CFLAGS: -Os -w -pipe
CXXFLAGS: -Os -w -pipe
CPPFLAGS: -isystem/home/mpschr/bin/bcbionextgen/tools/include
LDFLAGS: -L/home/mpschr/bin/bcbionextgen/tools/lib -Wl,-rpath,/home/mpschr/bin/bcbionextgen/tools/lib
MAKEFLAGS: -j24
CMAKE_PREFIX_PATH: /home/mpschr/bin/bcbionextgen/tools
PKG_CONFIG_LIBDIR: /home/mpschr/bin/bcbionextgen/tools/lib/pkgconfig:/usr/lib/pkgconfig
PATH: /home/mpschr/bin/bcbionextgen/tools/bin:/home/mpschr/anaconda3/bin:/home/mpschr/bin/jdk/jdk1.8.0_45/bin:/home/mpschr/anaconda3/bin:/home/mpschr/bin:/home/mpschr/bin/jdk/jdk1.8.0_45/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/mpschr/bin:/home/mpschr/.local/bin:/home/mpschr/bin:/home/mpschr/.local/bin:/home/mpschr/bin/bcbionextgen/tools/Library/ENV/scm
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