# This file contains information about your system that is useful for
# diagnosing a problem you may have. For technical assistance, please
# contact the Illumina Customer Support team <techsupport@illumina.com>
# and send them this file.

$_System = {
  'PID' : '25303',
  'OS' : 'linux',
  'PERL_VERSION' : 'v5.10.1',
  'PERL_EXECUTABLE' : '/usr/bin/perl'
};

$_ID-string = 'bcl2fastq-1.8.4';

$_Program = '/usr/local/bin/configureBclToFastq.pl';

$_Command-line = [
  '--sample-sheet',
  '/home/clinical/RUNS/170406_D00410_0399_BHHKV5BCXY/Data/Intensities/BaseCalls/SampleSheet.csv',
  '--ignore-missing-bcl',
  '--ignore-missing-stats',
  '--use-bases-mask',
  'Y126,I8,I8,Y126',
  '--fastq-cluster-count',
  '0',
  '--input-dir',
  '/home/clinical/RUNS/170406_D00410_0399_BHHKV5BCXY/Data/Intensities/BaseCalls',
  '--output-dir',
  '/home/clinical/DEMUX/170406_D00410_0399_BHHKV5BCXY/Unaligned8'
];

$_Locations = [
  '/usr/local/lib/bcl2fastq-1.8.4/perl',
  '/usr/local/lib64/perl5',
  '/usr/local/share/perl5',
  '/usr/lib64/perl5/vendor_perl',
  '/usr/share/perl5/vendor_perl',
  '/usr/lib64/perl5',
  '/usr/share/perl5',
  '.'
];

$_Modules = [
  '/usr/lib64/perl5/Config.pm',
  '/usr/lib64/perl5/Config_git.pl',
  '/usr/lib64/perl5/Config_heavy.pl',
  '/usr/lib64/perl5/Cwd.pm',
  '/usr/lib64/perl5/Data/Dumper.pm',
  '/usr/lib64/perl5/DynaLoader.pm',
  '/usr/lib64/perl5/Fcntl.pm',
  '/usr/lib64/perl5/File/Glob.pm',
  '/usr/lib64/perl5/IO.pm',
  '/usr/lib64/perl5/IO/File.pm',
  '/usr/lib64/perl5/IO/Handle.pm',
  '/usr/lib64/perl5/IO/Seekable.pm',
  '/usr/lib64/perl5/List/Util.pm',
  '/usr/lib64/perl5/POSIX.pm',
  '/usr/lib64/perl5/Scalar/Util.pm',
  '/usr/lib64/perl5/XML/Parser.pm',
  '/usr/lib64/perl5/XML/Parser/Expat.pm',
  '/usr/lib64/perl5/XML/Parser/Style/Tree.pm',
  '/usr/lib64/perl5/XSLoader.pm',
  '/usr/lib64/perl5/auto/POSIX/autosplit.ix',
  '/usr/lib64/perl5/auto/POSIX/load_imports.al',
  '/usr/lib64/perl5/lib.pm',
  '/usr/lib64/perl5/re.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/BaseCalls.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Common/IOLib.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Common/Log.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Common/Utils.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex/DemultiplexConfig.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex/Dx.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex/SampleSheet.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex/SampleSheet/Csv.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex/SampleSheet/Make.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex/SampleSheet/Xml.pm',
  '/usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Intensities.pm',
  '/usr/share/perl5/AutoLoader.pm',
  '/usr/share/perl5/Carp.pm',
  '/usr/share/perl5/Exporter.pm',
  '/usr/share/perl5/Exporter/Heavy.pm',
  '/usr/share/perl5/File/Basename.pm',
  '/usr/share/perl5/File/Copy.pm',
  '/usr/share/perl5/File/Path.pm',
  '/usr/share/perl5/File/Spec.pm',
  '/usr/share/perl5/File/Spec/Unix.pm',
  '/usr/share/perl5/Getopt/Long.pm',
  '/usr/share/perl5/Pod/Escapes.pm',
  '/usr/share/perl5/Pod/InputObjects.pm',
  '/usr/share/perl5/Pod/Parser.pm',
  '/usr/share/perl5/Pod/Select.pm',
  '/usr/share/perl5/Pod/Simple.pm',
  '/usr/share/perl5/Pod/Simple/BlackBox.pm',
  '/usr/share/perl5/Pod/Simple/LinkSection.pm',
  '/usr/share/perl5/Pod/Text.pm',
  '/usr/share/perl5/Pod/Usage.pm',
  '/usr/share/perl5/SelectSaver.pm',
  '/usr/share/perl5/Symbol.pm',
  '/usr/share/perl5/Term/ANSIColor.pm',
  '/usr/share/perl5/Text/ParseWords.pm',
  '/usr/share/perl5/Tie/Hash.pm',
  '/usr/share/perl5/UNIVERSAL.pm',
  '/usr/share/perl5/XML/Simple.pm',
  '/usr/share/perl5/base.pm',
  '/usr/share/perl5/bytes.pm',
  '/usr/share/perl5/constant.pm',
  '/usr/share/perl5/integer.pm',
  '/usr/share/perl5/overload.pm',
  '/usr/share/perl5/strict.pm',
  '/usr/share/perl5/unicore/Canonical.pl',
  '/usr/share/perl5/unicore/Exact.pl',
  '/usr/share/perl5/unicore/PVA.pl',
  '/usr/share/perl5/unicore/To/Fold.pl',
  '/usr/share/perl5/unicore/lib/gc_sc/Digit.pl',
  '/usr/share/perl5/unicore/lib/gc_sc/SpacePer.pl',
  '/usr/share/perl5/utf8.pm',
  '/usr/share/perl5/utf8_heavy.pl',
  '/usr/share/perl5/vars.pm',
  '/usr/share/perl5/warnings.pm',
  '/usr/share/perl5/warnings/register.pm'
];

$_Environment = {
  'QTINC' : '/usr/lib64/qt-3.3/include',
  'SSH_CLIENT' : '130.237.80.45 52126 22',
  'CVS_RSH' : 'ssh',
  'LESSOPEN' : '||/usr/bin/lesspipe.sh %s',
  'PWD' : '/home/clinical/RUNS/170406_D00410_0399_BHHKV5BCXY',
  'SELINUX_ROLE_REQUESTED' : '',
  'SELINUX_USE_CURRENT_RANGE' : '',
  'LANG' : 'en_US.UTF-8',
  'USER' : 'hiseq.clinical',
  'G_BROKEN_FILENAMES' : '1',
  'LOGNAME' : 'hiseq.clinical',
  'SHLVL' : '3',
  'SELINUX_LEVEL_REQUESTED' : '',
  'QTLIB' : '/usr/lib64/qt-3.3/lib',
  'PATH' : '/home/hiseq.clinical/miniconda2/bin/:/home/hiseq.clinical/.virtualenv/mysql/bin:/home/hiseq.clinical/.virtualenv/mysql/bin:/usr/lib64/qt-3.3/bin:/opt/rh/python27/root/usr/bin/:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/dell/srvadmin/bin',
  'VIRTUAL_ENV' : '/home/hiseq.clinical/.virtualenv/mysql',
  'HISTSIZE' : '1000',
  'TERM' : 'screen',
  'SSH_TTY' : '/dev/pts/0',
  'HOME' : '/home/hiseq.clinical',
  'CONDA_ENV_PATH' : '/home/hiseq.clinical/miniconda2/envs/nipt',
  'SSH_CONNECTION' : '130.237.80.45 52126 130.237.80.51 22',
  'MAIL' : '/var/spool/mail/hiseq.clinical',
  'QTDIR' : '/usr/lib64/qt-3.3',
  'CONDA_DEFAULT_ENV' : 'nipt',
  'WINDOW' : '0',
  'STY' : '22988.pts-0.clinical-preproc',
  'HOSTNAME' : 'clinical-preproc.scilifelab.se',
  '_' : '/usr/local/bin/configureBclToFastq.pl',
  'LS_COLORS' : 'rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lz=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.bz=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.rar=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:',
  'SHELL' : '/bin/bash',
  'TERMCAP' : 'SC|screen|VT 100/ANSI X3.64 virtual terminal:\\
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  'HISTCONTROL' : 'ignoredups'
};

$_Mask = 'YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY,IIIIIIII,IIIIIIII,YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY';

$_Barcodes/Lanes = {
                     '1' => {
                              'ATTACTCG-GTACTGAC' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106130',
                                                       'SAMPLE_ID' => 'MIC2206A8',
                                                       'PROJECT_ID' => '718258'
                                                     },
                              'GAATTCGT-GGCTCTGA' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106136',
                                                       'SAMPLE_ID' => 'MIC2208A44',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'CGCTCATT-CCTATCCT' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106132',
                                                       'SAMPLE_ID' => 'MIC2208A19',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'GAATTCGT-TATAGCCT' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106133',
                                                       'SAMPLE_ID' => 'MIC2208A41',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'Undetermined' => {
                                                  'CONTROL' => 'N',
                                                  'SPECIES' => 'unknown',
                                                  'DESCRIPTION' => 'Clusters with unmatched barcodes for lane 1',
                                                  'SAMPLE_ID' => 'lane1',
                                                  'PROJECT_ID' => 'Undetermined_indices'
                                                },
                              'CGCTCATT-ATAGAGGC' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106139',
                                                       'SAMPLE_ID' => 'MIC2206A37',
                                                       'PROJECT_ID' => '718258'
                                                     },
                              'CTGAAGCT-TAATCTTA' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106138',
                                                       'SAMPLE_ID' => 'MIC2208A54',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'GAATTCGT-ATAGAGGC' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106134',
                                                       'SAMPLE_ID' => 'MIC2208A42',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'GAATTCGT-AGGCGAAG' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106137',
                                                       'SAMPLE_ID' => 'MIC2208A45',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'GAATTCGT-CCTATCCT' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106135',
                                                       'SAMPLE_ID' => 'MIC2208A43',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'TCCGGAGA-GGCTCTGA' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106131',
                                                       'SAMPLE_ID' => 'MIC2206A12',
                                                       'PROJECT_ID' => '718258'
                                                     }
                            },
                     '2' => {
                              'ATTACTCG-GTACTGAC' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106130',
                                                       'SAMPLE_ID' => 'MIC2206A8',
                                                       'PROJECT_ID' => '718258'
                                                     },
                              'GAATTCGT-GGCTCTGA' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106136',
                                                       'SAMPLE_ID' => 'MIC2208A44',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'CGCTCATT-CCTATCCT' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106132',
                                                       'SAMPLE_ID' => 'MIC2208A19',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'GAATTCGT-TATAGCCT' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106133',
                                                       'SAMPLE_ID' => 'MIC2208A41',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'Undetermined' => {
                                                  'CONTROL' => 'N',
                                                  'SPECIES' => 'unknown',
                                                  'DESCRIPTION' => 'Clusters with unmatched barcodes for lane 2',
                                                  'SAMPLE_ID' => 'lane2',
                                                  'PROJECT_ID' => 'Undetermined_indices'
                                                },
                              'CGCTCATT-ATAGAGGC' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106139',
                                                       'SAMPLE_ID' => 'MIC2206A37',
                                                       'PROJECT_ID' => '718258'
                                                     },
                              'CTGAAGCT-TAATCTTA' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106138',
                                                       'SAMPLE_ID' => 'MIC2208A54',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'GAATTCGT-ATAGAGGC' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106134',
                                                       'SAMPLE_ID' => 'MIC2208A42',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'GAATTCGT-AGGCGAAG' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106137',
                                                       'SAMPLE_ID' => 'MIC2208A45',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'GAATTCGT-CCTATCCT' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106135',
                                                       'SAMPLE_ID' => 'MIC2208A43',
                                                       'PROJECT_ID' => '356717'
                                                     },
                              'TCCGGAGA-GGCTCTGA' => {
                                                       'CONTROL' => 'N',
                                                       'SPECIES' => 'hg19',
                                                       'DESCRIPTION' => '2-106131',
                                                       'SAMPLE_ID' => 'MIC2206A12',
                                                       'PROJECT_ID' => '718258'
                                                     }
                            }
                   };

