diff --git a/cpanfile b/cpanfile
index 7860a94..1ff55ff 100644
--- a/cpanfile
+++ b/cpanfile
@@ -1,5 +1,6 @@
 requires 'Bio::Seq';
 requires 'Bio::SeqIO';
+requires 'Class::Accessor';
 requires 'DBD::mysql';
 requires 'Date::Format';
 requires 'Devel::Cover';
diff --git a/lib/Pacbio/Command/Assembly/BaxToBam.pm b/lib/Pacbio/Command/Assembly/BaxToBam.pm
new file mode 100644
index 0000000..2d7f8af
--- /dev/null
+++ b/lib/Pacbio/Command/Assembly/BaxToBam.pm
@@ -0,0 +1,11 @@
+package Pacbio::Command::Assembly::BaxToBam;
+
+use strict;
+use warnings 'FATAL';
+
+class Pacbio::Command::Assembly::BaxToBam {
+    is => 'Command::Tree',
+    doc => 'helpers for bax2bam',
+};
+
+1;
diff --git a/lib/Pacbio/Command/Assembly/BaxToBam/GenerateCommands.pm b/lib/Pacbio/Command/Assembly/BaxToBam/GenerateCommands.pm
new file mode 100644
index 0000000..cc3bc56
--- /dev/null
+++ b/lib/Pacbio/Command/Assembly/BaxToBam/GenerateCommands.pm
@@ -0,0 +1,123 @@
+package Pacbio::Command::Assembly::BaxToBam::GenerateCommands;
+
+use strict;
+use warnings 'FATAL';
+
+use IO::File;
+use Pacbio::Run;
+use Path::Class;
+
+class Pacbio::Command::Assembly::BaxToBam::GenerateCommands {
+    is => 'Command::V2',
+    has_input => {
+        bam_to_bax_command => {
+            is => 'Text',
+            doc => 'Command to fill in with BAX files and logging files. BAX files will be appended to the command. Use %LOG for the log file base name for each cell.  Example: bsub -o /my-logging-dir/%LOG bam2bax',
+        },
+        run_directories => {
+            is => 'Text',
+            is_many => 1,
+            doc => 'Pacbio run directories',
+        },
+    },
+    has_optional_input => {
+        bam_output_directory => {
+            is => 'Text',
+            doc => 'Give the bam output directory to check if the bam already exists. If so, the bax2bam command for that cell will not be printed.',
+        },
+    },
+    has_optional_output => {
+        commands_file => {
+            is => 'Text',
+            default_value => '-',
+            doc => 'Output file to print commands. Defaults to STDOUT.',
+        },
+    },
+    has_optional_transient => {
+        _bam_output_directory => { is => 'Path::Class::Dir', },
+        _runs => { is => 'ARRAY', },
+        _commands_fh => { is => 'IO::Handle', },
+    },
+    doc => 'insert missing primary contigs from haplotigs',
+};
+
+sub __init__ {
+    my ($self) = @_;
+
+    my @runs;
+    for my $directory ( $self->run_directories ) {
+        push @runs, Pacbio::Run->new(
+            directory => Path::Class::dir($directory),
+            machine_type => 'rsii',
+        );
+    }
+    $self->_runs(\@runs);
+
+    my $commands_file = $self->commands_file;
+    if ( $commands_file and $commands_file ne '-' and -s $commands_file ) {
+        $self->fatal_message("Output commands file exists: $commands_file. Please change detination, or remove it.");
+    }
+
+    $self->_commands_fh(
+        ( $commands_file eq '-' )
+        ? 'STDOUT'
+        : IO::File->new($commands_file, 'r')
+    );
+
+    my $bam_output_directory = $self->bam_output_directory;
+    if ( $bam_output_directory ) {
+        $self->fatal_message('Given bam output directory, but it does not exist!') if not -d $bam_output_directory;
+        $self->_bam_output_directory( Path::Class::dir($bam_output_directory) );
+    }
+
+}
+
+sub execute {
+    my ($self) = @_;
+
+    $self->__init__;
+    for my $run ( @{$self->_runs} ) {
+        my $analyses = $run->analyses;
+        for my $analysis ( @$analyses ) {
+            my $bam = $self->_bam_output_for_analysis($analysis);
+            next if $bam and -s $bam;
+            my $cmd = $self->_bax_to_bam_command_for_analysis($analysis);
+            $self->_commands_fh->print("$cmd\n");
+        }
+    }
+
+    1;
+}
+
+sub _bam_output_for_analysis {
+    my ($self, $analysis) = @_;
+    return if not $self->bam_output_directory;
+    # m151026_060206_00116_c100928752550000001823208204291687_s1_p0.subreads.bam
+    # m151026_060206_00116_c100928752550000001823208204291687_s1_p0.bax.h5
+    my @bax_files = map { $_->stringify } grep { "$_" =~ /\.bax\.h5$/ } @{$analysis->analysis_files};
+    my @bax_basenames = List::Util::uniq( 
+        map { my $bn = $_->basename; my ($t) = split(/\./, $bn, 2); $t; } grep { "$_" =~ /\.bax\.h5$/ } @{$analysis->analysis_files}
+    );
+    $self->fatal_message('Expected one BAX file basename: %s', join(' ', @bax_basenames)) if @bax_basenames != 1;
+    $self->_bam_output_directory->file( join('.', $bax_basenames[0], 'subreads', 'bam') );
+}
+
+sub _bax_to_bam_command_for_analysis {
+    my ($self, $analysis) = @_;
+
+    my @bax_files = map { $_->stringify } grep { "$_" =~ /\.bax\.h5$/ } @{$analysis->analysis_files};
+    $self->fatal_message('Incorrect number (%d) of BAX files for run analysis: %s', scalar(@bax_files), $analysis->alias) if not @bax_files or @bax_files != 3;
+
+    # bsub -o /dir/%LOG bax2bam -o %OUT_BAM BAX_FILES
+    my $cmd = $self->bam_to_bax_command;
+
+    my $log_rex = qr/%LOG/;
+    if ( $cmd =~ /$log_rex/ ) {
+        my $log = join('.', $analysis->alias, 'out');
+        $cmd =~ s/$log_rex/$log/;
+    }
+
+    join(' ', $cmd, join(' ', @bax_files));
+}
+
+1;
diff --git a/lib/Pacbio/Run.pm b/lib/Pacbio/Run.pm
new file mode 100644
index 0000000..f3681fd
--- /dev/null
+++ b/lib/Pacbio/Run.pm
@@ -0,0 +1,65 @@
+package Pacbio::Run;
+
+use strict;
+use warnings 'FATAL';
+
+use base 'Class::Accessor';
+__PACKAGE__->mk_accessors(qw/ _analyses directory machine_type /);
+
+use List::MoreUtils;
+
+use Pacbio::Run::AnalysisFactoryForRsii;
+use Pacbio::Run::AnalysisFactoryForSequel;
+
+sub valid_machine_types { (qw/ rsii sequel /) }
+
+sub __name__ { join(' ', map { $_[0]->$_ } (qw/ directory machine_type /)) }
+
+sub new {
+    my ($class, %params) = @_;
+
+    my $self = bless \%params, $class;
+
+    die "No directory given!" if not $self->directory;
+    die "Directory given does not exist: ".$self->directory if not -d $self->directory->stringify;
+    die "No machine_type given!" if not $self->machine_type;
+    die "Invalid machine_type given: ".$self->machine_type if not List::MoreUtils::any { $self->machine_type eq $_ } $self->valid_machine_types;
+
+    $self;
+}
+
+sub analyses_for_sample {
+    my ($self, $sample_name_regex) = @_;
+    die "No sample name regex given!" if not $sample_name_regex;
+
+    my $analyses = $self->analyses;
+    my @sample_analyses;
+    for my $analysis ( @$analyses ) {
+        push @sample_analyses, $analysis if $analysis->sample_name =~ $sample_name_regex;
+    }
+
+    return if not @sample_analyses;
+    \@sample_analyses;
+}
+
+sub analyses_count {
+    my ($self) = @_;
+    my $analyses = $self->analyses;
+    ( $analyses ? scalar(@$analyses) : 0 );
+}
+
+sub analyses {
+    my ($self) = @_;
+    return $self->_analyses if $self->_analyses;
+    my $analyses;
+    if ( $self->machine_type eq 'rsii' ) {
+        $analyses = Pacbio::Run::AnalysisFactoryForRsii->build($self->directory)
+    }
+    else {
+        $analyses = Pacbio::Run::AnalysisFactoryForSequel->build($self->directory)
+    }
+    return if not $analyses;
+    $self->_analyses($analyses);
+}
+
+1;
diff --git a/lib/Pacbio/Run/Analysis.pm b/lib/Pacbio/Run/Analysis.pm
new file mode 100644
index 0000000..ad7206f
--- /dev/null
+++ b/lib/Pacbio/Run/Analysis.pm
@@ -0,0 +1,32 @@
+package Pacbio::Run::Analysis;
+
+use strict;
+use warnings 'FATAL';
+
+use base 'Class::Accessor';
+__PACKAGE__->mk_accessors(qw/ metadata_xml_file sample_name library_name plate_id version well analysis_files /);
+
+sub __name__ { join(' ', map { $_[0]->$_ } (qw/ plate_id well library_name /)); }
+
+sub new {
+    my ($class, %params) = @_;
+    $params{analysis_files} = [] if not $params{analysis_files};
+    bless \%params, $class;
+}
+
+sub add_analysis_files {
+    my ($self, @files) = @_;
+    die "No analysis file given!" if not @files;
+    my $analysis_files = $self->analysis_files;
+    push @$analysis_files, @files;
+    $self->analysis_files;
+}
+
+sub alias { # PLATE_WELL was: 6U00E3_1020_A01_1
+	my $self = shift;
+    my $alias = join('_', $self->plate_id, $self->well);
+    $alias =~ s/ /_/g;
+	$alias;
+}
+
+1;
diff --git a/lib/Pacbio/Run/AnalysisFactoryForRsii.pm b/lib/Pacbio/Run/AnalysisFactoryForRsii.pm
new file mode 100644
index 0000000..52c95e8
--- /dev/null
+++ b/lib/Pacbio/Run/AnalysisFactoryForRsii.pm
@@ -0,0 +1,92 @@
+package Pacbio::Run::AnalysisFactoryForRsii;
+
+use strict;
+use warnings 'FATAL';
+
+use Data::Dumper 'Dumper';
+use File::Find 'find';
+use List::Util;
+use Path::Class;
+use Pacbio::Run::Analysis;
+use XML::LibXML;
+
+sub build {
+    my ($class, $directory) = @_;
+
+    die "No run directory given." if not $directory;
+    die "Run directory given does not exist!" if not -d "$directory";
+
+    my (@analyses);
+    find(
+        {
+            wanted => sub{
+                if ( /metadata\.xml$/) {
+                    my $xml_info = _load_xml( $File::Find::name );
+                    my $analysis = Pacbio::Run::Analysis->new(
+                        metadata_xml_file => file( $File::Find::name ),
+                        %$xml_info,
+                    );
+                    push @analyses, $analysis;
+                }
+                elsif ( $File::Find::dir =~ /Analysis_Results/ and /\.h5$/ ) {
+                    die "No analyses created to add analysis files!" if not @analyses;
+                    $analyses[$#analyses]->add_analysis_files( file($File::Find::name) );
+                }
+            },
+        },
+        glob($directory->file('*')->stringify),
+    );
+
+    return if not @analyses;
+    \@analyses;
+}
+
+sub _load_xml {
+    my ($xml_file) = @_;
+
+    my $dom = XML::LibXML->load_xml(location => "$xml_file");
+    my $metadata_node = $dom->firstChild;
+    if ( not $metadata_node ) {
+        die "No metadata node found in $xml_file";
+    }
+
+    my $sample_node = List::Util::first { $_->nodeName eq 'Sample' } $metadata_node->childNodes;
+    if ( not $sample_node ) {
+        die "No sample node found!";
+    }
+
+    my $library_name = _load_from_parent_node($sample_node, 'Name');
+    my $well = _load_from_parent_node($sample_node, 'WellName');
+
+    my $sample_name = $library_name;
+    my $well_without_zeros = $well;
+    $well_without_zeros =~ s/0//g;
+    $sample_name =~ s/_$well_without_zeros$//;
+
+    {
+        sample_name => $sample_name,
+        library_name => $library_name,
+        plate_id => _load_from_parent_node($sample_node, 'PlateId'),
+        version => _load_from_parent_node($metadata_node, 'InstCtrlVer'),
+        well => $well,
+    };
+}
+
+sub _load_from_parent_node {
+    my ($parent_node, $node_name) = @_;
+    die "No parent node given!" if not $parent_node;
+    die "No node name node given!" if not $node_name;
+
+    my $node = List::Util::first { $_->nodeName eq $node_name } $parent_node->childNodes;
+    if ( not $node ) {
+        die "No $node_name node found!";
+    }
+
+    my $version = $node->to_literal;
+    if ( not $version ) {
+        die "No info found in $node_name node!";
+    }
+    $version;
+}
+
+1;
diff --git a/lib/Pacbio/Run/AnalysisFactoryForSequel.pm b/lib/Pacbio/Run/AnalysisFactoryForSequel.pm
new file mode 100644
index 0000000..0db3bf5
--- /dev/null
+++ b/lib/Pacbio/Run/AnalysisFactoryForSequel.pm
@@ -0,0 +1,145 @@
+package Pacbio::Run::AnalysisFactoryForSequel;
+
+use strict;
+use warnings 'FATAL';
+
+use Data::Dumper 'Dumper';
+use File::Find 'find';
+use List::Util;
+use Path::Class;
+use Pacbio::Run::Analysis;
+use XML::LibXML;
+
+sub build {
+    my ($class, $directory) = @_;
+
+    die "No run directory given." if not $directory;
+    die "Run directory given does not exist!" if not -d "$directory";
+
+    my (%well_meta_xml_files, %well_analysis_files);
+    find(
+        {
+            wanted => sub{
+                if ( /metadata\.xml$/ and ! /run/ ) {
+                    $well_meta_xml_files{ $File::Find::dir } = file( $File::Find::name );
+                }
+                elsif ( /\.subreads\.bam$/ ) {
+                    push @{$well_analysis_files{ $File::Find::dir }}, file($File::Find::name);
+                }
+            },
+        },
+        glob($directory->file('*')->stringify),
+    );
+
+    die "No meata data xml files found in $directory" if not %well_meta_xml_files;
+
+    my (@analyses);
+    for my $well_dir ( sort keys %well_meta_xml_files ) {
+        die "No analysis files for $well_dir" if not exists $well_analysis_files{$well_dir};
+        my $xml_info = _load_xml( $well_meta_xml_files{$well_dir} );
+        my $analysis = Pacbio::Run::Analysis->new(
+            metadata_xml_file => $well_meta_xml_files{$well_dir},
+            %$xml_info,
+        );
+        $analysis->add_analysis_files(sort @{$well_analysis_files{$well_dir}});
+        push @analyses, $analysis;
+    }
+
+    return if not @analyses;
+    \@analyses;
+}
+
+sub _load_xml {
+    my ($xml_file) = @_;
+
+    my $dom = XML::LibXML->load_xml(location => "$xml_file");
+
+    my ($data_model) = $dom->getElementsByTagName('pbdm:PacBioDataModel');
+    if ( not $data_model ) {
+        ($data_model) = $dom->getElementsByTagName('PacBioDataModel');
+    }
+
+    if ( not $data_model ) {
+        die "Could not find PacBioDataModel node!"
+    }
+
+    my $version = $data_model->getAttribute('Version');
+    die "No version found in PacBioDataModel node!" if not $version;
+    my $node_names = _node_names_for_version($version);
+
+    my %info;
+    my ($collection) = $dom->getElementsByTagName( $node_names->{collections} );
+    if ( not $collection ) {
+        die "No collection node found in $xml_file";
+    }
+
+    my ($collection_metadata) = $collection->getElementsByTagName( $node_names->{collection_metadata} );
+    if ( not $collection_metadata ) {
+        die "No collection metadata node found in $xml_file";
+    }
+
+    my ($run_details_node) = $collection_metadata->getElementsByTagName( $node_names->{run_details} );
+    if ( not $run_details_node ) {
+        die "No run details node found in $xml_file";
+    }
+    my ($run_name_node) = $collection_metadata->getElementsByTagName( $node_names->{run_name} );
+    if ( not $run_name_node ) {
+        die "No run name node found in $xml_file";
+    }
+    $info{plate_id} = $run_name_node->to_literal;
+
+    my ($version_node) = $collection_metadata->getElementsByTagName( $node_names->{instrument_control_version} );
+    if ( not $version_node ) {
+        die "No sample node found in $xml_file";
+    }
+    $info{version} = $version_node->to_literal;
+
+    my ($sample_node) = $collection_metadata->getElementsByTagName( $node_names->{well_sample} );
+    if ( not $sample_node ) {
+        die "No sample node found in $xml_file";
+    }
+    $info{library_name} = $sample_node->getAttribute('Name');
+    my @tokens = split(/_/, $info{library_name});
+    pop @tokens;
+    $info{sample_name} = join('_', @tokens);
+
+    my ($well_name_node) = $collection_metadata->getElementsByTagName( $node_names->{well_name} );
+    if ( not $well_name_node ) {
+        die "No well name node found in $xml_file";
+    }
+    $info{well} = $well_name_node->to_literal;
+
+    \%info;
+}
+
+sub _node_names_for_version {
+    my ($version) = @_;
+
+    if ( $version eq '4.0.0' ) {
+        return {
+            collections => 'pbmeta:Collections',
+            collection_metadata => 'pbmeta:CollectionMetadata',
+            run_details => 'pbmeta:RunDetails',
+            run_name => 'pbmeta:Name',
+            instrument_control_version => 'pbmeta:InstCtrlVer',
+            well_sample => 'pbmeta:WellSample',
+            well_name => 'pbmeta:WellName',
+        }
+    }
+    elsif ( $version eq '4.0.1' ) {
+        return {
+            collections => 'Collections',
+            collection_metadata => 'CollectionMetadata',
+            run_details => 'RunDetails',
+            run_name => 'Name',
+            instrument_control_version => 'InstCtrlVer',
+            well_sample => 'WellSample',
+            well_name => 'WellName',
+        }
+    }
+    else {
+        die "Unknown PacBio Data Model version: $version!";
+    }
+}
+
+1;
diff --git a/t/Pacbio-Command-Assembly-BaxToBam-GenerateCommands.t b/t/Pacbio-Command-Assembly-BaxToBam-GenerateCommands.t
new file mode 100644
index 0000000..c07c9af
--- /dev/null
+++ b/t/Pacbio-Command-Assembly-BaxToBam-GenerateCommands.t
@@ -0,0 +1,70 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings 'FATAL';
+
+use TenxTestEnv;
+
+use File::Slurp;
+use Test::Exception;
+use Test::More tests => 3;
+
+my %test = ( class => 'Pacbio::Command::Assembly::BaxToBam::GenerateCommands', );
+subtest 'setup' => sub{
+    plan tests => 3;
+
+    use_ok($test{class});
+
+    $test{data_dir} = TenxTestEnv::test_data_directory_for_class($test{class});
+    ok(-d $test{data_dir}->stringify, 'data dir exists');
+    $test{tempdir} = File::Temp::tempdir(CLEANUP => 1);
+
+    $test{run_directories} = TenxTestEnv::test_data_directory_for_class('Pacbio::Run');
+    ok(-d $test{run_directories}->stringify, 'run dirs exists');
+
+};
+
+subtest 'execute' => sub{
+    plan tests => 4;
+
+    my $cmd = $test{class}->create(
+        run_directories => [ $test{data_dir}->file('6U00E3')->stringify, ],
+        bam_to_bax_command => 'bsub -q long -o %LOG bam2bax',
+    );
+    ok($cmd, 'create command');
+
+    my $output;
+    open local(*STDOUT), '>', \$output or die $!;
+    lives_ok(sub{ $cmd->execute }, 'execute');
+    ok($cmd->result, 'command result');
+
+    my $expected_output = File::Slurp::slurp( $test{data_dir}->file('expected.out')->stringify );
+    my $base_test_data_dir = TenxTestEnv::test_data_directory();
+    $expected_output =~ s/\%TDD/$base_test_data_dir/g;
+    is($output, $expected_output, 'output commands matches');
+
+};
+
+subtest 'execute with some bams completed' => sub{
+    plan tests => 4;
+
+    my $cmd = $test{class}->create(
+        run_directories => [ $test{data_dir}->file('6U00E3')->stringify, ],
+        bam_to_bax_command => 'bsub -q long -o %LOG bam2bax',
+        bam_output_directory => $test{data_dir}->stringify,
+    );
+    ok($cmd, 'create command');
+
+    my $output;
+    open local(*STDOUT), '>', \$output or die $!;
+    lives_ok(sub{ $cmd->execute }, 'execute');
+    ok($cmd->result, 'command result');
+
+    my $expected_output = File::Slurp::slurp( $test{data_dir}->file('expected.some-done.out')->stringify );
+    my $base_test_data_dir = TenxTestEnv::test_data_directory();
+    $expected_output =~ s/\%TDD/$base_test_data_dir/g;
+    is($output, $expected_output, 'output commands matches');
+
+};
+
+done_testing();
diff --git a/t/Pacbio-Command-Assembly-BaxToBam.t b/t/Pacbio-Command-Assembly-BaxToBam.t
new file mode 100644
index 0000000..af50b6f
--- /dev/null
+++ b/t/Pacbio-Command-Assembly-BaxToBam.t
@@ -0,0 +1,10 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings 'FATAL';
+
+use TenxTestEnv;
+use Test::More tests => 1;
+
+use_ok('Pacbio::Command::Assembly::BaxToBam') or die;
+done_testing();
diff --git a/t/Pacbio-Run-Analysis.t b/t/Pacbio-Run-Analysis.t
new file mode 100644
index 0000000..41c7384
--- /dev/null
+++ b/t/Pacbio-Run-Analysis.t
@@ -0,0 +1,52 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings 'FATAL';
+
+use TenxTestEnv;
+
+use Test::More tests => 3;
+
+my %test = ( class => 'Pacbio::Run::Analysis', );
+subtest 'new' => sub{
+    plan tests => 9;
+
+    use_ok($test{class}) or die;
+
+    my %params = (
+        metadata_xml_file => 'xml', sample_name => 'SAMPLE', library_name => 'LIBRARY',
+        plate_id => 'PLATE', version => 'VERSION', well => 'WELL', analysis_files => [],
+    );
+    my $meta = $test{class}->new(%params);
+    ok($meta, 'create run');
+    $test{meta} = $meta;
+
+    ok($meta->metadata_xml_file, 'xml_file');
+    ok($meta->sample_name, 'sample_name');
+    ok($meta->library_name, 'library_name');
+    ok($meta->plate_id, 'plate_id');
+    ok($meta->version, 'version');
+    ok($meta->well, 'well');
+    ok($meta->analysis_files, 'analysis_files');
+
+};
+
+subtest 'add_analysis_files' => sub{
+    plan tests => 3;
+
+    my $meta = $test{meta};
+    is_deeply($meta->analysis_files, [], 'no analysis_files');
+    ok($meta->add_analysis_files('FILE'), 'add_analysis_files');
+    is_deeply($meta->analysis_files, ['FILE'], 'correct analysis_files');
+
+};
+
+subtest 'name and alias' => sub{
+    plan tests => 2;
+
+    is($test{meta}->__name__, 'PLATE WELL LIBRARY', 'correct __name__');
+    is($test{meta}->alias, 'PLATE_WELL', 'correct alias');
+
+};
+
+done_testing();
diff --git a/t/Pacbio-Run-AnalysisFactoryForRsii.t b/t/Pacbio-Run-AnalysisFactoryForRsii.t
new file mode 100644
index 0000000..8781c5f
--- /dev/null
+++ b/t/Pacbio-Run-AnalysisFactoryForRsii.t
@@ -0,0 +1,35 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings 'FATAL';
+
+use TenxTestEnv;
+
+use Path::Class;
+use Test::More tests => 1;
+use Test::Exception;
+
+my %setup = ( class => 'Pacbio::Run::AnalysisFactoryForRsii', );
+subtest 'new' => sub{
+    plan tests => 11;
+
+    use_ok($setup{class}) or die;
+
+    throws_ok(sub{ $setup{class}->build; }, qr/No run directory given/, 'new fails w/o directory');
+    throws_ok(sub{ $setup{class}->build('blah'); }, qr/Run directory given does not exist/, 'new fails w/ non existing directory');
+
+    my $directory = dir( TenxTestEnv::test_data_directory_for_class('Pacbio::Run') )->subdir('6U00FA');
+    ok(-d "$directory", "example run directory exists");
+
+    my $analyses = $setup{class}->build($directory);
+    is(@$analyses, 10, 'built the correct number of analyses');
+    is($analyses->[0]->metadata_xml_file, $directory->subdir('A01_1')->file('m160819_231415_00116_c101036512550000001823251411171640_s1_p0.metadata.xml'), 'metadata_xml_file');
+    is($analyses->[0]->sample_name, 'NA19434_4808o3_lib1_50pM', 'sample_name');
+    is($analyses->[0]->library_name, 'NA19434_4808o3_lib1_50pM_A1', 'library_name');
+    is($analyses->[0]->plate_id, '6U00FA', 'plate_id');
+    is($analyses->[0]->version, '2.3.0.3.154799', 'version');
+    is($analyses->[0]->well, 'A01', 'well');
+
+};
+
+done_testing();
diff --git a/t/Pacbio-Run-AnalysisFactoryForSequel.t b/t/Pacbio-Run-AnalysisFactoryForSequel.t
new file mode 100644
index 0000000..a0576c8
--- /dev/null
+++ b/t/Pacbio-Run-AnalysisFactoryForSequel.t
@@ -0,0 +1,60 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings 'FATAL';
+
+use TenxTestEnv;
+
+use Path::Class;
+use Test::More tests => 3;
+use Test::Exception;
+
+my %test = ( class => 'Pacbio::Run::AnalysisFactoryForSequel', );
+subtest 'setup and fails' => sub{
+    plan tests => 3;
+
+    use_ok($test{class}) or die;
+
+    throws_ok(sub{ $test{class}->build; }, qr/No run directory given/, 'new fails w/o directory');
+    throws_ok(sub{ $test{class}->build('blah'); }, qr/Run directory given does not exist/, 'new fails w/ non existing directory');
+};
+
+subtest 'new version 4.0.0' => sub{
+    plan tests => 9;
+
+    my $run_id= '6U00I7';
+    my $directory = dir( TenxTestEnv::test_data_directory_for_class('Pacbio::Run') )->subdir($run_id);
+    ok(-d "$directory", "example run directory exists");
+
+    my $analyses = $test{class}->build($directory);
+    is(@$analyses, 5, 'built the correct number of analyses');
+    is($analyses->[0]->metadata_xml_file, $directory->subdir('1_A01')->file('.m54111_170804_145334.metadata.xml'), 'metadata_xml_file');
+    is($analyses->[0]->sample_name, 'HG03486_Mende_4808Ll', 'sample_name');
+    is($analyses->[0]->library_name, 'HG03486_Mende_4808Ll_20pM', 'library_name');
+    is($analyses->[0]->plate_id, $run_id, 'plate_id');
+    is($analyses->[0]->version, '4.0.0.189873', 'version');
+    is($analyses->[0]->well, 'A01', 'well');
+    is_deeply($analyses->[0]->analysis_files, [ $directory->subdir('1_A01')->file('m54111_170804_145334.subreads.bam') ], 'analysis_files');
+
+};
+
+subtest 'new version 4.0.1' => sub{
+    plan tests => 9;
+
+    my $run_id= '6U00IG';
+    my $directory = dir( TenxTestEnv::test_data_directory_for_class('Pacbio::Run') )->subdir($run_id);
+    ok(-d "$directory", "example run directory exists");
+
+    my $analyses = $test{class}->build($directory);
+    is(@$analyses, 2, 'built the correct number of analyses');
+    is($analyses->[1]->metadata_xml_file, $directory->subdir('2_B01')->file('.m54111_170830_013202.metadata.xml'), 'metadata_xml_file');
+    is($analyses->[1]->sample_name, 'X.couchianus_4808Lu', 'sample_name');
+    is($analyses->[1]->library_name, 'X.couchianus_4808Lu_18pM', 'library_name');
+    is($analyses->[1]->plate_id, $run_id, 'plate_id');
+    is($analyses->[1]->version, '5.0.0.6235', 'version');
+    is($analyses->[1]->well, 'B01', 'well');
+    is_deeply($analyses->[1]->analysis_files, [ $directory->subdir('2_B01')->file('m54111_170830_013202.subreads.bam') ], 'analysis_files');
+
+};
+
+done_testing();
diff --git a/t/Pacbio-Run.t b/t/Pacbio-Run.t
new file mode 100644
index 0000000..38a6845
--- /dev/null
+++ b/t/Pacbio-Run.t
@@ -0,0 +1,54 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings 'FATAL';
+
+use TenxTestEnv;
+
+use Path::Class;
+use Test::More tests => 2;
+use Test::Exception;
+
+my %test = ( class => 'Pacbio::Run', );
+subtest 'new' => sub{
+    plan tests => 9;
+
+    use_ok($test{class}) or die;
+
+    my $directory = dir( TenxTestEnv::test_data_directory_for_class($test{class}) )->subdir('6U00E3');
+    ok(-d "$directory", "example run directory exists");
+
+    my $run = $test{class}->new(directory => $directory, machine_type => 'rsii');
+
+    ok($run, 'create run');
+    ok($run->directory, 'directory');
+    is($run->__name__, join(' ', $run->directory, $run->machine_type), '__name__');
+
+    $test{run} = $run;
+
+    throws_ok(sub{ $test{class}->new; }, qr/No directory given/, 'fails w/o directory');
+    throws_ok(sub{ $test{class}->new(directory => dir('blah')); }, qr/Directory given does not exist/, 'fails w/ invalid directory');
+    throws_ok(sub{ $test{class}->new(directory => $directory); }, qr/No machine_type given/, 'fails w/o machine_type');
+    throws_ok(sub{ $test{class}->new(directory => $directory, machine_type => 'blah'); }, qr/Invalid machine_type given/, 'fails w/ invalid machine_type');
+
+};
+
+subtest 'analyses' => sub{
+    plan tests => 6;
+
+    my $run = $test{run};
+	my $analyses = $run->analyses;
+    ok($analyses, 'run analyses');
+    is(@$analyses, 16, 'correct number of analyses');
+    is($run->analyses_count, 16, 'analyses_count');
+
+	my $sample_analyses = $run->analyses_for_sample(qr/HG02818/);
+    is(@$sample_analyses, 14, 'correct number of sample analyses');
+    my $expected_sample_analyses = [ grep { $_->sample_name =~ /HG02818/ } @$analyses ];
+    is_deeply($sample_analyses, $expected_sample_analyses, 'analyses_for_sample');
+
+    throws_ok(sub{ $test{run}->analyses_for_sample; }, qr/No sample name regex given/, 'analyses_for_sample fails w/o sample name regex');
+
+};
+
+done_testing();
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.bax.h5
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.bax.h5
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.log b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.log
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.log
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fasta b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fasta
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fasta
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fastq b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fastq
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fastq
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.bax.h5
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.bax.h5
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.log b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.log
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.log
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fasta b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fasta
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fasta
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fastq b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fastq
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fastq
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.bax.h5
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.bax.h5
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.log b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.log
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.log
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fasta b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fasta
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fasta
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fastq b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fastq
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fastq
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.bas.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.bas.h5
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.bas.h5
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.csv b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.csv
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.csv
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.xml b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.xml
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.xml
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.xfer.xml b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.xfer.xml
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.xfer.xml
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.xfer.xml b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.xfer.xml
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.xfer.xml
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.xfer.xml b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.xfer.xml
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.xfer.xml
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.mcd.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.mcd.h5
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.mcd.h5
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.metadata.xml b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.metadata.xml
new file mode 100644
index 0000000..b883bd2
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.metadata.xml
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A02_1/Analysis_Results/m160613_024817_00116_c100976392550000001823226708101600_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A02_1/Analysis_Results/m160613_024817_00116_c100976392550000001823226708101600_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B01_1/Analysis_Results/m160611_041253_00116_c100976122550000001823226708101631_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B01_1/Analysis_Results/m160611_041253_00116_c100976122550000001823226708101631_s1_p0.1.bax.h5
new file mode 100644
index 0000000..76848c8
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new file mode 100644
index 0000000..76848c8
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B02_1/Analysis_Results/m160613_070741_00116_c100976392550000001823226708101601_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B02_1/Analysis_Results/m160613_070741_00116_c100976392550000001823226708101601_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C01_1/Analysis_Results/m160611_103201_00116_c100976122550000001823226708101632_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C01_1/Analysis_Results/m160611_103201_00116_c100976122550000001823226708101632_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C02_1/Analysis_Results/m160613_112823_00116_c100976392550000001823226708101602_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C02_1/Analysis_Results/m160613_112823_00116_c100976392550000001823226708101602_s1_p0.1.bax.h5
new file mode 100644
index 0000000..76848c8
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D01_1/Analysis_Results/m160611_165410_00116_c100976122550000001823226708101633_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D01_1/Analysis_Results/m160611_165410_00116_c100976122550000001823226708101633_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D02_1/Analysis_Results/m160613_154904_00116_c100976392550000001823226708101603_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D02_1/Analysis_Results/m160613_154904_00116_c100976392550000001823226708101603_s1_p0.1.bax.h5
new file mode 100644
index 0000000..76848c8
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E01_1/Analysis_Results/m160611_231419_00116_c100976122550000001823226708101634_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E01_1/Analysis_Results/m160611_231419_00116_c100976122550000001823226708101634_s1_p0.1.bax.h5
new file mode 100644
index 0000000..76848c8
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E02_1/Analysis_Results/m160613_200939_00116_c100976392550000001823226708101604_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E02_1/Analysis_Results/m160613_200939_00116_c100976392550000001823226708101604_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F01_1/Analysis_Results/m160612_053356_00116_c100976122550000001823226708101635_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F01_1/Analysis_Results/m160612_053356_00116_c100976122550000001823226708101635_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F02_1/Analysis_Results/m160614_003005_00116_c100976392550000001823226708101605_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F02_1/Analysis_Results/m160614_003005_00116_c100976392550000001823226708101605_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G01_1/Analysis_Results/m160612_115607_00116_c100976122550000001823226708101636_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G01_1/Analysis_Results/m160612_115607_00116_c100976122550000001823226708101636_s1_p0.1.bax.h5
new file mode 100644
index 0000000..76848c8
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G02_1/Analysis_Results/m160614_045352_00116_c100976392550000001823226708101606_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G02_1/Analysis_Results/m160614_045352_00116_c100976392550000001823226708101606_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H01_1/Analysis_Results/m160612_181848_00116_c100976122550000001823226708101637_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H01_1/Analysis_Results/m160612_181848_00116_c100976122550000001823226708101637_s1_p0.1.bax.h5
new file mode 100644
index 0000000..76848c8
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.1.bax.h5 b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
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new file mode 100644
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+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.metadata.xml
@@ -0,0 +1 @@
+<?xml version="1.0" encoding="utf-8"?><Metadata xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="http://pacificbiosciences.com/PAP/Metadata.xsd"><InstCtrlVer>2.3.0.3.154799</InstCtrlVer><SigProcVer>NRT@172.31.128.10:8082, SwVer=2303.154799, HwVer=1.0</SigProcVer><Run><RunId>r001020_00116_160610</RunId><Name>6U00E3</Name><WhenCreated>2016-06-10T12:39:26</WhenCreated><WhenStarted>2016-06-10T19:33:27</WhenStarted></Run><Movie><WhenStarted>2016-06-14T09:24:53.70997+00:00</WhenStarted><DurationInSec>14400</DurationInSec><Number>0</Number></Movie><Sample><Name>4808lj_HG02818_Lib2_50pM_H2</Name><PlateId>6U00E3</PlateId><WellName>H02</WellName><Concentration>0</Concentration><SampleReuseEnabled>false</SampleReuseEnabled><StageHotstartEnabled>true</StageHotstartEnabled><SizeSelectionEnabled>true</SizeSelectionEnabled><UseCount>1</UseCount><DNAControlComplex>2kb_control</DNAControlComplex></Sample><InstrumentId>1</InstrumentId><InstrumentName>00116</InstrumentName><CollectionProtocol>MagBead OneCellPerWell v1</CollectionProtocol><CollectionNumber>16</CollectionNumber><CellIndex>7</CellIndex><SetNumber>1</SetNumber><EightPac><PartNumber>0018</PartNumber><LotNumber>232267</LotNumber><Barcode>10097639255000000182322670810160</Barcode><ExpirationDate>2016-08-10</ExpirationDate></EightPac><TemplatePrep><Name>DNA Template Prep Kit 3.0</Name><PartNumber>100259100</PartNumber><LotNumber>006928</LotNumber><Barcode>006928100259100022817</Barcode><ExpirationDate>2017-02-28</ExpirationDate><AdapterSequence>ATCTCTCTCttttcctcctcctccgttgttgttgttGAGAGAGAT</AdapterSequence><InsertSize>20000</InsertSize></TemplatePrep><BindingKit><Name>DNA/Polymerase Binding Kit P6 v2</Name><PartNumber>100372700</PartNumber><LotNumber>006724</LotNumber><Barcode>006724100372700100816</Barcode><ExpirationDate>2016-10-08</ExpirationDate><Control>2kb_control</Control><IsControlUsed>true</IsControlUsed></BindingKit><SequencingKit><Name>ReagentPlate1</Name><PartNumber>100612400</PartNumber><LotNumber>006925</LotNumber><Barcode>006925183100612400092416</Barcode><ExpirationDate>2016-09-24</ExpirationDate><Protocol>MagBeadReagentMixingProtocol_DWP</Protocol></SequencingKit><ReagentTube0><Name>ReagentTube1-0</Name><PartNumber>001028310</PartNumber><LotNumber>206520</LotNumber><Barcode>206520676001028310051218</Barcode><ExpirationDate>2018-05-12</ExpirationDate></ReagentTube0><ReagentTube1><Name>ReagentTube1-1</Name><PartNumber>100192000</PartNumber><LotNumber>007541</LotNumber><Barcode>007541930100192000053120</Barcode><ExpirationDate>2020-05-31</ExpirationDate></ReagentTube1><Primary><Protocol>BasecallerV1</Protocol><ConfigFileName>2-3-0_P6-C4.xml</ConfigFileName><ResultsFolder>Analysis_Results</ResultsFolder><CollectionPathUri>rsy://smb-cluster.gsc.wustl.edu/gc2716/production/paresults//6U00E3_1020/H02_1/</CollectionPathUri><CollectionFileCopy>Fasta</CollectionFileCopy><CollectionFileCopy>Fastq</CollectionFileCopy></Primary><Secondary><ProtocolName /><CellCountInJob>0</CellCountInJob></Secondary><Custom><KeyValue key="svc:/CentralDataSvc/#Display.Sample_Metadata.User_Defined_Field_1" label="Primary Investigator" /><KeyValue key="svc:/CentralDataSvc/#Display.Sample_Metadata.User_Defined_Field_2" label="Lab Number">PROD16_0069_RS1</KeyValue><KeyValue key="svc:/CentralDataSvc/#Display.Sample_Metadata.User_Defined_Field_3" label="User Defined Field 3" /><KeyValue key="svc:/CentralDataSvc/#Display.Sample_Metadata.User_Defined_Field_4" label="User Defined Field 4" /><KeyValue key="svc:/CentralDataSvc/#Display.Sample_Metadata.User_Defined_Field_5" label="User Defined Field 5" /><KeyValue key="svc:/CentralDataSvc/#Display.Sample_Metadata.User_Defined_Field_6" label="User Defined Field 6" /></Custom><ExpirationData><EightPacPastExpiration>0</EightPacPastExpiration><ReagentKitPastExpiration>0</ReagentKitPastExpiration><ReagentTube0PastExpiration>0</ReagentTube0PastExpiration><ReagentTube1PastExpiration>0</ReagentTube1PastExpiration></ExpirationData></Metadata>
\ No newline at end of file
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/expected.out b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/expected.out
new file mode 100644
index 0000000..e88da0f
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/expected.out
@@ -0,0 +1,16 @@
+bsub -q long -o 6U00E3_A01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_A02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A02_1/Analysis_Results/m160613_024817_00116_c100976392550000001823226708101600_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A02_1/Analysis_Results/m160613_024817_00116_c100976392550000001823226708101600_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A02_1/Analysis_Results/m160613_024817_00116_c100976392550000001823226708101600_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_B01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B01_1/Analysis_Results/m160611_041253_00116_c100976122550000001823226708101631_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B01_1/Analysis_Results/m160611_041253_00116_c100976122550000001823226708101631_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B01_1/Analysis_Results/m160611_041253_00116_c100976122550000001823226708101631_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_B02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B02_1/Analysis_Results/m160613_070741_00116_c100976392550000001823226708101601_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B02_1/Analysis_Results/m160613_070741_00116_c100976392550000001823226708101601_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B02_1/Analysis_Results/m160613_070741_00116_c100976392550000001823226708101601_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_C01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C01_1/Analysis_Results/m160611_103201_00116_c100976122550000001823226708101632_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C01_1/Analysis_Results/m160611_103201_00116_c100976122550000001823226708101632_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C01_1/Analysis_Results/m160611_103201_00116_c100976122550000001823226708101632_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_C02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C02_1/Analysis_Results/m160613_112823_00116_c100976392550000001823226708101602_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C02_1/Analysis_Results/m160613_112823_00116_c100976392550000001823226708101602_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C02_1/Analysis_Results/m160613_112823_00116_c100976392550000001823226708101602_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_D01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D01_1/Analysis_Results/m160611_165410_00116_c100976122550000001823226708101633_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D01_1/Analysis_Results/m160611_165410_00116_c100976122550000001823226708101633_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D01_1/Analysis_Results/m160611_165410_00116_c100976122550000001823226708101633_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_D02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D02_1/Analysis_Results/m160613_154904_00116_c100976392550000001823226708101603_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D02_1/Analysis_Results/m160613_154904_00116_c100976392550000001823226708101603_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D02_1/Analysis_Results/m160613_154904_00116_c100976392550000001823226708101603_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_E01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E01_1/Analysis_Results/m160611_231419_00116_c100976122550000001823226708101634_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E01_1/Analysis_Results/m160611_231419_00116_c100976122550000001823226708101634_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E01_1/Analysis_Results/m160611_231419_00116_c100976122550000001823226708101634_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_E02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E02_1/Analysis_Results/m160613_200939_00116_c100976392550000001823226708101604_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E02_1/Analysis_Results/m160613_200939_00116_c100976392550000001823226708101604_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E02_1/Analysis_Results/m160613_200939_00116_c100976392550000001823226708101604_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_F01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F01_1/Analysis_Results/m160612_053356_00116_c100976122550000001823226708101635_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F01_1/Analysis_Results/m160612_053356_00116_c100976122550000001823226708101635_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F01_1/Analysis_Results/m160612_053356_00116_c100976122550000001823226708101635_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_F02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F02_1/Analysis_Results/m160614_003005_00116_c100976392550000001823226708101605_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F02_1/Analysis_Results/m160614_003005_00116_c100976392550000001823226708101605_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F02_1/Analysis_Results/m160614_003005_00116_c100976392550000001823226708101605_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_G01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G01_1/Analysis_Results/m160612_115607_00116_c100976122550000001823226708101636_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G01_1/Analysis_Results/m160612_115607_00116_c100976122550000001823226708101636_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G01_1/Analysis_Results/m160612_115607_00116_c100976122550000001823226708101636_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_G02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G02_1/Analysis_Results/m160614_045352_00116_c100976392550000001823226708101606_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G02_1/Analysis_Results/m160614_045352_00116_c100976392550000001823226708101606_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G02_1/Analysis_Results/m160614_045352_00116_c100976392550000001823226708101606_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_H01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H01_1/Analysis_Results/m160612_181848_00116_c100976122550000001823226708101637_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H01_1/Analysis_Results/m160612_181848_00116_c100976122550000001823226708101637_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H01_1/Analysis_Results/m160612_181848_00116_c100976122550000001823226708101637_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_H02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.3.bax.h5
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/expected.some-done.out b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/expected.some-done.out
new file mode 100644
index 0000000..2bcaff4
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/expected.some-done.out
@@ -0,0 +1,14 @@
+bsub -q long -o 6U00E3_A02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A02_1/Analysis_Results/m160613_024817_00116_c100976392550000001823226708101600_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A02_1/Analysis_Results/m160613_024817_00116_c100976392550000001823226708101600_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/A02_1/Analysis_Results/m160613_024817_00116_c100976392550000001823226708101600_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_B01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B01_1/Analysis_Results/m160611_041253_00116_c100976122550000001823226708101631_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B01_1/Analysis_Results/m160611_041253_00116_c100976122550000001823226708101631_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B01_1/Analysis_Results/m160611_041253_00116_c100976122550000001823226708101631_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_B02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B02_1/Analysis_Results/m160613_070741_00116_c100976392550000001823226708101601_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B02_1/Analysis_Results/m160613_070741_00116_c100976392550000001823226708101601_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/B02_1/Analysis_Results/m160613_070741_00116_c100976392550000001823226708101601_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_C01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C01_1/Analysis_Results/m160611_103201_00116_c100976122550000001823226708101632_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C01_1/Analysis_Results/m160611_103201_00116_c100976122550000001823226708101632_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C01_1/Analysis_Results/m160611_103201_00116_c100976122550000001823226708101632_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_C02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C02_1/Analysis_Results/m160613_112823_00116_c100976392550000001823226708101602_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C02_1/Analysis_Results/m160613_112823_00116_c100976392550000001823226708101602_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/C02_1/Analysis_Results/m160613_112823_00116_c100976392550000001823226708101602_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_D01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D01_1/Analysis_Results/m160611_165410_00116_c100976122550000001823226708101633_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D01_1/Analysis_Results/m160611_165410_00116_c100976122550000001823226708101633_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D01_1/Analysis_Results/m160611_165410_00116_c100976122550000001823226708101633_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_D02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D02_1/Analysis_Results/m160613_154904_00116_c100976392550000001823226708101603_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D02_1/Analysis_Results/m160613_154904_00116_c100976392550000001823226708101603_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/D02_1/Analysis_Results/m160613_154904_00116_c100976392550000001823226708101603_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_E01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E01_1/Analysis_Results/m160611_231419_00116_c100976122550000001823226708101634_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E01_1/Analysis_Results/m160611_231419_00116_c100976122550000001823226708101634_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/E01_1/Analysis_Results/m160611_231419_00116_c100976122550000001823226708101634_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_F01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F01_1/Analysis_Results/m160612_053356_00116_c100976122550000001823226708101635_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F01_1/Analysis_Results/m160612_053356_00116_c100976122550000001823226708101635_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F01_1/Analysis_Results/m160612_053356_00116_c100976122550000001823226708101635_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_F02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F02_1/Analysis_Results/m160614_003005_00116_c100976392550000001823226708101605_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F02_1/Analysis_Results/m160614_003005_00116_c100976392550000001823226708101605_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/F02_1/Analysis_Results/m160614_003005_00116_c100976392550000001823226708101605_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_G01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G01_1/Analysis_Results/m160612_115607_00116_c100976122550000001823226708101636_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G01_1/Analysis_Results/m160612_115607_00116_c100976122550000001823226708101636_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G01_1/Analysis_Results/m160612_115607_00116_c100976122550000001823226708101636_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_G02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G02_1/Analysis_Results/m160614_045352_00116_c100976392550000001823226708101606_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G02_1/Analysis_Results/m160614_045352_00116_c100976392550000001823226708101606_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/G02_1/Analysis_Results/m160614_045352_00116_c100976392550000001823226708101606_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_H01.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H01_1/Analysis_Results/m160612_181848_00116_c100976122550000001823226708101637_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H01_1/Analysis_Results/m160612_181848_00116_c100976122550000001823226708101637_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H01_1/Analysis_Results/m160612_181848_00116_c100976122550000001823226708101637_s1_p0.3.bax.h5
+bsub -q long -o 6U00E3_H02.out bam2bax %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.1.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.2.bax.h5 %TDD/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.3.bax.h5
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.subreads.bam b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.subreads.bam
new file mode 100644
index 0000000..1a9580c
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.subreads.bam
@@ -0,0 +1 @@
+BAM for A01_1 m160610_215437_00116_c100976122550000001823226708101630_s1_p0
diff --git a/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/m160613_200939_00116_c100976392550000001823226708101604_s1_p0.subreads.bam b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/m160613_200939_00116_c100976392550000001823226708101604_s1_p0.subreads.bam
new file mode 100644
index 0000000..e5910c5
--- /dev/null
+++ b/t/data/Pacbio-Command-Assembly-BaxToBam-GenerateCommands/m160613_200939_00116_c100976392550000001823226708101604_s1_p0.subreads.bam
@@ -0,0 +1 @@
+BAM for E02_1 m160613_200939_00116_c100976392550000001823226708101604_s1_p0
diff --git a/t/data/Pacbio-Run/6U00E3-submission/6U00E3.tar b/t/data/Pacbio-Run/6U00E3-submission/6U00E3.tar
new file mode 100644
index 0000000..8e0af98
Binary files /dev/null and b/t/data/Pacbio-Run/6U00E3-submission/6U00E3.tar differ
diff --git a/t/data/Pacbio-Run/6U00E3-submission/6U00E3/6U00E3.experiment.xml b/t/data/Pacbio-Run/6U00E3-submission/6U00E3/6U00E3.experiment.xml
new file mode 100644
index 0000000..e18eb6f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3-submission/6U00E3/6U00E3.experiment.xml
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.experiment.xsd?view=co">
+  <EXPERIMENT alias="H_IJ-HG02818-HG02818_1-lib2" center_name="WUGSC">
+    <STUDY_REF>
+      <IDENTIFIERS>
+        <EXTERNAL_ID namespace="BioProject">BIOPROJECT</EXTERNAL_ID>
+      </IDENTIFIERS>
+    </STUDY_REF>
+    <DESIGN>
+      <DESIGN_DESCRIPTION></DESIGN_DESCRIPTION>
+      <SAMPLE_DESCRIPTOR>
+        <IDENTIFIERS>
+          <EXTERNAL_ID namespace="BioSample">BIOSAMPLE</EXTERNAL_ID>
+        </IDENTIFIERS>
+      </SAMPLE_DESCRIPTOR>
+      <LIBRARY_DESCRIPTOR>
+        <LIBRARY_NAME>H_IJ-HG02818-HG02818_1-lib2</LIBRARY_NAME>
+        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
+        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
+        <LIBRARY_SELECTION>unspecified</LIBRARY_SELECTION>
+        <LIBRARY_LAYOUT>
+          <SINGLE/>
+        </LIBRARY_LAYOUT>
+      </LIBRARY_DESCRIPTOR>
+    </DESIGN>
+    <PLATFORM>
+      <PACBIO_SMRT>
+        <INSTRUMENT_MODEL>PacBio RS II</INSTRUMENT_MODEL>
+      </PACBIO_SMRT>
+    </PLATFORM>
+    <PROCESSING>
+      <PIPELINE>
+        <PIPE_SECTION>
+          <STEP_INDEX></STEP_INDEX>
+          <PREV_STEP_INDEX></PREV_STEP_INDEX>
+          <PROGRAM>PacBio RS II</PROGRAM>
+          <VERSION>2.3.0.3.154799</VERSION>
+        </PIPE_SECTION>
+      </PIPELINE>
+    </PROCESSING>
+  </EXPERIMENT>
+</EXPERIMENT_SET>
diff --git a/t/data/Pacbio-Run/6U00E3-submission/6U00E3/6U00E3.run.xml b/t/data/Pacbio-Run/6U00E3-submission/6U00E3/6U00E3.run.xml
new file mode 100644
index 0000000..4047361
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3-submission/6U00E3/6U00E3.run.xml
@@ -0,0 +1,171 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<RUN_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.run.xsd?view=co">
+  <RUN alias="6U00E3_A01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160610_215437_00116_c100976122550000001823226708101630_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160610_215437_00116_c100976122550000001823226708101630_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_A02" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160613_024817_00116_c100976392550000001823226708101600_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_024817_00116_c100976392550000001823226708101600_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_024817_00116_c100976392550000001823226708101600_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_024817_00116_c100976392550000001823226708101600_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_024817_00116_c100976392550000001823226708101600_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_B01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160611_041253_00116_c100976122550000001823226708101631_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_041253_00116_c100976122550000001823226708101631_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_041253_00116_c100976122550000001823226708101631_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_041253_00116_c100976122550000001823226708101631_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_041253_00116_c100976122550000001823226708101631_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_B02" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160613_070741_00116_c100976392550000001823226708101601_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_070741_00116_c100976392550000001823226708101601_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_070741_00116_c100976392550000001823226708101601_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_070741_00116_c100976392550000001823226708101601_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_070741_00116_c100976392550000001823226708101601_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_C01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160611_103201_00116_c100976122550000001823226708101632_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_103201_00116_c100976122550000001823226708101632_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_103201_00116_c100976122550000001823226708101632_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_103201_00116_c100976122550000001823226708101632_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_103201_00116_c100976122550000001823226708101632_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_C02" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160613_112823_00116_c100976392550000001823226708101602_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_112823_00116_c100976392550000001823226708101602_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_112823_00116_c100976392550000001823226708101602_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_112823_00116_c100976392550000001823226708101602_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_112823_00116_c100976392550000001823226708101602_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_D01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160611_165410_00116_c100976122550000001823226708101633_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_165410_00116_c100976122550000001823226708101633_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_165410_00116_c100976122550000001823226708101633_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_165410_00116_c100976122550000001823226708101633_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_165410_00116_c100976122550000001823226708101633_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_D02" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160613_154904_00116_c100976392550000001823226708101603_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_154904_00116_c100976392550000001823226708101603_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_154904_00116_c100976392550000001823226708101603_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_154904_00116_c100976392550000001823226708101603_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_154904_00116_c100976392550000001823226708101603_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_E01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160611_231419_00116_c100976122550000001823226708101634_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_231419_00116_c100976122550000001823226708101634_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_231419_00116_c100976122550000001823226708101634_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_231419_00116_c100976122550000001823226708101634_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160611_231419_00116_c100976122550000001823226708101634_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_E02" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160613_200939_00116_c100976392550000001823226708101604_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_200939_00116_c100976392550000001823226708101604_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_200939_00116_c100976392550000001823226708101604_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_200939_00116_c100976392550000001823226708101604_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160613_200939_00116_c100976392550000001823226708101604_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_F01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160612_053356_00116_c100976122550000001823226708101635_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160612_053356_00116_c100976122550000001823226708101635_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160612_053356_00116_c100976122550000001823226708101635_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160612_053356_00116_c100976122550000001823226708101635_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160612_053356_00116_c100976122550000001823226708101635_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_F02" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160614_003005_00116_c100976392550000001823226708101605_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_003005_00116_c100976392550000001823226708101605_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_003005_00116_c100976392550000001823226708101605_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_003005_00116_c100976392550000001823226708101605_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_003005_00116_c100976392550000001823226708101605_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_G02" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160614_045352_00116_c100976392550000001823226708101606_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_045352_00116_c100976392550000001823226708101606_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_045352_00116_c100976392550000001823226708101606_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_045352_00116_c100976392550000001823226708101606_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_045352_00116_c100976392550000001823226708101606_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00E3_H02" center_name="WUGSC">
+    <EXPERIMENT_REF refname="H_IJ-HG02818-HG02818_1-lib2" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m160614_091421_00116_c100976392550000001823226708101607_s1_p0.1.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_091421_00116_c100976392550000001823226708101607_s1_p0.2.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_091421_00116_c100976392550000001823226708101607_s1_p0.3.bax.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_091421_00116_c100976392550000001823226708101607_s1_p0.bas.h5" filetype="PacBio_HDF5" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m160614_091421_00116_c100976392550000001823226708101607_s1_p0.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+</RUN_SET>
diff --git a/t/data/Pacbio-Run/6U00E3-submission/6U00E3/6U00E3.submission.xml b/t/data/Pacbio-Run/6U00E3-submission/6U00E3/6U00E3.submission.xml
new file mode 100644
index 0000000..65d1533
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3-submission/6U00E3/6U00E3.submission.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SUBMISSION_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.submission.xsd?view=co">
+  <SUBMISSION alias="6U00E3" center_name="WUGSC">
+    <CONTACTS>
+      <CONTACT name="LIMS" inform_on_status="mailto:mgi-submission@gowustl.onmicrosoft.com" inform_on_error="mailto:mgi-submission@gowustl.onmicrosoft.com"/>
+    </CONTACTS>
+    <ACTIONS>
+      <ACTION>
+        <RELEASE/>
+      </ACTION>
+      <ACTION>
+        <ADD source="6U00E3.experiment.xml" schema="experiment"/>
+      </ACTION>
+      <ACTION>
+        <ADD source="6U00E3.run.xml" schema="run"/>
+      </ACTION>
+    </ACTIONS>
+  </SUBMISSION>
+</SUBMISSION_SET>
diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.bax.h5 b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.bax.h5
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.bax.h5
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.log b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.log
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.log
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fasta b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fasta
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fasta
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fastq b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fastq
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.subreads.fastq
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.bax.h5 b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.bax.h5
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.bax.h5
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.log b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.log
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.log
@@ -0,0 +1 @@
+DATA
diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fasta b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fasta
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fasta
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fastq b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fastq
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.subreads.fastq
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.bax.h5 b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.bax.h5
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.bax.h5
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.log b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.log
new file mode 100644
index 0000000..76848c8
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@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fasta b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fasta
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fasta
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fastq b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fastq
new file mode 100644
index 0000000..76848c8
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+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.subreads.fastq
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.bas.h5 b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.bas.h5
new file mode 100644
index 0000000..76848c8
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+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.bas.h5
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.csv b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.csv
new file mode 100644
index 0000000..76848c8
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+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.csv
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.xml b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.xml
new file mode 100644
index 0000000..76848c8
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+++ b/t/data/Pacbio-Run/6U00E3/A01_1/Analysis_Results/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.sts.xml
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.xfer.xml b/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.1.xfer.xml
new file mode 100644
index 0000000..76848c8
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@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.xfer.xml b/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.xfer.xml
new file mode 100644
index 0000000..76848c8
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+++ b/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.2.xfer.xml
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.xfer.xml b/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.3.xfer.xml
new file mode 100644
index 0000000..76848c8
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@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.mcd.h5
new file mode 100644
index 0000000..76848c8
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@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00E3/A01_1/m160610_215437_00116_c100976122550000001823226708101630_s1_p0.metadata.xml
new file mode 100644
index 0000000..b883bd2
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diff --git a/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.3.subreads.fasta b/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.3.subreads.fasta
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.3.subreads.fasta
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.3.subreads.fastq b/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.3.subreads.fastq
new file mode 100644
index 0000000..76848c8
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@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.bas.h5 b/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.bas.h5
new file mode 100644
index 0000000..76848c8
--- /dev/null
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@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.sts.csv b/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.sts.csv
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.sts.csv
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.sts.xml b/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.sts.xml
new file mode 100644
index 0000000..76848c8
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+++ b/t/data/Pacbio-Run/6U00E3/H02_1/Analysis_Results/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.sts.xml
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.1.xfer.xml b/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.1.xfer.xml
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.1.xfer.xml
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.2.xfer.xml b/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.2.xfer.xml
new file mode 100644
index 0000000..76848c8
--- /dev/null
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@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.3.xfer.xml b/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.3.xfer.xml
new file mode 100644
index 0000000..76848c8
--- /dev/null
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@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.mcd.h5
new file mode 100644
index 0000000..76848c8
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.mcd.h5
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.metadata.xml
new file mode 100644
index 0000000..6ec93d2
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00E3/H02_1/m160614_091421_00116_c100976392550000001823226708101607_s1_p0.metadata.xml
@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.1.bax.h5 b/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.1.bax.h5
new file mode 100644
index 0000000..e69de29
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new file mode 100644
index 0000000..e69de29
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new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.1.subreads.fastq b/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.1.subreads.fastq
new file mode 100644
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new file mode 100644
index 0000000..e69de29
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new file mode 100644
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new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.2.subreads.fastq b/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.2.subreads.fastq
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.3.bax.h5 b/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.3.bax.h5
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.3.log b/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.3.log
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.3.subreads.fasta b/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.3.subreads.fasta
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.3.subreads.fastq b/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.3.subreads.fastq
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.bas.h5 b/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.bas.h5
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.sts.csv b/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.sts.csv
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.sts.xml b/t/data/Pacbio-Run/6U00FA/A01_1/Analysis_Results/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.sts.xml
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.1.xfer.xml b/t/data/Pacbio-Run/6U00FA/A01_1/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.1.xfer.xml
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.2.xfer.xml b/t/data/Pacbio-Run/6U00FA/A01_1/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.2.xfer.xml
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.3.xfer.xml b/t/data/Pacbio-Run/6U00FA/A01_1/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.3.xfer.xml
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00FA/A01_1/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.mcd.h5
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/A01_1/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00FA/A01_1/m160819_231415_00116_c101036512550000001823251411171640_s1_p0.metadata.xml
new file mode 100644
index 0000000..253354a
--- /dev/null
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@@ -0,0 +1 @@
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diff --git a/t/data/Pacbio-Run/6U00FA/B01_1/m160820_053721_00116_c101036512550000001823251411171641_s1_p0.2.xfer.xml b/t/data/Pacbio-Run/6U00FA/B01_1/m160820_053721_00116_c101036512550000001823251411171641_s1_p0.2.xfer.xml
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index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/B01_1/m160820_053721_00116_c101036512550000001823251411171641_s1_p0.3.xfer.xml b/t/data/Pacbio-Run/6U00FA/B01_1/m160820_053721_00116_c101036512550000001823251411171641_s1_p0.3.xfer.xml
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/B01_1/m160820_053721_00116_c101036512550000001823251411171641_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00FA/B01_1/m160820_053721_00116_c101036512550000001823251411171641_s1_p0.mcd.h5
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/B01_1/m160820_053721_00116_c101036512550000001823251411171641_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00FA/B01_1/m160820_053721_00116_c101036512550000001823251411171641_s1_p0.metadata.xml
new file mode 100644
index 0000000..8beffd4
--- /dev/null
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.1.bax.h5 b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.1.bax.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.1.subreads.fasta b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.1.subreads.fasta
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.1.subreads.fastq b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.1.subreads.fastq
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.2.bax.h5 b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.2.bax.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.2.subreads.fastq b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.2.subreads.fastq
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.3.bax.h5 b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.3.bax.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.3.log b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.3.log
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.3.subreads.fasta b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.3.subreads.fasta
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.3.subreads.fastq b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.3.subreads.fastq
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.bas.h5 b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.bas.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.sts.csv b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.sts.csv
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.sts.xml b/t/data/Pacbio-Run/6U00FA/B02_1/Analysis_Results/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.sts.xml
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.1.xfer.xml b/t/data/Pacbio-Run/6U00FA/B02_1/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.1.xfer.xml
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diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.3.xfer.xml b/t/data/Pacbio-Run/6U00FA/B02_1/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.3.xfer.xml
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index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00FA/B02_1/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.mcd.h5
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index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/B02_1/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00FA/B02_1/m160822_045426_00116_c101036752550000001823251411171641_s1_p0.metadata.xml
new file mode 100644
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index 0000000..e69de29
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diff --git a/t/data/Pacbio-Run/6U00FA/C01_1/Analysis_Results/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.bas.h5 b/t/data/Pacbio-Run/6U00FA/C01_1/Analysis_Results/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.bas.h5
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/C01_1/Analysis_Results/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.sts.csv b/t/data/Pacbio-Run/6U00FA/C01_1/Analysis_Results/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.sts.csv
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/C01_1/Analysis_Results/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.sts.xml b/t/data/Pacbio-Run/6U00FA/C01_1/Analysis_Results/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.sts.xml
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.1.xfer.xml b/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.1.xfer.xml
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.2.xfer.xml b/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.2.xfer.xml
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.3.xfer.xml b/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.3.xfer.xml
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.mcd.h5
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.metadata.xml
new file mode 100644
index 0000000..ac74d0e
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00FA/C01_1/m160820_120016_00116_c101036512550000001823251411171642_s1_p0.metadata.xml
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.1.bax.h5 b/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.1.subreads.fasta b/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.1.subreads.fasta
new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.2.subreads.fastq b/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.2.subreads.fastq
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.3.bax.h5 b/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.3.bax.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.3.log b/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.3.log
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.3.subreads.fasta b/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.3.subreads.fasta
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.3.subreads.fastq b/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.3.subreads.fastq
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.bas.h5 b/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.bas.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.sts.csv b/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.sts.csv
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.sts.xml b/t/data/Pacbio-Run/6U00FA/D01_1/Analysis_Results/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.sts.xml
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.1.xfer.xml b/t/data/Pacbio-Run/6U00FA/D01_1/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.1.xfer.xml
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new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.3.xfer.xml b/t/data/Pacbio-Run/6U00FA/D01_1/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.3.xfer.xml
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00FA/D01_1/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.mcd.h5
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/D01_1/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00FA/D01_1/m160820_182317_00116_c101036512550000001823251411171643_s1_p0.metadata.xml
new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.3.bax.h5 b/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.3.bax.h5
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.3.log b/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.3.log
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diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.3.subreads.fasta b/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.3.subreads.fasta
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.3.subreads.fastq b/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.3.subreads.fastq
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.bas.h5 b/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.bas.h5
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.sts.csv b/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.sts.csv
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.sts.xml b/t/data/Pacbio-Run/6U00FA/E01_1/Analysis_Results/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.sts.xml
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.1.xfer.xml b/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.1.xfer.xml
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.2.xfer.xml b/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.2.xfer.xml
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diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.3.xfer.xml b/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.3.xfer.xml
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.mcd.h5
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.metadata.xml
new file mode 100644
index 0000000..ff91856
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00FA/E01_1/m160821_004554_00116_c101036512550000001823251411171644_s1_p0.metadata.xml
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.1.bax.h5 b/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.1.bax.h5
new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.1.subreads.fasta b/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.1.subreads.fasta
new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.2.subreads.fastq b/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.2.subreads.fastq
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.3.bax.h5 b/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.3.bax.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.3.log b/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.3.log
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.3.subreads.fasta b/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.3.subreads.fasta
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.3.subreads.fastq b/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.3.subreads.fastq
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.bas.h5 b/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.bas.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.sts.csv b/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.sts.csv
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.sts.xml b/t/data/Pacbio-Run/6U00FA/F01_1/Analysis_Results/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.sts.xml
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00FA/F01_1/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.mcd.h5
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/F01_1/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00FA/F01_1/m160821_070940_00116_c101036512550000001823251411171645_s1_p0.metadata.xml
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.2.log b/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.2.log
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.2.subreads.fasta b/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.2.subreads.fasta
new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.3.bax.h5 b/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.3.bax.h5
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.3.log b/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.3.log
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.3.subreads.fasta b/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.3.subreads.fasta
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.3.subreads.fastq b/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.3.subreads.fastq
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.bas.h5 b/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.bas.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.sts.csv b/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.sts.csv
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.sts.xml b/t/data/Pacbio-Run/6U00FA/G01_1/Analysis_Results/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.sts.xml
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.1.xfer.xml b/t/data/Pacbio-Run/6U00FA/G01_1/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.1.xfer.xml
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.2.xfer.xml b/t/data/Pacbio-Run/6U00FA/G01_1/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.2.xfer.xml
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.3.xfer.xml b/t/data/Pacbio-Run/6U00FA/G01_1/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.3.xfer.xml
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00FA/G01_1/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.mcd.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/G01_1/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00FA/G01_1/m160821_133539_00116_c101036512550000001823251411171646_s1_p0.metadata.xml
new file mode 100644
index 0000000..ff8f2fe
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diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.1.bax.h5 b/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.1.bax.h5
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new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.2.subreads.fastq b/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.2.subreads.fastq
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.3.bax.h5 b/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.3.bax.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.3.log b/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.3.log
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diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.3.subreads.fasta b/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.3.subreads.fasta
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.3.subreads.fastq b/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.3.subreads.fastq
new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.bas.h5 b/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.bas.h5
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diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.sts.csv b/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.sts.csv
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diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.sts.xml b/t/data/Pacbio-Run/6U00FA/H01_1/Analysis_Results/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.sts.xml
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.mcd.h5 b/t/data/Pacbio-Run/6U00FA/H01_1/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.mcd.h5
new file mode 100644
index 0000000..e69de29
diff --git a/t/data/Pacbio-Run/6U00FA/H01_1/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.metadata.xml b/t/data/Pacbio-Run/6U00FA/H01_1/m160821_175820_00116_c101036512550000001823251411171647_s1_p0.metadata.xml
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diff --git a/t/data/Pacbio-Run/6U00I7-submission/6U00I7.tar b/t/data/Pacbio-Run/6U00I7-submission/6U00I7.tar
new file mode 100644
index 0000000..919f9fa
Binary files /dev/null and b/t/data/Pacbio-Run/6U00I7-submission/6U00I7.tar differ
diff --git a/t/data/Pacbio-Run/6U00I7-submission/6U00I7/6U00I7.experiment.xml b/t/data/Pacbio-Run/6U00I7-submission/6U00I7/6U00I7.experiment.xml
new file mode 100644
index 0000000..736d979
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7-submission/6U00I7/6U00I7.experiment.xml
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.experiment.xsd?view=co">
+  <EXPERIMENT alias="HG03486_Mende_4808Ll" center_name="WUGSC">
+    <STUDY_REF>
+      <IDENTIFIERS>
+        <EXTERNAL_ID namespace="BioProject">BIOPROJECT</EXTERNAL_ID>
+      </IDENTIFIERS>
+    </STUDY_REF>
+    <DESIGN>
+      <DESIGN_DESCRIPTION></DESIGN_DESCRIPTION>
+      <SAMPLE_DESCRIPTOR>
+        <IDENTIFIERS>
+          <EXTERNAL_ID namespace="BioSample">BIOSAMPLE</EXTERNAL_ID>
+        </IDENTIFIERS>
+      </SAMPLE_DESCRIPTOR>
+      <LIBRARY_DESCRIPTOR>
+        <LIBRARY_NAME>HG03486_Mende_4808Ll</LIBRARY_NAME>
+        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
+        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
+        <LIBRARY_SELECTION>unspecified</LIBRARY_SELECTION>
+        <LIBRARY_LAYOUT>
+          <SINGLE/>
+        </LIBRARY_LAYOUT>
+      </LIBRARY_DESCRIPTOR>
+    </DESIGN>
+    <PLATFORM>
+      <PACBIO_SMRT>
+        <INSTRUMENT_MODEL>PacBio RS II</INSTRUMENT_MODEL>
+      </PACBIO_SMRT>
+    </PLATFORM>
+    <PROCESSING>
+      <PIPELINE>
+        <PIPE_SECTION>
+          <STEP_INDEX></STEP_INDEX>
+          <PREV_STEP_INDEX></PREV_STEP_INDEX>
+          <PROGRAM>PacBio RS II</PROGRAM>
+          <VERSION>4.0.0.189873</VERSION>
+        </PIPE_SECTION>
+      </PIPELINE>
+    </PROCESSING>
+  </EXPERIMENT>
+</EXPERIMENT_SET>
diff --git a/t/data/Pacbio-Run/6U00I7-submission/6U00I7/6U00I7.run.xml b/t/data/Pacbio-Run/6U00I7-submission/6U00I7/6U00I7.run.xml
new file mode 100644
index 0000000..a6a9f11
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7-submission/6U00I7/6U00I7.run.xml
@@ -0,0 +1,48 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<RUN_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.run.xsd?view=co">
+  <RUN alias="6U00I7_A01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="HG03486_Mende_4808Ll" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m54111_170804_145334.subreads.bam" filetype="bam" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m54111_170804_145334.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00I7_B01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="HG03486_Mende_4808Ll" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m54111_170805_005230.subreads.bam" filetype="bam" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m54111_170805_005230.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00I7_C01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="HG03486_Mende_4808Ll" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m54111_170805_110221.subreads.bam" filetype="bam" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m54111_170805_110221.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00I7_D01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="HG03486_Mende_4808Ll" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m54111_170805_211205.subreads.bam" filetype="bam" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m54111_170805_211205.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+  <RUN alias="6U00I7_E01" center_name="WUGSC">
+    <EXPERIMENT_REF refname="HG03486_Mende_4808Ll" refcenter="WUGSC"/>
+    <DATA_BLOCK>
+      <FILES>
+        <FILE filename="m54111_170806_072207.subreads.bam" filetype="bam" checksum_method="MD5" checksum="md5sum"/>
+        <FILE filename="m54111_170806_072207.metadata.xml" filetype="xml" checksum_method="MD5" checksum="md5sum"/>
+      </FILES>
+    </DATA_BLOCK>
+  </RUN>
+</RUN_SET>
diff --git a/t/data/Pacbio-Run/6U00I7-submission/6U00I7/6U00I7.submission.xml b/t/data/Pacbio-Run/6U00I7-submission/6U00I7/6U00I7.submission.xml
new file mode 100644
index 0000000..bb0b648
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7-submission/6U00I7/6U00I7.submission.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SUBMISSION_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.submission.xsd?view=co">
+  <SUBMISSION alias="6U00I7" center_name="WUGSC">
+    <CONTACTS>
+      <CONTACT name="LIMS" inform_on_status="mailto:mgi-submission@gowustl.onmicrosoft.com" inform_on_error="mailto:mgi-submission@gowustl.onmicrosoft.com"/>
+    </CONTACTS>
+    <ACTIONS>
+      <ACTION>
+        <RELEASE/>
+      </ACTION>
+      <ACTION>
+        <ADD source="6U00I7.experiment.xml" schema="experiment"/>
+      </ACTION>
+      <ACTION>
+        <ADD source="6U00I7.run.xml" schema="run"/>
+      </ACTION>
+    </ACTIONS>
+  </SUBMISSION>
+</SUBMISSION_SET>
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/.m54111_170804_145334.metadata.xml b/t/data/Pacbio-Run/6U00I7/1_A01/.m54111_170804_145334.metadata.xml
new file mode 100644
index 0000000..053076f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/.m54111_170804_145334.metadata.xml
@@ -0,0 +1,134 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<pbdm:PacBioDataModel xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" Version="4.0.0">
+    <pbdm:ExperimentContainer CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbdm:InvestigatorName>Default</pbdm:InvestigatorName>
+        <pbdm:CreatedDate>0001-01-01</pbdm:CreatedDate>
+        <pbdm:Runs>
+            <pbdm:Run Status="Starting" CreatedBy="unknown" WhenStarted="2017-08-04T14:53:33.357294Z" UniqueId="589c6d5a-7bee-478a-ab35-497a2c17c64a" MetaType="Run" TimeStampedName="r54111_20170804_144420" Name="6U00I7" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+                <pbdm:Outputs>
+                    <pbdm:SubreadSets>
+                        <pbds:SubreadSet UniqueId="cbe7aa3a-5770-47fa-af11-89326697a32a" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_20pM-Cell1" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="d8733eb5-a1a1-4b69-b39f-55aa7bc0c8e3" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170804_145334" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="cbe7aa3a-5770-47fa-af11-89326697a32a" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_20pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>A01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="0" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>0</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>0</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320801" Barcode="BA050132636374552148325710" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/1_A01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/1_A01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                    </pbdm:SubreadSets>
+                </pbdm:Outputs>
+                <pbdm:RecordedEvents>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="Starting" Name="RunStateChange" CreatedAt="2017-08-04T14:46:17.480663Z"/>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="{&quot;Id&quot;:150064,&quot;Name&quot;:&quot;ActiveUseExceeded&quot;,&quot;Owner&quot;:&quot;svc:/i/runcontrol/&quot;,&quot;Severity&quot;:&quot;WARNING&quot;,&quot;Message&quot;:&quot;Reagents exceed active use:  | ReagentPlate-1.  Tubes exceed active use:  | Tube-1-2.&quot;,&quot;When&quot;:&quot;2017-08-04T14:44:54.543902Z&quot;}" Name="Alarm" CreatedAt="2017-08-04T14:46:17.486471Z"/>
+                </pbdm:RecordedEvents>
+            </pbdm:Run>
+        </pbdm:Runs>
+    </pbdm:ExperimentContainer>
+</pbdm:PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/.m54111_170804_145334.run.metadata.xml b/t/data/Pacbio-Run/6U00I7/1_A01/.m54111_170804_145334.run.metadata.xml
new file mode 100644
index 0000000..f16b40a
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/.m54111_170804_145334.run.metadata.xml
@@ -0,0 +1,594 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<pbdm:PacBioDataModel xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" Version="4.0.0">
+    <pbdm:ExperimentContainer CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbdm:InvestigatorName>Default</pbdm:InvestigatorName>
+        <pbdm:CreatedDate>0001-01-01</pbdm:CreatedDate>
+        <pbdm:Runs>
+            <pbdm:Run Status="Starting" CreatedBy="unknown" WhenStarted="2017-08-04T14:53:33.357294Z" UniqueId="589c6d5a-7bee-478a-ab35-497a2c17c64a" MetaType="Run" TimeStampedName="r54111_20170804_144420" Name="6U00I7" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+                <pbdm:Outputs>
+                    <pbdm:SubreadSets>
+                        <pbds:SubreadSet UniqueId="cbe7aa3a-5770-47fa-af11-89326697a32a" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_20pM-Cell1" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="d8733eb5-a1a1-4b69-b39f-55aa7bc0c8e3" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170804_145334" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="cbe7aa3a-5770-47fa-af11-89326697a32a" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_20pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>A01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="0" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>0</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>0</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320801" Barcode="BA050132636374552148325710" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/1_A01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/1_A01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                        <pbds:SubreadSet UniqueId="52af2651-bfda-4acc-a8ac-23d6a10fa705" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_25pM-Cell2" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="e3d73d7b-c301-4e3f-810b-c7ed69d8c581" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="52af2651-bfda-4acc-a8ac-23d6a10fa705" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_25pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>B01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>1</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>1</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320801" Barcode="320801101008000083017" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/2_B01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/2_B01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                        <pbds:SubreadSet UniqueId="5f2c7e7d-0f56-49ae-8c2c-afef6af5a047" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_30pM-Cell3" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="e1bd301f-3232-4d10-b515-eac47cfcb58a" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="5f2c7e7d-0f56-49ae-8c2c-afef6af5a047" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
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+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/5_E01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/5_E01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                    </pbdm:SubreadSets>
+                </pbdm:Outputs>
+                <pbdm:RecordedEvents>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="Starting" Name="RunStateChange" CreatedAt="2017-08-04T14:46:17.480663Z"/>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="{&quot;Id&quot;:150064,&quot;Name&quot;:&quot;ActiveUseExceeded&quot;,&quot;Owner&quot;:&quot;svc:/i/runcontrol/&quot;,&quot;Severity&quot;:&quot;WARNING&quot;,&quot;Message&quot;:&quot;Reagents exceed active use:  | ReagentPlate-1.  Tubes exceed active use:  | Tube-1-2.&quot;,&quot;When&quot;:&quot;2017-08-04T14:44:54.543902Z&quot;}" Name="Alarm" CreatedAt="2017-08-04T14:46:17.486471Z"/>
+                </pbdm:RecordedEvents>
+            </pbdm:Run>
+        </pbdm:Runs>
+    </pbdm:ExperimentContainer>
+</pbdm:PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.adapters.fasta b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.adapters.fasta
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.adapters.fasta
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.scraps.bam b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.scraps.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.scraps.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.scraps.bam.pbi b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.scraps.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.scraps.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.sts.xml b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.sts.xml
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.sts.xml
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.subreads.bam b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.subreads.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.subreads.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.subreads.bam.pbi b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.subreads.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.subreads.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.subreadset.xml b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.subreadset.xml
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.subreadset.xml
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.transferdone b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.transferdone
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/m54111_170804_145334.transferdone
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/1_A01/tmp-file-8165609474012237547.txt b/t/data/Pacbio-Run/6U00I7/1_A01/tmp-file-8165609474012237547.txt
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/1_A01/tmp-file-8165609474012237547.txt
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/.m54111_170805_005230.metadata.xml b/t/data/Pacbio-Run/6U00I7/2_B01/.m54111_170805_005230.metadata.xml
new file mode 100644
index 0000000..84a8aa0
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/.m54111_170805_005230.metadata.xml
@@ -0,0 +1,134 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<pbdm:PacBioDataModel xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" Version="4.0.0">
+    <pbdm:ExperimentContainer CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbdm:InvestigatorName>Default</pbdm:InvestigatorName>
+        <pbdm:CreatedDate>0001-01-01</pbdm:CreatedDate>
+        <pbdm:Runs>
+            <pbdm:Run Status="Starting" CreatedBy="unknown" WhenStarted="2017-08-04T14:53:33.357294Z" UniqueId="589c6d5a-7bee-478a-ab35-497a2c17c64a" MetaType="Run" TimeStampedName="r54111_20170804_144420" Name="6U00I7" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+                <pbdm:Outputs>
+                    <pbdm:SubreadSets>
+                        <pbds:SubreadSet UniqueId="52af2651-bfda-4acc-a8ac-23d6a10fa705" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_25pM-Cell2" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="e3d73d7b-c301-4e3f-810b-c7ed69d8c581" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170805_005230" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="52af2651-bfda-4acc-a8ac-23d6a10fa705" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_25pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>B01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>1</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>1</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320801" Barcode="BA050147636374911508526970" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/2_B01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/2_B01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                    </pbdm:SubreadSets>
+                </pbdm:Outputs>
+                <pbdm:RecordedEvents>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="Starting" Name="RunStateChange" CreatedAt="2017-08-04T14:46:17.480663Z"/>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="{&quot;Id&quot;:150064,&quot;Name&quot;:&quot;ActiveUseExceeded&quot;,&quot;Owner&quot;:&quot;svc:/i/runcontrol/&quot;,&quot;Severity&quot;:&quot;WARNING&quot;,&quot;Message&quot;:&quot;Reagents exceed active use:  | ReagentPlate-1.  Tubes exceed active use:  | Tube-1-2.&quot;,&quot;When&quot;:&quot;2017-08-04T14:44:54.543902Z&quot;}" Name="Alarm" CreatedAt="2017-08-04T14:46:17.486471Z"/>
+                </pbdm:RecordedEvents>
+            </pbdm:Run>
+        </pbdm:Runs>
+    </pbdm:ExperimentContainer>
+</pbdm:PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/.m54111_170805_005230.run.metadata.xml b/t/data/Pacbio-Run/6U00I7/2_B01/.m54111_170805_005230.run.metadata.xml
new file mode 100644
index 0000000..404c90f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/.m54111_170805_005230.run.metadata.xml
@@ -0,0 +1,594 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<pbdm:PacBioDataModel xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" Version="4.0.0">
+    <pbdm:ExperimentContainer CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbdm:InvestigatorName>Default</pbdm:InvestigatorName>
+        <pbdm:CreatedDate>0001-01-01</pbdm:CreatedDate>
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+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                    </pbdm:SubreadSets>
+                </pbdm:Outputs>
+                <pbdm:RecordedEvents>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="Starting" Name="RunStateChange" CreatedAt="2017-08-04T14:46:17.480663Z"/>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="{&quot;Id&quot;:150064,&quot;Name&quot;:&quot;ActiveUseExceeded&quot;,&quot;Owner&quot;:&quot;svc:/i/runcontrol/&quot;,&quot;Severity&quot;:&quot;WARNING&quot;,&quot;Message&quot;:&quot;Reagents exceed active use:  | ReagentPlate-1.  Tubes exceed active use:  | Tube-1-2.&quot;,&quot;When&quot;:&quot;2017-08-04T14:44:54.543902Z&quot;}" Name="Alarm" CreatedAt="2017-08-04T14:46:17.486471Z"/>
+                </pbdm:RecordedEvents>
+            </pbdm:Run>
+        </pbdm:Runs>
+    </pbdm:ExperimentContainer>
+</pbdm:PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.adapters.fasta b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.adapters.fasta
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.adapters.fasta
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.scraps.bam b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.scraps.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.scraps.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.scraps.bam.pbi b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.scraps.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.scraps.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.sts.xml b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.sts.xml
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.sts.xml
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.subreads.bam b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.subreads.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.subreads.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.subreads.bam.pbi b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.subreads.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.subreads.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.subreadset.xml b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.subreadset.xml
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.subreadset.xml
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.transferdone b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.transferdone
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/m54111_170805_005230.transferdone
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/2_B01/tmp-file-5564990877457481769.txt b/t/data/Pacbio-Run/6U00I7/2_B01/tmp-file-5564990877457481769.txt
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/2_B01/tmp-file-5564990877457481769.txt
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/.m54111_170805_110221.metadata.xml b/t/data/Pacbio-Run/6U00I7/3_C01/.m54111_170805_110221.metadata.xml
new file mode 100644
index 0000000..e7b2def
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/.m54111_170805_110221.metadata.xml
@@ -0,0 +1,134 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<pbdm:PacBioDataModel xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" Version="4.0.0">
+    <pbdm:ExperimentContainer CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbdm:InvestigatorName>Default</pbdm:InvestigatorName>
+        <pbdm:CreatedDate>0001-01-01</pbdm:CreatedDate>
+        <pbdm:Runs>
+            <pbdm:Run Status="Starting" CreatedBy="unknown" WhenStarted="2017-08-04T14:53:33.357294Z" UniqueId="589c6d5a-7bee-478a-ab35-497a2c17c64a" MetaType="Run" TimeStampedName="r54111_20170804_144420" Name="6U00I7" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+                <pbdm:Outputs>
+                    <pbdm:SubreadSets>
+                        <pbds:SubreadSet UniqueId="5f2c7e7d-0f56-49ae-8c2c-afef6af5a047" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_30pM-Cell3" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="e1bd301f-3232-4d10-b515-eac47cfcb58a" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170805_110221" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="5f2c7e7d-0f56-49ae-8c2c-afef6af5a047" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_30pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>C01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="2" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>2</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>2</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320801" Barcode="BA050219636375277412518650" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/3_C01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/3_C01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                    </pbdm:SubreadSets>
+                </pbdm:Outputs>
+                <pbdm:RecordedEvents>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="Starting" Name="RunStateChange" CreatedAt="2017-08-04T14:46:17.480663Z"/>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="{&quot;Id&quot;:150064,&quot;Name&quot;:&quot;ActiveUseExceeded&quot;,&quot;Owner&quot;:&quot;svc:/i/runcontrol/&quot;,&quot;Severity&quot;:&quot;WARNING&quot;,&quot;Message&quot;:&quot;Reagents exceed active use:  | ReagentPlate-1.  Tubes exceed active use:  | Tube-1-2.&quot;,&quot;When&quot;:&quot;2017-08-04T14:44:54.543902Z&quot;}" Name="Alarm" CreatedAt="2017-08-04T14:46:17.486471Z"/>
+                </pbdm:RecordedEvents>
+            </pbdm:Run>
+        </pbdm:Runs>
+    </pbdm:ExperimentContainer>
+</pbdm:PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/.m54111_170805_110221.run.metadata.xml b/t/data/Pacbio-Run/6U00I7/3_C01/.m54111_170805_110221.run.metadata.xml
new file mode 100644
index 0000000..79d696a
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/.m54111_170805_110221.run.metadata.xml
@@ -0,0 +1,594 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<pbdm:PacBioDataModel xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" Version="4.0.0">
+    <pbdm:ExperimentContainer CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbdm:InvestigatorName>Default</pbdm:InvestigatorName>
+        <pbdm:CreatedDate>0001-01-01</pbdm:CreatedDate>
+        <pbdm:Runs>
+            <pbdm:Run Status="Starting" CreatedBy="unknown" WhenStarted="2017-08-04T14:53:33.357294Z" UniqueId="589c6d5a-7bee-478a-ab35-497a2c17c64a" MetaType="Run" TimeStampedName="r54111_20170804_144420" Name="6U00I7" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+                <pbdm:Outputs>
+                    <pbdm:SubreadSets>
+                        <pbds:SubreadSet UniqueId="cbe7aa3a-5770-47fa-af11-89326697a32a" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_20pM-Cell1" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="d8733eb5-a1a1-4b69-b39f-55aa7bc0c8e3" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170804_145334" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="cbe7aa3a-5770-47fa-af11-89326697a32a" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_20pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
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+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="{&quot;Id&quot;:150064,&quot;Name&quot;:&quot;ActiveUseExceeded&quot;,&quot;Owner&quot;:&quot;svc:/i/runcontrol/&quot;,&quot;Severity&quot;:&quot;WARNING&quot;,&quot;Message&quot;:&quot;Reagents exceed active use:  | ReagentPlate-1.  Tubes exceed active use:  | Tube-1-2.&quot;,&quot;When&quot;:&quot;2017-08-04T14:44:54.543902Z&quot;}" Name="Alarm" CreatedAt="2017-08-04T14:46:17.486471Z"/>
+                </pbdm:RecordedEvents>
+            </pbdm:Run>
+        </pbdm:Runs>
+    </pbdm:ExperimentContainer>
+</pbdm:PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.adapters.fasta b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.adapters.fasta
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.adapters.fasta
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.scraps.bam b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.scraps.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.scraps.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.scraps.bam.pbi b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.scraps.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.scraps.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.sts.xml b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.sts.xml
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.sts.xml
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.subreads.bam b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.subreads.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.subreads.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.subreads.bam.pbi b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.subreads.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.subreads.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.subreadset.xml b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.subreadset.xml
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.subreadset.xml
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.transferdone b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.transferdone
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/m54111_170805_110221.transferdone
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/3_C01/tmp-file-6175509889408621182.txt b/t/data/Pacbio-Run/6U00I7/3_C01/tmp-file-6175509889408621182.txt
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/3_C01/tmp-file-6175509889408621182.txt
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/.m54111_170805_211205.metadata.xml b/t/data/Pacbio-Run/6U00I7/4_D01/.m54111_170805_211205.metadata.xml
new file mode 100644
index 0000000..3f595e0
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/.m54111_170805_211205.metadata.xml
@@ -0,0 +1,134 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<pbdm:PacBioDataModel xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" Version="4.0.0">
+    <pbdm:ExperimentContainer CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbdm:InvestigatorName>Default</pbdm:InvestigatorName>
+        <pbdm:CreatedDate>0001-01-01</pbdm:CreatedDate>
+        <pbdm:Runs>
+            <pbdm:Run Status="Starting" CreatedBy="unknown" WhenStarted="2017-08-04T14:53:33.357294Z" UniqueId="589c6d5a-7bee-478a-ab35-497a2c17c64a" MetaType="Run" TimeStampedName="r54111_20170804_144420" Name="6U00I7" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+                <pbdm:Outputs>
+                    <pbdm:SubreadSets>
+                        <pbds:SubreadSet UniqueId="040ccb55-c5bf-410a-921b-af65c465720c" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_35pM-Cell4" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="d5c117b7-ae81-4bbd-a826-e4a0772346b3" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170805_211205" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="040ccb55-c5bf-410a-921b-af65c465720c" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_35pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>D01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="3" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>3</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>3</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320801" Barcode="BA050211636375643257203110" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/4_D01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/4_D01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                    </pbdm:SubreadSets>
+                </pbdm:Outputs>
+                <pbdm:RecordedEvents>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="Starting" Name="RunStateChange" CreatedAt="2017-08-04T14:46:17.480663Z"/>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="{&quot;Id&quot;:150064,&quot;Name&quot;:&quot;ActiveUseExceeded&quot;,&quot;Owner&quot;:&quot;svc:/i/runcontrol/&quot;,&quot;Severity&quot;:&quot;WARNING&quot;,&quot;Message&quot;:&quot;Reagents exceed active use:  | ReagentPlate-1.  Tubes exceed active use:  | Tube-1-2.&quot;,&quot;When&quot;:&quot;2017-08-04T14:44:54.543902Z&quot;}" Name="Alarm" CreatedAt="2017-08-04T14:46:17.486471Z"/>
+                </pbdm:RecordedEvents>
+            </pbdm:Run>
+        </pbdm:Runs>
+    </pbdm:ExperimentContainer>
+</pbdm:PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/.m54111_170805_211205.run.metadata.xml b/t/data/Pacbio-Run/6U00I7/4_D01/.m54111_170805_211205.run.metadata.xml
new file mode 100644
index 0000000..81a11e5
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/.m54111_170805_211205.run.metadata.xml
@@ -0,0 +1,594 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<pbdm:PacBioDataModel xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" Version="4.0.0">
+    <pbdm:ExperimentContainer CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbdm:InvestigatorName>Default</pbdm:InvestigatorName>
+        <pbdm:CreatedDate>0001-01-01</pbdm:CreatedDate>
+        <pbdm:Runs>
+            <pbdm:Run Status="Starting" CreatedBy="unknown" WhenStarted="2017-08-04T14:53:33.357294Z" UniqueId="589c6d5a-7bee-478a-ab35-497a2c17c64a" MetaType="Run" TimeStampedName="r54111_20170804_144420" Name="6U00I7" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+                <pbdm:Outputs>
+                    <pbdm:SubreadSets>
+                        <pbds:SubreadSet UniqueId="cbe7aa3a-5770-47fa-af11-89326697a32a" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_20pM-Cell1" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="d8733eb5-a1a1-4b69-b39f-55aa7bc0c8e3" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170804_145334" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="cbe7aa3a-5770-47fa-af11-89326697a32a" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_20pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>A01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="0" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
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+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
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+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                        <pbds:SubreadSet UniqueId="040ccb55-c5bf-410a-921b-af65c465720c" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_35pM-Cell4" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="d5c117b7-ae81-4bbd-a826-e4a0772346b3" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170805_211205" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="040ccb55-c5bf-410a-921b-af65c465720c" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
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+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_35pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
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+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="3" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>3</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>3</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320801" Barcode="BA050211636375643257203110" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/4_D01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/4_D01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
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+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
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+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
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+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
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+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="a0c3edb6-b106-465e-bb40-acf127cd0324" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="88dea5aa-8b5b-4fb0-bfbc-e21adc29d5e4" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
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+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
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+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="4" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>4</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>4</pbmeta:CellIndex>
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+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
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+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
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+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
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+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/5_E01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/5_E01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
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+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                    </pbdm:SubreadSets>
+                </pbdm:Outputs>
+                <pbdm:RecordedEvents>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="Starting" Name="RunStateChange" CreatedAt="2017-08-04T14:46:17.480663Z"/>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="{&quot;Id&quot;:150064,&quot;Name&quot;:&quot;ActiveUseExceeded&quot;,&quot;Owner&quot;:&quot;svc:/i/runcontrol/&quot;,&quot;Severity&quot;:&quot;WARNING&quot;,&quot;Message&quot;:&quot;Reagents exceed active use:  | ReagentPlate-1.  Tubes exceed active use:  | Tube-1-2.&quot;,&quot;When&quot;:&quot;2017-08-04T14:44:54.543902Z&quot;}" Name="Alarm" CreatedAt="2017-08-04T14:46:17.486471Z"/>
+                </pbdm:RecordedEvents>
+            </pbdm:Run>
+        </pbdm:Runs>
+    </pbdm:ExperimentContainer>
+</pbdm:PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.adapters.fasta b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.adapters.fasta
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.adapters.fasta
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.scraps.bam b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.scraps.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.scraps.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.scraps.bam.pbi b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.scraps.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.scraps.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.sts.xml b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.sts.xml
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.sts.xml
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.subreads.bam b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.subreads.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.subreads.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.subreads.bam.pbi b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.subreads.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.subreads.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.subreadset.xml b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.subreadset.xml
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.subreadset.xml
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.transferdone b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.transferdone
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/m54111_170805_211205.transferdone
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/4_D01/tmp-file-5279275195801925944.txt b/t/data/Pacbio-Run/6U00I7/4_D01/tmp-file-5279275195801925944.txt
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/4_D01/tmp-file-5279275195801925944.txt
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/.m54111_170806_072207.metadata.xml b/t/data/Pacbio-Run/6U00I7/5_E01/.m54111_170806_072207.metadata.xml
new file mode 100644
index 0000000..fdf6610
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/.m54111_170806_072207.metadata.xml
@@ -0,0 +1,134 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<pbdm:PacBioDataModel xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" Version="4.0.0">
+    <pbdm:ExperimentContainer CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbdm:InvestigatorName>Default</pbdm:InvestigatorName>
+        <pbdm:CreatedDate>0001-01-01</pbdm:CreatedDate>
+        <pbdm:Runs>
+            <pbdm:Run Status="Starting" CreatedBy="unknown" WhenStarted="2017-08-04T14:53:33.357294Z" UniqueId="589c6d5a-7bee-478a-ab35-497a2c17c64a" MetaType="Run" TimeStampedName="r54111_20170804_144420" Name="6U00I7" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+                <pbdm:Outputs>
+                    <pbdm:SubreadSets>
+                        <pbds:SubreadSet UniqueId="88dea5aa-8b5b-4fb0-bfbc-e21adc29d5e4" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_40pM-Cell5" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="a0c3edb6-b106-465e-bb40-acf127cd0324" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170806_072207" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="88dea5aa-8b5b-4fb0-bfbc-e21adc29d5e4" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_40pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>E01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="4" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>4</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>4</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320772" Barcode="BA050495636376009278413540" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/5_E01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/5_E01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                    </pbdm:SubreadSets>
+                </pbdm:Outputs>
+                <pbdm:RecordedEvents>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="Starting" Name="RunStateChange" CreatedAt="2017-08-04T14:46:17.480663Z"/>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="{&quot;Id&quot;:150064,&quot;Name&quot;:&quot;ActiveUseExceeded&quot;,&quot;Owner&quot;:&quot;svc:/i/runcontrol/&quot;,&quot;Severity&quot;:&quot;WARNING&quot;,&quot;Message&quot;:&quot;Reagents exceed active use:  | ReagentPlate-1.  Tubes exceed active use:  | Tube-1-2.&quot;,&quot;When&quot;:&quot;2017-08-04T14:44:54.543902Z&quot;}" Name="Alarm" CreatedAt="2017-08-04T14:46:17.486471Z"/>
+                </pbdm:RecordedEvents>
+            </pbdm:Run>
+        </pbdm:Runs>
+    </pbdm:ExperimentContainer>
+</pbdm:PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/.m54111_170806_072207.run.metadata.xml b/t/data/Pacbio-Run/6U00I7/5_E01/.m54111_170806_072207.run.metadata.xml
new file mode 100644
index 0000000..c2c4ed3
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/.m54111_170806_072207.run.metadata.xml
@@ -0,0 +1,594 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<pbdm:PacBioDataModel xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" Version="4.0.0">
+    <pbdm:ExperimentContainer CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbdm:InvestigatorName>Default</pbdm:InvestigatorName>
+        <pbdm:CreatedDate>0001-01-01</pbdm:CreatedDate>
+        <pbdm:Runs>
+            <pbdm:Run Status="Starting" CreatedBy="unknown" WhenStarted="2017-08-04T14:53:33.357294Z" UniqueId="589c6d5a-7bee-478a-ab35-497a2c17c64a" MetaType="Run" TimeStampedName="r54111_20170804_144420" Name="6U00I7" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+                <pbdm:Outputs>
+                    <pbdm:SubreadSets>
+                        <pbds:SubreadSet UniqueId="cbe7aa3a-5770-47fa-af11-89326697a32a" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_20pM-Cell1" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="d8733eb5-a1a1-4b69-b39f-55aa7bc0c8e3" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170804_145334" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="cbe7aa3a-5770-47fa-af11-89326697a32a" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_20pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>A01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="0" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>0</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>0</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320801" Barcode="BA050132636374552148325710" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
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+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_35pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>D01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="3" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>3</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>3</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320801" Barcode="BA050211636375643257203110" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/4_D01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/4_D01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                        <pbds:SubreadSet UniqueId="88dea5aa-8b5b-4fb0-bfbc-e21adc29d5e4" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-44-04T14:44:20.775Z" Name="HG03486_Mende_4808Ll_40pM-Cell5" CreatedAt="2017-08-04T19:58:19.431Z">
+                            <pbbase:ExternalResources>
+<pbbase:ExternalResource UniqueId="a0c3edb6-b106-465e-bb40-acf127cd0324" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-44-04T14:44:20.775Z"/>
+                            </pbbase:ExternalResources>
+                            <pbds:DataSetMetadata>
+<pbds:TotalLength>0</pbds:TotalLength>
+<pbds:NumRecords>0</pbds:NumRecords>
+<pbmeta:Collections>
+    <pbmeta:CollectionMetadata Context="m54111_170806_072207" Status="Ready" InstrumentId="54111" InstrumentName="54111" UniqueId="88dea5aa-8b5b-4fb0-bfbc-e21adc29d5e4" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-44-04T14:44:20.775Z" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+        <pbmeta:InstCtrlVer>4.0.0.189873</pbmeta:InstCtrlVer>
+        <pbmeta:SigProcVer>4.0.0-189308</pbmeta:SigProcVer>
+        <pbmeta:RunDetails>
+            <pbmeta:TimeStampedName>r54111_20170804_144420</pbmeta:TimeStampedName>
+            <pbmeta:Name>6U00I7</pbmeta:Name>
+            <pbmeta:WhenCreated>2017-08-04T19:58:19.431Z</pbmeta:WhenCreated>
+            <pbmeta:WhenStarted>2017-08-04T14:53:33.357294Z</pbmeta:WhenStarted>
+        </pbmeta:RunDetails>
+        <pbmeta:WellSample Name="HG03486_Mende_4808Ll_40pM" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00">
+            <pbmeta:WellName>E01</pbmeta:WellName>
+            <pbmeta:Concentration>0.0</pbmeta:Concentration>
+            <pbmeta:InsertSize>20000</pbmeta:InsertSize>
+            <pbmeta:SampleReuseEnabled>false</pbmeta:SampleReuseEnabled>
+            <pbmeta:StageHotstartEnabled>false</pbmeta:StageHotstartEnabled>
+            <pbmeta:SizeSelectionEnabled>false</pbmeta:SizeSelectionEnabled>
+            <pbmeta:UseCount>0</pbmeta:UseCount>
+        </pbmeta:WellSample>
+        <pbmeta:Automation Name="Workflow_Magbead.py">
+            <pbbase:AutomationParameters>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="600" Name="MovieLength" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="ReuseSample" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="0" Name="ExtensionTime" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="ExtendFirst" CreatedAt="2017-08-04T19:58:19.431Z" ModifiedAt="0001-01-01T00:00:00"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="True" Name="GentleWash"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="1" Name="CellNFCIndex"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="4" Name="CollectionNumber"/>
+                <pbbase:AutomationParameter ValueDataType="String" SimpleValue="False" Name="UseStageHotStart"/>
+                <pbbase:AutomationParameter ValueDataType="Int32" SimpleValue="20000" Name="InsertSize"/>
+                <pbbase:AutomationParameter ValueDataType="Boolean" SimpleValue="False" Name="HasN2Switch"/>
+                <pbbase:AutomationParameter ValueDataType="Double" SimpleValue="4" Name="SNRCut"/>
+            </pbbase:AutomationParameters>
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:Automation>
+        <pbmeta:CollectionNumber>4</pbmeta:CollectionNumber>
+        <pbmeta:CellIndex>4</pbmeta:CellIndex>
+        <pbmeta:CellPac PartNumber="101-008-000" LotNumber="320772" Barcode="BA050495636376009278413540" ExpirationDate="2017-08-30">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:CellPac>
+        <pbmeta:TemplatePrepKit MinInsertSize="500" MaxInsertSize="20000" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" Name="SMRTbell™ Template Prep Kit">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbbase:LeftAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:LeftAdaptorSequence>
+            <pbbase:RightAdaptorSequence>ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</pbbase:RightAdaptorSequence>
+        </pbmeta:TemplatePrepKit>
+        <pbmeta:BindingKit PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" Name="Sequel™ Binding Kit 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+        </pbmeta:BindingKit>
+        <pbmeta:SequencingKitPlate PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28" Name="Sequel™ Sequencing Plate 2.0">
+            <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            <pbrk:ReagentTubes PartNumber="100-619-700" LotNumber="010025" ExpirationDate="2019-08-16">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+            <pbrk:ReagentTubes PartNumber="100-619-600" LotNumber="008604" ExpirationDate="2020-11-30">
+                <pbbase:Defaults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:nil="true"/>
+            </pbrk:ReagentTubes>
+        </pbmeta:SequencingKitPlate>
+        <pbmeta:Primary>
+            <pbmeta:AutomationName>SequelAlpha</pbmeta:AutomationName>
+            <pbmeta:ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</pbmeta:ConfigFileName>
+            <pbmeta:SequencingCondition>DefaultPrimarySequencingCondition</pbmeta:SequencingCondition>
+            <pbmeta:OutputOptions>
+                <pbmeta:ResultsFolder>r54111_20170804_144420/5_E01/</pbmeta:ResultsFolder>
+                <pbmeta:CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170804_144420/5_E01/</pbmeta:CollectionPathUri>
+                <pbmeta:CopyFiles>
+                    <pbmeta:CollectionFileCopy>Fasta</pbmeta:CollectionFileCopy>
+                    <pbmeta:CollectionFileCopy>Bam</pbmeta:CollectionFileCopy>
+                </pbmeta:CopyFiles>
+                <pbmeta:Readout>Bases_Without_QVs</pbmeta:Readout>
+                <pbmeta:MetricsVerbosity>Minimal</pbmeta:MetricsVerbosity>
+                <pbmeta:TransferResource>
+                    <pbmeta:Id>wustl_srs</pbmeta:Id>
+                    <pbmeta:TransferScheme>SRS</pbmeta:TransferScheme>
+                    <pbmeta:Name>WUSTL SRS</pbmeta:Name>
+                    <pbmeta:Description>Transfer Scheme for WUSTL SRS</pbmeta:Description>
+                    <pbmeta:DestPath>/gscmnt/gc13036/production/smrtlink_data_root</pbmeta:DestPath>
+                </pbmeta:TransferResource>
+            </pbmeta:OutputOptions>
+        </pbmeta:Primary>
+        <pbmeta:Secondary>
+            <pbmeta:AutomationName>DefaultSecondaryAutomationName</pbmeta:AutomationName>
+            <pbmeta:AutomationParameters>
+                <pbmeta:AutomationParameter ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00"/>
+            </pbmeta:AutomationParameters>
+            <pbmeta:CellCountInJob>0</pbmeta:CellCountInJob>
+        </pbmeta:Secondary>
+        <pbmeta:UserDefinedFields>
+            <pbbase:DataEntities ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" Name=" LIMS_IMPORT "/>
+        </pbmeta:UserDefinedFields>
+        <pbmeta:ComponentVersions>
+            <pbmeta:VersionInfo Name="ics" Version="4.0.0.189873"/>
+            <pbmeta:VersionInfo Name="iui" Version="4.0.0.189891"/>
+            <pbmeta:VersionInfo Name="pa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="paws" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="ppa" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="realtime" Version="4.0.0-189308"/>
+            <pbmeta:VersionInfo Name="transfer" Version="4.0.0-189805"/>
+            <pbmeta:VersionInfo Name="smrtlink-analysisservices-gui" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtinub" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrtlink" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtimisc" Version="4.0.0.189856"/>
+            <pbmeta:VersionInfo Name="smrttools" Version="4.0.0.190159"/>
+            <pbmeta:VersionInfo Name="smrtview" Version="4.0.0.189856"/>
+        </pbmeta:ComponentVersions>
+    </pbmeta:CollectionMetadata>
+</pbmeta:Collections>
+                            </pbds:DataSetMetadata>
+                        </pbds:SubreadSet>
+                    </pbdm:SubreadSets>
+                </pbdm:Outputs>
+                <pbdm:RecordedEvents>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="Starting" Name="RunStateChange" CreatedAt="2017-08-04T14:46:17.480663Z"/>
+                    <pbdm:RecordedEvent Context="589c6d5a-7bee-478a-ab35-497a2c17c64a" SimpleValue="{&quot;Id&quot;:150064,&quot;Name&quot;:&quot;ActiveUseExceeded&quot;,&quot;Owner&quot;:&quot;svc:/i/runcontrol/&quot;,&quot;Severity&quot;:&quot;WARNING&quot;,&quot;Message&quot;:&quot;Reagents exceed active use:  | ReagentPlate-1.  Tubes exceed active use:  | Tube-1-2.&quot;,&quot;When&quot;:&quot;2017-08-04T14:44:54.543902Z&quot;}" Name="Alarm" CreatedAt="2017-08-04T14:46:17.486471Z"/>
+                </pbdm:RecordedEvents>
+            </pbdm:Run>
+        </pbdm:Runs>
+    </pbdm:ExperimentContainer>
+</pbdm:PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.adapters.fasta b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.adapters.fasta
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.adapters.fasta
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.scraps.bam b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.scraps.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.scraps.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.scraps.bam.pbi b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.scraps.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.scraps.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.sts.xml b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.sts.xml
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.sts.xml
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.subreads.bam b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.subreads.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.subreads.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.subreads.bam.pbi b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.subreads.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.subreads.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.subreadset.xml b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.subreadset.xml
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.subreadset.xml
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.transferdone b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.transferdone
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/m54111_170806_072207.transferdone
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/5_E01/tmp-file-2259719094073772459.txt b/t/data/Pacbio-Run/6U00I7/5_E01/tmp-file-2259719094073772459.txt
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/5_E01/tmp-file-2259719094073772459.txt
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00I7/files b/t/data/Pacbio-Run/6U00I7/files
new file mode 100644
index 0000000..34f8925
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/files
@@ -0,0 +1,55 @@
+3_C01/m54111_170805_110221.scraps.bam
+3_C01/m54111_170805_110221.adapters.fasta
+3_C01/m54111_170805_110221.subreads.bam
+3_C01/m54111_170805_110221.transferdone
+3_C01/m54111_170805_110221.scraps.bam.pbi
+3_C01/.m54111_170805_110221.run.metadata.xml
+3_C01/tmp-file-6175509889408621182.txt
+3_C01/m54111_170805_110221.sts.xml
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+3_C01/.m54111_170805_110221.metadata.xml
+3_C01/m54111_170805_110221.subreads.bam.pbi
+2_B01/m54111_170805_005230.subreadset.xml
+2_B01/m54111_170805_005230.sts.xml
+2_B01/m54111_170805_005230.transferdone
+2_B01/.m54111_170805_005230.run.metadata.xml
+2_B01/m54111_170805_005230.subreads.bam
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+2_B01/m54111_170805_005230.scraps.bam.pbi
+2_B01/.m54111_170805_005230.metadata.xml
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+2_B01/m54111_170805_005230.subreads.bam.pbi
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+4_D01/m54111_170805_211205.subreadset.xml
+4_D01/.m54111_170805_211205.run.metadata.xml
+4_D01/m54111_170805_211205.transferdone
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+4_D01/m54111_170805_211205.subreads.bam
+4_D01/tmp-file-5279275195801925944.txt
+4_D01/m54111_170805_211205.scraps.bam
+4_D01/m54111_170805_211205.sts.xml
+4_D01/.m54111_170805_211205.metadata.xml
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+4_D01/m54111_170805_211205.subreads.bam.pbi
+5_E01/.m54111_170806_072207.metadata.xml
+5_E01/.m54111_170806_072207.run.metadata.xml
+5_E01/m54111_170806_072207.subreadset.xml
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+5_E01/m54111_170806_072207.transferdone
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+5_E01/m54111_170806_072207.subreads.bam
+5_E01/m54111_170806_072207.scraps.bam.pbi
+5_E01/m54111_170806_072207.sts.xml
+5_E01/m54111_170806_072207.adapters.fasta
+5_E01/m54111_170806_072207.scraps.bam
+1_A01/m54111_170804_145334.subreads.bam.pbi
+1_A01/.m54111_170804_145334.run.metadata.xml
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+1_A01/m54111_170804_145334.scraps.bam
+1_A01/tmp-file-8165609474012237547.txt
+1_A01/m54111_170804_145334.sts.xml
+1_A01/.m54111_170804_145334.metadata.xml
+1_A01/m54111_170804_145334.adapters.fasta
+1_A01/m54111_170804_145334.subreads.bam
+1_A01/m54111_170804_145334.scraps.bam.pbi
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diff --git a/t/data/Pacbio-Run/6U00I7/metadatafiles b/t/data/Pacbio-Run/6U00I7/metadatafiles
new file mode 100644
index 0000000..4ef737f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00I7/metadatafiles
@@ -0,0 +1,10 @@
+3_C01/.m54111_170805_110221.run.metadata.xml
+3_C01/.m54111_170805_110221.metadata.xml
+2_B01/.m54111_170805_005230.run.metadata.xml
+2_B01/.m54111_170805_005230.metadata.xml
+4_D01/.m54111_170805_211205.run.metadata.xml
+4_D01/.m54111_170805_211205.metadata.xml
+5_E01/.m54111_170806_072207.metadata.xml
+5_E01/.m54111_170806_072207.run.metadata.xml
+1_A01/.m54111_170804_145334.run.metadata.xml
+1_A01/.m54111_170804_145334.metadata.xml
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/.m54111_170829_153300.metadata.xml b/t/data/Pacbio-Run/6U00IG/1_A01/.m54111_170829_153300.metadata.xml
new file mode 100644
index 0000000..46cce5c
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/.m54111_170829_153300.metadata.xml
@@ -0,0 +1,122 @@
+<PacBioDataModel xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd PacBioDataModel.xsd" Version="4.0.1" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd">
+	<ExperimentContainer CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+		<InvestigatorName>Default</InvestigatorName>
+		<CreatedDate>0001-01-01</CreatedDate>
+		<Runs>
+			<Run Name="6U00IG" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" UniqueId="2d2563e3-0a00-4b9a-87a7-cd8ec0afe327" MetaType="Run" TimeStampedName="r54111_20170829_145220" Status="Ready" CreatedBy="admin" StartedBy="unknown">
+				<Outputs>
+					<SubreadSets>
+						<SubreadSet Name="X.couchianus_4808Lu_9pM-Cell1" CreatedAt="2017-08-29T19:55:11.464Z" UniqueId="83a61432-fb33-405d-96d4-3101c133840c" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-52-29T14:52:20.079Z" xmlns="http://pacificbiosciences.com/PacBioDatasets.xsd">
+							<ExternalResources xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+								<ExternalResource UniqueId="a4ba80a3-6802-45df-bfd0-bd3a1ccda4b8" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-52-29T14:52:20.079Z" />
+							</ExternalResources>
+							<DataSetMetadata>
+								<TotalLength>0</TotalLength>
+								<NumRecords>0</NumRecords>
+								<Collections xmlns="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd">
+									<CollectionMetadata CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" UniqueId="83a61432-fb33-405d-96d4-3101c133840c" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-52-29T14:52:20.079Z" Status="Ready" InstrumentId="54111" InstrumentName="54111" Context="m54111_170829_153300">
+										<InstCtrlVer>5.0.0.6235</InstCtrlVer>
+										<SigProcVer>5.0.0.6236</SigProcVer>
+										<RunDetails>
+											<TimeStampedName>r54111_20170829_145220</TimeStampedName>
+											<Name>6U00IG</Name>
+											<CreatedBy>admin</CreatedBy>
+											<WhenCreated>2017-08-29T19:55:11.464Z</WhenCreated>
+											<StartedBy>unknown</StartedBy>
+											<WhenStarted>0001-01-01T00:00:00</WhenStarted>
+										</RunDetails>
+										<WellSample Name="X.couchianus_4808Lu_9pM" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+											<WellName>A01</WellName>
+											<Concentration>0</Concentration>
+											<InsertSize>20000</InsertSize>
+											<SampleReuseEnabled>false</SampleReuseEnabled>
+											<StageHotstartEnabled>false</StageHotstartEnabled>
+											<SizeSelectionEnabled>false</SizeSelectionEnabled>
+											<UseCount>0</UseCount>
+										</WellSample>
+										<Automation Name="Workflow_Magbead.py">
+											<AutomationParameters xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+												<AutomationParameter Name="MovieLength" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="600" />
+												<AutomationParameter Name="ReuseSample" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="False" />
+												<AutomationParameter Name="ExtensionTime" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="0" />
+												<AutomationParameter Name="ExtendFirst" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="GentleWash" ValueDataType="Boolean" SimpleValue="True" />
+												<AutomationParameter Name="CellNFCIndex" ValueDataType="Int32" SimpleValue="1" />
+												<AutomationParameter Name="CollectionNumber" ValueDataType="Int32" SimpleValue="0" />
+												<AutomationParameter Name="UseStageHotStart" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="InsertSize" ValueDataType="Int32" SimpleValue="20000" />
+												<AutomationParameter Name="HasN2Switch" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="SNRCut" ValueDataType="Double" SimpleValue="3.75" />
+											</AutomationParameters>
+										</Automation>
+										<CollectionNumber>0</CollectionNumber>
+										<CellIndex>0</CellIndex>
+										<CellPac Name="SMRT®Cell 1M (4/Pack)" Description="The Sequel SMRT Cell 1M (4/Pack) are nanofabricated consumables each patterned with 1,000,000 wells called zero-mode waveguides (ZMWs). They are packaged together in a streamlined 4 SMRT Cell format (4/tray). One SMRT Cell is utilized in each sequencing reaction, and experiments can be run in single or in batch mode, giving your projects a greater level of flexibility." Version="2.0" PartNumber="101-008-000" LotNumber="320801" Barcode="BA050191" ExpirationDate="2017-08-30" />
+										<TemplatePrepKit Name="SMRTbell™ Template Prep Kit" Description="The SMRTbell™ Template Prep Kit contains reagent supplies to perform SMRTbell library preparations of primer-annealed SMRTbell libraries for insert sizes ranging from 500 bp to over 20 kb." Tags="Template Prep Kit, TPK" Version="1.0" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" MinInsertSize="500" MaxInsertSize="20000">
+											<LeftAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</LeftAdaptorSequence>
+											<LeftPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</LeftPrimerSequence>
+											<RightAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</RightAdaptorSequence>
+											<RightPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</RightPrimerSequence>
+										</TemplatePrepKit>
+										<BindingKit Name="Sequel™ Binding Kit 2.0" Description="The Sequel Binding Kit 2.0 contains reagent supplies to bind prepared DNA template libraries to the Sequel Polymerase 1.0 in preparation for sequencing on the Sequel System. The result is a DNA polymerase/template complex. Sequel Binding Kit 1.0 should be used only with Sequel Sequencing Kit 1.0. Reagent quantities support 24 binding reactions." Tags="Binding Kit, BDK" Version="1.0" PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" />
+										<SequencingKitPlate Name="Sequel™ Sequencing Plate 2.0" Description="The DNA Sequencing Kit contains a sequencing reagent plate with chemistry for single molecule real-time sequencing on the PacBio RS. Reagent quantities support 8 sequencing reactions to be used in conjunction with SMRT® Cell 4Pac(s).  (8 Cells max/Each Row supplies reagents for 1 Sequel SMRT Cell)" Tags="Sequencing Kit, SQK" Version="2.0" PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28">
+											<ReagentTubes Name="Sequel™ OS Enzyme" PartNumber="100-619-700" LotNumber="010025" Barcode="010025100619700081619" ExpirationDate="2019-08-16" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+											<ReagentTubes Name="Sequel™ SMRT®Cell Oil" PartNumber="100-619-600" LotNumber="008604" Barcode="008604100619600113020" ExpirationDate="2020-11-30" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+										</SequencingKitPlate>
+										<Primary>
+											<AutomationName>SequelAlpha</AutomationName>
+											<ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</ConfigFileName>
+											<SequencingCondition>DefaultPrimarySequencingCondition</SequencingCondition>
+											<OutputOptions>
+												<ResultsFolder>r54111_20170829_145220/1_A01/</ResultsFolder>
+												<CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170829_145220/1_A01/</CollectionPathUri>
+												<CopyFiles>
+													<CollectionFileCopy>Fasta</CollectionFileCopy>
+													<CollectionFileCopy>Bam</CollectionFileCopy>
+												</CopyFiles>
+												<Readout>Bases_Without_QVs</Readout>
+												<MetricsVerbosity>Minimal</MetricsVerbosity>
+												<TransferResource>
+													<Id>wustl_srs</Id>
+													<TransferScheme>SRS</TransferScheme>
+													<Name>WUSTL SRS</Name>
+													<Description>Transfer Scheme for WUSTL SRS</Description>
+													<DestPath>/gscmnt/gc13036/production/smrtlink_data_root</DestPath>
+												</TransferResource>
+											</OutputOptions>
+										</Primary>
+										<Secondary>
+											<AutomationName>DefaultSecondaryAutomationName</AutomationName>
+											<AutomationParameters>
+												<AutomationParameter Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" />
+											</AutomationParameters>
+											<CellCountInJob>0</CellCountInJob>
+										</Secondary>
+										<UserDefinedFields>
+											<DataEntities Name=" LIMS_IMPORT " ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" />
+										</UserDefinedFields>
+										<ComponentVersions>
+											<VersionInfo Name="ics" Version="5.0.0.6235" />
+											<VersionInfo Name="iui" Version="5.0.0.6235" />
+											<VersionInfo Name="pa" Version="5.0.0.6236" />
+											<VersionInfo Name="paws" Version="5.0.0.6236" />
+											<VersionInfo Name="ppa" Version="5.0.0.6236" />
+											<VersionInfo Name="realtime" Version="5.0.0.6236" />
+											<VersionInfo Name="transfer" Version="5.0.0.6236" />
+											<VersionInfo Name="smrttools" Version="5.0.0.6784" />
+											<VersionInfo Name="smrtinub" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtimisc" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtview" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink-analysisservices-gui" Version="5.0.0.6752" />
+										</ComponentVersions>
+									</CollectionMetadata>
+								</Collections>
+							</DataSetMetadata>
+						</SubreadSet>
+					</SubreadSets>
+				</Outputs>
+			</Run>
+		</Runs>
+	</ExperimentContainer>
+</PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/.m54111_170829_153300.run.metadata.xml b/t/data/Pacbio-Run/6U00IG/1_A01/.m54111_170829_153300.run.metadata.xml
new file mode 100644
index 0000000..6c19bbc
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/.m54111_170829_153300.run.metadata.xml
@@ -0,0 +1,230 @@
+<PacBioDataModel xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd PacBioDataModel.xsd" Version="4.0.1" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd">
+	<ExperimentContainer CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+		<InvestigatorName>Default</InvestigatorName>
+		<CreatedDate>0001-01-01</CreatedDate>
+		<Runs>
+			<Run Name="6U00IG" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" UniqueId="2d2563e3-0a00-4b9a-87a7-cd8ec0afe327" MetaType="Run" TimeStampedName="r54111_20170829_145220" Status="Ready" CreatedBy="admin" StartedBy="unknown">
+				<Outputs>
+					<SubreadSets>
+						<SubreadSet Name="X.couchianus_4808Lu_9pM-Cell1" CreatedAt="2017-08-29T19:55:11.464Z" UniqueId="83a61432-fb33-405d-96d4-3101c133840c" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-52-29T14:52:20.079Z" xmlns="http://pacificbiosciences.com/PacBioDatasets.xsd">
+							<ExternalResources xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+								<ExternalResource UniqueId="a4ba80a3-6802-45df-bfd0-bd3a1ccda4b8" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-52-29T14:52:20.079Z" />
+							</ExternalResources>
+							<DataSetMetadata>
+								<TotalLength>0</TotalLength>
+								<NumRecords>0</NumRecords>
+								<Collections xmlns="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd">
+									<CollectionMetadata CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" UniqueId="83a61432-fb33-405d-96d4-3101c133840c" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-52-29T14:52:20.079Z" Status="Ready" InstrumentId="54111" InstrumentName="54111" Context="m54111_170829_153300">
+										<InstCtrlVer>5.0.0.6235</InstCtrlVer>
+										<SigProcVer>5.0.0.6236</SigProcVer>
+										<RunDetails>
+											<TimeStampedName>r54111_20170829_145220</TimeStampedName>
+											<Name>6U00IG</Name>
+											<CreatedBy>admin</CreatedBy>
+											<WhenCreated>2017-08-29T19:55:11.464Z</WhenCreated>
+											<StartedBy>unknown</StartedBy>
+											<WhenStarted>0001-01-01T00:00:00</WhenStarted>
+										</RunDetails>
+										<WellSample Name="X.couchianus_4808Lu_9pM" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+											<WellName>A01</WellName>
+											<Concentration>0</Concentration>
+											<InsertSize>20000</InsertSize>
+											<SampleReuseEnabled>false</SampleReuseEnabled>
+											<StageHotstartEnabled>false</StageHotstartEnabled>
+											<SizeSelectionEnabled>false</SizeSelectionEnabled>
+											<UseCount>0</UseCount>
+										</WellSample>
+										<Automation Name="Workflow_Magbead.py">
+											<AutomationParameters xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+												<AutomationParameter Name="MovieLength" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="600" />
+												<AutomationParameter Name="ReuseSample" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="False" />
+												<AutomationParameter Name="ExtensionTime" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="0" />
+												<AutomationParameter Name="ExtendFirst" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="GentleWash" ValueDataType="Boolean" SimpleValue="True" />
+												<AutomationParameter Name="CellNFCIndex" ValueDataType="Int32" SimpleValue="1" />
+												<AutomationParameter Name="CollectionNumber" ValueDataType="Int32" SimpleValue="0" />
+												<AutomationParameter Name="UseStageHotStart" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="InsertSize" ValueDataType="Int32" SimpleValue="20000" />
+												<AutomationParameter Name="HasN2Switch" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="SNRCut" ValueDataType="Double" SimpleValue="3.75" />
+											</AutomationParameters>
+										</Automation>
+										<CollectionNumber>0</CollectionNumber>
+										<CellIndex>0</CellIndex>
+										<CellPac Name="SMRT®Cell 1M (4/Pack)" Description="The Sequel SMRT Cell 1M (4/Pack) are nanofabricated consumables each patterned with 1,000,000 wells called zero-mode waveguides (ZMWs). They are packaged together in a streamlined 4 SMRT Cell format (4/tray). One SMRT Cell is utilized in each sequencing reaction, and experiments can be run in single or in batch mode, giving your projects a greater level of flexibility." Version="2.0" PartNumber="101-008-000" LotNumber="320801" Barcode="BA050191" ExpirationDate="2017-08-30" />
+										<TemplatePrepKit Name="SMRTbell™ Template Prep Kit" Description="The SMRTbell™ Template Prep Kit contains reagent supplies to perform SMRTbell library preparations of primer-annealed SMRTbell libraries for insert sizes ranging from 500 bp to over 20 kb." Tags="Template Prep Kit, TPK" Version="1.0" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" MinInsertSize="500" MaxInsertSize="20000">
+											<LeftAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</LeftAdaptorSequence>
+											<LeftPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</LeftPrimerSequence>
+											<RightAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</RightAdaptorSequence>
+											<RightPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</RightPrimerSequence>
+										</TemplatePrepKit>
+										<BindingKit Name="Sequel™ Binding Kit 2.0" Description="The Sequel Binding Kit 2.0 contains reagent supplies to bind prepared DNA template libraries to the Sequel Polymerase 1.0 in preparation for sequencing on the Sequel System. The result is a DNA polymerase/template complex. Sequel Binding Kit 1.0 should be used only with Sequel Sequencing Kit 1.0. Reagent quantities support 24 binding reactions." Tags="Binding Kit, BDK" Version="1.0" PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" />
+										<SequencingKitPlate Name="Sequel™ Sequencing Plate 2.0" Description="The DNA Sequencing Kit contains a sequencing reagent plate with chemistry for single molecule real-time sequencing on the PacBio RS. Reagent quantities support 8 sequencing reactions to be used in conjunction with SMRT® Cell 4Pac(s).  (8 Cells max/Each Row supplies reagents for 1 Sequel SMRT Cell)" Tags="Sequencing Kit, SQK" Version="2.0" PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28">
+											<ReagentTubes Name="Sequel™ OS Enzyme" PartNumber="100-619-700" LotNumber="010025" Barcode="010025100619700081619" ExpirationDate="2019-08-16" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+											<ReagentTubes Name="Sequel™ SMRT®Cell Oil" PartNumber="100-619-600" LotNumber="008604" Barcode="008604100619600113020" ExpirationDate="2020-11-30" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+										</SequencingKitPlate>
+										<Primary>
+											<AutomationName>SequelAlpha</AutomationName>
+											<ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</ConfigFileName>
+											<SequencingCondition>DefaultPrimarySequencingCondition</SequencingCondition>
+											<OutputOptions>
+												<ResultsFolder>r54111_20170829_145220/1_A01/</ResultsFolder>
+												<CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170829_145220/1_A01/</CollectionPathUri>
+												<CopyFiles>
+													<CollectionFileCopy>Fasta</CollectionFileCopy>
+													<CollectionFileCopy>Bam</CollectionFileCopy>
+												</CopyFiles>
+												<Readout>Bases_Without_QVs</Readout>
+												<MetricsVerbosity>Minimal</MetricsVerbosity>
+												<TransferResource>
+													<Id>wustl_srs</Id>
+													<TransferScheme>SRS</TransferScheme>
+													<Name>WUSTL SRS</Name>
+													<Description>Transfer Scheme for WUSTL SRS</Description>
+													<DestPath>/gscmnt/gc13036/production/smrtlink_data_root</DestPath>
+												</TransferResource>
+											</OutputOptions>
+										</Primary>
+										<Secondary>
+											<AutomationName>DefaultSecondaryAutomationName</AutomationName>
+											<AutomationParameters>
+												<AutomationParameter Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" />
+											</AutomationParameters>
+											<CellCountInJob>0</CellCountInJob>
+										</Secondary>
+										<UserDefinedFields>
+											<DataEntities Name=" LIMS_IMPORT " ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" />
+										</UserDefinedFields>
+										<ComponentVersions>
+											<VersionInfo Name="ics" Version="5.0.0.6235" />
+											<VersionInfo Name="iui" Version="5.0.0.6235" />
+											<VersionInfo Name="pa" Version="5.0.0.6236" />
+											<VersionInfo Name="paws" Version="5.0.0.6236" />
+											<VersionInfo Name="ppa" Version="5.0.0.6236" />
+											<VersionInfo Name="realtime" Version="5.0.0.6236" />
+											<VersionInfo Name="transfer" Version="5.0.0.6236" />
+											<VersionInfo Name="smrttools" Version="5.0.0.6784" />
+											<VersionInfo Name="smrtinub" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtimisc" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtview" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink-analysisservices-gui" Version="5.0.0.6752" />
+										</ComponentVersions>
+									</CollectionMetadata>
+								</Collections>
+							</DataSetMetadata>
+						</SubreadSet>
+						<SubreadSet Name="X.couchianus_4808Lu_18pM-Cell2" CreatedAt="2017-08-29T19:55:11.464Z" UniqueId="2e23ac02-4eff-4da8-9e2a-b6d87951934e" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-52-29T14:52:20.079Z" xmlns="http://pacificbiosciences.com/PacBioDatasets.xsd">
+							<ExternalResources xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+								<ExternalResource UniqueId="df570ad7-90ff-4725-bd84-ea9e65f4f55b" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-52-29T14:52:20.079Z" />
+							</ExternalResources>
+							<DataSetMetadata>
+								<TotalLength>0</TotalLength>
+								<NumRecords>0</NumRecords>
+								<Collections xmlns="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd">
+									<CollectionMetadata CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" UniqueId="2e23ac02-4eff-4da8-9e2a-b6d87951934e" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-52-29T14:52:20.079Z" Status="Ready" InstrumentId="54111" InstrumentName="54111">
+										<InstCtrlVer>5.0.0.6235</InstCtrlVer>
+										<SigProcVer>5.0.0.6236</SigProcVer>
+										<RunDetails>
+											<TimeStampedName>r54111_20170829_145220</TimeStampedName>
+											<Name>6U00IG</Name>
+											<CreatedBy>admin</CreatedBy>
+											<WhenCreated>2017-08-29T19:55:11.464Z</WhenCreated>
+											<StartedBy>unknown</StartedBy>
+											<WhenStarted>0001-01-01T00:00:00</WhenStarted>
+										</RunDetails>
+										<WellSample Name="X.couchianus_4808Lu_18pM" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+											<WellName>B01</WellName>
+											<Concentration>0</Concentration>
+											<InsertSize>20000</InsertSize>
+											<SampleReuseEnabled>false</SampleReuseEnabled>
+											<StageHotstartEnabled>false</StageHotstartEnabled>
+											<SizeSelectionEnabled>false</SizeSelectionEnabled>
+											<UseCount>0</UseCount>
+										</WellSample>
+										<Automation Name="Workflow_Magbead.py">
+											<AutomationParameters xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+												<AutomationParameter Name="MovieLength" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="600" />
+												<AutomationParameter Name="ReuseSample" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="False" />
+												<AutomationParameter Name="ExtensionTime" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="0" />
+												<AutomationParameter Name="ExtendFirst" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="GentleWash" ValueDataType="Boolean" SimpleValue="True" />
+												<AutomationParameter Name="CellNFCIndex" ValueDataType="Int32" SimpleValue="1" />
+												<AutomationParameter Name="CollectionNumber" ValueDataType="Int32" SimpleValue="1" />
+												<AutomationParameter Name="UseStageHotStart" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="InsertSize" ValueDataType="Int32" SimpleValue="20000" />
+												<AutomationParameter Name="HasN2Switch" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="SNRCut" ValueDataType="Double" SimpleValue="3.75" />
+											</AutomationParameters>
+										</Automation>
+										<CollectionNumber>1</CollectionNumber>
+										<CellIndex>1</CellIndex>
+										<CellPac Name="SMRT®Cell 1M (4/Pack)" Description="The Sequel SMRT Cell 1M (4/Pack) are nanofabricated consumables each patterned with 1,000,000 wells called zero-mode waveguides (ZMWs). They are packaged together in a streamlined 4 SMRT Cell format (4/tray). One SMRT Cell is utilized in each sequencing reaction, and experiments can be run in single or in batch mode, giving your projects a greater level of flexibility." Version="2.0" PartNumber="101-008-000" LotNumber="320801" Barcode="320801101008000083017" ExpirationDate="2017-08-30" />
+										<TemplatePrepKit Name="SMRTbell™ Template Prep Kit" Description="The SMRTbell™ Template Prep Kit contains reagent supplies to perform SMRTbell library preparations of primer-annealed SMRTbell libraries for insert sizes ranging from 500 bp to over 20 kb." Tags="Template Prep Kit, TPK" Version="1.0" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" MinInsertSize="500" MaxInsertSize="20000">
+											<LeftAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</LeftAdaptorSequence>
+											<LeftPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</LeftPrimerSequence>
+											<RightAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</RightAdaptorSequence>
+											<RightPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</RightPrimerSequence>
+										</TemplatePrepKit>
+										<BindingKit Name="Sequel™ Binding Kit 2.0" Description="The Sequel Binding Kit 2.0 contains reagent supplies to bind prepared DNA template libraries to the Sequel Polymerase 1.0 in preparation for sequencing on the Sequel System. The result is a DNA polymerase/template complex. Sequel Binding Kit 1.0 should be used only with Sequel Sequencing Kit 1.0. Reagent quantities support 24 binding reactions." Tags="Binding Kit, BDK" Version="1.0" PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" />
+										<SequencingKitPlate Name="Sequel™ Sequencing Plate 2.0" Description="The DNA Sequencing Kit contains a sequencing reagent plate with chemistry for single molecule real-time sequencing on the PacBio RS. Reagent quantities support 8 sequencing reactions to be used in conjunction with SMRT® Cell 4Pac(s).  (8 Cells max/Each Row supplies reagents for 1 Sequel SMRT Cell)" Tags="Sequencing Kit, SQK" Version="2.0" PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28">
+											<ReagentTubes Name="Sequel™ OS Enzyme" PartNumber="100-619-700" LotNumber="010025" Barcode="010025100619700081619" ExpirationDate="2019-08-16" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+											<ReagentTubes Name="Sequel™ SMRT®Cell Oil" PartNumber="100-619-600" LotNumber="008604" Barcode="008604100619600113020" ExpirationDate="2020-11-30" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+										</SequencingKitPlate>
+										<Primary>
+											<AutomationName>SequelAlpha</AutomationName>
+											<ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</ConfigFileName>
+											<SequencingCondition>DefaultPrimarySequencingCondition</SequencingCondition>
+											<OutputOptions>
+												<ResultsFolder>r54111_20170829_145220/2_B01/</ResultsFolder>
+												<CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170829_145220/2_B01/</CollectionPathUri>
+												<CopyFiles>
+													<CollectionFileCopy>Fasta</CollectionFileCopy>
+													<CollectionFileCopy>Bam</CollectionFileCopy>
+												</CopyFiles>
+												<Readout>Bases_Without_QVs</Readout>
+												<MetricsVerbosity>Minimal</MetricsVerbosity>
+												<TransferResource>
+													<Id>wustl_srs</Id>
+													<TransferScheme>SRS</TransferScheme>
+													<Name>WUSTL SRS</Name>
+													<Description>Transfer Scheme for WUSTL SRS</Description>
+													<DestPath>/gscmnt/gc13036/production/smrtlink_data_root</DestPath>
+												</TransferResource>
+											</OutputOptions>
+										</Primary>
+										<Secondary>
+											<AutomationName>DefaultSecondaryAutomationName</AutomationName>
+											<AutomationParameters>
+												<AutomationParameter Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" />
+											</AutomationParameters>
+											<CellCountInJob>0</CellCountInJob>
+										</Secondary>
+										<UserDefinedFields>
+											<DataEntities Name=" LIMS_IMPORT " ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" />
+										</UserDefinedFields>
+										<ComponentVersions>
+											<VersionInfo Name="ics" Version="5.0.0.6235" />
+											<VersionInfo Name="iui" Version="5.0.0.6235" />
+											<VersionInfo Name="pa" Version="5.0.0.6236" />
+											<VersionInfo Name="paws" Version="5.0.0.6236" />
+											<VersionInfo Name="ppa" Version="5.0.0.6236" />
+											<VersionInfo Name="realtime" Version="5.0.0.6236" />
+											<VersionInfo Name="transfer" Version="5.0.0.6236" />
+											<VersionInfo Name="smrttools" Version="5.0.0.6784" />
+											<VersionInfo Name="smrtinub" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtimisc" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtview" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink-analysisservices-gui" Version="5.0.0.6752" />
+										</ComponentVersions>
+									</CollectionMetadata>
+								</Collections>
+							</DataSetMetadata>
+						</SubreadSet>
+					</SubreadSets>
+				</Outputs>
+			</Run>
+		</Runs>
+	</ExperimentContainer>
+</PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.adapters.fasta b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.adapters.fasta
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.adapters.fasta
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.baz2bam_1.log b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.baz2bam_1.log
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.baz2bam_1.log
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.scraps.bam b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.scraps.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.scraps.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.scraps.bam.pbi b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.scraps.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.scraps.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.sts.xml b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.sts.xml
new file mode 100644
index 0000000..51b63cf
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.sts.xml
@@ -0,0 +1 @@
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Level: Channel C</ns:MetricDescription></BaselineLevelDist><BaselineLevelDist 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\ No newline at end of file
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.subreads.bam b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.subreads.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.subreads.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.subreads.bam.pbi b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.subreads.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.subreads.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.subreadset.xml b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.subreadset.xml
new file mode 100644
index 0000000..a0a021d
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.subreadset.xml
@@ -0,0 +1,121 @@
+<pbds:SubreadSet CreatedAt="2017-08-29T19:55:11.464Z" MetaType="PacBio.DataSet.SubreadSet" Name="X.couchianus_4808Lu_9pM-Cell1" Tags="subreadset" TimeStampedName="54111-SubreadSetCollection-2017-52-29T14:52:20.079Z" UniqueId="83a61432-fb33-405d-96d4-3101c133840c" Version="4.0.1" xmlns="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioSecondaryDataModel.xsd">
+    <pbbase:ExternalResources>
+        <pbbase:ExternalResource Description="Points to the subreads bam file." MetaType="PacBio.SubreadFile.SubreadBamFile" Name="subreads bam" ResourceId="m54111_170829_153300.subreads.bam" TimeStampedName="pacbio_subreadfile_subreadbamfile-170830_041937898" UniqueId="fe5780d7-5591-4671-bcfc-ce4603c1de47" Version="4.0.1">
+            <pbbase:FileIndices>
+                <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="m54111_170829_153300.subreads.bam.pbi" TimeStampedName="pacbio_index_pacbioindex-170830_041937898" UniqueId="88d44050-0188-4dfa-83e2-47dc79a2c227" Version="4.0.1" />
+            </pbbase:FileIndices>
+            <pbbase:ExternalResources>
+                <pbbase:ExternalResource Description="Points to the scraps bam file." MetaType="PacBio.SubreadFile.ScrapsBamFile" Name="scraps bam" ResourceId="m54111_170829_153300.scraps.bam" TimeStampedName="pacbio_subreadfile_scrapsbamfile-170830_041937904" UniqueId="ef858434-273d-4304-9e5f-b99928554798" Version="4.0.1">
+                    <pbbase:FileIndices>
+                        <pbbase:FileIndex MetaType="PacBio.Index.PacBioIndex" ResourceId="m54111_170829_153300.scraps.bam.pbi" TimeStampedName="pacbio_index_pacbioindex-170830_041937904" UniqueId="74aa05ff-9588-4b86-b771-3addfffd6da6" Version="4.0.1" />
+                    </pbbase:FileIndices>
+                </pbbase:ExternalResource>
+                <pbbase:ExternalResource Description="Points to the adapters.fasta file." MetaType="PacBio.SubreadFile.AdapterFastaFile" Name="Adapters FASTA" ResourceId="m54111_170829_153300.adapters.fasta" TimeStampedName="pacbio_subreadfile_adapterfastafile-170830_041937904" UniqueId="35815b09-c9dd-4983-9cf1-017e98f5ed86" Version="4.0.1" />
+                <pbbase:ExternalResource Description="Points to the summary sts.xml file." MetaType="PacBio.SubreadFile.ChipStatsFile" Name="Chipstats XML" ResourceId="m54111_170829_153300.sts.xml" TimeStampedName="pacbio_subreadfile_chipstatsfile-170830_041937904" UniqueId="d426cc77-8fdf-415e-9b4d-b5e7d273035f" Version="4.0.1" />
+            </pbbase:ExternalResources>
+        </pbbase:ExternalResource>
+    </pbbase:ExternalResources>
+    <pbds:DataSetMetadata>
+        <pbds:TotalLength>675664348</pbds:TotalLength>
+        <pbds:NumRecords>68422</pbds:NumRecords>
+        <Collections xmlns="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd">
+            <CollectionMetadata CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" UniqueId="83a61432-fb33-405d-96d4-3101c133840c" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-52-29T14:52:20.079Z" Status="Ready" InstrumentId="54111" InstrumentName="54111" Context="m54111_170829_153300">
+                <InstCtrlVer>5.0.0.6235</InstCtrlVer>
+                <SigProcVer>5.0.0.6236</SigProcVer>
+                <RunDetails>
+                    <TimeStampedName>r54111_20170829_145220</TimeStampedName>
+                    <Name>6U00IG</Name>
+                    <CreatedBy>admin</CreatedBy>
+                    <WhenCreated>2017-08-29T19:55:11.464Z</WhenCreated>
+                    <StartedBy>unknown</StartedBy>
+                    <WhenStarted>0001-01-01T00:00:00</WhenStarted>
+                </RunDetails>
+                <WellSample Name="X.couchianus_4808Lu_9pM" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+                    <WellName>A01</WellName>
+                    <Concentration>0</Concentration>
+                    <InsertSize>20000</InsertSize>
+                    <SampleReuseEnabled>false</SampleReuseEnabled>
+                    <StageHotstartEnabled>false</StageHotstartEnabled>
+                    <SizeSelectionEnabled>false</SizeSelectionEnabled>
+                    <UseCount>0</UseCount>
+                </WellSample>
+                <Automation Name="Workflow_Magbead.py">
+                    <AutomationParameters xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+                        <AutomationParameter Name="MovieLength" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="600" />
+                        <AutomationParameter Name="ReuseSample" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="False" />
+                        <AutomationParameter Name="ExtensionTime" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="0" />
+                        <AutomationParameter Name="ExtendFirst" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Boolean" SimpleValue="False" />
+                        <AutomationParameter Name="GentleWash" ValueDataType="Boolean" SimpleValue="True" />
+                        <AutomationParameter Name="CellNFCIndex" ValueDataType="Int32" SimpleValue="1" />
+                        <AutomationParameter Name="CollectionNumber" ValueDataType="Int32" SimpleValue="0" />
+                        <AutomationParameter Name="UseStageHotStart" ValueDataType="Boolean" SimpleValue="False" />
+                        <AutomationParameter Name="InsertSize" ValueDataType="Int32" SimpleValue="20000" />
+                        <AutomationParameter Name="HasN2Switch" ValueDataType="Boolean" SimpleValue="False" />
+                        <AutomationParameter Name="SNRCut" ValueDataType="Double" SimpleValue="3.75" />
+                    </AutomationParameters>
+                </Automation>
+                <CollectionNumber>0</CollectionNumber>
+                <CellIndex>0</CellIndex>
+                <CellPac Name="SMRT®Cell 1M (4/Pack)" Description="The Sequel SMRT Cell 1M (4/Pack) are nanofabricated consumables each patterned with 1,000,000 wells called zero-mode waveguides (ZMWs). They are packaged together in a streamlined 4 SMRT Cell format (4/tray). One SMRT Cell is utilized in each sequencing reaction, and experiments can be run in single or in batch mode, giving your projects a greater level of flexibility." Version="2.0" PartNumber="101-008-000" LotNumber="320801" Barcode="BA050191" ExpirationDate="2017-08-30" />
+                <TemplatePrepKit Name="SMRTbell™ Template Prep Kit" Description="The SMRTbell™ Template Prep Kit contains reagent supplies to perform SMRTbell library preparations of primer-annealed SMRTbell libraries for insert sizes ranging from 500 bp to over 20 kb." Tags="Template Prep Kit, TPK" Version="1.0" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" MinInsertSize="500" MaxInsertSize="20000">
+                    <LeftAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</LeftAdaptorSequence>
+                    <LeftPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</LeftPrimerSequence>
+                    <RightAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</RightAdaptorSequence>
+                    <RightPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</RightPrimerSequence>
+                </TemplatePrepKit>
+                <BindingKit Name="Sequel™ Binding Kit 2.0" Description="The Sequel Binding Kit 2.0 contains reagent supplies to bind prepared DNA template libraries to the Sequel Polymerase 1.0 in preparation for sequencing on the Sequel System. The result is a DNA polymerase/template complex. Sequel Binding Kit 1.0 should be used only with Sequel Sequencing Kit 1.0. Reagent quantities support 24 binding reactions." Tags="Binding Kit, BDK" Version="1.0" PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" />
+                <SequencingKitPlate Name="Sequel™ Sequencing Plate 2.0" Description="The DNA Sequencing Kit contains a sequencing reagent plate with chemistry for single molecule real-time sequencing on the PacBio RS. Reagent quantities support 8 sequencing reactions to be used in conjunction with SMRT® Cell 4Pac(s).  (8 Cells max/Each Row supplies reagents for 1 Sequel SMRT Cell)" Tags="Sequencing Kit, SQK" Version="2.0" PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28">
+                    <ReagentTubes Name="Sequel™ OS Enzyme" PartNumber="100-619-700" LotNumber="010025" Barcode="010025100619700081619" ExpirationDate="2019-08-16" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+                    <ReagentTubes Name="Sequel™ SMRT®Cell Oil" PartNumber="100-619-600" LotNumber="008604" Barcode="008604100619600113020" ExpirationDate="2020-11-30" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+                </SequencingKitPlate>
+                <Primary>
+                    <AutomationName>SequelAlpha</AutomationName>
+                    <ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</ConfigFileName>
+                    <SequencingCondition>DefaultPrimarySequencingCondition</SequencingCondition>
+                    <OutputOptions>
+                        <ResultsFolder>r54111_20170829_145220/1_A01/</ResultsFolder>
+                        <CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170829_145220/1_A01/</CollectionPathUri>
+                        <CopyFiles>
+                            <CollectionFileCopy>Fasta</CollectionFileCopy>
+                            <CollectionFileCopy>Bam</CollectionFileCopy>
+                        </CopyFiles>
+                        <Readout>Bases_Without_QVs</Readout>
+                        <MetricsVerbosity>Minimal</MetricsVerbosity>
+                        <TransferResource>
+                            <Id>wustl_srs</Id>
+                            <TransferScheme>SRS</TransferScheme>
+                            <Name>WUSTL SRS</Name>
+                            <Description>Transfer Scheme for WUSTL SRS</Description>
+                            <DestPath>/gscmnt/gc13036/production/smrtlink_data_root</DestPath>
+                        </TransferResource>
+                    </OutputOptions>
+                </Primary>
+                <Secondary>
+                    <AutomationName>DefaultSecondaryAutomationName</AutomationName>
+                    <AutomationParameters>
+                        <AutomationParameter Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" />
+                    </AutomationParameters>
+                    <CellCountInJob>0</CellCountInJob>
+                </Secondary>
+                <UserDefinedFields>
+                    <DataEntities Name=" LIMS_IMPORT " ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" />
+                </UserDefinedFields>
+                <ComponentVersions>
+                    <VersionInfo Name="ics" Version="5.0.0.6235" />
+                    <VersionInfo Name="iui" Version="5.0.0.6235" />
+                    <VersionInfo Name="pa" Version="5.0.0.6236" />
+                    <VersionInfo Name="paws" Version="5.0.0.6236" />
+                    <VersionInfo Name="ppa" Version="5.0.0.6236" />
+                    <VersionInfo Name="realtime" Version="5.0.0.6236" />
+                    <VersionInfo Name="transfer" Version="5.0.0.6236" />
+                    <VersionInfo Name="smrttools" Version="5.0.0.6784" />
+                    <VersionInfo Name="smrtinub" Version="5.0.0.6656" />
+                    <VersionInfo Name="smrtlink" Version="5.0.0.6792" />
+                    <VersionInfo Name="smrtimisc" Version="5.0.0.6792" />
+                    <VersionInfo Name="smrtview" Version="5.0.0.6656" />
+                    <VersionInfo Name="smrtlink-analysisservices-gui" Version="5.0.0.6752" />
+                </ComponentVersions>
+            </CollectionMetadata>
+        </Collections>
+    </pbds:DataSetMetadata>
+</pbds:SubreadSet>
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.transferdone b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.transferdone
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/m54111_170829_153300.transferdone
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/1_A01/tmp-file-4b626e16-2356-4bee-9781-b29a63c7e40c.txt b/t/data/Pacbio-Run/6U00IG/1_A01/tmp-file-4b626e16-2356-4bee-9781-b29a63c7e40c.txt
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/1_A01/tmp-file-4b626e16-2356-4bee-9781-b29a63c7e40c.txt
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/2_B01/.m54111_170830_013202.metadata.xml b/t/data/Pacbio-Run/6U00IG/2_B01/.m54111_170830_013202.metadata.xml
new file mode 100644
index 0000000..98959ed
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/2_B01/.m54111_170830_013202.metadata.xml
@@ -0,0 +1,122 @@
+<PacBioDataModel xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd PacBioDataModel.xsd" Version="4.0.1" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd">
+	<ExperimentContainer CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+		<InvestigatorName>Default</InvestigatorName>
+		<CreatedDate>0001-01-01</CreatedDate>
+		<Runs>
+			<Run Name="6U00IG" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" UniqueId="2d2563e3-0a00-4b9a-87a7-cd8ec0afe327" MetaType="Run" TimeStampedName="r54111_20170829_145220" Status="Ready" CreatedBy="admin" StartedBy="unknown">
+				<Outputs>
+					<SubreadSets>
+						<SubreadSet Name="X.couchianus_4808Lu_18pM-Cell2" CreatedAt="2017-08-29T19:55:11.464Z" UniqueId="2e23ac02-4eff-4da8-9e2a-b6d87951934e" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-52-29T14:52:20.079Z" xmlns="http://pacificbiosciences.com/PacBioDatasets.xsd">
+							<ExternalResources xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+								<ExternalResource UniqueId="df570ad7-90ff-4725-bd84-ea9e65f4f55b" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-52-29T14:52:20.079Z" />
+							</ExternalResources>
+							<DataSetMetadata>
+								<TotalLength>0</TotalLength>
+								<NumRecords>0</NumRecords>
+								<Collections xmlns="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd">
+									<CollectionMetadata CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" UniqueId="2e23ac02-4eff-4da8-9e2a-b6d87951934e" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-52-29T14:52:20.079Z" Status="Ready" InstrumentId="54111" InstrumentName="54111" Context="m54111_170830_013202">
+										<InstCtrlVer>5.0.0.6235</InstCtrlVer>
+										<SigProcVer>5.0.0.6236</SigProcVer>
+										<RunDetails>
+											<TimeStampedName>r54111_20170829_145220</TimeStampedName>
+											<Name>6U00IG</Name>
+											<CreatedBy>admin</CreatedBy>
+											<WhenCreated>2017-08-29T19:55:11.464Z</WhenCreated>
+											<StartedBy>unknown</StartedBy>
+											<WhenStarted>0001-01-01T00:00:00</WhenStarted>
+										</RunDetails>
+										<WellSample Name="X.couchianus_4808Lu_18pM" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+											<WellName>B01</WellName>
+											<Concentration>0</Concentration>
+											<InsertSize>20000</InsertSize>
+											<SampleReuseEnabled>false</SampleReuseEnabled>
+											<StageHotstartEnabled>false</StageHotstartEnabled>
+											<SizeSelectionEnabled>false</SizeSelectionEnabled>
+											<UseCount>0</UseCount>
+										</WellSample>
+										<Automation Name="Workflow_Magbead.py">
+											<AutomationParameters xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+												<AutomationParameter Name="MovieLength" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="600" />
+												<AutomationParameter Name="ReuseSample" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="False" />
+												<AutomationParameter Name="ExtensionTime" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="0" />
+												<AutomationParameter Name="ExtendFirst" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="GentleWash" ValueDataType="Boolean" SimpleValue="True" />
+												<AutomationParameter Name="CellNFCIndex" ValueDataType="Int32" SimpleValue="1" />
+												<AutomationParameter Name="CollectionNumber" ValueDataType="Int32" SimpleValue="1" />
+												<AutomationParameter Name="UseStageHotStart" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="InsertSize" ValueDataType="Int32" SimpleValue="20000" />
+												<AutomationParameter Name="HasN2Switch" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="SNRCut" ValueDataType="Double" SimpleValue="3.75" />
+											</AutomationParameters>
+										</Automation>
+										<CollectionNumber>1</CollectionNumber>
+										<CellIndex>1</CellIndex>
+										<CellPac Name="SMRT®Cell 1M (4/Pack)" Description="The Sequel SMRT Cell 1M (4/Pack) are nanofabricated consumables each patterned with 1,000,000 wells called zero-mode waveguides (ZMWs). They are packaged together in a streamlined 4 SMRT Cell format (4/tray). One SMRT Cell is utilized in each sequencing reaction, and experiments can be run in single or in batch mode, giving your projects a greater level of flexibility." Version="2.0" PartNumber="101-008-000" LotNumber="320801" Barcode="BA050145" ExpirationDate="2017-08-30" />
+										<TemplatePrepKit Name="SMRTbell™ Template Prep Kit" Description="The SMRTbell™ Template Prep Kit contains reagent supplies to perform SMRTbell library preparations of primer-annealed SMRTbell libraries for insert sizes ranging from 500 bp to over 20 kb." Tags="Template Prep Kit, TPK" Version="1.0" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" MinInsertSize="500" MaxInsertSize="20000">
+											<LeftAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</LeftAdaptorSequence>
+											<LeftPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</LeftPrimerSequence>
+											<RightAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</RightAdaptorSequence>
+											<RightPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</RightPrimerSequence>
+										</TemplatePrepKit>
+										<BindingKit Name="Sequel™ Binding Kit 2.0" Description="The Sequel Binding Kit 2.0 contains reagent supplies to bind prepared DNA template libraries to the Sequel Polymerase 1.0 in preparation for sequencing on the Sequel System. The result is a DNA polymerase/template complex. Sequel Binding Kit 1.0 should be used only with Sequel Sequencing Kit 1.0. Reagent quantities support 24 binding reactions." Tags="Binding Kit, BDK" Version="1.0" PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" />
+										<SequencingKitPlate Name="Sequel™ Sequencing Plate 2.0" Description="The DNA Sequencing Kit contains a sequencing reagent plate with chemistry for single molecule real-time sequencing on the PacBio RS. Reagent quantities support 8 sequencing reactions to be used in conjunction with SMRT® Cell 4Pac(s).  (8 Cells max/Each Row supplies reagents for 1 Sequel SMRT Cell)" Tags="Sequencing Kit, SQK" Version="2.0" PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28">
+											<ReagentTubes Name="Sequel™ OS Enzyme" PartNumber="100-619-700" LotNumber="010025" Barcode="010025100619700081619" ExpirationDate="2019-08-16" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+											<ReagentTubes Name="Sequel™ SMRT®Cell Oil" PartNumber="100-619-600" LotNumber="008604" Barcode="008604100619600113020" ExpirationDate="2020-11-30" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+										</SequencingKitPlate>
+										<Primary>
+											<AutomationName>SequelAlpha</AutomationName>
+											<ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</ConfigFileName>
+											<SequencingCondition>DefaultPrimarySequencingCondition</SequencingCondition>
+											<OutputOptions>
+												<ResultsFolder>r54111_20170829_145220/2_B01/</ResultsFolder>
+												<CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170829_145220/2_B01/</CollectionPathUri>
+												<CopyFiles>
+													<CollectionFileCopy>Fasta</CollectionFileCopy>
+													<CollectionFileCopy>Bam</CollectionFileCopy>
+												</CopyFiles>
+												<Readout>Bases_Without_QVs</Readout>
+												<MetricsVerbosity>Minimal</MetricsVerbosity>
+												<TransferResource>
+													<Id>wustl_srs</Id>
+													<TransferScheme>SRS</TransferScheme>
+													<Name>WUSTL SRS</Name>
+													<Description>Transfer Scheme for WUSTL SRS</Description>
+													<DestPath>/gscmnt/gc13036/production/smrtlink_data_root</DestPath>
+												</TransferResource>
+											</OutputOptions>
+										</Primary>
+										<Secondary>
+											<AutomationName>DefaultSecondaryAutomationName</AutomationName>
+											<AutomationParameters>
+												<AutomationParameter Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" />
+											</AutomationParameters>
+											<CellCountInJob>0</CellCountInJob>
+										</Secondary>
+										<UserDefinedFields>
+											<DataEntities Name=" LIMS_IMPORT " ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" />
+										</UserDefinedFields>
+										<ComponentVersions>
+											<VersionInfo Name="ics" Version="5.0.0.6235" />
+											<VersionInfo Name="iui" Version="5.0.0.6235" />
+											<VersionInfo Name="pa" Version="5.0.0.6236" />
+											<VersionInfo Name="paws" Version="5.0.0.6236" />
+											<VersionInfo Name="ppa" Version="5.0.0.6236" />
+											<VersionInfo Name="realtime" Version="5.0.0.6236" />
+											<VersionInfo Name="transfer" Version="5.0.0.6236" />
+											<VersionInfo Name="smrttools" Version="5.0.0.6784" />
+											<VersionInfo Name="smrtinub" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtimisc" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtview" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink-analysisservices-gui" Version="5.0.0.6752" />
+										</ComponentVersions>
+									</CollectionMetadata>
+								</Collections>
+							</DataSetMetadata>
+						</SubreadSet>
+					</SubreadSets>
+				</Outputs>
+			</Run>
+		</Runs>
+	</ExperimentContainer>
+</PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00IG/2_B01/.m54111_170830_013202.run.metadata.xml b/t/data/Pacbio-Run/6U00IG/2_B01/.m54111_170830_013202.run.metadata.xml
new file mode 100644
index 0000000..74e8a21
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/2_B01/.m54111_170830_013202.run.metadata.xml
@@ -0,0 +1,230 @@
+<PacBioDataModel xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd PacBioDataModel.xsd" Version="4.0.1" xmlns="http://pacificbiosciences.com/PacBioDataModel.xsd">
+	<ExperimentContainer CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+		<InvestigatorName>Default</InvestigatorName>
+		<CreatedDate>0001-01-01</CreatedDate>
+		<Runs>
+			<Run Name="6U00IG" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" UniqueId="2d2563e3-0a00-4b9a-87a7-cd8ec0afe327" MetaType="Run" TimeStampedName="r54111_20170829_145220" Status="Ready" CreatedBy="admin" StartedBy="unknown">
+				<Outputs>
+					<SubreadSets>
+						<SubreadSet Name="X.couchianus_4808Lu_9pM-Cell1" CreatedAt="2017-08-29T19:55:11.464Z" UniqueId="83a61432-fb33-405d-96d4-3101c133840c" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-52-29T14:52:20.079Z" xmlns="http://pacificbiosciences.com/PacBioDatasets.xsd">
+							<ExternalResources xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+								<ExternalResource UniqueId="a4ba80a3-6802-45df-bfd0-bd3a1ccda4b8" MetaType="ExternalResource" TimeStampedName="54111-ExternalResource-2017-52-29T14:52:20.079Z" />
+							</ExternalResources>
+							<DataSetMetadata>
+								<TotalLength>0</TotalLength>
+								<NumRecords>0</NumRecords>
+								<Collections xmlns="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd">
+									<CollectionMetadata CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" UniqueId="83a61432-fb33-405d-96d4-3101c133840c" MetaType="CollectionMetadata" TimeStampedName="54111-CollectionMetadata-2017-52-29T14:52:20.079Z" Status="Ready" InstrumentId="54111" InstrumentName="54111">
+										<InstCtrlVer>5.0.0.6235</InstCtrlVer>
+										<SigProcVer>5.0.0.6236</SigProcVer>
+										<RunDetails>
+											<TimeStampedName>r54111_20170829_145220</TimeStampedName>
+											<Name>6U00IG</Name>
+											<CreatedBy>admin</CreatedBy>
+											<WhenCreated>2017-08-29T19:55:11.464Z</WhenCreated>
+											<StartedBy>unknown</StartedBy>
+											<WhenStarted>0001-01-01T00:00:00</WhenStarted>
+										</RunDetails>
+										<WellSample Name="X.couchianus_4808Lu_9pM" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+											<WellName>A01</WellName>
+											<Concentration>0</Concentration>
+											<InsertSize>20000</InsertSize>
+											<SampleReuseEnabled>false</SampleReuseEnabled>
+											<StageHotstartEnabled>false</StageHotstartEnabled>
+											<SizeSelectionEnabled>false</SizeSelectionEnabled>
+											<UseCount>0</UseCount>
+										</WellSample>
+										<Automation Name="Workflow_Magbead.py">
+											<AutomationParameters xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+												<AutomationParameter Name="MovieLength" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="600" />
+												<AutomationParameter Name="ReuseSample" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="False" />
+												<AutomationParameter Name="ExtensionTime" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="0" />
+												<AutomationParameter Name="ExtendFirst" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="GentleWash" ValueDataType="Boolean" SimpleValue="True" />
+												<AutomationParameter Name="CellNFCIndex" ValueDataType="Int32" SimpleValue="1" />
+												<AutomationParameter Name="CollectionNumber" ValueDataType="Int32" SimpleValue="0" />
+												<AutomationParameter Name="UseStageHotStart" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="InsertSize" ValueDataType="Int32" SimpleValue="20000" />
+												<AutomationParameter Name="HasN2Switch" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="SNRCut" ValueDataType="Double" SimpleValue="3.75" />
+											</AutomationParameters>
+										</Automation>
+										<CollectionNumber>0</CollectionNumber>
+										<CellIndex>0</CellIndex>
+										<CellPac Name="SMRT®Cell 1M (4/Pack)" Description="The Sequel SMRT Cell 1M (4/Pack) are nanofabricated consumables each patterned with 1,000,000 wells called zero-mode waveguides (ZMWs). They are packaged together in a streamlined 4 SMRT Cell format (4/tray). One SMRT Cell is utilized in each sequencing reaction, and experiments can be run in single or in batch mode, giving your projects a greater level of flexibility." Version="2.0" PartNumber="101-008-000" LotNumber="320801" Barcode="320801101008000083017" ExpirationDate="2017-08-30" />
+										<TemplatePrepKit Name="SMRTbell™ Template Prep Kit" Description="The SMRTbell™ Template Prep Kit contains reagent supplies to perform SMRTbell library preparations of primer-annealed SMRTbell libraries for insert sizes ranging from 500 bp to over 20 kb." Tags="Template Prep Kit, TPK" Version="1.0" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" MinInsertSize="500" MaxInsertSize="20000">
+											<LeftAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</LeftAdaptorSequence>
+											<LeftPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</LeftPrimerSequence>
+											<RightAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</RightAdaptorSequence>
+											<RightPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</RightPrimerSequence>
+										</TemplatePrepKit>
+										<BindingKit Name="Sequel™ Binding Kit 2.0" Description="The Sequel Binding Kit 2.0 contains reagent supplies to bind prepared DNA template libraries to the Sequel Polymerase 1.0 in preparation for sequencing on the Sequel System. The result is a DNA polymerase/template complex. Sequel Binding Kit 1.0 should be used only with Sequel Sequencing Kit 1.0. Reagent quantities support 24 binding reactions." Tags="Binding Kit, BDK" Version="1.0" PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" />
+										<SequencingKitPlate Name="Sequel™ Sequencing Plate 2.0" Description="The DNA Sequencing Kit contains a sequencing reagent plate with chemistry for single molecule real-time sequencing on the PacBio RS. Reagent quantities support 8 sequencing reactions to be used in conjunction with SMRT® Cell 4Pac(s).  (8 Cells max/Each Row supplies reagents for 1 Sequel SMRT Cell)" Tags="Sequencing Kit, SQK" Version="2.0" PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28">
+											<ReagentTubes Name="Sequel™ OS Enzyme" PartNumber="100-619-700" LotNumber="010025" Barcode="010025100619700081619" ExpirationDate="2019-08-16" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
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+											<ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</ConfigFileName>
+											<SequencingCondition>DefaultPrimarySequencingCondition</SequencingCondition>
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+												<ResultsFolder>r54111_20170829_145220/1_A01/</ResultsFolder>
+												<CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170829_145220/1_A01/</CollectionPathUri>
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+													<CollectionFileCopy>Fasta</CollectionFileCopy>
+													<CollectionFileCopy>Bam</CollectionFileCopy>
+												</CopyFiles>
+												<Readout>Bases_Without_QVs</Readout>
+												<MetricsVerbosity>Minimal</MetricsVerbosity>
+												<TransferResource>
+													<Id>wustl_srs</Id>
+													<TransferScheme>SRS</TransferScheme>
+													<Name>WUSTL SRS</Name>
+													<Description>Transfer Scheme for WUSTL SRS</Description>
+													<DestPath>/gscmnt/gc13036/production/smrtlink_data_root</DestPath>
+												</TransferResource>
+											</OutputOptions>
+										</Primary>
+										<Secondary>
+											<AutomationName>DefaultSecondaryAutomationName</AutomationName>
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+												<AutomationParameter Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" />
+											</AutomationParameters>
+											<CellCountInJob>0</CellCountInJob>
+										</Secondary>
+										<UserDefinedFields>
+											<DataEntities Name=" LIMS_IMPORT " ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" />
+										</UserDefinedFields>
+										<ComponentVersions>
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+											<VersionInfo Name="ppa" Version="5.0.0.6236" />
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+											<VersionInfo Name="smrtinub" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtimisc" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtview" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink-analysisservices-gui" Version="5.0.0.6752" />
+										</ComponentVersions>
+									</CollectionMetadata>
+								</Collections>
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+						</SubreadSet>
+						<SubreadSet Name="X.couchianus_4808Lu_18pM-Cell2" CreatedAt="2017-08-29T19:55:11.464Z" UniqueId="2e23ac02-4eff-4da8-9e2a-b6d87951934e" MetaType="SubreadSetCollection" TimeStampedName="54111-SubreadSetCollection-2017-52-29T14:52:20.079Z" xmlns="http://pacificbiosciences.com/PacBioDatasets.xsd">
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+							</ExternalResources>
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+										<SigProcVer>5.0.0.6236</SigProcVer>
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+											<TimeStampedName>r54111_20170829_145220</TimeStampedName>
+											<Name>6U00IG</Name>
+											<CreatedBy>admin</CreatedBy>
+											<WhenCreated>2017-08-29T19:55:11.464Z</WhenCreated>
+											<StartedBy>unknown</StartedBy>
+											<WhenStarted>0001-01-01T00:00:00</WhenStarted>
+										</RunDetails>
+										<WellSample Name="X.couchianus_4808Lu_18pM" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00">
+											<WellName>B01</WellName>
+											<Concentration>0</Concentration>
+											<InsertSize>20000</InsertSize>
+											<SampleReuseEnabled>false</SampleReuseEnabled>
+											<StageHotstartEnabled>false</StageHotstartEnabled>
+											<SizeSelectionEnabled>false</SizeSelectionEnabled>
+											<UseCount>0</UseCount>
+										</WellSample>
+										<Automation Name="Workflow_Magbead.py">
+											<AutomationParameters xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">
+												<AutomationParameter Name="MovieLength" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="600" />
+												<AutomationParameter Name="ReuseSample" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="False" />
+												<AutomationParameter Name="ExtensionTime" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Double" SimpleValue="0" />
+												<AutomationParameter Name="ExtendFirst" CreatedAt="2017-08-29T19:55:11.464Z" ModifiedAt="0001-01-01T00:00:00" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="GentleWash" ValueDataType="Boolean" SimpleValue="True" />
+												<AutomationParameter Name="CellNFCIndex" ValueDataType="Int32" SimpleValue="1" />
+												<AutomationParameter Name="CollectionNumber" ValueDataType="Int32" SimpleValue="1" />
+												<AutomationParameter Name="UseStageHotStart" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="InsertSize" ValueDataType="Int32" SimpleValue="20000" />
+												<AutomationParameter Name="HasN2Switch" ValueDataType="Boolean" SimpleValue="False" />
+												<AutomationParameter Name="SNRCut" ValueDataType="Double" SimpleValue="3.75" />
+											</AutomationParameters>
+										</Automation>
+										<CollectionNumber>1</CollectionNumber>
+										<CellIndex>1</CellIndex>
+										<CellPac Name="SMRT®Cell 1M (4/Pack)" Description="The Sequel SMRT Cell 1M (4/Pack) are nanofabricated consumables each patterned with 1,000,000 wells called zero-mode waveguides (ZMWs). They are packaged together in a streamlined 4 SMRT Cell format (4/tray). One SMRT Cell is utilized in each sequencing reaction, and experiments can be run in single or in batch mode, giving your projects a greater level of flexibility." Version="2.0" PartNumber="101-008-000" LotNumber="320801" Barcode="BA050145" ExpirationDate="2017-08-30" />
+										<TemplatePrepKit Name="SMRTbell™ Template Prep Kit" Description="The SMRTbell™ Template Prep Kit contains reagent supplies to perform SMRTbell library preparations of primer-annealed SMRTbell libraries for insert sizes ranging from 500 bp to over 20 kb." Tags="Template Prep Kit, TPK" Version="1.0" PartNumber="100-259-100" LotNumber="008939" Barcode="008939100259100100717" ExpirationDate="2017-10-07" MinInsertSize="500" MaxInsertSize="20000">
+											<LeftAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</LeftAdaptorSequence>
+											<LeftPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</LeftPrimerSequence>
+											<RightAdaptorSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT</RightAdaptorSequence>
+											<RightPrimerSequence xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd">aacggaggaggagga</RightPrimerSequence>
+										</TemplatePrepKit>
+										<BindingKit Name="Sequel™ Binding Kit 2.0" Description="The Sequel Binding Kit 2.0 contains reagent supplies to bind prepared DNA template libraries to the Sequel Polymerase 1.0 in preparation for sequencing on the Sequel System. The result is a DNA polymerase/template complex. Sequel Binding Kit 1.0 should be used only with Sequel Sequencing Kit 1.0. Reagent quantities support 24 binding reactions." Tags="Binding Kit, BDK" Version="1.0" PartNumber="100-862-200" LotNumber="161221" Barcode="161221100862200111017" ExpirationDate="2017-11-10" />
+										<SequencingKitPlate Name="Sequel™ Sequencing Plate 2.0" Description="The DNA Sequencing Kit contains a sequencing reagent plate with chemistry for single molecule real-time sequencing on the PacBio RS. Reagent quantities support 8 sequencing reactions to be used in conjunction with SMRT® Cell 4Pac(s).  (8 Cells max/Each Row supplies reagents for 1 Sequel SMRT Cell)" Tags="Sequencing Kit, SQK" Version="2.0" PartNumber="100-861-800" LotNumber="010353" Barcode="010353100861800102817" ExpirationDate="2017-10-28">
+											<ReagentTubes Name="Sequel™ OS Enzyme" PartNumber="100-619-700" LotNumber="010025" Barcode="010025100619700081619" ExpirationDate="2019-08-16" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+											<ReagentTubes Name="Sequel™ SMRT®Cell Oil" PartNumber="100-619-600" LotNumber="008604" Barcode="008604100619600113020" ExpirationDate="2020-11-30" xmlns="http://pacificbiosciences.com/PacBioReagentKit.xsd" />
+										</SequencingKitPlate>
+										<Primary>
+											<AutomationName>SequelAlpha</AutomationName>
+											<ConfigFileName>SqlPoC_SubCrf_2C2A-t2.xml</ConfigFileName>
+											<SequencingCondition>DefaultPrimarySequencingCondition</SequencingCondition>
+											<OutputOptions>
+												<ResultsFolder>r54111_20170829_145220/2_B01/</ResultsFolder>
+												<CollectionPathUri>/gscmnt/gc13036/production/smrtlink_data_root/r54111_20170829_145220/2_B01/</CollectionPathUri>
+												<CopyFiles>
+													<CollectionFileCopy>Fasta</CollectionFileCopy>
+													<CollectionFileCopy>Bam</CollectionFileCopy>
+												</CopyFiles>
+												<Readout>Bases_Without_QVs</Readout>
+												<MetricsVerbosity>Minimal</MetricsVerbosity>
+												<TransferResource>
+													<Id>wustl_srs</Id>
+													<TransferScheme>SRS</TransferScheme>
+													<Name>WUSTL SRS</Name>
+													<Description>Transfer Scheme for WUSTL SRS</Description>
+													<DestPath>/gscmnt/gc13036/production/smrtlink_data_root</DestPath>
+												</TransferResource>
+											</OutputOptions>
+										</Primary>
+										<Secondary>
+											<AutomationName>DefaultSecondaryAutomationName</AutomationName>
+											<AutomationParameters>
+												<AutomationParameter Name="Reference" CreatedAt="0001-01-01T00:00:00" ModifiedAt="0001-01-01T00:00:00" ValueDataType="String" SimpleValue="DefaultSecondaryAnalysisReferenceName" />
+											</AutomationParameters>
+											<CellCountInJob>0</CellCountInJob>
+										</Secondary>
+										<UserDefinedFields>
+											<DataEntities Name=" LIMS_IMPORT " ValueDataType="String" SimpleValue="DefaultUserDefinedFieldLIMS" xmlns="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" />
+										</UserDefinedFields>
+										<ComponentVersions>
+											<VersionInfo Name="ics" Version="5.0.0.6235" />
+											<VersionInfo Name="iui" Version="5.0.0.6235" />
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+											<VersionInfo Name="paws" Version="5.0.0.6236" />
+											<VersionInfo Name="ppa" Version="5.0.0.6236" />
+											<VersionInfo Name="realtime" Version="5.0.0.6236" />
+											<VersionInfo Name="transfer" Version="5.0.0.6236" />
+											<VersionInfo Name="smrttools" Version="5.0.0.6784" />
+											<VersionInfo Name="smrtinub" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtimisc" Version="5.0.0.6792" />
+											<VersionInfo Name="smrtview" Version="5.0.0.6656" />
+											<VersionInfo Name="smrtlink-analysisservices-gui" Version="5.0.0.6752" />
+										</ComponentVersions>
+									</CollectionMetadata>
+								</Collections>
+							</DataSetMetadata>
+						</SubreadSet>
+					</SubreadSets>
+				</Outputs>
+			</Run>
+		</Runs>
+	</ExperimentContainer>
+</PacBioDataModel>
diff --git a/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.adapters.fasta b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.adapters.fasta
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.adapters.fasta
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.baz2bam_1.log b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.baz2bam_1.log
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.baz2bam_1.log
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.scraps.bam b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.scraps.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.scraps.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.scraps.bam.pbi b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.scraps.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.scraps.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.subreads.bam b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.subreads.bam
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.subreads.bam
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.subreads.bam.pbi b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.subreads.bam.pbi
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.subreads.bam.pbi
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.transferdone b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.transferdone
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/2_B01/m54111_170830_013202.transferdone
@@ -0,0 +1 @@
+1
diff --git a/t/data/Pacbio-Run/6U00IG/2_B01/tmp-file-175c3b94-c2ea-49e5-b4e2-b5066cb462b3.txt b/t/data/Pacbio-Run/6U00IG/2_B01/tmp-file-175c3b94-c2ea-49e5-b4e2-b5066cb462b3.txt
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/t/data/Pacbio-Run/6U00IG/2_B01/tmp-file-175c3b94-c2ea-49e5-b4e2-b5066cb462b3.txt
@@ -0,0 +1 @@
+1