diff --git a/Changes b/Changes index abb14df9..86e7a07c 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,16 @@ LIST OF CHANGES +release 39.11 + - auto QC loader query costruction: do not use invalid option + - wh loader: skip loading results for multi-component entities + - to retrieve lane-level results for multi-component entities, + ask for lanes and plexes separately + - stop loading Illumina qc data that came from chached_query table + of the npg_qc database (pf_cluster_count, raw_cluster_count, pf_bases) + - load q30 and q40 yields from qX_yield autoqc check results + - load bam_flagstats target metrics into iseq_product_metrics table + - a script to launch warehouse loader script for certain runs + release 39.10 - two gbs metrics to be added to the iseq_product_metrics table diff --git a/MANIFEST b/MANIFEST index 4639ca2a..ac2e9f4e 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1,10 +1,9 @@ -Build.PL -Changes -MANIFEST -README bin/npg_mlwarehouse_fkrepair bin/npg_run_statuses2mlwarehouse bin/npg_runs2mlwarehouse +bin/warehouse_loader_launcher +Build.PL +Changes lib/npg_tracking/daemon/fkrepair.pm lib/npg_warehouse/fk_repair.pm lib/npg_warehouse/loader/autoqc.pm @@ -12,12 +11,19 @@ lib/npg_warehouse/loader/base.pm lib/npg_warehouse/loader/fqc.pm lib/npg_warehouse/loader/npg.pm lib/npg_warehouse/loader/qc.pm -lib/npg_warehouse/loader/run_status.pm lib/npg_warehouse/loader/run.pm -lib/st/api/lims/ml_warehouse/driver.pm +lib/npg_warehouse/loader/run_status.pm lib/st/api/lims/ml_warehouse.pm -lib/st/api/lims/ml_warehouse_fc_cache.pm +lib/st/api/lims/ml_warehouse/driver.pm lib/st/api/lims/ml_warehouse_auto.pm +lib/st/api/lims/ml_warehouse_fc_cache.pm +MANIFEST This list of files +README +t/00-critic.t +t/00-distribution.t +t/00-pod.t +t/00-podcoverage.t +t/00-scripts_compile.t t/10-npg_warehouse-fkrepair.t t/10-npg_warehouse-loader-autoqc.t t/10-npg_warehouse-loader-fqc.t @@ -28,13 +34,6 @@ t/10-npg_warehouse-loader-run_status.t t/10-st-api-lims-ml_warehouse.t t/20-npg_warehouse-loader-run.t t/30-npg_tracking-daemon-fkrepair.t -t/00-critic.t -t/00-distribution.t -t/00-podcoverage.t -t/00-pod.t -t/00-scripts_compile.t -t/perlcriticrc -t/util.pm t/data/fixtures/npg/000-InstrumentStatusDict.yml t/data/fixtures/npg/000-RunStatusDict.yml t/data/fixtures/npg/000-Tag.yml @@ -45,17 +44,15 @@ t/data/fixtures/npg/300-Run.yml t/data/fixtures/npg/400-RunLane.yml t/data/fixtures/npg/400-RunStatus.yml t/data/fixtures/npg/400-TagRun.yml -t/data/fixtures/npgqc/CacheQuery.yml -t/data/fixtures/npgqc/ClusterDensity.yml -t/data/fixtures/npgqc/Fastqcheck.yml -t/data/fixtures/npgqc/MqcLibraryOutcomeDict.yml -t/data/fixtures/npgqc/MqcOutcomeDict.yml t/data/fixtures/npgqc/100-SeqComponent.yml t/data/fixtures/npgqc/100-SeqComposition.yml t/data/fixtures/npgqc/200-SeqComponentComposition.yml t/data/fixtures/npgqc/300-InsertSize.yml t/data/fixtures/npgqc/300-QXYield.yml t/data/fixtures/npgqc/300-TagMetrics.yml +t/data/fixtures/npgqc/ClusterDensity.yml +t/data/fixtures/npgqc/MqcLibraryOutcomeDict.yml +t/data/fixtures/npgqc/MqcOutcomeDict.yml t/data/fixtures/wh/000-Sample.yml t/data/fixtures/wh/000-Study.yml t/data/fixtures/wh/100-IseqFlowcell.yml @@ -65,6 +62,7 @@ t/data/fixtures_stlims_wh/000-Sample.yml t/data/fixtures_stlims_wh/000-Study.yml t/data/fixtures_stlims_wh/100-IseqFlowcell.yml t/data/fixtures_stlims_wh/100-StudyUser.yml +t/data/fixtures_stlims_wh/200-IseqProductMetric.yml t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.insert_size.json t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.qX_yield.json t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#1.insert_size.json @@ -78,7 +76,7 @@ t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-14394 t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.qX_yield.json t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.ref_match.json t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.sequence_error.json -t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_3_tag_decode_stats.json +t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_3.tag_decode_stats.json t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.adapter.json t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.contamination.json t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.gc_bias.json @@ -87,87 +85,104 @@ t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-14394 t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.qX_yield.json t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.ref_match.json t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.sequence_error.json -t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4_tag_decode_stats.json -t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_5_tag_decode_stats.json -t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_6_tag_decode_stats.json -t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_7_tag_decode_stats.json +t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.tag_decode_stats.json +t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_5.tag_decode_stats.json +t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_6.tag_decode_stats.json +t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_7.tag_decode_stats.json t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_8.insert_size.json -t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_8_tag_decode_stats.json +t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_8.tag_decode_stats.json 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+t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/qc/6642_2.tag_metrics.json +t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/qc/6642_2_human.split_stats.json +t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/qc/6642_3.bam_flagstats.json +t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/qc/6642_4.bam_flagstats.json +t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/qc/6642_4.verify_bam_id.json t/data/runfolders/180130_MS6_24975_A_MS6073474-300V2/Data/Intensities/BAM_basecalls_20180221-165427/no_cal/archive/lane1/qc/24975_1#1.rna_seqc.json -t/data/runfolders/180423_MS7_25710_A_MS6392545-300V2/Data/Intensities/BAM_basecalls_20180501-112028/no_cal/archive/qc/25710_1.tag_metrics.json +t/data/runfolders/180130_MS6_24975_A_MS6073474-300V2/Data/Intensities/BAM_basecalls_20180221-165427/no_cal/archive/qc/24975_1.tag_metrics.json t/data/runfolders/180423_MS7_25710_A_MS6392545-300V2/Data/Intensities/BAM_basecalls_20180501-112028/no_cal/archive/lane1/qc/25710_1#60.genotype_call.json +t/data/runfolders/180423_MS7_25710_A_MS6392545-300V2/Data/Intensities/BAM_basecalls_20180501-112028/no_cal/archive/qc/25710_1.tag_metrics.json +t/data/runfolders/181008_HX1_27116_B_HNYKNCCXY/Data/Intensities/BAM_basecalls_20181015-171739/no_cal/archive/lane1/qc/27116_1#1.bam_flagstats.json +t/data/runfolders/with_merges/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex1/qc/26291#1.insert_size.json +t/data/runfolders/with_merges/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/qc/26291_1.ref_match.json +t/data/runfolders/with_merges/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/qc/26291_1.tag_metrics.json +t/perlcriticrc +t/util.pm diff --git a/bin/warehouse_loader_launcher b/bin/warehouse_loader_launcher new file mode 100755 index 00000000..81ce6260 --- /dev/null +++ b/bin/warehouse_loader_launcher @@ -0,0 +1,186 @@ +#!/usr/bin/env perl + +use strict; +use warnings; +use FindBin qw($Bin); +use lib ( -d "$Bin/../lib/perl5" ? "$Bin/../lib/perl5" : "$Bin/../lib" ); +use DateTime; +use DateTime::Duration; +use Getopt::Long; +use Pod::Usage; +use Readonly; + +use npg_tracking::Schema; + +our $VERSION = '0'; + +Readonly::Scalar my $ML_WH_LOADER_COMMAND => 'npg_runs2mlwarehouse'; +Readonly::Scalar my $SS_WH_LOADER_COMMAND => 'warehouse_loader'; +Readonly::Array my @RUN_STATUSES => + ('secondary analysis in progress', 'qc review pending'); +Readonly::Scalar my $NUM_HOURS_LOOK_BACK => 3; + +my $look_back = $NUM_HOURS_LOOK_BACK; +my $run_statuses = \@RUN_STATUSES; +my $dry_run = 0; +my $old_wh = 0; +my $help; + +GetOptions ( + 'help' => \$help, + 'dry_run!' => \$dry_run, + 'sswh!' => \$old_wh, + 'num_hours=i' => \$look_back, + 'run_status=s@' => \$run_statuses, + ); + +if ($help) { pod2usage(0); } + +my $date = DateTime->now(); +my $script_name = $old_wh ? $SS_WH_LOADER_COMMAND : $ML_WH_LOADER_COMMAND; + +warn "$date == Running warehouse_loader_launcher, looking back " . + ($look_back ? "$look_back hours" : 'without limit') . qq[\n]; +warn 'Considering statuses: ' . join(q[, ], @{$run_statuses}) . qq[\n]; +warn "Will use $script_name warehouse loader\n"; +if ($dry_run) { + warn "DRY RUN\n"; +} + +my $query = { 'run_status_dict.description' => $run_statuses, + 'run_statuses.iscurrent' => 1 }; +if ($look_back) { + $date->subtract(DateTime::Duration->new(hours => $look_back)); + $date = sprintf q[%s], $date; + $query->{'run_statuses.date'} = {q[>], $date}; +} + +my @rows = npg_tracking::Schema->connect() + ->resultset('Run') + ->search( $query, + { join => { 'run_statuses' => 'run_status_dict' } } )->all(); + +my @id_runs = (); +foreach my $run (@rows) { + my @dirs = glob $run->folder_path_glob; + if (@dirs) { + my $id_run = $run->id_run; + warn "Run $id_run: found " . join(q[, ], @dirs) . qq[\n]; + push @id_runs, $id_run; + } +} + +if (@id_runs) { + # This script might be run as a cron job. If we srecify a full path + # to the wh loader, we do not need to set PATH for the job. + my $command = join q[ --id_run ], + "$Bin/$script_name --verbose", + sort {$a <=> $b} @id_runs; + warn qq[Will run command:\n"$command"\n]; + if (!$dry_run) { + system($command) == 0 or die 'Failed to execute comand'; + } +} else { + warn "No eligible runs\n"; +} + +0; + +__END__ + +=head1 NAME + +warehouse_loader_launcher + +=head1 SYNOPSIS + +Finds runs that recently reached "secondary analysis in progress" +or "qc review pending" status and calls ml warehouse loader (default) +or the sequencescape (old) warehouse loader for those runs whose +run folder location is visible on the host where this script is running. + +By default looks at statuses with dates within last 3 hours. + +=head1 USAGE + + warehouse_loader_launcher + warehouse_loader_launcher --dry_run + warehouse_loader_launcher --num_hours 24 + warehouse_loader_launcher --num_hours 0 # no time limit on status + warehouse_loader_launcher --run_status 'archival pending' --run_status 'archival in progress' + warehouse_loader_launcher --sswh # to launch the old warehouse loader + +=head1 DESCRIPTION + +=head1 REQUIRED ARGUMENTS + +None + +=head1 OPTIONS + + --help - brief help message + --dry_run - a boolean flag; if true, the script prints what will + happen and exists + --num_hours - number of hours to look back at status dates + --run_status - an array of run status descriptions + --sswh - a boolean flag, switching from ml to ss warehouse + +=head1 EXIT STATUS + +0 + +=head1 CONFIGURATION + +=head1 DIAGNOSTICS + +=head1 DEPENDENCIES + +=over + +=item strict + +=item warnings + +=item lib + +=item FindBin + +=item Getopt::Long + +=item Pod::Usage + +=item npg_tracking::Schema + +=item DateTime + +=item DateTime::Duration + +=item Readonly + +=back + +=head1 INCOMPATIBILITIES + +=head1 BUGS AND LIMITATIONS + +=head1 AUTHOR + +Marina Gourtovaia + +=head1 LICENSE AND COPYRIGHT + +Copyright (C) 2018 by Genome Research Limited + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . + diff --git a/lib/npg_warehouse/loader/autoqc.pm b/lib/npg_warehouse/loader/autoqc.pm index 508f20fb..deca317a 100644 --- a/lib/npg_warehouse/loader/autoqc.pm +++ b/lib/npg_warehouse/loader/autoqc.pm @@ -6,8 +6,9 @@ use MooseX::StrictConstructor; use Readonly; use npg_qc::autoqc::qc_store; -use npg_qc::autoqc::qc_store::options qw/$ALL/; +use npg_qc::autoqc::qc_store::options qw/$LANES $PLEXES/; use npg_qc::autoqc::qc_store::query; +use npg_qc::autoqc::results::collection; our $VERSION = '0'; @@ -46,6 +47,7 @@ Readonly::Hash our %AUTOQC_MAPPING => { 'rna_intronic_rate' => 'intronic_rate', 'rna_transcripts_detected' => 'transcripts_detected', 'rna_globin_percent_tpm' => 'globin_pct_tpm', + 'rna_mitochondrial_percent_tpm' => 'mt_pct_tpm', }, genotype_call => { 'gbs_call_rate' => 'genotype_call_rate', @@ -53,8 +55,7 @@ Readonly::Hash our %AUTOQC_MAPPING => { }, }; -Readonly::Scalar our $Q_TWENTY => 20; -Readonly::Scalar our $HUNDRED => 100; +Readonly::Scalar my $HUNDRED => 100; =head1 NAME @@ -86,20 +87,13 @@ has 'verbose' => ( isa => 'Bool', =head2 autoqc_store -A driver to retrieve autoqc objects. If DB storage is not available, -it will give no error, so no need to mock DB for this one in tests. -Just mock the staging area in your tests +A driver to retrieve autoqc objects, required attribute. =cut has 'autoqc_store' => ( isa => 'npg_qc::autoqc::qc_store', is => 'ro', - required => 0, - lazy_build => 1, + required => 1, ); -sub _build_autoqc_store { - my $self = shift; - return npg_qc::autoqc::qc_store->new(verbose => $self->verbose); -} =head2 plex_key @@ -180,22 +174,22 @@ sub _insert_size { sub _qX_yield { my ($self, $result, $autoqc) = @_; - if ($result->threshold_quality != $Q_TWENTY) { - croak 'Need Q20 quality, got ' . $result->threshold_quality; - } - my $data = {}; - if (defined $result->yield1) { - $data->{q20_yield_kb_forward_read} = $result->yield1; - } - if (defined $result->yield2) { - $data->{q20_yield_kb_reverse_read} = $result->yield2; + foreach my $read (qw/1 2/) { + foreach my $quality (qw/20 30 40/) { + my $autoqc_method_name = sprintf 'yield%s_q%s', $read, $quality; + my $wh_column_name = sprintf 'q%s_yield_kb_%s_read', + $quality, ($read eq '1') ? 'forward' : 'reverse'; + my $value = $result->$autoqc_method_name; + if (defined $value) { + $data->{$wh_column_name} = $result->$autoqc_method_name; + } + } } $self->_copy_fields($data, $autoqc, $result->position, $result->tag_index); return; } - sub _ref_match { my ($self, $result, $autoqc) = @_; @@ -335,6 +329,13 @@ sub _bam_flagstats { ? ($result->mate_mapped_defferent_chr_5 * $HUNDRED / $num_reads) : 0.00); $self->_copy_fields({chimeric_reads_percent => $chimeric_reads}, $autoqc, $position, $tag_index); + foreach my $method (qw(target_filter target_length target_mapped_reads + target_proper_pair_mapped_reads target_mapped_bases target_coverage_threshold + target_percent_gt_coverage_threshold)) { + if(my $r = $result->$method ) { + $self->_copy_fields({$method => $r}, $autoqc, $position, $tag_index); + } + } return; } @@ -400,10 +401,6 @@ sub _genotype { sub _autoqc_check { my ($self, $result, $autoqc) = @_; - my $num_components = $result->composition->num_components(); - if ($num_components > 1){ - croak q[Too many components for check ] . $result->class_name; - } my $component = $result->composition->get_component(0); my $position = $component->position; my $tag_index = $component->tag_index; @@ -428,29 +425,38 @@ sub _autoqc_check { =head2 retrieve -Retrieves autoqc results for a run +Retrieves autoqc results for a run. Skips results for multi-component entities. =cut sub retrieve { my ($self, $id_run, $npg_schema) = @_; - my $query = npg_qc::autoqc::qc_store::query->new( - id_run => $id_run, - option => $ALL, - npg_tracking_schema=> $npg_schema, - propagate_npg_tracking_schema => 1); - - my $autoqc = {}; - my $collection = $self->autoqc_store->load($query); + my $query1 = npg_qc::autoqc::qc_store::query->new( + id_run => $id_run, + option => $LANES, + npg_tracking_schema => $npg_schema + ); + my $query2 = npg_qc::autoqc::qc_store::query->new( + id_run => $id_run, + option => $PLEXES, + npg_tracking_schema => $npg_schema + ); + my $collection = npg_qc::autoqc::results::collection->join_collections( + $self->autoqc_store->load($query1), $self->autoqc_store->load($query2)); $collection->sort_collection(q[check_name]); # tag metrics object are after tag decode stats now + my $i = $collection->size - 1; + my $autoqc = {}; while ($i >= 0) { # iterating from tail to head my $result = $collection->get($i); + $i--; + if ($result->composition->num_components() > 1) { + next; + } my $method_name = exists $AUTOQC_MAPPING{$result->class_name} ? q[_autoqc_check] : q[_] . $result->class_name; if ($self->can($method_name)) { $self->$method_name($result, $autoqc); } - $i--; } return $autoqc; } diff --git a/lib/npg_warehouse/loader/qc.pm b/lib/npg_warehouse/loader/qc.pm index b068fdc0..071e2dde 100644 --- a/lib/npg_warehouse/loader/qc.pm +++ b/lib/npg_warehouse/loader/qc.pm @@ -1,19 +1,17 @@ package npg_warehouse::loader::qc; -use Carp; use Moose; +use namespace::autoclean; use MooseX::StrictConstructor; -use Math::Round qw / round /; +use Carp; use Readonly; use npg_qc::Schema; our $VERSION = '0'; -Readonly::Array my @CLUSTER_DENSITY_COLUMNS => qw/ raw_cluster_density - pf_cluster_density /; -Readonly::Hash my %QUALITIES => { 'thirty' => 'q30', 'forty' => 'q40',}; -Readonly::Scalar my $THOUSAND => 1000; +Readonly::Array my @CLUSTER_DENSITY_COLUMNS => qw/ raw_cluster_density + pf_cluster_density /; =head1 NAME @@ -23,24 +21,13 @@ npg_warehouse::loader::qc =head1 DESCRIPTION -A retriever for NPG QC data to be loaded to the warehouse table +A retriever for NPG QC data to be loaded to the warehouse. =head1 SUBROUTINES/METHODS -=head2 verbose - -Verbose flag - -=cut -has 'verbose' => ( isa => 'Bool', - is => 'ro', - required => 0, - default => 0, - ); - =head2 schema_qc -DBIx schema object for the NPGQC database +DBIx schema object for the NPG QC database =cut has 'schema_qc' => ( isa => 'npg_qc::Schema', @@ -49,38 +36,13 @@ has 'schema_qc' => ( isa => 'npg_qc::Schema', lazy_build => 1, ); sub _build_schema_qc { - my $self = shift; - my $schema = npg_qc::Schema->connect(); - if($self->verbose) { - carp q[Connected to the qc db, schema object ] . $schema; - } - return $schema; + return npg_qc::Schema->connect(); } -=head2 reverse_end_index - -reverse_end_index - -=cut -has 'reverse_end_index' => ( isa => 'Int', - is => 'ro', - required => 1, - ); - -=head2 plex_key - -Name of the key to use in data structures for plex data. - -=cut -has 'plex_key' => ( isa => 'Str', - is => 'ro', - required => 1, - ); - - =head2 retrieve_cluster_density -Returns a hash containing per lane cluster densities +Returns a hash containing per lane cluster density +values. =cut sub retrieve_cluster_density { @@ -105,120 +67,12 @@ sub retrieve_cluster_density { return $density; } - -=head2 retrieve_summary - -Returns a hash containing per lane/end NPG QC information - -=cut -sub retrieve_summary { - my ($self, $id_run, $end, $has_two_runfolders) = @_; - - if (!defined $id_run) { - croak 'Run id argument should be set'; - } - if (!defined $end) { - croak 'End argument should be set'; - } - if (!defined $has_two_runfolders) { - croak 'Two run folders flag argument should be set'; - } - - my $ends = [$end]; - my $lanes = {}; - if (!$has_two_runfolders) { - if ($end == $self->reverse_end_index) { - croak qq[Reverse end index AND run with one runfolder for run $id_run]; - } - push @{$ends}, $self->reverse_end_index; - } - - my $rs_all = $self->schema_qc->resultset('CacheQuery')->search( - { - id_run => $id_run, - end => $ends, - is_current => 1, - type => 'lane_summary', - }, - { - columns => [ qw/results/], - }, - ); - my $rs; - while ($rs = $rs_all->next) { - my $result = $rs->results; - if ($result) { - my $rows_ref; - my $semi_colon_count = $result =~ tr/;/;/; - ##no critic (ProhibitEscapedMetacharacters) - if ($semi_colon_count == 1 && $result =~ /[$]rows_ref[ ]=[ ]\[\{.*?\}\];\z/xms) { - eval $result; ## no critic (ProhibitStringyEval,RequireCheckingReturnValueOfEval) - } else { - croak 'Too many statements in returned code: ' . $result; - } - - foreach my $lane_hash (@{$rows_ref}) { - $lanes->{$lane_hash->{lane}}->{$lane_hash->{end}} = $lane_hash; - } - } - } - return $lanes; -} - -=head2 retrieve_yields - -Returns a hash containing per lane q30 base counts - -=cut -sub retrieve_yields { - my ($self, $id_run) = @_; - - if (!defined $id_run) { - croak 'Run id argument should be set'; - } - my $lanes = {}; - - my $rs_all = $self->schema_qc->resultset('Fastqcheck')->search( - { - id_run => $id_run, - split => 'none', - }, - { - columns => [ qw/section position tag_index thirty forty/ ], - }, - ); - while (my $r= $rs_all->next) { - my $read = $r->section; - if ($read =~ /forward|reverse/smx) { - foreach my $q (keys %QUALITIES) { - my $value = $r->$q; - if (defined $value) { - if ($value) { - $value = round($value/$THOUSAND); - } - my $column_name = join q[_], $QUALITIES{$q}, 'yield_kb', $read, 'read'; - my $tag_index = $r->tag_index; - my $position = $r->position; - if(!defined $tag_index) { - $lanes->{$position}->{$column_name} = $value; - } else { - $lanes->{$position}->{$self->plex_key}->{$tag_index}->{$column_name} = $value; - } - } - } - } - } - - return $lanes; -} - __PACKAGE__->meta->make_immutable; 1; __END__ - =head1 DIAGNOSTICS =head1 CONFIGURATION AND ENVIRONMENT @@ -235,7 +89,7 @@ __END__ =item MooseX::StrictConstructor -=item Math::Round qw/round/ +=item namespace::autoclean =item npg_qc::Schema @@ -247,11 +101,11 @@ __END__ =head1 AUTHOR -Andy Brown and Marina Gourtovaia +Marina Gourtovaia =head1 LICENSE AND COPYRIGHT -Copyright (C) 2014 Genome Research Limited +Copyright (C) 2018 Genome Research Limited This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by diff --git a/lib/npg_warehouse/loader/run.pm b/lib/npg_warehouse/loader/run.pm index d0e92a36..e09719da 100644 --- a/lib/npg_warehouse/loader/run.pm +++ b/lib/npg_warehouse/loader/run.pm @@ -17,8 +17,8 @@ use npg_warehouse::loader::npg; extends 'npg_warehouse::loader::base'; with qw/ - npg_tracking::glossary::run - npg_tracking::glossary::flowcell + npg_tracking::glossary::run + npg_tracking::glossary::flowcell /; with 'WTSI::DNAP::Warehouse::Schema::Query::IseqFlowcell'; @@ -171,13 +171,6 @@ sub _build__flowcell_table_fks_exist { return scalar keys %{$self->_flowcell_table_fks} ? 1 : 0; } -=head2 _autoqc_store - -A driver to retrieve autoqc objects. If DB storage is not available, -it will give no error, so no need to mock DB for this one in tests. -Just mock the staging area in your tests - -=cut has '_autoqc_store' => ( isa => 'npg_qc::autoqc::qc_store', is => 'ro', required => 0, @@ -190,11 +183,6 @@ sub _build__autoqc_store { qc_schema => $self->schema_qc); } -=head2 _run_lane_rs - -Result set object for run lanes that have to be loaded - -=cut has '_run_lane_rs' => ( isa => 'ArrayRef', is => 'ro', required => 0, @@ -280,10 +268,7 @@ has '_npgqc_data_retriever' => ( isa => 'npg_warehouse::loader::qc', ); sub _build__npgqc_data_retriever { my $self = shift; - return npg_warehouse::loader::qc->new(schema_qc => $self->schema_qc, - verbose => $self->verbose, - reverse_end_index => $REVERSE_END_INDEX, - plex_key => $PLEXES_KEY); + return npg_warehouse::loader::qc->new(schema_qc => $self->schema_qc); } has '_fqc_data_retriever' => ( isa => 'npg_warehouse::loader::fqc', @@ -298,27 +283,6 @@ sub _build__fqc_data_retriever { plex_key => $PLEXES_KEY); } -has '_run_end_summary' => ( isa => 'HashRef', - is => 'ro', - required => 0, - lazy_build => 1, -); -sub _build__run_end_summary { - my $self = shift; - return $self->_npgqc_data_retriever->retrieve_summary( - $self->id_run, $FORWARD_END_INDEX, $self->_run_lane_rs->[0]->run->is_paired); -} - -has '_qyields' => ( isa => 'HashRef', - is => 'ro', - required => 0, - lazy_build => 1, -); -sub _build__qyields { - my $self = shift; - return $self->_npgqc_data_retriever->retrieve_yields($self->id_run); -} - has '_cluster_density' => ( isa => 'HashRef', is => 'ro', required => 0, @@ -365,31 +329,17 @@ sub _build__data { $values->{$column} = $self->_cluster_density->{$position}->{$column}; } - if (exists $self->_run_end_summary->{$position}->{$FORWARD_END_INDEX}) { - $values->{'raw_cluster_count'} = - $self->_run_end_summary->{$position}->{$FORWARD_END_INDEX}->{'clusters_raw'}; - $values->{'pf_cluster_count'} = - $self->_run_end_summary->{$position}->{$FORWARD_END_INDEX}->{'clusters_pf'}; - $values->{'pf_bases'} = - $self->_run_end_summary->{$position}->{$FORWARD_END_INDEX}->{'lane_yield'}; - if (exists $self->_run_end_summary->{$position}->{$REVERSE_END_INDEX}) { - $values->{'pf_bases'} += - $self->_run_end_summary->{$position}->{$REVERSE_END_INDEX}->{'lane_yield'}; - } - } - my $lane_is_indexed = $self->_lane_is_indexed($position); my $product_values; my $plexes = {}; - foreach my $data_hash (($self->_qyields, $self->_autoqc_data)) { - if ($data_hash->{$position}) { - _copy_plex_values($plexes, $data_hash, $position); - foreach my $column (keys %{$data_hash->{$position}}) { - $values->{$column} = $data_hash->{$position}->{$column}; - if ( !$lane_is_indexed ) { - $product_values->{$column} = $data_hash->{$position}->{$column}; - } + my $data_hash = $self->_autoqc_data; + if ($data_hash->{$position}) { + _copy_plex_values($plexes, $data_hash, $position); + foreach my $column (keys %{$data_hash->{$position}}) { + $values->{$column} = $data_hash->{$position}->{$column}; + if ( !$lane_is_indexed ) { + $product_values->{$column} = $data_hash->{$position}->{$column}; } } } diff --git a/t/10-npg_warehouse-loader-autoqc.t b/t/10-npg_warehouse-loader-autoqc.t index 802bedf2..a3a02096 100644 --- a/t/10-npg_warehouse-loader-autoqc.t +++ b/t/10-npg_warehouse-loader-autoqc.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 126; +use Test::More tests => 137; use Test::Exception; use Moose::Meta::Class; @@ -13,14 +13,10 @@ my $store = npg_qc::autoqc::qc_store->new(use_db => 0); my $plex_key = q[plexes]; my $util = Moose::Meta::Class->create_anon_class( roles => [qw/npg_testing::db/])->new_object({}); -my $schema_npg; -eval { $schema_npg = $util->create_test_db(q[npg_tracking::Schema], q[t/data/fixtures/npg]); 1 } - or die 'failed to create npg test db - test prerequisite'; +my $schema_npg = $util->create_test_db(q[npg_tracking::Schema], q[t/data/fixtures/npg]); my $folder_glob = q[t/data/runfolders/]; my $user_id = 7; -local $ENV{TEST_DIR} = q[t]; - { throws_ok {npg_warehouse::loader::autoqc->new(autoqc_store => $store)} qr/Attribute \(plex_key\) is required/, @@ -40,7 +36,7 @@ local $ENV{TEST_DIR} = q[t]; { my $autoqc = npg_warehouse::loader::autoqc->new( - autoqc_store => npg_qc::autoqc::qc_store->new(use_db => 0,verbose => 0,), + autoqc_store => npg_qc::autoqc::qc_store->new(use_db => 0), plex_key => $plex_key,); throws_ok {$autoqc->retrieve()} qr/Attribute \(id_run\) does not pass the type constraint/, @@ -54,10 +50,7 @@ local $ENV{TEST_DIR} = q[t]; ); my $result = npg_qc::autoqc::results::qX_yield->new( path => q[dodo], id_run=>22, position=>1, threshold_quality => 30,); - throws_ok {$autoqc->_qX_yield($result, {})} - qr/Need Q20 quality, got 30/, 'error when quality is not 20'; - $result->threshold_quality(20); - lives_ok {$autoqc->_qX_yield($result, {})} 'lives with quality 20'; + lives_ok {$autoqc->_qX_yield($result, {})} 'lives with quality 30'; $result->yield1(200); my $h = {}; $autoqc->_qX_yield($result, $h); @@ -78,7 +71,7 @@ local $ENV{TEST_DIR} = q[t]; { my $id_run = 4799; - lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run, })->set_tag($user_id, 'staging')} + lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run})->set_tag($user_id, 'staging')} 'staging tag is set - test prerequisite'; lives_ok {$schema_npg->resultset('Run') ->update_or_create({folder_path_glob => $folder_glob, folder_name => '100330_HS21_4799', id_run => $id_run, })} @@ -114,7 +107,7 @@ local $ENV{TEST_DIR} = q[t]; { my $id_run = 4333; - lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run, })->set_tag($user_id, 'staging')} + lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run})->set_tag($user_id, 'staging')} 'staging tag is set - test prerequisite'; lives_ok {$schema_npg->resultset('Run') ->update_or_create({folder_path_glob => $folder_glob, folder_name => '100330_IL21_4333', id_run => $id_run, })} @@ -150,7 +143,7 @@ local $ENV{TEST_DIR} = q[t]; { my $id_run = 6624; - lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run, })->set_tag($user_id, 'staging')} + lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run})->set_tag($user_id, 'staging')} 'staging tag is set - test prerequisite'; lives_ok {$schema_npg->resultset('Run') ->update_or_create({folder_path_glob => $folder_glob, folder_name => '110731_HS17_06624_A_B00T5ACXX', id_run => $id_run, })} @@ -200,7 +193,7 @@ local $ENV{TEST_DIR} = q[t]; my $id_run = 6642; lives_ok {$schema_npg->resultset('Run')->update_or_create({folder_path_glob => $folder_glob, id_run => $id_run, })} 'forder glob reset lives - test prerequisite'; - lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run, })->set_tag($user_id, 'staging')} + lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run})->set_tag($user_id, 'staging')} 'staging tag is set - test prerequisite'; my $auto = npg_warehouse::loader::autoqc->new(autoqc_store => $store,plex_key => $plex_key)->retrieve($id_run, $schema_npg); @@ -242,6 +235,7 @@ local $ENV{TEST_DIR} = q[t]; cmp_ok(sprintf('%.10f',$auto->{1}->{$plex_key}->{1}->{rna_rrna_rate}), q(==), 0.020362793, 'rna - rrna rate'); cmp_ok(sprintf('%.10f',$auto->{1}->{$plex_key}->{1}->{rna_transcripts_detected}), q(==), 71321, 'rna - transcripts detected'); cmp_ok(sprintf('%.10f',$auto->{1}->{$plex_key}->{1}->{rna_globin_percent_tpm}), q(==), 2.71, 'rna - globin percent tpm'); + cmp_ok(sprintf('%.10f',$auto->{1}->{$plex_key}->{1}->{rna_mitochondrial_percent_tpm}), q(==), 6.56, 'rna - mitochondrial percent tpm'); ok(! exists $auto->{1}->{$plex_key}->{1}->{rna_rrna}, 'rna - rrna not present'); } @@ -249,7 +243,7 @@ local $ENV{TEST_DIR} = q[t]; my $id_run = 25710; lives_ok {$schema_npg->resultset('Run')->update_or_create({folder_path_glob => $folder_glob, id_run => $id_run, })} 'folder glob reset lives - test prerequisite'; - lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run, })->set_tag($user_id, 'staging')} + lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run})->set_tag($user_id, 'staging')} 'staging tag is set - test prerequisite'; my $auto; lives_ok {$auto = npg_warehouse::loader::autoqc->new(autoqc_store => $store, plex_key => $plex_key )->retrieve($id_run, $schema_npg)} @@ -259,4 +253,92 @@ local $ENV{TEST_DIR} = q[t]; cmp_ok(sprintf('%.10f',$auto->{1}->{$plex_key}->{60}->{gbs_pass_rate}), q(==), 0.99, 'gbs - pass rate'); } +{ + my $id_run = 27116; + lives_ok {$schema_npg->resultset('Run')->update_or_create({folder_path_glob => $folder_glob, id_run => $id_run, })} + 'folder glob reset lives - test prerequisite'; + lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run})->set_tag($user_id, 'staging')} + 'staging tag is set - test prerequisite'; + my $auto; + lives_ok {$auto = npg_warehouse::loader::autoqc->new(autoqc_store => $store, plex_key => $plex_key )->retrieve($id_run, $schema_npg)} + 'data for run 27116 retrieved'; + + is ($auto->{1}->{$plex_key}->{1}->{target_filter}, 'F0xF04_target', 'target - target_filter'); + cmp_ok(sprintf('%.2f',$auto->{1}->{$plex_key}->{1}->{target_coverage_threshold}), q(==), 15, 'target - target_coverage_threshold'); + cmp_ok(sprintf('%.2f',$auto->{1}->{$plex_key}->{1}->{target_length}), q(==), '2945869055', 'target - target_length'); + cmp_ok(sprintf('%.2f',$auto->{1}->{$plex_key}->{1}->{target_mapped_bases}), q(==), 8700474137, 'target - target_mapped_bases'); + cmp_ok(sprintf('%.2f',$auto->{1}->{$plex_key}->{1}->{target_mapped_reads}), q(==), 58704583, 'target - target_mapped_reads'); + cmp_ok(sprintf('%.2f',$auto->{1}->{$plex_key}->{1}->{target_percent_gt_coverage_threshold}), q(==), 0.15, 'target - target_percent_gt_coverage_threshold'); + cmp_ok(sprintf('%.2f',$auto->{1}->{$plex_key}->{1}->{target_proper_pair_mapped_reads}), q(==), 57355728, 'target - target_proper_pair_mapped_reads'); +} + +{ + $schema_npg->resultset('Run')->update_or_create({ + folder_path_glob => $folder_glob, + id_run => 26291, + folder_name => 'with_merges', + id_instrument_format => 10, + team => 'A'}); + $schema_npg->resultset('Run')->find({id_run => 26291})->set_tag($user_id, 'staging'); + my $auto = npg_warehouse::loader::autoqc->new(autoqc_store => $store, plex_key => $plex_key) + ->retrieve(26291, $schema_npg); + + my $expected = { + '1' => { + 'tag_hops_power' => 1, + 'ref_match2_name' => 'Pan troglodytes CHIMP2.1.4', + 'tags_decode_cv' => '15.14', + 'tag_hops_percent' => '1.431923', + 'ref_match1_percent' => '95.5', + 'ref_match2_percent' => '89.1', + 'ref_match1_name' => 'Homo sapiens 1000Genomes', + 'tags_decode_percent' => '93.77', + 'plexes' => { + '7' => {'tag_decode_percent' => '6.90', + 'tag_sequence' => 'ACACATTC-CTGTCGGT', + 'tag_decode_count' => '68726651'}, + '9' => {'tag_decode_count' => '110359514', + 'tag_decode_percent' => '11.10', + 'tag_sequence' => 'ACAGCCTT-CACACGCG'}, + '12' => {'tag_decode_count' => '66558340', + 'tag_sequence' => 'TTGCCATC-ACGCGTCA', + 'tag_decode_percent' => '6.70'}, + '5' => {'tag_decode_percent' => '8', + 'tag_sequence' => 'ACACACCT-GGCAACTG', + 'tag_decode_count' => '79299831' }, + '11' => {'tag_decode_percent' => '7.80', + 'tag_sequence' => 'ACAGGCAG-AGCAAGTT', + 'tag_decode_count' => '77788454'}, + '888' => {'tag_sequence' => 'ACAACGCA-TCTTTCCC', + 'tag_decode_percent' => '0', + 'tag_decode_count' => '9'}, + '3' => {'tag_decode_percent' => '8.70', + 'tag_sequence' => 'ACACTAAC-ACAGTGAA', + 'tag_decode_count' => '86434858'}, + '6' => {'tag_decode_count' => '63169296', + 'tag_sequence' => 'GGTGTCCG-CAGCGTCT', + 'tag_decode_percent' => '6.30'}, + '0' => {'tag_decode_count' => '62102003', + 'tag_decode_percent' => '6.20'}, + '10' => {'tag_sequence' => 'TTGCAGTA-AGCCAACA', + 'tag_decode_percent' => '7.10', + 'tag_decode_count' => '70535174'}, + '8' => {'tag_sequence' => 'TTGCTTAA-TCGGCGTT', + 'tag_decode_percent' => '7.30', + 'tag_decode_count' => '72387564'}, + '1' => {'tag_decode_percent' => '8.10', + 'tag_sequence' => 'AACACATA-AATTCTAA', + 'tag_decode_count' => '81073574'}, + '4' => {'tag_decode_count' => '81708200', + 'tag_decode_percent' => '8.20', + 'tag_sequence' => 'TTGTGTTC-AGATGTGA'}, + '2' => {'tag_sequence' => 'TGGTGTCT-TTCATCTG', + 'tag_decode_percent' => '7.70', + 'tag_decode_count' => '76726441'} + },} + }; + + is_deeply ($auto, $expected, 'lane-level results in, multi-component plex skipped'); +} + 1; diff --git a/t/10-npg_warehouse-loader-qc.t b/t/10-npg_warehouse-loader-qc.t index c0467156..6d1fa15f 100644 --- a/t/10-npg_warehouse-loader-qc.t +++ b/t/10-npg_warehouse-loader-qc.t @@ -1,200 +1,41 @@ use strict; use warnings; -use Test::More tests => 20; +use Test::More tests => 5; use Test::Exception; -use Test::Deep; use Moose::Meta::Class; use npg_testing::db; use_ok('npg_warehouse::loader::qc'); -################################################################ -# Test cases description -################################################################ -#batch_id # id_run # paired_id_run # paired_read # wh # npg # qc -################################################################ -#2044 # 1272 # 1246 # 1 # 1 # 1 # 1 -#4354 # 3500 # 3529 # 1 # 1 # 1 # 1 -#4178 # 3323 # 3351 # 1 # 1 # 1 # 1 -#4445 # 3622 # # 0 # 1 # 1 # 1 -#4915 # 3965 # # 1 # 1 # 1 # 1 -#4965 # 4025 # # 1 # 1 # 1 # 1 -#4380 # 3519 # # # # 1 # -#5169 # 4138 # # # # 1 # this run is cancelled without qc complete status -#5498 # 4333 # # 1 # # 1 # 1 tag decoding stats added - # 4779 # -################################################################ - my $util = Moose::Meta::Class->create_anon_class( roles => [qw/npg_testing::db/])->new_object({}); -my $schema_qc; -my $index = 2; - -lives_ok{ $schema_qc = $util->create_test_db(q[npg_qc::Schema], - q[t/data/fixtures/npgqc]) } 'qc test db created'; +my $schema_qc = $util->create_test_db( + q[npg_qc::Schema], q[t/data/fixtures/npgqc]); { - throws_ok {npg_warehouse::loader::qc->new(schema_qc => $schema_qc, plex_key => 'plex') } - qr/Attribute \(reverse_end_index\) is required /, - 'error if reverse index is not set'; - my $q; lives_ok { - $q = npg_warehouse::loader::qc->new( - schema_qc => $schema_qc, - reverse_end_index => $index, - plex_key => 'plex' - ) + $q = npg_warehouse::loader::qc->new(schema_qc => $schema_qc) } 'object instantiated by passing schema objects to the constructor'; isa_ok ($q, 'npg_warehouse::loader::qc'); - is ($q->reverse_end_index, $index, 'reverse index set correctly'); - is ($q->verbose, 0, 'verbose mode is off by default'); -} - -{ - my $q = npg_warehouse::loader::qc->new( schema_qc => $schema_qc, - reverse_end_index => $index, - plex_key => 'plex'); - throws_ok {$q->retrieve_cluster_density()} qr/Run id argument should be set/, 'error if id_run arg not set'; - throws_ok {$q->retrieve_summary()} qr/Run id argument should be set/, 'error if id_run arg not set'; - throws_ok {$q->retrieve_summary(22)} qr/End argument should be set/, 'error if end arg not set'; - throws_ok {$q->retrieve_summary(22,1)} qr/Two run folders flag argument should be set/, 'error if two run folders flag arg not set'; - throws_ok {$q->retrieve_yields()} qr/Run id argument should be set/, 'error if id_run arg not set'; -} - -{ - my $q = npg_warehouse::loader::qc->new( schema_qc => $schema_qc, - reverse_end_index => $index, - plex_key => 'plex'); - throws_ok {$q->retrieve_summary( 1, 2, 0)} qr/Reverse end index AND run with one runfolder/, 'error in get_run_qc_summary on a combination of a second read and one runfolder args'; - - cmp_deeply($q->retrieve_summary( 22, 1, 1), {}, 'qc summary is an empty hash if run is not in the db'); - - my $rows_ref = [{'clusters_pf' => '81851','lane_yield' => '363418','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '2.40','clusters_pf_sd' => '4659','perc_pf_clusters' => '83.41','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '3','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.46','clusters_raw_sd' => '4765','lane' => '1','first_cycle_int' => '69','clusters_raw' => '98126','end' => '1','perc_int_20_cycles' => '75.60','align_score_sd' => undef},{'clusters_pf' => '95506','lane_yield' => '424046','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.43','clusters_pf_sd' => '2161','perc_pf_clusters' => '84.83','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '1','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '0.97','clusters_raw_sd' => '2905','lane' => '2','first_cycle_int' => '45','clusters_raw' => '112604','end' => '1','perc_int_20_cycles' => '76.67','align_score_sd' => undef},{'clusters_pf' => '133450','lane_yield' => '592516','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.64','clusters_pf_sd' => '2551','perc_pf_clusters' => '78.75','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '1','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.69','clusters_raw_sd' => '3975','lane' => '3','first_cycle_int' => '49','clusters_raw' => '169519','end' => '1','perc_int_20_cycles' => '74.23','align_score_sd' => undef},{'clusters_pf' => '132313','lane_yield' => '587469','perc_pf_align_sd' => '0.04','perc_pf_clusters_sd' => '1.62','clusters_pf_sd' => '3790','perc_pf_clusters' => '83.17','align_score' => '178.07','perc_pf_align' => '99.13','perc_error_rate' => '0.22','first_cycle_int_sd' => '2','perc_error_rate_sd' => '0.01','perc_int_20_cycles_sd' => '1.58','clusters_raw_sd' => '7318','lane' => '4','first_cycle_int' => '74','clusters_raw' => '159216','end' => '1','perc_int_20_cycles' => '79.46','align_score_sd' => '0.12'},{'clusters_pf' => '125077','lane_yield' => '555341','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.93','clusters_pf_sd' => '1939','perc_pf_clusters' => '82.55','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '1','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.03','clusters_raw_sd' => '3519','lane' => '5','first_cycle_int' => '46','clusters_raw' => '151558','end' => '1','perc_int_20_cycles' => '76.82','align_score_sd' => undef},{'clusters_pf' => '131445','lane_yield' => '583616','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.65','clusters_pf_sd' => '4088','perc_pf_clusters' => '60.65','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '1','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.15','clusters_raw_sd' => '1848','lane' => '6','first_cycle_int' => '56','clusters_raw' => '216692','end' => '1','perc_int_20_cycles' => '65.04','align_score_sd' => undef},{'clusters_pf' => '102878','lane_yield' => '456778','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.96','clusters_pf_sd' => '5659','perc_pf_clusters' => '50.11','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '2','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.46','clusters_raw_sd' => '3720','lane' => '7','first_cycle_int' => '58','clusters_raw' => '205196','end' => '1','perc_int_20_cycles' => '64.96','align_score_sd' => undef},{'clusters_pf' => '49202','lane_yield' => '218459','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.58','clusters_pf_sd' => '4114','perc_pf_clusters' => '89.22','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '8','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.97','clusters_raw_sd' => '4518','lane' => '8','first_cycle_int' => '58','clusters_raw' => '55147','end' => '1','perc_int_20_cycles' => '73.03','align_score_sd' => undef}]; - my $h = $q->retrieve_summary( 3622, 1, 1); - my @a; - foreach my $key (sort keys %{$h}) { - push @a, $h->{$key}->{1}; - } - cmp_deeply( \@a, $rows_ref, 'qc summary for run 3622 end 1'); -} - -{ - my $q = npg_warehouse::loader::qc->new( schema_qc => $schema_qc, - reverse_end_index => $index, - plex_key => 'plex'); - is (scalar keys %{$q->retrieve_cluster_density(3323)}, 0, 'no cluster densities for run 3622'); -} + throws_ok {$q->retrieve_cluster_density()} qr/Run id argument should be set/, + 'error if id_run arg not set'; -{ my $expected = { - 1 => {'raw_cluster_density' => 95465.880, 'pf_cluster_density' => 11496.220,}, - 2 => {'raw_cluster_density' => 325143.800, 'pf_cluster_density' => 82325.490,}, - 3 => {'raw_cluster_density' => 335626.700, 'pf_cluster_density' => 171361.900,}, - 4 => {'raw_cluster_density' => 175608.400, 'pf_cluster_density' => 161077.600,}, - 5 => {'raw_cluster_density' => 443386.900, 'pf_cluster_density' => 380473.100,}, - 6 => {'raw_cluster_density' => 454826.200, 'pf_cluster_density' => 397424.100,}, - 7 => {'raw_cluster_density' => 611192.000, 'pf_cluster_density' => 465809.300,}, - 8 => {'raw_cluster_density' => 511924.700, 'pf_cluster_density' => 377133.300,}, + 1 => {'raw_cluster_density' => 95465.880, 'pf_cluster_density' => 11496.220,}, + 2 => {'raw_cluster_density' => 325143.800, 'pf_cluster_density' => 82325.490,}, + 3 => {'raw_cluster_density' => 335626.700, 'pf_cluster_density' => 171361.900,}, + 4 => {'raw_cluster_density' => 175608.400, 'pf_cluster_density' => 161077.600,}, + 5 => {'raw_cluster_density' => 443386.900, 'pf_cluster_density' => 380473.100,}, + 6 => {'raw_cluster_density' => 454826.200, 'pf_cluster_density' => 397424.100,}, + 7 => {'raw_cluster_density' => 611192.000, 'pf_cluster_density' => 465809.300,}, + 8 => {'raw_cluster_density' => 511924.700, 'pf_cluster_density' => 377133.300,}, }; - my $q = npg_warehouse::loader::qc->new( schema_qc => $schema_qc, - reverse_end_index => $index, - plex_key => 'plex'); - my $values = $q->retrieve_cluster_density(4333); - cmp_deeply ($q->retrieve_cluster_density(4333), $expected, 'cluster densities for run 4333'); -} - -{ - my $expected = { - '1' => { - 'q30_yield_kb_reverse_read' => '105906', - 'q30_yield_kb_forward_read' => '98073', - 'q40_yield_kb_forward_read' => '0' - }, - '2' => { - 'q30_yield_kb_reverse_read' => '1003112', - 'q30_yield_kb_forward_read' => '563558' - }, - '3' => { - 'q30_yield_kb_reverse_read' => '1011728', - 'q30_yield_kb_forward_read' => '981688' - }, - '4' => { - 'q30_yield_kb_reverse_read' => '714510', - 'q30_yield_kb_forward_read' => '745267', - 'q40_yield_kb_forward_read' => '56', - 'q40_yield_kb_reverse_read' => '37', - }, - '5' => { - 'q30_yield_kb_reverse_read' => '1523282', - 'q30_yield_kb_forward_read' => '1670331' - }, - '6' => { - 'q30_yield_kb_reverse_read' => '1530965', - 'q30_yield_kb_forward_read' => '1689674' - }, - '7' => { - 'q30_yield_kb_reverse_read' => '997068', - 'q30_yield_kb_forward_read' => '1668517' - }, - '8' => { - 'q30_yield_kb_forward_read' => '1111015' - }, - }; - my $q = npg_warehouse::loader::qc->new( schema_qc => $schema_qc, - reverse_end_index => $index, - plex_key => 'plex'); - my $values = $q->retrieve_yields(4333); - cmp_deeply ($values, $expected, 'q30 and q40 yields for run 4333 - all lanes not pools'); - ok(!exists $values->{1}->{plex}, 'no plexes retrieved'); - - $expected = { - - '2' => { - 'q30_yield_kb_reverse_read' => '9820023', - 'q30_yield_kb_forward_read' => '10236374', - 'q40_yield_kb_forward_read' => '6887095', - 'q40_yield_kb_reverse_read' => '5633534', - 'plex' => { '168' => { - 'q30_yield_kb_reverse_read' => '304', - 'q30_yield_kb_forward_read' => '326', - 'q40_yield_kb_forward_read' => '210', - 'q40_yield_kb_reverse_read' => '168', - } - } - }, - '4' => { - 'q30_yield_kb_reverse_read' => '11820778', - 'q30_yield_kb_forward_read' => '12548670', - 'q40_yield_kb_forward_read' => '8315876', - 'q40_yield_kb_reverse_read' => '5937501', - 'plex' => { '0' => { - 'q30_yield_kb_reverse_read' => '99353', - 'q30_yield_kb_forward_read' => '113296', - 'q40_yield_kb_forward_read' => '72788', - 'q40_yield_kb_reverse_read' => '48668', - }, - '2' => { - 'q30_yield_kb_reverse_read' => '1526977', - 'q30_yield_kb_forward_read' => '1603453', - 'q40_yield_kb_forward_read' => '1074747', - 'q40_yield_kb_reverse_read' => '780841', - }, - '8' => { - 'q30_yield_kb_reverse_read' => '1610054', - 'q30_yield_kb_forward_read' => '1700217', - 'q40_yield_kb_forward_read' => '1129798', - 'q40_yield_kb_reverse_read' => '811467', - }, - } - }, - }; - - $values = $q->retrieve_yields(6624); - cmp_deeply ($values, $expected, 'q30 and q40 yields for two pooled lanes of run 6624'); + is_deeply ($q->retrieve_cluster_density(4333), $expected, + 'cluster densities for run 4333'); } 1; diff --git a/t/10-npg_warehouse-loader-run.t b/t/10-npg_warehouse-loader-run.t index 3ccca9a9..8da0e8ba 100644 --- a/t/10-npg_warehouse-loader-run.t +++ b/t/10-npg_warehouse-loader-run.t @@ -15,14 +15,11 @@ my $RUN_LANE_TABLE_NAME = q[IseqRunLaneMetric]; my $PRODUCT_TABLE_NAME = q[IseqProductMetric]; my $LIMS_FK_COLUMN_NAME = q[id_iseq_flowcell_tmp]; my @basic_run_lane_columns = qw/cycles - pf_cluster_count - pf_bases paired_read cancelled run_priority instrument_name instrument_model - raw_cluster_count raw_cluster_density pf_cluster_density q30_yield_kb_forward_read @@ -50,7 +47,7 @@ lives_ok{ $schema_npg = $util->create_test_db(q[npg_tracking::Schema], lives_ok{ $schema_qc = $util->create_test_db(q[npg_qc::Schema], q[t/data/fixtures/npgqc]) } 'npgqc test db created'; -my $autoqc_store = npg_qc::autoqc::qc_store->new(use_db => 0, verbose => 0); +my $autoqc_store = npg_qc::autoqc::qc_store->new(use_db => 0); my $folder_glob = q[t/data/runfolders/]; my $user_id = 7; @@ -89,6 +86,7 @@ subtest 'old paired (two runfolders) run' => sub { my %in = %{$init}; $in{'id_run'} = 1246; + delete $in{'_autoqc_store'}; my $loader; lives_ok {$loader = npg_warehouse::loader::run->new(\%in)} @@ -96,7 +94,7 @@ subtest 'old paired (two runfolders) run' => sub { isa_ok ($loader, 'npg_warehouse::loader::run'); ok (!$loader->_old_forward_id_run, 'old forward id run is not set'); $loader->load(); - my $rs = $schema_wh->resultset($RUN_LANE_TABLE_NAME)->search({id_run => 1246,}); + my $rs = $schema_wh->resultset($RUN_LANE_TABLE_NAME)->search({id_run => 1246}); is ($rs->count, 8, '8 run-lane rows for run 1246'); $in{'id_run'} = 1272; @@ -115,7 +113,7 @@ subtest 'old paired (two runfolders) run' => sub { is ($r->run_pending->datetime, '2008-08-19T09:55:12', 'run pending for position 1'); my @found = (); - my @expected = (37,25284,617430,1,0,1,'IL20','1G',38831,undef,undef,3,0,4,0); + my @expected = (37,1,0,1,'IL20','1G',undef,undef,3,0,4,0); foreach my $column (@basic_run_lane_columns) { push @found, $r->$column; } @@ -141,6 +139,7 @@ subtest 'old paired (two runfolders) run' => sub { ->update_or_create({batch_id => undef, flowcell_id => undef, id_run => 1246, })} 'both batch and flowcell ids unset - test prerequisite'; %in = %{$init}; + delete $in{'_autoqc_store'}; $in{'id_run'} = 1246; $in{'explain'} = 1; lives_ok {$loader = npg_warehouse::loader::run->new(\%in)} @@ -173,7 +172,7 @@ subtest 'old paired (two runfolders) run' => sub { }; subtest 'old paired (two runfolders) run' => sub { - plan tests => 11; + plan tests => 8; my %in = %{$init}; $in{'id_run'} = 4138; @@ -186,9 +185,6 @@ subtest 'old paired (two runfolders) run' => sub { $loader = npg_warehouse::loader::run->new(\%in); $loader->load(); my $r = $schema_wh->resultset($RUN_LANE_TABLE_NAME)->search({id_run => 3965,position=>1},)->next; - is ($r->raw_cluster_count, 185608, 'clusters_raw as expected'); - is ($r->pf_bases, 1430265+1430265 , - 'pf_bases is summed up for two ends for a paired single folder run'); is ($r->paired_read, 1, 'paired read flag updated correctly'); is ($r->tags_decode_percent, undef, 'tags_decode_percent NULL where not loaded'); is ($r->instrument_name, q[IL36] , 'instr name'); @@ -201,7 +197,6 @@ subtest 'old paired (two runfolders) run' => sub { $loader = npg_warehouse::loader::run->new(\%in); $loader->load(); $r = $schema_wh->resultset($RUN_LANE_TABLE_NAME)->search({id_run => 3323,position=>1},)->next; - is($r->raw_cluster_density, undef, 'raw_cluster_density undefined'); is($r->pf_cluster_density, undef, 'pf_cluster_density undefined'); }; @@ -623,8 +618,8 @@ subtest 'linking to lims data' => sub { $in{'id_run'} = $id_run; $in{'_autoqc_store'} = npg_qc::autoqc::qc_store->new(use_db => 1, qc_schema => $schema_qc, verbose => 0); my $loader = npg_warehouse::loader::run->new(\%in); - warning_like { $loader->load() } - qr/Run 4486: multiple flowcell table records for library, pt key 1/, + warnings_exist { $loader->load() } + [qr/Run 4486: multiple flowcell table records for library, pt key 1/], 'warning about duplicate entries'; my $rs = $schema_wh->resultset($RUN_LANE_TABLE_NAME)->search({id_run => $id_run},); is($rs->count, 8, '8 rows in run-lane table'); @@ -704,7 +699,7 @@ subtest 'not loading early stage runs' => sub { }; subtest 'rna run' => sub { - plan tests => 14; + plan tests => 15; my $id_run = 24975; lives_ok {$schema_npg->resultset('Run')->find({id_run => $id_run, })->set_tag($user_id, 'staging')} @@ -732,6 +727,7 @@ subtest 'rna run' => sub { cmp_ok(sprintf('%.10f',$r->rna_rrna_rate), q(==), 0.020362793, 'loaded rrna rate matches source'); cmp_ok(sprintf('%.10f',$r->rna_transcripts_detected), q(==), 71321, 'loaded transcripts detected matches source'); cmp_ok(sprintf('%.10f',$r->rna_globin_percent_tpm), q(==), 2.71, 'loaded globin pct tpm matches source'); + cmp_ok(sprintf('%.10f',$r->rna_mitochondrial_percent_tpm), q(==), 6.56, 'loaded mitochondrial pct tpm matches source'); }; subtest 'gbs run' => sub { diff --git a/t/data/fixtures/npg/000-RunStatusDict.yml b/t/data/fixtures/npg/000-RunStatusDict.yml index 7b473be4..eb083341 100644 --- a/t/data/fixtures/npg/000-RunStatusDict.yml +++ b/t/data/fixtures/npg/000-RunStatusDict.yml @@ -50,15 +50,15 @@ - description: analysis prelim id_run_status_dict: 14 iscurrent: 0 - temporal_index: ~ + temporal_index: 997 - description: analysis prelim complete id_run_status_dict: 15 iscurrent: 0 - temporal_index: ~ + temporal_index: 998 - description: run quarantined id_run_status_dict: 16 iscurrent: 0 - temporal_index: ~ + temporal_index: 999 - description: archival pending id_run_status_dict: 17 iscurrent: 1 diff --git a/t/data/fixtures/npg/300-Run.yml b/t/data/fixtures/npg/300-Run.yml index 066d550c..cffd934a 100644 --- a/t/data/fixtures/npg/300-Run.yml +++ b/t/data/fixtures/npg/300-Run.yml @@ -246,3 +246,16 @@ is_paired: 0 priority: 4 team: '"C"' +- actual_cycle_count: 318 + batch_id: 64491 + expected_cycle_count: 318 + flowcell_id: HNYKNCCXY + folder_name: 181008_HX1_27116_B_HNYKNCCXY + folder_path_glob: '/{export,nfs}/sf32/ILorHSany_sf32/*/' + id_instrument: 117 + id_instrument_format: 12 + id_run: 27116 + id_run_pair: 0 + is_paired: 0 + priority: 1 + team: '"C"' diff --git a/t/data/fixtures/npg/400-RunLane.yml b/t/data/fixtures/npg/400-RunLane.yml index 8ef85f9a..8f73f014 100644 --- a/t/data/fixtures/npg/400-RunLane.yml +++ b/t/data/fixtures/npg/400-RunLane.yml @@ -689,4 +689,9 @@ position: 1 tile_count: 12 tracks: 1 +- id_run: 27116 + id_run_lane: 159883 + position: 1 + tile_count: 92 + tracks: 1 diff --git a/t/data/fixtures/npgqc/100-SeqComponent.yml b/t/data/fixtures/npgqc/100-SeqComponent.yml index fb131496..1ecc0a1c 100644 --- a/t/data/fixtures/npgqc/100-SeqComponent.yml +++ b/t/data/fixtures/npgqc/100-SeqComponent.yml @@ -1,4 +1,10 @@ --- +- digest: 1d9248b5f58d2993022f6ed0cc4fa39406624e635fbf4fd096f71c8c78158874 + id_run: 1246 + id_seq_component: 1900530 + position: 1 + subset: ~ + tag_index: ~ - digest: b1e0d289552a75047c464b1045bd02cb5ae7288f440aac667d15a6c7bfb96cd1 id_run: 4486 id_seq_component: 1601531 diff --git a/t/data/fixtures/npgqc/100-SeqComposition.yml b/t/data/fixtures/npgqc/100-SeqComposition.yml index 87a961c0..85085df6 100644 --- a/t/data/fixtures/npgqc/100-SeqComposition.yml +++ b/t/data/fixtures/npgqc/100-SeqComposition.yml @@ -1,4 +1,7 @@ --- +- digest: ef63c4828fef3a9a149ccbd79f32186ff1d13a5ebd6eb179b937a5ed1ed869f7 + id_seq_composition: 1904398 + size: 1 - digest: 64afd30c30f702a1b3d33434f90ffb843b406493050e574c5cca93c5ef169a9d id_seq_composition: 1601271 size: 1 diff --git a/t/data/fixtures/npgqc/200-SeqComponentComposition.yml b/t/data/fixtures/npgqc/200-SeqComponentComposition.yml index 3ac7936b..520b6cba 100644 --- a/t/data/fixtures/npgqc/200-SeqComponentComposition.yml +++ b/t/data/fixtures/npgqc/200-SeqComponentComposition.yml @@ -1,4 +1,8 @@ --- +- id_seq_comcom: 1900530 + id_seq_component: 1900530 + id_seq_composition: 1904398 + size: 1 - id_seq_comcom: 1601531 id_seq_component: 1601531 id_seq_composition: 1601530 diff --git a/t/data/fixtures/npgqc/300-QXYield.yml b/t/data/fixtures/npgqc/300-QXYield.yml index a0d0bd2e..7430385e 100644 --- a/t/data/fixtures/npgqc/300-QXYield.yml +++ b/t/data/fixtures/npgqc/300-QXYield.yml @@ -1,4 +1,24 @@ --- +- comments: ~ + filename1: 1246_1_1.fastqcheck + filename2: 1246_1_2.fastqcheck + id_qx_yield: 6000 + id_run: 1246 + id_seq_composition: 1904398 + info: '{"Check":"npg_qc::autoqc::checks::qX_yield","Check_version":"8943"}' + pass: 1 + path: archive + position: 1 + tag_index: ~ + threshold_quality: 20 + threshold_yield1: 700541 + threshold_yield2: 700541 + yield1: 274 + yield2: 236 + yield1_q30: 3 + yield2_q30: 0 + yield1_q40: 4 + yield2_q40: 0 - comments: ~ filename1: 4486_1_1.fastqcheck filename2: 4486_1_2.fastqcheck diff --git a/t/data/fixtures/npgqc/CacheQuery.yml b/t/data/fixtures/npgqc/CacheQuery.yml deleted file mode 100644 index 6d38827b..00000000 --- a/t/data/fixtures/npgqc/CacheQuery.yml +++ /dev/null @@ -1,89 +0,0 @@ ---- -- cache_time: 2009-07-31 13:47:43 - end: 1 - id_cache_query: 1 - id_run: 1246 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '25284','lane_yield' => '308715','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.70','clusters_pf_sd' => '1290','perc_pf_clusters' => '65.17','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '592','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '6.56','clusters_raw_sd' => '2404','lane' => '1','first_cycle_int' => '2459','clusters_raw' => '38831','end' => '1','perc_int_20_cycles' => '84.15','align_score_sd' => undef},{'clusters_pf' => '25941','lane_yield' => '316739','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.85','clusters_pf_sd' => '1147','perc_pf_clusters' => '66.54','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '575','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '6.96','clusters_raw_sd' => '2259','lane' => '2','first_cycle_int' => '2537','clusters_raw' => '39029','end' => '1','perc_int_20_cycles' => '85.36','align_score_sd' => undef},{'clusters_pf' => '26135','lane_yield' => '319105','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.98','clusters_pf_sd' => '1310','perc_pf_clusters' => '66.21','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '637','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '6.92','clusters_raw_sd' => '2528','lane' => '3','first_cycle_int' => '2580','clusters_raw' => '39520','end' => '1','perc_int_20_cycles' => '84.91','align_score_sd' => undef},{'clusters_pf' => '21633','lane_yield' => '264135','perc_pf_align_sd' => '0.75','perc_pf_clusters_sd' => '2.19','clusters_pf_sd' => '1474','perc_pf_clusters' => '66.38','align_score' => '62.44','perc_pf_align' => '96.54','perc_error_rate' => '0.69','first_cycle_int_sd' => '806','perc_error_rate_sd' => '0.53','perc_int_20_cycles_sd' => '10.26','clusters_raw_sd' => '2074','lane' => '4','first_cycle_int' => '3333','clusters_raw' => '32596','end' => '1','perc_int_20_cycles' => '94.18','align_score_sd' => '5.03'},{'clusters_pf' => '25481','lane_yield' => '311129','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '4.45','clusters_pf_sd' => '1808','perc_pf_clusters' => '65.16','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '638','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '8.92','clusters_raw_sd' => '2189','lane' => '5','first_cycle_int' => '2751','clusters_raw' => '39160','end' => '1','perc_int_20_cycles' => '79.37','align_score_sd' => undef},{'clusters_pf' => '24844','lane_yield' => '303341','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '5.19','clusters_pf_sd' => '2171','perc_pf_clusters' => '66.71','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '617','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '8.50','clusters_raw_sd' => '2089','lane' => '6','first_cycle_int' => '2689','clusters_raw' => '37270','end' => '1','perc_int_20_cycles' => '80.41','align_score_sd' => undef},{'clusters_pf' => '22947','lane_yield' => '280179','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '5.17','clusters_pf_sd' => '3262','perc_pf_clusters' => '65.03','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '858','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '14.92','clusters_raw_sd' => '5707','lane' => '7','first_cycle_int' => '2291','clusters_raw' => '35523','end' => '1','perc_int_20_cycles' => '84.94','align_score_sd' => undef},{'clusters_pf' => '24944','lane_yield' => '304561','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '3.89','clusters_pf_sd' => '1752','perc_pf_clusters' => '64.47','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '616','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '8.28','clusters_raw_sd' => '2189','lane' => '8','first_cycle_int' => '2602','clusters_raw' => '38723','end' => '1','perc_int_20_cycles' => '77.61','align_score_sd' => undef}];" - ssha_sql: datPueX4+RiF8SDntMhnCdEFTCs= - type: lane_summary -- cache_time: 2009-07-31 13:47:43 - end: 1 - id_cache_query: 2 - id_run: 1246 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '25284','lane_yield' => '308715','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.70','clusters_pf_sd' => '1290','perc_pf_clusters' => '65.17','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '135','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '259.83','clusters_raw_sd' => '2404','lane' => '1','first_cycle_int' => '258','clusters_raw' => '38831','end' => '2','perc_int_20_cycles' => '445.58','align_score_sd' => undef},{'clusters_pf' => '25941','lane_yield' => '316739','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.85','clusters_pf_sd' => '1147','perc_pf_clusters' => '66.54','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '182','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '252.09','clusters_raw_sd' => '2259','lane' => '2','first_cycle_int' => '340','clusters_raw' => '39029','end' => '2','perc_int_20_cycles' => '403.27','align_score_sd' => undef},{'clusters_pf' => '26135','lane_yield' => '319105','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.98','clusters_pf_sd' => '1310','perc_pf_clusters' => '66.21','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '206','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '223.63','clusters_raw_sd' => '2528','lane' => '3','first_cycle_int' => '398','clusters_raw' => '39520','end' => '2','perc_int_20_cycles' => '348.90','align_score_sd' => undef},{'clusters_pf' => '21633','lane_yield' => '264135','perc_pf_align_sd' => '2.29','perc_pf_clusters_sd' => '2.19','clusters_pf_sd' => '1474','perc_pf_clusters' => '66.38','align_score' => '40.52','perc_pf_align' => '89.04','perc_error_rate' => '1.61','first_cycle_int_sd' => '332','perc_error_rate_sd' => '0.32','perc_int_20_cycles_sd' => '189.39','clusters_raw_sd' => '2074','lane' => '4','first_cycle_int' => '654','clusters_raw' => '32596','end' => '2','perc_int_20_cycles' => '324.47','align_score_sd' => '5.79'},{'clusters_pf' => '25481','lane_yield' => '311129','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '4.45','clusters_pf_sd' => '1808','perc_pf_clusters' => '65.16','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '223','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '158.81','clusters_raw_sd' => '2189','lane' => '5','first_cycle_int' => '484','clusters_raw' => '39160','end' => '2','perc_int_20_cycles' => '257.66','align_score_sd' => undef},{'clusters_pf' => '24844','lane_yield' => '303341','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '5.19','clusters_pf_sd' => '2171','perc_pf_clusters' => '66.71','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '213','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '113.47','clusters_raw_sd' => '2089','lane' => '6','first_cycle_int' => '516','clusters_raw' => '37270','end' => '2','perc_int_20_cycles' => '210.82','align_score_sd' => undef},{'clusters_pf' => '22947','lane_yield' => '280179','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '5.17','clusters_pf_sd' => '3262','perc_pf_clusters' => '65.03','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '235','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '122.07','clusters_raw_sd' => '5707','lane' => '7','first_cycle_int' => '446','clusters_raw' => '35523','end' => '2','perc_int_20_cycles' => '205.26','align_score_sd' => undef},{'clusters_pf' => '24944','lane_yield' => '304561','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '3.89','clusters_pf_sd' => '1752','perc_pf_clusters' => '64.47','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '207','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '97.85','clusters_raw_sd' => '2189','lane' => '8','first_cycle_int' => '541','clusters_raw' => '38723','end' => '2','perc_int_20_cycles' => '181.39','align_score_sd' => undef}];" - ssha_sql: jVTmOjkliAxJoY1Sfu7ZUdxahHQ= - type: lane_summary -- cache_time: 2009-07-31 13:47:43 - end: 1 - id_cache_query: 7941 - id_run: 3323 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '27157','lane_yield' => '247672','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '5.35','clusters_pf_sd' => '18562','perc_pf_clusters' => '85.50','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '13','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '5.08','clusters_raw_sd' => '18837','lane' => '1','first_cycle_int' => '123','clusters_raw' => '30749','end' => '1','perc_int_20_cycles' => '81.27','align_score_sd' => undef},{'clusters_pf' => '30034','lane_yield' => '273909','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '3.43','clusters_pf_sd' => '18297','perc_pf_clusters' => '89.49','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '8','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '0.91','clusters_raw_sd' => '18658','lane' => '2','first_cycle_int' => '147','clusters_raw' => '32950','end' => '1','perc_int_20_cycles' => '87.24','align_score_sd' => undef},{'clusters_pf' => '18847','lane_yield' => '171880','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '6.07','clusters_pf_sd' => '11408','perc_pf_clusters' => '83.89','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '6','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '0.73','clusters_raw_sd' => '11341','lane' => '3','first_cycle_int' => '153','clusters_raw' => '21734','end' => '1','perc_int_20_cycles' => '87.96','align_score_sd' => undef},{'clusters_pf' => '104290','lane_yield' => '951121','perc_pf_align_sd' => '0.17','perc_pf_clusters_sd' => '1.28','clusters_pf_sd' => '16046','perc_pf_clusters' => '92.82','align_score' => '138.42','perc_pf_align' => '98.71','perc_error_rate' => '0.90','first_cycle_int_sd' => '9','perc_error_rate_sd' => '0.25','perc_int_20_cycles_sd' => '2.30','clusters_raw_sd' => '18799','lane' => '4','first_cycle_int' => '147','clusters_raw' => '112594','end' => '1','perc_int_20_cycles' => '84.17','align_score_sd' => '2.62'},{'clusters_pf' => '78039','lane_yield' => '711715','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.72','clusters_pf_sd' => '4939','perc_pf_clusters' => '88.67','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.57','clusters_raw_sd' => '7308','lane' => '5','first_cycle_int' => '129','clusters_raw' => '88144','end' => '1','perc_int_20_cycles' => '85.34','align_score_sd' => undef},{'clusters_pf' => '58843','lane_yield' => '536650','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.28','clusters_pf_sd' => '15040','perc_pf_clusters' => '93.19','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '5','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.02','clusters_raw_sd' => '17143','lane' => '6','first_cycle_int' => '139','clusters_raw' => '63330','end' => '1','perc_int_20_cycles' => '88.18','align_score_sd' => undef},{'clusters_pf' => '131126','lane_yield' => '1195867','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '4.55','clusters_pf_sd' => '5337','perc_pf_clusters' => '77.72','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '2','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.39','clusters_raw_sd' => '7906','lane' => '7','first_cycle_int' => '74','clusters_raw' => '169071','end' => '1','perc_int_20_cycles' => '82.78','align_score_sd' => undef},{'clusters_pf' => '136797','lane_yield' => '1247587','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '5.05','clusters_pf_sd' => '8681','perc_pf_clusters' => '68.64','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '6','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '11.27','clusters_raw_sd' => '4541','lane' => '8','first_cycle_int' => '76','clusters_raw' => '199492','end' => '1','perc_int_20_cycles' => '70.02','align_score_sd' => undef}];" - ssha_sql: 3PDS3t7uRAzHs4oHn7IpD1gAxW0= - type: lane_summary -- cache_time: 2009-07-31 13:47:48 - end: 2 - id_cache_query: 7943 - id_run: 3323 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '27157','lane_yield' => '247672','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '5.35','clusters_pf_sd' => '18562','perc_pf_clusters' => '85.50','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '10','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '4.35','clusters_raw_sd' => '18837','lane' => '1','first_cycle_int' => '71','clusters_raw' => '30749','end' => '2','perc_int_20_cycles' => '86.52','align_score_sd' => undef},{'clusters_pf' => '30034','lane_yield' => '273909','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '3.43','clusters_pf_sd' => '18297','perc_pf_clusters' => '89.49','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '8','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '4.42','clusters_raw_sd' => '18658','lane' => '2','first_cycle_int' => '83','clusters_raw' => '32950','end' => '2','perc_int_20_cycles' => '87.93','align_score_sd' => undef},{'clusters_pf' => '18847','lane_yield' => '171880','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '6.07','clusters_pf_sd' => '11408','perc_pf_clusters' => '83.89','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '9','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '4.82','clusters_raw_sd' => '11341','lane' => '3','first_cycle_int' => '89','clusters_raw' => '21734','end' => '2','perc_int_20_cycles' => '88.55','align_score_sd' => undef},{'clusters_pf' => '104290','lane_yield' => '951121','perc_pf_align_sd' => '0.35','perc_pf_clusters_sd' => '1.28','clusters_pf_sd' => '16046','perc_pf_clusters' => '92.82','align_score' => '137.57','perc_pf_align' => '97.39','perc_error_rate' => '0.75','first_cycle_int_sd' => '7','perc_error_rate_sd' => '0.09','perc_int_20_cycles_sd' => '5.16','clusters_raw_sd' => '18799','lane' => '4','first_cycle_int' => '83','clusters_raw' => '112594','end' => '2','perc_int_20_cycles' => '87.38','align_score_sd' => '1.35'},{'clusters_pf' => '78039','lane_yield' => '711715','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.72','clusters_pf_sd' => '4939','perc_pf_clusters' => '88.67','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '9','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '6.21','clusters_raw_sd' => '7308','lane' => '5','first_cycle_int' => '74','clusters_raw' => '88144','end' => '2','perc_int_20_cycles' => '90.15','align_score_sd' => undef},{'clusters_pf' => '58843','lane_yield' => '536650','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.28','clusters_pf_sd' => '15040','perc_pf_clusters' => '93.19','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '10','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '5.66','clusters_raw_sd' => '17143','lane' => '6','first_cycle_int' => '83','clusters_raw' => '63330','end' => '2','perc_int_20_cycles' => '89.63','align_score_sd' => undef},{'clusters_pf' => '131126','lane_yield' => '1195867','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '4.55','clusters_pf_sd' => '5337','perc_pf_clusters' => '77.72','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '5','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.90','clusters_raw_sd' => '7906','lane' => '7','first_cycle_int' => '40','clusters_raw' => '169071','end' => '2','perc_int_20_cycles' => '83.73','align_score_sd' => undef},{'clusters_pf' => '136797','lane_yield' => '1247587','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '5.05','clusters_pf_sd' => '8681','perc_pf_clusters' => '68.64','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '3','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '10.28','clusters_raw_sd' => '4541','lane' => '8','first_cycle_int' => '30','clusters_raw' => '199492','end' => '2','perc_int_20_cycles' => '75.64','align_score_sd' => undef}];" - ssha_sql: SW6XYVwswglORd6B8Rl3fDUdHmw= - type: lane_summary -- cache_time: 2009-08-19 12:54:41 - end: 1 - id_cache_query: 8230 - id_run: 3500 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '146973','lane_yield' => '1340393','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '6.86','clusters_pf_sd' => '16508','perc_pf_clusters' => '85.97','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '6','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '12.45','clusters_raw_sd' => '14009','lane' => '1','first_cycle_int' => '83','clusters_raw' => '170054','end' => '1','perc_int_20_cycles' => '74.77','align_score_sd' => undef},{'clusters_pf' => '96550','lane_yield' => '880538','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.14','clusters_pf_sd' => '4969','perc_pf_clusters' => '92.27','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '2','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.50','clusters_raw_sd' => '5641','lane' => '2','first_cycle_int' => '85','clusters_raw' => '104658','end' => '1','perc_int_20_cycles' => '77.79','align_score_sd' => undef},{'clusters_pf' => '80207','lane_yield' => '731487','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.29','clusters_pf_sd' => '4237','perc_pf_clusters' => '92.97','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '2','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.76','clusters_raw_sd' => '4591','lane' => '3','first_cycle_int' => '83','clusters_raw' => '86276','end' => '1','perc_int_20_cycles' => '80.20','align_score_sd' => undef},{'clusters_pf' => '151185','lane_yield' => '1378806','perc_pf_align_sd' => '0.04','perc_pf_clusters_sd' => '0.54','clusters_pf_sd' => '7398','perc_pf_clusters' => '90.54','align_score' => '139.39','perc_pf_align' => '98.96','perc_error_rate' => '0.75','first_cycle_int_sd' => '3','perc_error_rate_sd' => '0.14','perc_int_20_cycles_sd' => '1.81','clusters_raw_sd' => '8642','lane' => '4','first_cycle_int' => '93','clusters_raw' => '167012','end' => '1','perc_int_20_cycles' => '78.03','align_score_sd' => '1.78'},{'clusters_pf' => '103046','lane_yield' => '939781','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '8.42','clusters_pf_sd' => '10901','perc_pf_clusters' => '91.77','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '8','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '7.87','clusters_raw_sd' => '6154','lane' => '5','first_cycle_int' => '73','clusters_raw' => '112387','end' => '1','perc_int_20_cycles' => '78.92','align_score_sd' => undef},{'clusters_pf' => '159714','lane_yield' => '1456593','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.90','clusters_pf_sd' => '2892','perc_pf_clusters' => '85.96','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '2','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.90','clusters_raw_sd' => '3676','lane' => '6','first_cycle_int' => '47','clusters_raw' => '185842','end' => '1','perc_int_20_cycles' => '74.89','align_score_sd' => undef},{'clusters_pf' => '49018','lane_yield' => '447048','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.19','clusters_pf_sd' => '2682','perc_pf_clusters' => '93.21','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '2','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.80','clusters_raw_sd' => '2853','lane' => '7','first_cycle_int' => '65','clusters_raw' => '52587','end' => '1','perc_int_20_cycles' => '83.90','align_score_sd' => undef},{'clusters_pf' => '176221','lane_yield' => '1607137','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '4.01','clusters_pf_sd' => '10447','perc_pf_clusters' => '81.75','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '6','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.09','clusters_raw_sd' => '11418','lane' => '8','first_cycle_int' => '57','clusters_raw' => '215777','end' => '1','perc_int_20_cycles' => '70.79','align_score_sd' => undef}];" - ssha_sql: c2umynmR8eMva0dXJMs7uJU5fO8= - type: lane_summary -- cache_time: 2009-08-19 12:54:45 - end: 2 - id_cache_query: 8232 - id_run: 3500 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '146973','lane_yield' => '1340393','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '6.86','clusters_pf_sd' => '16508','perc_pf_clusters' => '85.97','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.12','clusters_raw_sd' => '14009','lane' => '1','first_cycle_int' => '50','clusters_raw' => '170054','end' => '2','perc_int_20_cycles' => '86.92','align_score_sd' => undef},{'clusters_pf' => '96550','lane_yield' => '880538','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.14','clusters_pf_sd' => '4969','perc_pf_clusters' => '92.27','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '2','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.13','clusters_raw_sd' => '5641','lane' => '2','first_cycle_int' => '50','clusters_raw' => '104658','end' => '2','perc_int_20_cycles' => '87.10','align_score_sd' => undef},{'clusters_pf' => '80207','lane_yield' => '731487','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.29','clusters_pf_sd' => '4237','perc_pf_clusters' => '92.97','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '2','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.91','clusters_raw_sd' => '4591','lane' => '3','first_cycle_int' => '51','clusters_raw' => '86276','end' => '2','perc_int_20_cycles' => '86.59','align_score_sd' => undef},{'clusters_pf' => '151185','lane_yield' => '1378806','perc_pf_align_sd' => '0.22','perc_pf_clusters_sd' => '0.54','clusters_pf_sd' => '7398','perc_pf_clusters' => '90.54','align_score' => '135.55','perc_pf_align' => '97.67','perc_error_rate' => '0.93','first_cycle_int_sd' => '2','perc_error_rate_sd' => '0.13','perc_int_20_cycles_sd' => '1.66','clusters_raw_sd' => '8642','lane' => '4','first_cycle_int' => '61','clusters_raw' => '167012','end' => '2','perc_int_20_cycles' => '87.10','align_score_sd' => '1.63'},{'clusters_pf' => '103046','lane_yield' => '939781','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '8.42','clusters_pf_sd' => '10901','perc_pf_clusters' => '91.77','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '5','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '8.12','clusters_raw_sd' => '6154','lane' => '5','first_cycle_int' => '50','clusters_raw' => '112387','end' => '2','perc_int_20_cycles' => '86.21','align_score_sd' => undef},{'clusters_pf' => '159714','lane_yield' => '1456593','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.90','clusters_pf_sd' => '2892','perc_pf_clusters' => '85.96','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '1','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.91','clusters_raw_sd' => '3676','lane' => '6','first_cycle_int' => '28','clusters_raw' => '185842','end' => '2','perc_int_20_cycles' => '78.74','align_score_sd' => undef},{'clusters_pf' => '49018','lane_yield' => '447048','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.19','clusters_pf_sd' => '2682','perc_pf_clusters' => '93.21','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '2','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.05','clusters_raw_sd' => '2853','lane' => '7','first_cycle_int' => '43','clusters_raw' => '52587','end' => '2','perc_int_20_cycles' => '86.61','align_score_sd' => undef},{'clusters_pf' => '176221','lane_yield' => '1607137','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '4.01','clusters_pf_sd' => '10447','perc_pf_clusters' => '81.75','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '3','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.11','clusters_raw_sd' => '11418','lane' => '8','first_cycle_int' => '30','clusters_raw' => '215777','end' => '2','perc_int_20_cycles' => '75.25','align_score_sd' => undef}];" - ssha_sql: 4fGWA1fw5YYDu6GeSnxgdCit75g= - type: lane_summary -- cache_time: 2009-09-10 14:46:22 - end: 1 - id_cache_query: 8688 - id_run: 3622 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '81851','lane_yield' => '363418','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '2.40','clusters_pf_sd' => '4659','perc_pf_clusters' => '83.41','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '3','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.46','clusters_raw_sd' => '4765','lane' => '1','first_cycle_int' => '69','clusters_raw' => '98126','end' => '1','perc_int_20_cycles' => '75.60','align_score_sd' => undef},{'clusters_pf' => '95506','lane_yield' => '424046','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.43','clusters_pf_sd' => '2161','perc_pf_clusters' => '84.83','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '1','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '0.97','clusters_raw_sd' => '2905','lane' => '2','first_cycle_int' => '45','clusters_raw' => '112604','end' => '1','perc_int_20_cycles' => '76.67','align_score_sd' => undef},{'clusters_pf' => '133450','lane_yield' => '592516','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.64','clusters_pf_sd' => '2551','perc_pf_clusters' => '78.75','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '1','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.69','clusters_raw_sd' => '3975','lane' => '3','first_cycle_int' => '49','clusters_raw' => '169519','end' => '1','perc_int_20_cycles' => '74.23','align_score_sd' => undef},{'clusters_pf' => '132313','lane_yield' => '587469','perc_pf_align_sd' => '0.04','perc_pf_clusters_sd' => '1.62','clusters_pf_sd' => '3790','perc_pf_clusters' => '83.17','align_score' => '178.07','perc_pf_align' => '99.13','perc_error_rate' => '0.22','first_cycle_int_sd' => '2','perc_error_rate_sd' => '0.01','perc_int_20_cycles_sd' => '1.58','clusters_raw_sd' => '7318','lane' => '4','first_cycle_int' => '74','clusters_raw' => '159216','end' => '1','perc_int_20_cycles' => '79.46','align_score_sd' => '0.12'},{'clusters_pf' => '125077','lane_yield' => '555341','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.93','clusters_pf_sd' => '1939','perc_pf_clusters' => '82.55','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '1','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.03','clusters_raw_sd' => '3519','lane' => '5','first_cycle_int' => '46','clusters_raw' => '151558','end' => '1','perc_int_20_cycles' => '76.82','align_score_sd' => undef},{'clusters_pf' => '131445','lane_yield' => '583616','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.65','clusters_pf_sd' => '4088','perc_pf_clusters' => '60.65','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '1','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.15','clusters_raw_sd' => '1848','lane' => '6','first_cycle_int' => '56','clusters_raw' => '216692','end' => '1','perc_int_20_cycles' => '65.04','align_score_sd' => undef},{'clusters_pf' => '102878','lane_yield' => '456778','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.96','clusters_pf_sd' => '5659','perc_pf_clusters' => '50.11','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '2','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.46','clusters_raw_sd' => '3720','lane' => '7','first_cycle_int' => '58','clusters_raw' => '205196','end' => '1','perc_int_20_cycles' => '64.96','align_score_sd' => undef},{'clusters_pf' => '49202','lane_yield' => '218459','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.58','clusters_pf_sd' => '4114','perc_pf_clusters' => '89.22','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '8','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.97','clusters_raw_sd' => '4518','lane' => '8','first_cycle_int' => '58','clusters_raw' => '55147','end' => '1','perc_int_20_cycles' => '73.03','align_score_sd' => undef}];" - ssha_sql: h5wwwRFTAanFrjKzFqhoJXwGrjQ= - type: lane_summary -- cache_time: 2009-11-27 14:56:52 - end: 1 - id_cache_query: 10099 - id_run: 3965 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '156827','lane_yield' => '1430265','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.84','clusters_pf_sd' => '5086','perc_pf_clusters' => '84.49','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '12','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.05','clusters_raw_sd' => '4075','lane' => '1','first_cycle_int' => '145','clusters_raw' => '185608','end' => '1','perc_int_20_cycles' => '83.87','align_score_sd' => undef},{'clusters_pf' => '159552','lane_yield' => '1455115','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '3.38','clusters_pf_sd' => '4995','perc_pf_clusters' => '83.73','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '9','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.48','clusters_raw_sd' => '3805','lane' => '2','first_cycle_int' => '154','clusters_raw' => '190654','end' => '1','perc_int_20_cycles' => '82.25','align_score_sd' => undef},{'clusters_pf' => '159854','lane_yield' => '1457870','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '2.41','clusters_pf_sd' => '5115','perc_pf_clusters' => '85.21','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '10','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.00','clusters_raw_sd' => '3131','lane' => '3','first_cycle_int' => '154','clusters_raw' => '187598','end' => '1','perc_int_20_cycles' => '83.54','align_score_sd' => undef},{'clusters_pf' => '160665','lane_yield' => '1465265','perc_pf_align_sd' => '0.26','perc_pf_clusters_sd' => '3.36','clusters_pf_sd' => '5661','perc_pf_clusters' => '84.13','align_score' => '378.41','perc_pf_align' => '96.56','perc_error_rate' => '1.87','first_cycle_int_sd' => '13','perc_error_rate_sd' => '0.48','perc_int_20_cycles_sd' => '4.70','clusters_raw_sd' => '6362','lane' => '4','first_cycle_int' => '194','clusters_raw' => '191125','end' => '1','perc_int_20_cycles' => '83.55','align_score_sd' => '6.02'},{'clusters_pf' => '159007','lane_yield' => '1450144','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '2.36','clusters_pf_sd' => '5188','perc_pf_clusters' => '85.07','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '8','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.78','clusters_raw_sd' => '5739','lane' => '5','first_cycle_int' => '162','clusters_raw' => '186976','end' => '1','perc_int_20_cycles' => '82.98','align_score_sd' => undef},{'clusters_pf' => '157697','lane_yield' => '1438199','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.87','clusters_pf_sd' => '11491','perc_pf_clusters' => '85.25','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '9','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.72','clusters_raw_sd' => '14715','lane' => '6','first_cycle_int' => '160','clusters_raw' => '185157','end' => '1','perc_int_20_cycles' => '82.28','align_score_sd' => undef},{'clusters_pf' => '155821','lane_yield' => '1421090','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.71','clusters_pf_sd' => '13340','perc_pf_clusters' => '86.20','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '19','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.16','clusters_raw_sd' => '16743','lane' => '7','first_cycle_int' => '149','clusters_raw' => '180918','end' => '1','perc_int_20_cycles' => '82.68','align_score_sd' => undef},{'clusters_pf' => '30465','lane_yield' => '277838','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.59','clusters_pf_sd' => '1596','perc_pf_clusters' => '88.89','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '20','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.36','clusters_raw_sd' => '1703','lane' => '8','first_cycle_int' => '199','clusters_raw' => '34274','end' => '1','perc_int_20_cycles' => '85.05','align_score_sd' => undef}];" - ssha_sql: AxEObUUB/JIjEZQaWBznHwb1e7M= - type: lane_summary -- cache_time: 2009-11-27 14:56:57 - end: 2 - id_cache_query: 10101 - id_run: 3965 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '156827','lane_yield' => '1430265','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.84','clusters_pf_sd' => '5086','perc_pf_clusters' => '84.49','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '6','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.30','clusters_raw_sd' => '4075','lane' => '1','first_cycle_int' => '77','clusters_raw' => '185608','end' => '2','perc_int_20_cycles' => '94.41','align_score_sd' => undef},{'clusters_pf' => '159552','lane_yield' => '1455115','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '3.38','clusters_pf_sd' => '4995','perc_pf_clusters' => '83.73','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.29','clusters_raw_sd' => '3805','lane' => '2','first_cycle_int' => '76','clusters_raw' => '190654','end' => '2','perc_int_20_cycles' => '90.65','align_score_sd' => undef},{'clusters_pf' => '159854','lane_yield' => '1457870','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '2.41','clusters_pf_sd' => '5115','perc_pf_clusters' => '85.21','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '3','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.58','clusters_raw_sd' => '3131','lane' => '3','first_cycle_int' => '79','clusters_raw' => '187598','end' => '2','perc_int_20_cycles' => '92.49','align_score_sd' => undef},{'clusters_pf' => '160665','lane_yield' => '1465265','perc_pf_align_sd' => '1.76','perc_pf_clusters_sd' => '3.36','clusters_pf_sd' => '5661','perc_pf_clusters' => '84.13','align_score' => '318.72','perc_pf_align' => '86.73','perc_error_rate' => '4.12','first_cycle_int_sd' => '7','perc_error_rate_sd' => '0.65','perc_int_20_cycles_sd' => '3.00','clusters_raw_sd' => '6362','lane' => '4','first_cycle_int' => '113','clusters_raw' => '191125','end' => '2','perc_int_20_cycles' => '86.94','align_score_sd' => '12.01'},{'clusters_pf' => '159007','lane_yield' => '1450144','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '2.36','clusters_pf_sd' => '5188','perc_pf_clusters' => '85.07','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '6','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.14','clusters_raw_sd' => '5739','lane' => '5','first_cycle_int' => '86','clusters_raw' => '186976','end' => '2','perc_int_20_cycles' => '92.52','align_score_sd' => undef},{'clusters_pf' => '157697','lane_yield' => '1438199','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.87','clusters_pf_sd' => '11491','perc_pf_clusters' => '85.25','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '6','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.74','clusters_raw_sd' => '14715','lane' => '6','first_cycle_int' => '90','clusters_raw' => '185157','end' => '2','perc_int_20_cycles' => '91.22','align_score_sd' => undef},{'clusters_pf' => '155821','lane_yield' => '1421090','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.71','clusters_pf_sd' => '13340','perc_pf_clusters' => '86.20','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '9','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '3.49','clusters_raw_sd' => '16743','lane' => '7','first_cycle_int' => '83','clusters_raw' => '180918','end' => '2','perc_int_20_cycles' => '93.49','align_score_sd' => undef},{'clusters_pf' => '30465','lane_yield' => '277838','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '1.59','clusters_pf_sd' => '1596','perc_pf_clusters' => '88.89','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '14','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '7.15','clusters_raw_sd' => '1703','lane' => '8','first_cycle_int' => '119','clusters_raw' => '34274','end' => '2','perc_int_20_cycles' => '94.91','align_score_sd' => undef}];" - ssha_sql: 7YiFM0mumXcViIgViIX6HOev6TA= - type: lane_summary -- cache_time: 2009-11-19 16:10:42 - end: 1 - id_cache_query: 9907 - id_run: 4025 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '182035','lane_yield' => '1660159','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '2.66','clusters_pf_sd' => '5259','perc_pf_clusters' => '71.87','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.07','clusters_raw_sd' => '3718','lane' => '1','first_cycle_int' => '163','clusters_raw' => '253377','end' => '1','perc_int_20_cycles' => '76.19','align_score_sd' => undef},{'clusters_pf' => '157882','lane_yield' => '1439885','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '3.32','clusters_pf_sd' => '10344','perc_pf_clusters' => '60.62','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '3','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.45','clusters_raw_sd' => '3236','lane' => '2','first_cycle_int' => '159','clusters_raw' => '260295','end' => '1','perc_int_20_cycles' => '67.99','align_score_sd' => undef},{'clusters_pf' => '169670','lane_yield' => '1547390','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '2.82','clusters_pf_sd' => '8117','perc_pf_clusters' => '64.27','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '3','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.64','clusters_raw_sd' => '1765','lane' => '3','first_cycle_int' => '161','clusters_raw' => '263947','end' => '1','perc_int_20_cycles' => '71.59','align_score_sd' => undef},{'clusters_pf' => '182549','lane_yield' => '1664849','perc_pf_align_sd' => '0.08','perc_pf_clusters_sd' => '1.58','clusters_pf_sd' => '4802','perc_pf_clusters' => '86.40','align_score' => '396.14','perc_pf_align' => '97.08','perc_error_rate' => '0.64','first_cycle_int_sd' => '6','perc_error_rate_sd' => '0.08','perc_int_20_cycles_sd' => '2.00','clusters_raw_sd' => '9272','lane' => '4','first_cycle_int' => '186','clusters_raw' => '211438','end' => '1','perc_int_20_cycles' => '83.89','align_score_sd' => '0.73'},{'clusters_pf' => '153020','lane_yield' => '1395543','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.98','clusters_pf_sd' => '8811','perc_pf_clusters' => '89.91','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.08','clusters_raw_sd' => '11610','lane' => '5','first_cycle_int' => '170','clusters_raw' => '170314','end' => '1','perc_int_20_cycles' => '85.11','align_score_sd' => undef},{'clusters_pf' => '126512','lane_yield' => '1153787','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.47','clusters_pf_sd' => '8941','perc_pf_clusters' => '91.85','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.65','clusters_raw_sd' => '10176','lane' => '6','first_cycle_int' => '176','clusters_raw' => '137775','end' => '1','perc_int_20_cycles' => '84.72','align_score_sd' => undef},{'clusters_pf' => '153855','lane_yield' => '1403159','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.81','clusters_pf_sd' => '7702','perc_pf_clusters' => '89.60','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.14','clusters_raw_sd' => '10123','lane' => '7','first_cycle_int' => '161','clusters_raw' => '171793','end' => '1','perc_int_20_cycles' => '85.58','align_score_sd' => undef},{'clusters_pf' => '136321','lane_yield' => '1243250','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.61','clusters_pf_sd' => '8089','perc_pf_clusters' => '91.01','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '15','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.22','clusters_raw_sd' => '9745','lane' => '8','first_cycle_int' => '179','clusters_raw' => '149839','end' => '1','perc_int_20_cycles' => '83.01','align_score_sd' => undef}];" - ssha_sql: RpEcVpj05b+U+3O3gMOPkjF+9r0= - type: lane_summary -- cache_time: 2009-11-19 16:10:48 - end: 2 - id_cache_query: 9909 - id_run: 4025 - is_current: 1 - results: "$rows_ref = [{'clusters_pf' => '182035','lane_yield' => '1660159','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '2.66','clusters_pf_sd' => '5259','perc_pf_clusters' => '71.87','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.80','clusters_raw_sd' => '3718','lane' => '1','first_cycle_int' => '97','clusters_raw' => '253377','end' => '2','perc_int_20_cycles' => '82.99','align_score_sd' => undef},{'clusters_pf' => '157882','lane_yield' => '1439885','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '3.32','clusters_pf_sd' => '10344','perc_pf_clusters' => '60.62','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.57','clusters_raw_sd' => '3236','lane' => '2','first_cycle_int' => '94','clusters_raw' => '260295','end' => '2','perc_int_20_cycles' => '74.94','align_score_sd' => undef},{'clusters_pf' => '169670','lane_yield' => '1547390','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '2.82','clusters_pf_sd' => '8117','perc_pf_clusters' => '64.27','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '3','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.83','clusters_raw_sd' => '1765','lane' => '3','first_cycle_int' => '95','clusters_raw' => '263947','end' => '2','perc_int_20_cycles' => '77.67','align_score_sd' => undef},{'clusters_pf' => '182549','lane_yield' => '1664849','perc_pf_align_sd' => '0.16','perc_pf_clusters_sd' => '1.58','clusters_pf_sd' => '4802','perc_pf_clusters' => '86.40','align_score' => '390.59','perc_pf_align' => '95.98','perc_error_rate' => '0.70','first_cycle_int_sd' => '3','perc_error_rate_sd' => '0.11','perc_int_20_cycles_sd' => '1.93','clusters_raw_sd' => '9272','lane' => '4','first_cycle_int' => '128','clusters_raw' => '211438','end' => '2','perc_int_20_cycles' => '84.49','align_score_sd' => '1.81'},{'clusters_pf' => '153020','lane_yield' => '1395543','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.98','clusters_pf_sd' => '8811','perc_pf_clusters' => '89.91','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.24','clusters_raw_sd' => '11610','lane' => '5','first_cycle_int' => '121','clusters_raw' => '170314','end' => '2','perc_int_20_cycles' => '86.21','align_score_sd' => undef},{'clusters_pf' => '126512','lane_yield' => '1153787','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.47','clusters_pf_sd' => '8941','perc_pf_clusters' => '91.85','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '12','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '7.93','clusters_raw_sd' => '10176','lane' => '6','first_cycle_int' => '121','clusters_raw' => '137775','end' => '2','perc_int_20_cycles' => '84.32','align_score_sd' => undef},{'clusters_pf' => '153855','lane_yield' => '1403159','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.81','clusters_pf_sd' => '7702','perc_pf_clusters' => '89.60','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '4','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '1.23','clusters_raw_sd' => '10123','lane' => '7','first_cycle_int' => '115','clusters_raw' => '171793','end' => '2','perc_int_20_cycles' => '86.17','align_score_sd' => undef},{'clusters_pf' => '136321','lane_yield' => '1243250','perc_pf_align_sd' => undef,'perc_pf_clusters_sd' => '0.61','clusters_pf_sd' => '8089','perc_pf_clusters' => '91.01','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '9','perc_error_rate_sd' => undef,'perc_int_20_cycles_sd' => '2.31','clusters_raw_sd' => '9745','lane' => '8','first_cycle_int' => '125','clusters_raw' => '149839','end' => '2','perc_int_20_cycles' => '83.65','align_score_sd' => undef}];" - ssha_sql: Mswj2CvVilws4KpxGuZKGzuXFrc= - type: lane_summary diff --git a/t/data/fixtures/npgqc/Fastqcheck.yml b/t/data/fixtures/npgqc/Fastqcheck.yml deleted file mode 100644 index 86f9369a..00000000 --- a/t/data/fixtures/npgqc/Fastqcheck.yml +++ /dev/null @@ -1,342 +0,0 @@ ---- -- section: 'forward' - id_fastqcheck: 1 - id_run: 1246 - position: 1 - file_name: '1246_1_1' - forty: 4000 - thirty: 3090 - twenty: 274104 - twentyfive: 50 -- section: 'reverse' - id_fastqcheck: 2 - id_run: 1246 - position: 1 - file_name: '1246_1_2' - forty: 0 - thirty: 0 - twenty: 235566 - twentyfive: 49 -- section: 'forward' - id_fastqcheck: 28115 - id_run: 4333 - position: 1 - file_name: '4333_1_1' - forty: 35 - thirty: 98072564 - twenty: 132721857 - twentyfive: 121121876 -- section: 'forward' - id_fastqcheck: 28117 - id_run: 4333 - position: 2 - file_name: '4333_2_1' - thirty: 563558260 - twenty: 951073764 - twentyfive: 807139434 -- section: 'forward' - id_fastqcheck: 28122 - id_run: 4333 - position: 3 - file_name: '4333_3_1' - thirty: 981688118 - twenty: 1137893082 - twentyfive: 1087426863 -- section: 'forward' - id_fastqcheck: 28113 - id_run: 4333 - position: 4 - file_name: '4333_4_1' - forty: 56344 - thirty: 745267162 - twenty: 778390148 - twentyfive: 768926438 -- section: 'forward' - id_fastqcheck: 28123 - id_run: 4333 - position: 5 - file_name: '4333_5_1' - thirty: 1670331429 - twenty: 1830577672 - twentyfive: 1779675924 -- section: 'forward' - id_fastqcheck: 28134 - id_run: 4333 - position: 6 - file_name: '4333_6_1' - thirty: 1689674298 - twenty: 1877415887 - twentyfive: 1817415998 -- section: 'forward' - id_fastqcheck: 28133 - id_run: 4333 - position: 7 - file_name: '4333_7_1' - thirty: 1668517367 - twenty: 2034558190 - twentyfive: 1911047483 -- section: 'forward' - id_fastqcheck: 28124 - id_run: 4333 - position: 8 - file_name: '4333_8_1' - thirty: 1111014601 - twenty: 1399434675 - twentyfive: 1307276781 -- section: 'reverse' - id_fastqcheck: 28120 - id_run: 4333 - position: 1 - file_name: '4333_1_2' - thirty: 105906317 - twenty: 125942648 - twentyfive: 117656947 -- section: 'reverse' - id_fastqcheck: 28114 - id_run: 4333 - position: 2 - file_name: '4333_2_2' - thirty: 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twenty: 773102326 - twentyfive: 679237805 -- section: 'index' - id_fastqcheck: 28121 - id_run: 4333 - position: 1 - file_name: '4333_1_t' - thirty: 10513721 - twenty: 11005313 - twentyfive: 10830877 -- section: 'index' - id_fastqcheck: 28118 - id_run: 4333 - position: 2 - file_name: '4333_2_t' - thirty: 112000721 - twenty: 113865458 - twentyfive: 113282728 -- section: 'index' - id_fastqcheck: 28119 - id_run: 4333 - position: 3 - file_name: '4333_3_t' - thirty: 118386920 - twenty: 121422482 - twentyfive: 120537110 -- section: 'index' - id_fastqcheck: 28111 - id_run: 4333 - position: 4 - file_name: '4333_4_t' - thirty: 82350880 - twenty: 82350880 - twentyfive: 82350880 -- section: 'index' - id_fastqcheck: 28126 - id_run: 4333 - position: 5 - file_name: '4333_5_t' - thirty: 171061624 - twenty: 174435229 - twentyfive: 173442993 -- section: 'index' - id_fastqcheck: 28132 - id_run: 4333 - position: 6 - file_name: '4333_6_t' - thirty: 175619370 - twenty: 179490331 - twentyfive: 178267922 -- section: 'index' - id_fastqcheck: 28127 - id_run: 4333 - position: 7 - file_name: '4333_7_t' - thirty: 148449232 - twenty: 157195445 - twentyfive: 154595220 -- section: 'index' - id_fastqcheck: 28125 - id_run: 4333 - position: 8 - file_name: '4333_8_t' - thirty: 94672923 - twenty: 99702984 - twentyfive: 98265824 -- file_name: 6624_2_1.fastqcheck - forty: 6887094682 - id_fastqcheck: 165397 - id_run: 6624 - position: 2 - section: forward - tag_index: -1 - thirty: 10236374221 - twenty: 10846342349 -- file_name: 6624_2_t.fastqcheck - forty: 0 - id_fastqcheck: 165412 - id_run: 6624 - position: 2 - section: index - tag_index: -1 - thirty: 856969902 - twenty: 875657719 -- file_name: 6624_2_2.fastqcheck - forty: 5633533960 - id_fastqcheck: 165409 - id_run: 6624 - position: 2 - section: reverse - tag_index: -1 - thirty: 9820022923 - twenty: 10648483799 -- file_name: 6624_2_1#168.fastqcheck - forty: 209878 - id_fastqcheck: 165389 - id_run: 6624 - position: 2 - section: forward - tag_index: 168 - thirty: 325932 - twenty: 354569 -- file_name: 6624_2_2#168.fastqcheck - forty: 167676 - id_fastqcheck: 165401 - id_run: 6624 - position: 2 - section: reverse - tag_index: 168 - thirty: 303701 - twenty: 341381 -- file_name: 6624_4_1.fastqcheck - forty: 8315875545 - id_fastqcheck: 165454 - id_run: 6624 - position: 4 - section: forward - tag_index: -1 - thirty: 12548669808 - twenty: 13270014168 -- file_name: 6624_4_t.fastqcheck - forty: 0 - id_fastqcheck: 165470 - id_run: 6624 - position: 4 - section: index - tag_index: -1 - thirty: 1035469413 - twenty: 1070311707 -- file_name: 6624_4_2.fastqcheck - forty: 5937501073 - id_fastqcheck: 165467 - id_run: 6624 - position: 4 - section: reverse - tag_index: -1 - thirty: 11820778392 - twenty: 13000145044 -- file_name: 6624_4_1#0.fastqcheck - forty: 72788029 - id_fastqcheck: 165444 - id_run: 6624 - position: 4 - section: forward - tag_index: 0 - thirty: 113296149 - twenty: 121904124 -- file_name: 6624_4_2#0.fastqcheck - forty: 48667858 - id_fastqcheck: 165457 - id_run: 6624 - position: 4 - section: reverse - tag_index: 0 - thirty: 99353038 - twenty: 113474281 -- file_name: 6624_4_1#2.fastqcheck - forty: 1074746952 - id_fastqcheck: 165447 - id_run: 6624 - position: 4 - section: forward - tag_index: 2 - thirty: 1603453114 - twenty: 1691859718 -- file_name: 6624_4_2#2.fastqcheck - forty: 780840677 - id_fastqcheck: 165460 - id_run: 6624 - position: 4 - section: reverse - tag_index: 2 - thirty: 1526977324 - twenty: 1669263847 -- file_name: 6624_4_1#8.fastqcheck - forty: 1129798191 - id_fastqcheck: 165453 - id_run: 6624 - position: 4 - section: forward - tag_index: 8 - thirty: 1700217473 - twenty: 1797740769 -- file_name: 6624_4_2#8.fastqcheck - forty: 811467430 - id_fastqcheck: 165466 - id_run: 6624 - position: 4 - section: reverse - tag_index: 8 - thirty: 1610054425 - twenty: 1768299774 - - - diff --git a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.insert_size.json b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.insert_size.json index a0ce6613..abda9b23 100644 --- a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.insert_size.json +++ b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.insert_size.json @@ -1 +1 @@ -{"min_isize":51,"quartile1":172000,"position":"3","tag_index":"0","num_well_aligned_reads":9597,"comments":"Insert size is not defined","median":189,"bin_width":3,"reference":"/nfs/repository/d0031/references/PhiX/Illumina/all/bwa/phix-illumina.fa","info":{"Additional_Modules":"npg_qc::autoqc::align::Xreads_insert_size 8943;npg_common::extractor::fastq 8343;npg_qc::autoqc::align::alignment_paired 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+{"std":96,"quartile3":207,"id_run":4799,"quartile1":172000,"num_well_aligned_reads":9597,"bins":[10,9,9,10,15,23,17,16,25,23,30,28,29,39,39,40,39,53,41,39,52,60,53,55,55,75,61,73,62,70,84,69,73,87,86,95,91,130,148,230,298,377,424,472,492,438,466,441,387,393,358,323,332,309,277,278,249,212,170,119,77,48,44,32,26,23,21,14,13,10,16,10,10,5,10,9,9,3,7,5,3,4,4,9,7,0,3,7,4,2,1,2,0,0,2,2,1,1],"min_isize":51,"bin_width":3,"composition":{"__CLASS__":"npg_tracking::glossary::composition-87.3-54-gf4380c3","components":[{"position":3,"tag_index":0,"__CLASS__":"npg_tracking::glossary::composition::component::illumina-87.3-54-gf4380c3","id_run":4799}]},"path":"archive/lane3","paired_reads_direction_in":"1","position":3,"filenames":["4523_4_1.fastq","4523_4_2.fastq"],"sample_size":10000,"mean":232,"comments":"Insert size is not defined","__CLASS__":"npg_qc::autoqc::results::insert_size","tag_index":0,"reference":"/nfs/repository/d0031/references/PhiX/Illumina/all/bwa/phix-illumina.fa","info":{"Check_version":"8943","Check":"npg_qc::autoqc::checks::insert_size","Additional_Modules":"npg_qc::autoqc::align::Xreads_insert_size 8943;npg_common::extractor::fastq 8343;npg_qc::autoqc::align::alignment_paired 8943","Aligner":"bwa","Aligner_version":"0.5.5 (r1273)"},"median":189} diff --git a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.qX_yield.json b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.qX_yield.json index afb6103e..ca9db0af 100644 --- a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.qX_yield.json +++ b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.qX_yield.json @@ -1 +1 @@ -{"info":{"Check":"npg_qc::autoqc::checks::qX_yield","Check_version":"8943"},"yield2":39877,"pass":0,"filename1":"4523_1_1.fastqcheck","threshold_yield2":350270,"position":"3","tag_index":"0","path":"/nfs/sf11/IL21/analysis/100330_IL21_4523/Data/Intensities/Bustard1.6.0a14_06-04-2010_RTA/GERALD_06-04-2010_RTA/archive","id_run":"4799","threshold_quality":20,"__CLASS__":"npg_qc::autoqc::results::qX_yield-8943","threshold_yield1":350270,"yield1":46671,"filename2":"4523_1_2.fastqcheck"} \ No newline at end of file +{"id_run":4799,"yield2":39877,"yield1":46671,"threshold_yield1":350270,"filename1":"4523_1_1.fastqcheck","threshold_yield2":350270,"threshold_quality":20,"__CLASS__":"npg_qc::autoqc::results::qX_yield","composition":{"__CLASS__":"npg_tracking::glossary::composition-87.3-54-gf4380c3","components":[{"id_run":4799,"position":3,"tag_index":0,"__CLASS__":"npg_tracking::glossary::composition::component::illumina-87.3-54-gf4380c3"}]},"position":3,"pass":"0","filename2":"4523_1_2.fastqcheck","tag_index":0,"info":{"Check_version":"8943","Check":"npg_qc::autoqc::checks::qX_yield"},"path":"archive/lane3"} diff --git a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#1.insert_size.json b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#1.insert_size.json index e49c1f59..93a7da87 100644 --- a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#1.insert_size.json +++ b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#1.insert_size.json @@ -1 +1 @@ -{"min_isize":51,"quartile1":172000,"position":"3","tag_index":"1","num_well_aligned_reads":9597,"comments":"Insert size is not defined","median":189,"bin_width":3,"reference":"/nfs/repository/d0031/references/PhiX/Illumina/all/bwa/phix-illumina.fa","info":{"Additional_Modules":"npg_qc::autoqc::align::Xreads_insert_size 8943;npg_common::extractor::fastq 8343;npg_qc::autoqc::align::alignment_paired 8943","Check":"npg_qc::autoqc::checks::insert_size","Aligner":"bwa","Aligner_version":"0.5.5 (r1273)","Check_version":"8943"},"sample_size":10000,"std":96,"path":"/nfs/sf11/IL21/analysis/100330_IL21_4523/Data/Intensities/Bustard1.6.0a14_06-04-2010_RTA/GERALD_06-04-2010_RTA/archive","mean":232,"id_run":"4799","__CLASS__":"npg_qc::autoqc::results::insert_size-8943","quartile3":207,"bins":[10,9,9,10,15,23,17,16,25,23,30,28,29,39,39,40,39,53,41,39,52,60,53,55,55,75,61,73,62,70,84,69,73,87,86,95,91,130,148,230,298,377,424,472,492,438,466,441,387,393,358,323,332,309,277,278,249,212,170,119,77,48,44,32,26,23,21,14,13,10,16,10,10,5,10,9,9,3,7,5,3,4,4,9,7,0,3,7,4,2,1,2,0,0,2,2,1,1],"filenames":["4523_4_1.fastq","4523_4_2.fastq"]} \ No newline at end of file +{"reference":"/nfs/repository/d0031/references/PhiX/Illumina/all/bwa/phix-illumina.fa","tag_index":1,"info":{"Check_version":"8943","Additional_Modules":"npg_qc::autoqc::align::Xreads_insert_size 8943;npg_common::extractor::fastq 8343;npg_qc::autoqc::align::alignment_paired 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diff --git a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#2.insert_size.json b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#2.insert_size.json index 0e1ba8c9..83f4d1fc 100644 --- a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#2.insert_size.json +++ b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#2.insert_size.json @@ -1 +1 @@ -{"min_isize":51,"quartile1":172000,"position":"3","tag_index":"2","num_well_aligned_reads":9597,"comments":"Insert size is not defined","median":189,"bin_width":3,"reference":"/nfs/repository/d0031/references/PhiX/Illumina/all/bwa/phix-illumina.fa","info":{"Additional_Modules":"npg_qc::autoqc::align::Xreads_insert_size 8943;npg_common::extractor::fastq 8343;npg_qc::autoqc::align::alignment_paired 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--git a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#3.qX_yield.json b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#3.qX_yield.json index fc4b544a..fc00650e 100644 --- a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#3.qX_yield.json +++ b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#3.qX_yield.json @@ -1 +1 @@ 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a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.adapter.json +++ b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.adapter.json @@ -1 +1 @@ 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diff --git a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.contamination.json b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.contamination.json index 7fe521f0..13be2703 100644 --- a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.contamination.json +++ b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.contamination.json @@ -1 +1 @@ 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organism names Failed to retrieve binary reference.","id_run":"4523"} \ No newline at end of file +{"comments":"no reference for taxon id 9615 Failed to map Dog;Canis lupus familiaris;Maningrida24Tv2;Transmissable Dog Cancer to known organism names Failed to retrieve binary reference.","info":{"Check":"npg_qc::autoqc::checks::sequence_error","Check_version":"8943"},"position":1,"composition":{"components":[{"id_run":4799,"__CLASS__":"npg_tracking::glossary::composition::component::illumina-87.3-54-gf4380c3","position":1}],"__CLASS__":"npg_tracking::glossary::composition-87.3-54-gf4380c3"},"path":"archive","__CLASS__":"npg_qc::autoqc::results::sequence_error","id_run":4799} diff --git a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_3.tag_decode_stats.json b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_3.tag_decode_stats.json new file mode 100644 index 00000000..c40873ad --- /dev/null +++ b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_3.tag_decode_stats.json @@ -0,0 +1 @@ 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b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_3_tag_decode_stats.json deleted file mode 100644 index ec723317..00000000 --- a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_3_tag_decode_stats.json +++ /dev/null @@ -1 +0,0 @@ -{"info":{},"errors_good":{"1":"158667","0":"26863390","no_match":"259367"},"pass":1,"distribution_good":{"8":"4560784","6":"3728","4":"5060619","1":"3080996","3":"2453590","7":"6081841","2":"1555308","5":"4225191"},"position":"3","distribution_all":{"8":"5182574","6":"4544","4":"5691478","1":"3515808","3":"2742046","7":"6823049","2":"1746783","5":"4754975"},"id_run":"4752","__CLASS__":"npg_qc::autoqc::results::tag_decode_stats-8829","errors_all":{"1":"736060","0":"29725197","no_match":"1060663"},"tag_code":{"8":"ACTTGA","6":"GCCAAT","4":"TGACCA","1":"ATCACG","3":"TTAGGC","7":"CAGATC","2":"CGATGT","5":"ACAGTG"}} \ No newline at end of file diff --git a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.adapter.json b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.adapter.json index 6dd0f235..9acc2bda 100644 --- a/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.adapter.json +++ b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.adapter.json @@ -1 +1 @@ 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b/t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.qX_yield.json @@ -1 +1 @@ -{"info":{"Check":"npg_qc::autoqc::checks::qX_yield","Check_version":"8943"},"yield2":1393269,"pass":1,"filename1":"4523_4_1.fastqcheck","threshold_yield2":350270,"position":"4","path":"/nfs/sf11/IL21/analysis/100330_IL21_4523/Data/Intensities/Bustard1.6.0a14_06-04-2010_RTA/GERALD_06-04-2010_RTA/archive","id_run":"4799","threshold_quality":20,"__CLASS__":"npg_qc::autoqc::results::qX_yield-8943","threshold_yield1":350270,"yield1":1455655,"filename2":"4523_4_2.fastqcheck"} \ No newline at end of file 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diff --git a/t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1.gc_fraction.json b/t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1.gc_fraction.json index cb9224f5..fca672f9 100644 --- a/t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1.gc_fraction.json +++ b/t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1.gc_fraction.json @@ -1 +1 @@ -{"info":{"Check":"npg_qc::autoqc::checks::gc_fraction","Check_version":"8943"},"forward_read_gc_percent":45.2905811623247,"threshold_difference":20,"position":"1","path":"/nfs/sf11/IL21/analysis/100330_IL21_4523/Data/Intensities/Bustard1.6.0a14_06-04-2010_RTA/GERALD_06-04-2010_RTA/archive","comments":"no reference for taxon id 9615 Failed to map Dog;Canis lupus familiaris;Maningrida24Tv2;Transmissable Dog Cancer to known 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\ No newline at end of file diff --git a/t/data/runfolders/with_merges/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/qc/26291_1.tag_metrics.json b/t/data/runfolders/with_merges/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/qc/26291_1.tag_metrics.json new file mode 100644 index 00000000..d39fd4b3 --- /dev/null +++ b/t/data/runfolders/with_merges/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/qc/26291_1.tag_metrics.json @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/t/perlcriticrc b/t/perlcriticrc index 87642ee0..160d3306 100644 --- a/t/perlcriticrc +++ b/t/perlcriticrc @@ -5,4 +5,4 @@ [Documentation::RequirePodSections] lib_sections = NAME | SYNOPSIS | DESCRIPTION | SUBROUTINES/METHODS | BUGS AND LIMITATIONS | DEPENDENCIES | CONFIGURATION AND ENVIRONMENT | INCOMPATIBILITIES | AUTHOR | LICENSE AND COPYRIGHT [Documentation::PodSpelling] -stop_words = accessors FindBin flowcell NPG npg DBIx NPGQC qc arg dev plex Gourtovaia autoqc Readonly boolean LIMs mqc +stop_words = accessors FindBin flowcell NPG npg DBIx NPGQC qc arg dev plex Gourtovaia autoqc Readonly boolean LIMs mqc multi sequencescape DateTime