From a5f3ea00ab29294e57a1fab76526d439335d05af Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 20 Mar 2024 15:39:58 +0000 Subject: [PATCH 1/5] PacBio iRODS data - set QC state metadata ... when it is safe to do so. --- lib/WTSI/NPG/HTS/PacBio/Annotator.pm | 45 ++++++++++++++++++++ lib/WTSI/NPG/HTS/PacBio/MetaUpdater.pm | 3 +- t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm | 36 +++++++++++++++- 3 files changed, 81 insertions(+), 3 deletions(-) diff --git a/lib/WTSI/NPG/HTS/PacBio/Annotator.pm b/lib/WTSI/NPG/HTS/PacBio/Annotator.pm index d32e011a..d85aba4d 100644 --- a/lib/WTSI/NPG/HTS/PacBio/Annotator.pm +++ b/lib/WTSI/NPG/HTS/PacBio/Annotator.pm @@ -225,6 +225,51 @@ sub make_tag_metadata { return $self->_make_multi_value_metadata(\@run_records, $method_attr); } +=head2 make_qc_metadata + + Arg [n] PacBio run database records, + List[WTSI::DNAP::Warehouse::Schema::Result::PacBioRun]. ++ + Example : my @avus = $ann->make_qc_metadata(@run_records); + Description: Return QC outcome AVU metadata for a single product. + + An empty list is returned if the input list contains + either no records or multiple records or the only record + is not linked to a record in the pac_bio_product_metrics + table. + + This method should be called in the context of a single + iRODS object. If, according to a record in the pac_bio_run + table, a well contains multiple samples, but in practice + no deplexing was done, when trying to establish data + provenance we might get multiple pac_bio_run table rows. + Opting out of assigning a QC outcome in this case is + a conscious conservative decision that was made at the + time of writing (March 2024). + + Returntype : List[HashRef] + +=cut + +sub make_qc_metadata { + my ($self, @run_records) = @_; + + my @avus = (); + if (@run_records == 1) { + my @product_metrics = $run_records[0]->pac_bio_product_metrics()->all(); + # Absence of linked product records is not unknown, one linked product + # record is normal, multiple linked records is, most likely, an error. + if (@product_metrics == 1) { + my $qc_outcome = $product_metrics[0]->qc(); + if (defined $qc_outcome) { + push @avus, $self->make_avu($QC_STATE, $qc_outcome); + } + } + } + + return @avus; +} + sub _make_multi_value_metadata { my ($self, $objs, $method_attr) = @_; # The method_attr argument is a map of method name to attribute name diff --git a/lib/WTSI/NPG/HTS/PacBio/MetaUpdater.pm b/lib/WTSI/NPG/HTS/PacBio/MetaUpdater.pm index 15367e1e..819137bc 100644 --- a/lib/WTSI/NPG/HTS/PacBio/MetaUpdater.pm +++ b/lib/WTSI/NPG/HTS/PacBio/MetaUpdater.pm @@ -78,7 +78,8 @@ sub update_secondary_metadata { try { my @run_records = $self->find_pacbio_runs( $id_run, $well, $tag_id, $plate_number); - my @secondary_avus = $self->make_secondary_metadata(@run_records); + my @secondary_avus = map { $self->$_(@run_records) } + qw/make_secondary_metadata make_qc_metadata/; $obj->update_secondary_metadata(@secondary_avus); $self->info("Updated metadata on '$path' ", diff --git a/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm index 0b42f5b6..d1b5903a 100644 --- a/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm +++ b/t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm @@ -73,7 +73,7 @@ sub require : Test(1) { require_ok('WTSI::NPG::HTS::PacBio::MetaUpdater'); } -sub update_secondary_metadata : Test(7) { +sub update_secondary_metadata : Test(8) { my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, strict_baton_version => 0); my $updater = WTSI::NPG::HTS::PacBio::MetaUpdater->new @@ -135,7 +135,20 @@ sub update_secondary_metadata : Test(7) { 'plate_number', $plate_number); # Update primary metadata my $new_study_name = 'Updated for the test'; $study_row->update({name => $new_study_name}); # Update study name in mlwh - + # Create a linked product row with QC outcome defined. + my $rw_row = $wh_schema->resultset('PacBioRunWellMetric')->create({ + pac_bio_run_name => $run_name, + well_label => $well_label, + plate_number => $plate_number, + id_pac_bio_product => 'A' x 64, + instrument_type => 'SomeType' + }); + my $p_row = $wh_schema->resultset('PacBioProductMetric')->create({ + id_pac_bio_rw_metrics_tmp => $rw_row->id_pac_bio_rw_metrics_tmp, + id_pac_bio_tmp => $row->id_pac_bio_tmp, + id_pac_bio_product => $rw_row->id_pac_bio_product + }); + # Call the updater again. $updater->update_secondary_metadata(\@paths_to_update); @@ -165,6 +178,25 @@ sub update_secondary_metadata : Test(7) { is_deeply($updated_as_dict, $expected_as_dict, 'Updated metadata is correct after the update'); + + $p_row->update({qc => 1}); + $expected_as_dict->{$QC_STATE} = 1; + for my $key ((map { $_ . '_history'} ($STUDY_NAME, $PACBIO_STUDY_NAME))) { + delete $expected_as_dict->{$key}; + } + # Call the updater again. + $updater->update_secondary_metadata(\@paths_to_update); + # Inspect the metadata after the update. + $updated = WTSI::NPG::HTS::DataObject->new + (collection => $irods_tmp_coll, + data_object => $data_file, + irods => $irods)->metadata; + + $updated_as_dict = {}; + for my $meta (@{$updated}) { + $updated_as_dict->{$meta->{'attribute'}} = $meta->{'value'}; + } + is($expected_as_dict->{$QC_STATE}, 1, 'Updated metadata contains qc outcome'); } 1; From 7adbf00e5d1dc0e297bba15dab030cac12d89c0d Mon Sep 17 00:00:00 2001 From: Carol Scott Date: Wed, 3 Apr 2024 15:54:00 +0100 Subject: [PATCH 2/5] Allow non deplexed Revio cells to publish now --- MANIFEST | 24 + .../NPG/HTS/PacBio/Sequel/RunPublisher.pm | 27 +- .../m84098_240321_114027_s1.fail_reads.bam | 0 ...m84098_240321_114027_s1.fail_reads.bam.pbi | 0 .../m84098_240321_114027_s1.hifi_reads.bam | 0 ...m84098_240321_114027_s1.hifi_reads.bam.pbi | 0 .../m84098_240321_114027_s1.primary_qc.tar.xz | 0 .../metadata/Transfer_Test_240321_105751.txt | 0 .../m84098_240321_114027_s1.metadata.xml | 168 ++++++ ..._114027_s1.sequencing_control.subreads.bam | 0 ...027_s1.sequencing_control.subreads.bam.pbi | 0 .../metadata/m84098_240321_114027_s1.sts.xml | 0 .../m84098_240321_114027_s1.transferdone | 0 ...1_114027_s1_basic_preview_4hr.metadata.xml | 168 ++++++ ...1_114027_s1_full_preview_23hr.metadata.xml | 168 ++++++ ..._114027_s1.fail_reads.consensusreadset.xml | 174 ++++++ ..._114027_s1.hifi_reads.consensusreadset.xml | 246 ++++++++ .../m84098_240321_114027_s1.ccs_report.json | 244 ++++++++ .../m84098_240321_114027_s1.ccs_report.txt | 57 ++ ...40321_114027_s1.fail_reads.5mc_report.json | 542 ++++++++++++++++++ ...40321_114027_s1.hifi_reads.5mc_report.json | 542 ++++++++++++++++++ .../m84098_240321_114027_s1.pbreports.log | 0 .../m84098_240321_114027_s1.reports.zip | 0 .../m84098_240321_114027_s1.summary.json | 1 + ...m84098_240321_114027_s1.zmw_metrics.csv.gz | 0 ...84098_240321_114027_s1.zmw_metrics.json.gz | 0 t/fixtures/ml_warehouse/300-PacBioRun.yml | 30 + .../NPG/HTS/PacBio/Sequel/RunPublisherTest.pm | 51 ++ 28 files changed, 2432 insertions(+), 10 deletions(-) create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam.pbi create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam.pbi create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/m84098_240321_114027_s1.primary_qc.tar.xz create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/Transfer_Test_240321_105751.txt create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.metadata.xml create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam.pbi create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sts.xml create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.transferdone create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_basic_preview_4hr.metadata.xml create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_full_preview_23hr.metadata.xml create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.fail_reads.consensusreadset.xml create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.hifi_reads.consensusreadset.xml create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.json create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.txt create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.fail_reads.5mc_report.json create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.hifi_reads.5mc_report.json create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.pbreports.log create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.reports.zip create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.summary.json create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.csv.gz create mode 100644 t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.json.gz diff --git a/MANIFEST b/MANIFEST index cc8379b5..3c40b8c7 100644 --- a/MANIFEST +++ b/MANIFEST @@ -16577,6 +16577,30 @@ t/data/pacbio/sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_11074 t/data/pacbio/sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.summary.json t/data/pacbio/sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.zmw_metrics.csv.gz t/data/pacbio/sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.zmw_metrics.json.gz +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam.pbi +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam.pbi +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/m84098_240321_114027_s1.primary_qc.tar.xz +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_basic_preview_4hr.metadata.xml +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_full_preview_23hr.metadata.xml +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.metadata.xml +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam.pbi +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sts.xml +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.transferdone +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/Transfer_Test_240321_105751.txt +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.fail_reads.consensusreadset.xml +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.hifi_reads.consensusreadset.xml +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.json +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.txt +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.fail_reads.5mc_report.json +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.hifi_reads.5mc_report.json +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.pbreports.log +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.reports.zip +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.summary.json +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.csv.gz +t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.json.gz t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.bam t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.bam.pbi t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.consensusreadset.xml diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisher.pm b/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisher.pm index 87faa97e..b48e578b 100644 --- a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisher.pm +++ b/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisher.pm @@ -27,14 +27,11 @@ our $SEQUENCE_INDEX_FORMAT = 'pbi'; our $SEQUENCE_PRODUCT = 'subreads'; our $SEQUENCE_AUXILIARY = 'scraps'; -# CCS Sequence file types - Sequel IIe +# CCS Sequence file types our $CCS_SEQUENCE_PRODUCT = 'reads'; our $HIFI_SEQUENCE_PRODUCT = 'hifi_reads'; our $HIFIUB_SEQUENCE_PRODUCT = 'unbarcoded.hifi_reads'; - -# CCS Sequence file types - Revio -our $REV_HIFIUB_SEQ_PRODUCT = 'hifi_reads.unassigned'; - +our $REV_HIFIUB_SEQ_PRODUCT = 'hifi_reads.unassigned'; ## Processing types our $OFFINSTRUMENT = 'OffInstrument'; @@ -43,6 +40,7 @@ our $ONINSTRUMENTHO = 'OnInstrumentHifiOnly'; our $ONINSTRUMENTDP = 'OnInstrumentDeplex'; our $ONINSTRUMENTSR = 'OnInstrumentPlusSubreads'; our $ONINST_REVIO1 = 'OnInstrumentRevioOne'; +our $ONINST_REVIO2 = 'OnInstrumentRevioTwo'; # Generic file prefix our $FILE_PREFIX_PATTERN = 'm[0-9a-z]+_\d+_\d+'; @@ -97,6 +95,11 @@ sub _build_movie_pattern { .q{[.]}. $REV_HIFIUB_SEQ_PRODUCT .q{[.]}. $SEQUENCE_FILE_FORMAT .q{$}, undef, 1)->[0] ) { $revio++; + } elsif ( defined $self->list_files($smrt_name, $REVIO_PREFIX_PATTERN + .q{[.]}. $HIFI_SEQUENCE_PRODUCT .q{[.]}. $SEQUENCE_FILE_FORMAT + .q{$}, undef, 1)->[0] ) { + ## non deplexed data now supported for Revio + $revio++; } last if $revio > 0; } @@ -166,7 +169,8 @@ sub publish_files { ($num_files_cell, $num_processed_cell, $num_errors_cell) = $self->_publish_on_instrument_cell($smrt_name, $process_type); } - elsif ($process_type eq $ONINST_REVIO1) { + elsif (($process_type eq $ONINST_REVIO1) || + ($process_type eq $ONINST_REVIO2)) { ($num_files_cell, $num_processed_cell, $num_errors_cell) = $self->_publish_revio_instrument_cell($smrt_name, $process_type); } @@ -211,7 +215,7 @@ sub _processing_type { } elsif (defined $self->list_files($smrt_name, $self->_movie_pattern .q{[.]}. $HIFI_SEQUENCE_PRODUCT .q{[.]}. $SEQUENCE_FILE_FORMAT .q{$})->[0]) { - $type = $ONINSTRUMENTHO; + $type = ($self->_is_onrevio) ? $ONINST_REVIO2 : $ONINSTRUMENTHO; } elsif (defined $self->list_files($smrt_name, $self->_movie_pattern .q{[.]}. $HIFIUB_SEQUENCE_PRODUCT .q{[.]}. $SEQUENCE_FILE_FORMAT .q{$})->[0]) { @@ -325,8 +329,7 @@ sub _publish_revio_instrument_cell { my $pub_xml = q[sts]; - my ($nfb, $npb, $neb) = $self->_publish_deplexed_files - ($smrt_name); + my ($nfb, $npb, $neb) = $self->_publish_deplexed_files($smrt_name); my ($nfx, $npx, $nex) = $self->publish_xml_files ($smrt_name, $pub_xml); my ($nfa, $npa, $nea) = $self->publish_aux_files @@ -641,6 +644,9 @@ sub publish_image_archive { q{hifi_reads.lima_summary.txt|summary.json|fail_reads.json|hifi_reads.json|}. q{ccs_report.json|fail_reads.unassigned.json|hifi_reads.unassigned.json}; } + elsif ($process_type eq $ONINST_REVIO2) { + $file_types = q{ccs_report.txt|summary.json|ccs_report.json}; + } my $file_pattern1 = $self->_movie_pattern .q{.}. $file_types . q{$}; my $file_count = scalar split m/[|]/msx, $file_types; @@ -649,7 +655,8 @@ sub publish_image_archive { push @runfolder_files, @{$runfolder_file1}; # Optional 5mC report file - my $fmc_pattern = ($process_type eq $ONINST_REVIO1) ? + my $fmc_pattern = + (($process_type eq $ONINST_REVIO1) || ($process_type eq $ONINST_REVIO2)) ? q{fail_reads.5mc_report.json|hifi_reads.5mc_report.json} : q{5mc_report.json}; my $file_pattern2 = $self->_movie_pattern .q{.}. $fmc_pattern .q{$}; my $runfolder_file2 = $self->list_files($smrt_name,$file_pattern2); diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam.pbi b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam.pbi new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam.pbi b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam.pbi new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/m84098_240321_114027_s1.primary_qc.tar.xz b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/m84098_240321_114027_s1.primary_qc.tar.xz new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/Transfer_Test_240321_105751.txt b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/Transfer_Test_240321_105751.txt new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.metadata.xml b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.metadata.xml new file mode 100644 index 00000000..0e1b89f8 --- /dev/null +++ b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.metadata.xml @@ -0,0 +1,168 @@ + + + + Default + 2024-03-21 + + + + + + + + + + 0 + 0 + + + 19294 + 1 + + + r84098_20240321_105751 + TRACTION-RUN-1199 + ju5 + 2024-03-21T09:09:10.924Z + unknown + 2024-03-21T11:33:24.1187243Z + + + A01 + unspecified + 0 + 253 + 13641 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240321_105751/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240321_105751/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam.pbi b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam.pbi new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sts.xml b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sts.xml new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.transferdone b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.transferdone new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_basic_preview_4hr.metadata.xml b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_basic_preview_4hr.metadata.xml new file mode 100644 index 00000000..007da869 --- /dev/null +++ b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_basic_preview_4hr.metadata.xml @@ -0,0 +1,168 @@ + + + + Default + 2024-03-21 + + + + + + + + + + 0 + 0 + + + 19294 + 1 + + + r84098_20240321_105751 + TRACTION-RUN-1199 + ju5 + 2024-03-21T09:09:10.924Z + unknown + 2024-03-21T11:33:24.1187243Z + + + A01 + unspecified + 0 + 253 + 13641 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240321_105751/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240321_105751/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_full_preview_23hr.metadata.xml b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_full_preview_23hr.metadata.xml new file mode 100644 index 00000000..007da869 --- /dev/null +++ b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_full_preview_23hr.metadata.xml @@ -0,0 +1,168 @@ + + + + Default + 2024-03-21 + + + + + + + + + + 0 + 0 + + + 19294 + 1 + + + r84098_20240321_105751 + TRACTION-RUN-1199 + ju5 + 2024-03-21T09:09:10.924Z + unknown + 2024-03-21T11:33:24.1187243Z + + + A01 + unspecified + 0 + 253 + 13641 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240321_105751/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240321_105751/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.fail_reads.consensusreadset.xml b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.fail_reads.consensusreadset.xml new file mode 100644 index 00000000..6881d8aa --- /dev/null +++ b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.fail_reads.consensusreadset.xml @@ -0,0 +1,174 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + 50734162563 + 3568177 + + + 19294 + + + r84098_20240321_105751 + TRACTION-RUN-1199 + ju5 + 2024-03-21T09:09:10.924Z + unknown + 2024-03-21T11:33:24.1187243Z + + + A01 + unspecified + 0 + 253 + 13641 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240321_105751/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240321_105751/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.hifi_reads.consensusreadset.xml b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.hifi_reads.consensusreadset.xml new file mode 100644 index 00000000..3473f79b --- /dev/null +++ b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.hifi_reads.consensusreadset.xml @@ -0,0 +1,246 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 50734162563 + 3568177 + + + 19294 + + + r84098_20240321_105751 + TRACTION-RUN-1199 + ju5 + 2024-03-21T09:09:10.924Z + unknown + 2024-03-21T11:33:24.1187243Z + + + A01 + unspecified + 0 + 253 + 13641 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240321_105751/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240321_105751/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.json b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.json new file mode 100644 index 00000000..b829e3f0 --- /dev/null +++ b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.json @@ -0,0 +1,244 @@ +{ + "_comment": "Created by pbcopper v2.4.0", + "attributes": [ + { + "id": "ccs_processing.zmw_input", + "name": "ZMWs input", + "value": 6954078 + }, + { + "id": "ccs_processing.zmw_passed_yield", + "name": "ZMWs pass filters", + "value": 3657602 + }, + { + "id": "ccs_processing.zmw_filtered_yield", + "name": "ZMWs fail filters", + "value": 3296476 + }, + { + "id": "ccs_processing.zmw_2_pass_shortcut", + "name": "ZMWs shortcut filters", + "value": 0 + }, + { + "id": "ccs_processing.zmw_tandem_repeat", + "name": "ZMWs with tandem repeats", + "value": 30706 + }, + { + "id": "ccs_processing.zmw_filtered_poor_snr", + "name": "Below SNR threshold", + "value": 70374 + }, + { + "id": "ccs_processing.zmw_filtered_median_length_filter", + "name": "Median length filter", + "value": 956636 + }, + { + "id": "ccs_processing.zmw_filtered_too_few_passes", + "name": "Lacking full passes", + "value": 1560501 + }, + { + "id": "ccs_processing.zmw_filtered_heteroduplexes", + "name": "Heteroduplex insertions", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_coverage_drops", + "name": "Coverage drops", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_insufficient_draft_cov", + "name": "Insufficient draft cov", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_draft_too_different", + "name": "Draft too different", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_draft_failure", + "name": "Draft generation error", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_draft_too_long", + "name": "Draft above --max-length", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_draft_too_short", + "name": "Draft below --min-length", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_read_failed_polish", + "name": "Reads failed polishing", + "value": 3927 + }, + { + "id": "ccs_processing.zmw_filtered_empty_window_during_polishing", + "name": "Empty coverage windows", + "value": 6198 + }, + { + "id": "ccs_processing.zmw_filtered_non_convergent", + "name": "CCS did not converge", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_adapter_concatenation", + "name": "CCS adapter concatenation", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_adapter_palindrom", + "name": "CCS adapter palindrome", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_adapter_residue", + "name": "CCS adapter residue", + "value": 11 + }, + { + "id": "ccs_processing.zmw_filtered_fl_subread", + "name": "ZMW with full-length subread", + "value": 693529 + }, + { + "id": "ccs_processing.zmw_filtered_control_failure", + "name": "ZMW with control failure", + "value": 4155 + }, + { + "id": "ccs_processing.zmw_filtered_control_success", + "name": "ZMW with control success", + "value": 1145 + }, + { + "id": "ccs_processing.zmw_filtered_below_rq", + "name": "CCS below minimum RQ", + "value": 0 + }, + { + "id": "ccs_processing.zmw_filtered_unknown_error", + "name": "Unknown error", + "value": 0 + }, + { + "id": "ccs_processing.zmw_missing_adapters", + "name": "ZMWs missing adapters", + "value": 33615 + }, + { + "id": "ccs_processing.number_of_ccs_reads_q20", + "name": "HiFi Reads", + "value": 3568177 + }, + { + "id": "ccs_processing.total_number_of_ccs_bases_q20", + "name": "HiFi Yield (bp)", + "value": 50734162563 + }, + { + "id": "ccs_processing.mean_ccs_readlength_q20", + "name": "HiFi Read Length (mean, bp)", + "value": 14218 + }, + { + "id": "ccs_processing.median_ccs_readlength_q20", + "name": "HiFi Read Length (median, bp)", + "value": 14194 + }, + { + "id": "ccs_processing.ccs_readlength_n50_q20", + "name": "HiFi Read Length N50 (bp)", + "value": 14194 + }, + { + "id": "ccs_processing.median_qv_q20", + "name": "HiFi Read Quality (median)", + "value": 32 + }, + { + "id": "ccs_processing.mean_npasses_q20", + "name": "HiFi Number of Passes (mean)", + "value": 10 + }, + { + "id": "ccs_processing.number_of_ccs_reads_lq", + "name": "=Q30 Reads", + "value": 2283999 + }, + { + "id": "ccs_processing.total_number_of_ccs_bases_q30", + "name": ">=Q30 Yield (bp)", + "value": 32438019319 + }, + { + "id": "ccs_processing.mean_ccs_readlength_q30", + "name": ">=Q30 Read Length (mean, bp)", + "value": 14202 + }, + { + "id": "ccs_processing.median_ccs_readlength_q30", + "name": ">=Q30 Read Length (median, bp)", + "value": 14199 + }, + { + "id": "ccs_processing.median_qv_q30", + "name": ">=Q30 Read Quality (median)", + "value": 34 + }, + { + "id": "ccs_processing.base_count_q30", + "name": "Base quality >=Q30 (bp)", + "value": 49153092114 + }, + { + "id": "ccs_processing.base_percentage_q30", + "name": "Base quality >=Q30 (%)", + "value": 96.9 + } + ], + "dataset_uuids": [ + "d28a0340-481d-44e3-80d8-e1546c98343e" + ], + "id": "ccs_processing", + "plotGroups": [], + "tables": [], + "title": "CCS Processing Report", + "uuid": "4e403cce-d93a-49e4-993e-86cf765c50d1", + "version": "1.0.1" +} diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.txt b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.txt new file mode 100644 index 00000000..9979ba7c --- /dev/null +++ b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.txt @@ -0,0 +1,57 @@ +ZMWs input : 6,954,078 + +ZMWs pass filters : 3,657,602 (52.60%) +ZMWs fail filters : 3,296,476 (47.40%) +ZMWs shortcut filters : 0 (0.000%) + +ZMWs with tandem repeats : 30,706 (0.931%) + +Exclusive failed counts +Below SNR threshold : 70,374 (2.135%) +Median length filter : 956,636 (29.02%) +Lacking full passes : 1,560,501 (47.34%) +Heteroduplex insertions : 0 (0.000%) +Coverage drops : 0 (0.000%) +Insufficient draft cov : 0 (0.000%) +Draft too different : 0 (0.000%) +Draft generation error : 0 (0.000%) +Draft above --max-length : 0 (0.000%) +Draft below --min-length : 0 (0.000%) +Reads failed polishing : 3,927 (0.119%) +Empty coverage windows : 6,198 (0.188%) +CCS did not converge : 0 (0.000%) +CCS adapter concatenation : 0 (0.000%) +CCS adapter palindrome : 0 (0.000%) +CCS adapter residue : 11 (0.000%) +ZMW with full-length subread : 693,529 (21.04%) +ZMW with control failure : 4,155 (0.126%) +ZMW with control success : 1,145 (0.035%) +CCS below minimum RQ : 0 (0.000%) +Unknown error : 0 (0.000%) + +Additional passing metrics +ZMWs missing adapters : 33,615 (0.919%) + +- - - - - - - - - - - - - - - : - - - - - + +HiFi Reads : 3,568,177 +HiFi Yield (bp) : 50,734,162,563 +HiFi Read Length (mean, bp) : 14,218 +HiFi Read Length (median, bp) : 14,194 +HiFi Read Length N50 (bp) : 14,194 +HiFi Read Quality (median) : 32 +HiFi Number of Passes (mean) : 10 + +=Q30 Reads : 2,283,999 +>=Q30 Yield (bp) : 32,438,019,319 +>=Q30 Read Length (mean, bp) : 14,202 +>=Q30 Read Length (median, bp): 14,199 +>=Q30 Read Quality (median) : 34 + +Base quality >=Q30 (bp) : 49,153,092,114 (96.9%) diff --git 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b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.reports.zip new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.summary.json b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.summary.json new file mode 100644 index 00000000..e570c130 --- /dev/null +++ b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.summary.json @@ -0,0 +1 @@ +{"hifi_mean_qv":31.6,"hifi_mean_read_length":14219,"number_hifi_reads":3568177,"q30_base_percentage":96.9,"version":"3"} diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.csv.gz b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.csv.gz new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.json.gz b/t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.json.gz new file mode 100644 index 00000000..e69de29b diff --git a/t/fixtures/ml_warehouse/300-PacBioRun.yml b/t/fixtures/ml_warehouse/300-PacBioRun.yml index 90097a4a..b5185d3f 100644 --- a/t/fixtures/ml_warehouse/300-PacBioRun.yml +++ b/t/fixtures/ml_warehouse/300-PacBioRun.yml @@ -2424,3 +2424,33 @@ library_created_at: ~ pac_bio_run_name: TRACTION-RUN-1130 pac_bio_library_tube_barcode: TRAC-2-7582 +- id_pac_bio_tmp: 121059 + last_updated: 2024-03-21 08:59:02 + recorded_at: 2024-03-21 08:59:02 + id_sample_tmp: 8409942 + id_study_tmp: 5735 + id_pac_bio_run_lims: TRACTION-RUN-1199 + pac_bio_run_uuid: 7c19d2e4-c908-47ba-bd37-e1234635ee15 + cost_code: S10613 + id_lims: Traction + tag_identifier: ~ + tag_sequence: ~ + tag_set_id_lims: ~ + tag_set_name: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag2_identifier: ~ + pipeline_id_lims: Pacbio_IsoSeq + plate_barcode: ~ + plate_uuid_lims: 76458489-3fd9-4245-8cbf-4e64c6660675 + plate_number: 1 + well_label: A1 + well_uuid_lims: e894a0b1-da57-4626-a021-faeb3daff03a + pac_bio_library_tube_id_lims: 11684 + pac_bio_library_tube_uuid: 927693e2-7b6d-43b8-8df0-3c58e88c074b + pac_bio_library_tube_name: 7323STDY14717195 + pac_bio_library_tube_legacy_id: ~ + library_created_at: ~ + pac_bio_run_name: TRACTION-RUN-1199 + pac_bio_library_tube_barcode: TRAC-2-8178 diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherTest.pm index 406b5067..487a65d0 100644 --- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherTest.pm +++ b/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherTest.pm @@ -586,6 +586,57 @@ sub publish_files_on_instrument_6 : Test(79) { } +sub publish_files_on_instrument_7 : Test(4) { + ## revio v13 - hifi data not deplexed + + my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, + strict_baton_version => 0); + my $runfolder_path = "$data_path/r84098_20240321_105751"; + my $dest_coll = "$irods_tmp_coll/publish_files"; + + my $client = WTSI::NPG::HTS::PacBio::Sequel::APIClient->new(); + + my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); + my $tmprf_path = catdir($tmpdir->dirname, 'r84098_20240321_105751'); + dircopy($runfolder_path,$tmprf_path) or die $!; + chmod (0770, "$tmprf_path/1_A01") or die "Chmod 0770 directory failed : $!"; + + my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new + (api_client => $client, + dest_collection => $dest_coll, + irods => $irods, + mlwh_schema => $wh_schema, + runfolder_path => $tmprf_path); + + my @expected_paths = + map { catfile("$dest_coll/1_A01", $_) } + ('m84098_240321_114027_s1.fail_reads.bam', + 'm84098_240321_114027_s1.fail_reads.bam.pbi', + 'm84098_240321_114027_s1.fail_reads.consensusreadset.xml', + 'm84098_240321_114027_s1.hifi_reads.bam', + 'm84098_240321_114027_s1.hifi_reads.bam.pbi', + 'm84098_240321_114027_s1.hifi_reads.consensusreadset.xml', + 'm84098_240321_114027_s1.primary_qc.tar.xz', + 'm84098_240321_114027_s1.reports.zip', + 'm84098_240321_114027_s1.sequencing_control.subreads.bam', + 'm84098_240321_114027_s1.sequencing_control.subreads.bam.pbi', + 'm84098_240321_114027_s1.sts.xml', + 'm84098_240321_114027_s1.zmw_metrics.json.gz', + 'merged_analysis_report.json', + ); + + my ($num_files, $num_processed, $num_errors) = $pub->publish_files; + cmp_ok($num_files, '==', 13); + cmp_ok($num_processed, '==', 13); + cmp_ok($num_errors, '==', 0); + + my @observed_paths = observed_data_objects($irods, $dest_coll); + is_deeply(\@observed_paths, \@expected_paths, + 'Published correctly named on instrument files') or + diag explain \@observed_paths; + +} + sub publish_files_off_instrument : Test(3) { my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, strict_baton_version => 0); From cfcf83525ff355b15b97483208876d7b185ad27e Mon Sep 17 00:00:00 2001 From: Carol Scott Date: Mon, 15 Apr 2024 12:11:07 +0100 Subject: [PATCH 3/5] Analysis loading changes post SMRT Link v13 --- MANIFEST | 91 ++---- bin/npg_pacbio_analysis_monitor.pl | 9 +- .../NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm | 14 +- .../HTS/PacBio/Sequel/AnalysisPublisher.pm | 25 +- t/data/mlwh_json/pacbio.json | 2 +- ...iplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.bam | 0 ...x.bc1009_BAK8A_OA--bc1009_BAK8A_OA.bam.pbi | 0 ...A_OA--bc1009_BAK8A_OA.consensusreadset.xml | 0 .../execution/demultiplex.lima.counts | 2 - .../execution/demultiplex.lima.guess.txt | 9 - .../execution/demultiplex.lima.summary.txt | 24 -- .../execution/demultiplex.removed.bam | 0 .../execution/demultiplex.removed.bam.pbi | 0 .../demultiplex.removed.consensusreadset.xml | 0 .../execution/merged_analysis_report.json | 1 - ...5099-4efb-9702-0f97bf22dc59.subreadset.xml | 168 ---------- ...iplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam | 0 ...x.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam.pbi | 0 ...B_OA--bc1019_BAK8B_OA.consensusreadset.xml | 0 .../demultiplex.consensusreadset.xml | 0 .../call-lima/execution/demultiplex.json | 19 -- .../execution/demultiplex.lima.counts | 2 - .../execution/demultiplex.lima.guess.txt | 2 - .../execution/demultiplex.lima.report | 0 .../execution/demultiplex.lima.summary.txt | 24 -- .../execution/demultiplex.unbarcoded.bam | 0 .../execution/demultiplex.unbarcoded.bam.pbi | 0 ...emultiplex.unbarcoded.consensusreadset.xml | 0 .../execution/lima_guesses_report.json | 39 --- .../execution/merged_analysis_report.json | 1 - ...m64229e_221104_164228.consensusreadset.xml | 156 --------- ...iplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam | 0 ...x.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam.pbi | 0 ...B_OA--bc1019_BAK8B_OA.consensusreadset.xml | 0 .../demultiplex.consensusreadset.xml | 0 .../call-lima/execution/demultiplex.json | 19 -- .../execution/demultiplex.lima.counts | 2 - .../execution/demultiplex.lima.guess.txt | 2 - .../execution/demultiplex.lima.report | 0 .../execution/demultiplex.lima.summary.txt | 24 -- .../execution/demultiplex.unbarcoded.bam | 0 .../execution/demultiplex.unbarcoded.bam.pbi | 0 ...emultiplex.unbarcoded.consensusreadset.xml | 0 .../execution/lima_guesses_report.json | 39 --- .../execution/merged_analysis_report.json | 1 - ...m64229e_221104_164228.consensusreadset.xml | 156 --------- ...12b8-45e6-bc10-b0790f8d6758.subreadset.xml | 148 --------- .../m64016_190608_025655.ccs.bam | 0 .../m64016_190608_025655.ccs.bam.pbi | 0 .../merged_analysis_report.json | 1 - ...8918-4ef1-8649-f44adaac75d3.subreadset.xml | 158 --------- .../lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam | 0 ...a.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam.pbi | 0 ...2_BAK8B_OA--bc1022_BAK8B_OA.subreadset.xml | 0 .../barcoding.tasks.lima-0/lima.removed.bam | 0 .../lima.removed.bam.pbi | 0 .../lima.removed.subreadset.xml | 0 t/fixtures/ml_warehouse/300-PacBioRun.yml | 31 ++ .../HTS/PacBio/Sequel/AnalysisMonitorTest.pm | 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t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1012_5p--bc1012_3p.consensusreadset.xml t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/merged_analysis_report.json t/data/pacbio/sequel_analysis/0000004117/entry-points/222a1be3-85b1-12b3-b3bc-9742f8e22f95.consensusreadset.xml -t/data/pacbio/sequel_analysis/0000010313/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml -t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.consensusreadset.xml -t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.json -t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.counts -t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.guess.txt -t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.report 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-t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam -t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam.pbi -t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.consensusreadset.xml -t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/lima_guesses_report.json -t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/merged_analysis_report.json -t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam -t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam.pbi -t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.consensusreadset.xml -t/data/pacbio/sequel_analysis/001185/entry-points/2c677e30-8918-4ef1-8649-f44adaac75d3.subreadset.xml -t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam -t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam.pbi -t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subreadset.xml -t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.bam -t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.bam.pbi -t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.subreadset.xml -t/data/pacbio/sequel_analysis/001612/entry-points/07d85801-6a09-4728-982c-e3c048f95bd8.subreadset.xml -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc12--lbc12.bam -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc12--lbc12.bam.pbi -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc12--lbc12.subreadset.xml -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc5--lbc5.bam -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc5--lbc5.bam.pbi -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc5--lbc5.subreadset.xml -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lima.counts -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lima.guess.txt -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lima.summary.txt -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.removed.bam -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.removed.bam.pbi -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.removed.subreadset.xml -t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/merged_analysis_report.json -t/data/pacbio/sequel_analysis/000226/entry-points/acf46f00-12b8-45e6-bc10-b0790f8d6758.subreadset.xml -t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/m64016_190608_025655.ccs.bam -t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/m64016_190608_025655.ccs.bam.pbi -t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/merged_analysis_report.json +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/lima_guesses.report.json +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.json +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi +t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml +t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml +t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.consensusreadset.xml +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/lima_guesses.report.json +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.json +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi +t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml +t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml +t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.consensusreadset.xml t/data/pacbio_meta_updater/m131209_183112_00127_c100579142550000001823092301191430_s1_p0.1.bax.h5 t/data/pacbio_seq_data_object/m54097_161031_165824.subreads.bam t/data/pacbio_seq_data_object/m54097_161207_133626.subreads.bam diff --git a/bin/npg_pacbio_analysis_monitor.pl b/bin/npg_pacbio_analysis_monitor.pl index 234b6fc2..5de04fa0 100755 --- a/bin/npg_pacbio_analysis_monitor.pl +++ b/bin/npg_pacbio_analysis_monitor.pl @@ -19,13 +19,11 @@ Readonly::Scalar my $DEFAULT_INTERVAL_DAYS => 14; Readonly::Scalar my $DEFAULT_OLDER_THAN_DAYS => 0; -Readonly::Scalar my $DEFAULT_SUBDIR => 0; my $api_uri; my $collection; my $debug; my $interval = $DEFAULT_INTERVAL_DAYS; -my $is_sub = $DEFAULT_SUBDIR; my $log4perl_config; my $older_than = $DEFAULT_OLDER_THAN_DAYS; my $pipeline_name; @@ -38,7 +36,6 @@ pod2usage(-verbose => 2, -exitval => 0); }, 'interval=i' => \$interval, - 'is_sub' => \$is_sub, 'logconf=s' => \$log4perl_config, 'older-than|older_than=i' => \$older_than, 'pipeline-name|pipeline_name=s' => \$pipeline_name, @@ -62,7 +59,6 @@ my @init_args = (interval => $interval, irods => $irods, - is_sub => $is_sub, mlwh_schema => $wh_schema, older_than => $older_than, ); @@ -110,7 +106,7 @@ =head1 NAME =head1 SYNOPSIS npg_pacbio_analysis_monitor - [--collection ] [--debug] [--interval days] [--is_sub] + [--collection ] [--debug] [--interval days] [--logconf ] [--older-than days] [--pipeline_name ] [--task_name ] [--api-uri] [--verbose] @@ -120,9 +116,6 @@ =head1 SYNOPSIS --debug Enable debug level logging. Optional, defaults to false. --help Display help. - --is_sub Data to be loaded is in sub-direcories of the - main analysis output directroy. Optional, defaults - to false. --interval Interval of time in days for analysis loading. Optional, defaults to 14. diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm b/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm index d601362f..24961165 100644 --- a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm +++ b/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm @@ -24,14 +24,14 @@ has 'pipeline_name' => (isa => 'Str', is => 'ro', required => 1, - default => 'pbsmrtpipe.pipelines.sa3_ds_barcode2', + default => 'cromwell.workflows.pb_demux_ccs', documentation => 'A specified pipeline name to identify relevant jobs'); has 'task_name' => (isa => 'Str', is => 'ro', required => 1, - default => 'barcoding.tasks.lima-0', + default => 'call-lima/execution', documentation => 'A specified task name to identify relevant output directories'); has 'job_root' => @@ -41,13 +41,6 @@ has 'job_root' => default => 'cromwell-job', documentation => 'Root directory for job processing output'); -has 'is_sub' => - (isa => 'Bool', - is => 'ro', - required => 0, - default => 0, - documentation => 'Data to be loaded is in the sub-directories of main output directory'); - =head2 publish_analysed_cells @@ -119,9 +112,6 @@ sub _publish_analysis_path { if ($self->dest_collection) { push @init_args, dest_collection => $self->dest_collection; } - if ($self->is_sub == 1 ) { - push @init_args, is_oninstrument => 1; - } my $publisher = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new(@init_args); diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm b/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm index b6461e21..5487ed9c 100644 --- a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm +++ b/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm @@ -32,6 +32,7 @@ our $SMT_METADATA_SET = q{hifi_reads.consensusreadset}; # Location of source metadata file our $ENTRY_DIR = 'entry-points'; +our $OUTPUT_DIR = 'outputs'; # Generic moviename file prefix our $MOVIENAME_PATTERN = 'm[0-9a-z]+_\d+_\d+'; @@ -40,8 +41,8 @@ our $MOVIENAME_PATTERN = 'm[0-9a-z]+_\d+_\d+'; our $WELL_DIRECTORY_PATTERN = '\d+_[A-Z]\d+$'; # Additional sequence filenames permitted for loading -our @FNAME_PERMITTED = qw[fail_reads removed ccs hifi_reads fl_transcripts sequencing_control.subreads]; -our @FNAME_NON_DEPLEXED = qw[unassigned removed sequencing_control.subreads]; +our @FNAME_PERMITTED = qw[fail_reads removed ccs hifi_reads fl_transcripts sequencing_control.subreads unbarcoded]; +our @FNAME_NON_DEPLEXED = qw[unassigned removed sequencing_control.subreads unbarcoded]; our @FNAME_FAILED = qw[fail_reads]; # Data processing level @@ -323,7 +324,8 @@ sub list_files { } } } else { - @files = $self->list_directory($self->runfolder_path, filter => $type); + @files = $self->list_directory + ($self->runfolder_path, filter => $type, recurse => 1); } return \@files; @@ -369,25 +371,34 @@ has '_metadata' => sub _build_metadata{ my ($self) = @_; - my $entry_path = catdir($self->analysis_path, $ENTRY_DIR); + my $entry_path = catdir($self->analysis_path, $ENTRY_DIR); + my $output_path = catdir($self->analysis_path, $OUTPUT_DIR); my @metafiles; - if ($self->is_oninstrument == 1 && ! -d $entry_path && $self->is_smtwelve == 1) { + if (-d $output_path && ! -d $entry_path) { + # As all analysis cell based all metafiles should have the correct run name, + # well and plate number as no merged cell analysis - so just pick one. + my @files = $self->list_directory + ($output_path, filter => $METADATA_SET .q[.]. $METADATA_FORMAT . q[$]); + push @metafiles, $files[0]; + } elsif ($self->is_oninstrument == 1 && ! -d $entry_path && $self->is_smtwelve == 1) { + # Revio @metafiles = $self->list_directory ($self->analysis_path, filter => $self->movie_pattern .q[.]. $SMT_METADATA_SET .q[.]. $METADATA_FORMAT .q[$], recurse => 1) } elsif ($self->is_oninstrument == 1 && ! -d $entry_path) { + # Sequel IIe - as will never be upgraded from ICS v11 @metafiles = $self->list_directory ($self->analysis_path, filter => $self->movie_pattern .q[.]. $METADATA_SET .q[.]. $METADATA_FORMAT .q[$]) - } else { + } elsif (-d $entry_path) { @metafiles = $self->list_directory ($entry_path, filter => $METADATA_FORMAT . q[$], recurse => 1); } if (@metafiles != 1) { - $self->logcroak('Expect one xml file in '. $self->analysis_path . ' (entry_dir)'); + $self->logcroak('Expect one xml file in '. $self->analysis_path); } return WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file ($metafiles[0], $METADATA_PREFIX); diff --git a/t/data/mlwh_json/pacbio.json b/t/data/mlwh_json/pacbio.json index e8b9cc70..16817feb 100644 --- a/t/data/mlwh_json/pacbio.json +++ b/t/data/mlwh_json/pacbio.json @@ -1 +1 @@ -{"version":"1.0","products":[{"irods_data_relative_path":"lima_output.lbc5--lbc5.bam","id_product":"6948c60e9ee9117255f1123e2c403013596339eda68b6b8e8867bc132023955d","irods_root_collection":"/testZone/home/irods/RunPublisherTest.XXXXX.0/publish_files/2_B01/","pipeline_name":"npg-prod","seq_platform_name":"pacbio"}, {"irods_data_relative_path":"lima_output.lbc12--lbc12.bam","id_product":"40ff7f2193f3b515a6c69ab284622c935097a63ccbf3eaf09cc39b5ff44468af","irods_root_collection":"/testZone/home/irods/RunPublisherTest.XXXXX.0/publish_files/2_B01/","pipeline_name":"npg-prod","seq_platform_name":"pacbio"}]} \ No newline at end of file +{"version":"1.0","products":[{"id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_root_collection":"/testZone/home/irods/RunPublisherTest.XXXXX.0/publish_sequence_files/1_A01/","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","pipeline_name":"npg-prod","seq_platform_name":"pacbio"}]} diff --git a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.bam b/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.bam deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.bam.pbi b/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.bam.pbi deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.consensusreadset.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.counts b/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.counts deleted file mode 100644 index 8501d10c..00000000 --- a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.counts +++ /dev/null @@ -1,2 +0,0 @@ -IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore -4 4 bc1009_BAK8A_OA bc1009_BAK8A_OA 1117 5 diff --git a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.guess.txt b/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.guess.txt deleted file mode 100644 index 8bd6525e..00000000 --- a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.guess.txt +++ /dev/null @@ -1,9 +0,0 @@ -IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed NumZMWs MeanScore Picked -3 3 bc1008_BAK8A_OA bc1008_BAK8A_OA 3 71 0 -4 4 bc1009_BAK8A_OA bc1009_BAK8A_OA 1 28 0 -5 5 bc1010_BAK8A_OA bc1010_BAK8A_OA 1 29 0 -6 6 bc1011_BAK8A_OA bc1011_BAK8A_OA 3 24 0 -7 7 bc1012_BAK8A_OA bc1012_BAK8A_OA 5 79 0 -10 10 bc1017_BAK8B_OA bc1017_BAK8B_OA 49385 89 1 -14 14 bc1021_BAK8B_OA bc1021_BAK8B_OA 1 17 0 -15 15 bc1022_BAK8B_OA bc1022_BAK8B_OA 1 100 0 diff --git a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.summary.txt b/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.summary.txt deleted file mode 100644 index c166e54f..00000000 --- a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.summary.txt +++ /dev/null @@ -1,24 +0,0 @@ -ZMWs input (A) : 80139 -ZMWs above all thresholds (B) : 1117 (1%) -ZMWs below any threshold (C) : 79022 (99%) - -ZMW marginals for (C): -Below min length : 2 (0%) -Below min score : 73425 (93%) -Below min end score : 73425 (93%) -Below min passes : 0 (0%) -Below min score lead : 73425 (93%) -Below min ref span : 79022 (100%) -Without SMRTbell adapter : 0 (0%) - -ZMWs for (B): -With same pair : 1117 (100%) -Coefficient of correlation : 0% - -ZMWs for (A): -Allow diff pair : 80139 (100%) -Allow same pair : 80139 (100%) - -Reads for (B): -Above length : 1117 (100%) -Below length : 0 (0%) diff --git a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam b/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam.pbi b/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam.pbi deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.consensusreadset.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json b/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json deleted file mode 100644 index ef2ab406..00000000 --- a/t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json +++ /dev/null @@ -1 +0,0 @@ -{"__CLASS__":"WTSI::NPG::HTS::PacBio::Sequel::Reportdata-2.28.0","created_at":"2021-04-12T07:30:03","meta_data":{"__CLASS__":"WTSI::NPG::HTS::PacBio::Metadata-2.28.0","ccsreads_uuid":"a8ddfa78-f166-4547-ada4-72bd46f608af","cell_index":"1","collection_number":"1","file_path":"/nfs/pacbio_data/smrtlink/userdata/jobs_root/0000/0000003/0000003280/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml","instrument_name":"64221E","is_ccs":"true","movie_name":"m64221e_210410_143943","results_folder":"r64221e_20210409_135810/2_B01/","run_name":"81230","sample_load_name":"DN787408U-C2","subreads_uuid":"081746ec-5099-4efb-9702-0f97bf22dc59","ts_run_name":"r64221e_20210409_135810","version_info":{"chemistry":"10.0.0.108341","ics":"10.0.0.111772","iui":"10.0.0.111772","pa":"10.0.0.111772","paws":"10.0.0.111772","ppa":"10.0.0.111772","realtime":"10.0.0.111772","smrtimisc":"10.0.0.108728","smrtinub":"10.0.0.108728","smrtlink":"10.0.0.108728","smrtlink-analysisservices-gui":"10.0.0.108728","smrttools":"10.0.0.108728","transfer":"10.0.0.111772"},"well_name":"B01"},"reports":{"barcode_ccs.report.json":[{"id":"barcode.n_barcodes","name":"Unique Barcodes","value":1},{"id":"barcode.n_barcoded_reads","name":"Barcoded Reads","value":1117},{"id":"barcode.mean_reads","name":"Mean Reads","value":1117},{"id":"barcode.max_reads","name":"Max. Reads","value":1117},{"id":"barcode.min_reads","name":"Min. Reads","value":1117},{"id":"barcode.mean_read_length","name":"Mean Read Length","value":14004},{"id":"barcode.n_unbarcoded_reads","name":"Unbarcoded Reads","value":79022},{"id":"barcode.percent_barcoded_bases","name":"Percent Bases in Barcoded Reads","value":0.0139577593642927},{"id":"barcode.percent_barcoded_reads","name":"Percent Barcoded Reads","value":0.0139382822346174}],"ccs.report.json":[{"id":"ccs2.number_of_ccs_reads","name":"HiFi Reads","value":80139},{"id":"ccs2.total_number_of_ccs_bases","name":"HiFi Yield (bp)","value":1120808794},{"id":"ccs2.mean_ccs_readlength","name":"HiFi Read Length (mean, bp)","value":13985},{"id":"ccs2.median_accuracy","name":"HiFi Read Quality (median)","value":"Q30"},{"id":"ccs2.mean_npasses","name":"HiFi Number of Passes (mean)","value":9},{"id":"ccs2.n_low_quality_reads","name":" - - - - - - - - - - - - - - - - - - 16277928039 - 1384621 - - - - - - - - - - 0 - - 10.0.0.111772 - 10.0.0.111772 - - r64221e_20210409_135810 - 81230 - chc - 2021-04-09T13:46:43.199Z - unknown - 0001-01-01T00:00:00 - - - B01 - lowDNAInput - 0.0 - 140.0 - 11867 - false - true - false - false - false - 0 - Sequel® II DNA Internal Control 1.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - 1 - 0 - - - Spider_1p0_NTO - - - - >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTGTCTAGGTCATCTCAACGTAGCTTTGACATATAACTTATCTAAAGTAATCCCTGCACACCTGTATGCATTATGCTTGCTATACACGCGGACACAGGCATATCATTTATTTTTTGCCATGTCCATTAATTGTTCAATAATTTTACTCACGGTATTTAATTTGATGTTGTGTTATATAGAATTGGAATTAAACTTATAAGGATGCTTAGACGTTGCATTATAAAAGTTTATGTACTAAGTATTTAAGACATTGGCATATGATTATAGCTTGACATTATTAAAAATTAATTAATTAAATCTCACACAATACTTATTCAAGACATTTTTACTAAGATAACCAAAGGAATGCGAACAAAATAATACTTAAAATATAAGACTTAGAAGTAATATGATCCAATAGTTACATATAGTACACTAAGTTCCTAAATTATATAACTTTAAAACAAAGTTACGAAATTTGGAAATAATTTTATTTAATCATATTTTCATAATAATGAAATACTGTTTATTTCAGTGGCGAAAAGAGATAATACGATTTTATAGTGATAGAATATCCTTGAAATATCTAAAGATAAAATTAGAAACTTTCTCTTTTCGCTGTAAAGCTATATGACTTAAAAATAACTTATACGCAAAGTATATTGCAGTGGAAACCCAAGAGTATAGTAGCCATGTAATCTCGGGTTCGAAACTACACGCCGCGCACGTAGTCAGATGGTCTGAAACTTGTCTGGGGCTGTTTGTTGACGGATGGAGACTTCACTAAGTGGCGTCAGGCGATGCGCACACACGGGACTCAATCCCGTAGCATGTTATGTGTCGTTCGAAACTCGTGCGTTCGAGATTTACGCCACATTGCCGGCTGGTCCAAGGACGTTATCTACCAGATGATACGGTCCAATTCGTAAGTTTGACTCACATAGTCGCGAACCGCGGAGCTGGAGAACAATAATTACCGGATGATTAGTTGACCATACGCACTATCATGCTCCGTGACTCAGTTTCCGCCATGGAGTTCTCACAGCCCCGTGTGTACCATAACTGCAGTAAGTAAGGACCTTGTTCGGAGGCCGACTCGTATTTCATATGATCTTAGTCTCGCCACCTTATCGCACGAATTGGGGGTGTCTTTTAGCCGACTCCGGCACGATCCGCCGGGAAGTTACTCGACCAGTTGCGGGACGCCCTAGTATGTTCGTATTACGTTCGATGCGTAAGCACCCCAGAGATTTTTGGCGGACGTTTCGGTAAATCATAGTAGAACCGGAGCGGTAAAGCTATTGATAACACGCAGGGACGAGCCAGTCGTCTAAGCTCCTCAGGGGTACCGTTCGCCGGACTACAGCCTGTCCCCGGCGGCCGCAACTGGGCTGCGATCCAGCCCCCGCTCCAAAAGGATGACTCGACCTTGCGCCTCGCGTACTCTGCTCTCGAGCTGTCTCCGTGGGCAATGCCGGCTCACGCTGTGGGGAACCCTGGACGCCCGGGCCGAGCCGACGTGGCCCCGCCCAGGCCTTTTCGTCGATCGCAGCTATGTACCCTGTGCTGGCCAGCGCTACTGCGCCGGCCATTAGCGGTGCGCTCTCGACTCGGCCCCAACGTAGACGGCGTCGCTGGCCGGATTCAAAGAAGTGAGCTACTACCATCGCGTGACGCCCTGCGGGCCTGAGTAACCGTGCACGAAGGACACCCCGTTCGTGGCGGGGGTTGCCTCCGCGACGGTCGCCAACGTTGGGGGTCGGTGCATTCAGGCGACGAGGGACCGCTGGTTTCCGGAGAGCGGCCTGTGCTCACACAGGTGCGGTCCATGGGGCCTGTGGATCCGGTTCTCCCACGCGTAGCGCCGGCGTTAGCATGGACGCTAAATAAGTATACGCCGGCAAAGGGAGTGTAGGCCGGCCCGAGGGCAATCGCGGTTACCGGGGTGGGGGAGCTCCCCGCACCAGCCTTGATGTGGTGTGCGAGCG - - - - ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT - aacggaggaggagga - ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT - aacggaggaggagga - - - - - - - - - - - - SequelAlpha - SqlPoC_SubCrf_2C2A-t2.xml - DefaultPrimarySequencingCondition - - OffInstrument - true - - - r64221e_20210409_135810/2_B01/ - /nfs/sf28/pacbio/r64221e_20210409_135810/2_B01/ - - Fasta - Bam - - Bases_Without_QVs - Minimal - - new-resource - RSYNC - Sanger sequel - Sanger transfer settings - /nfs/sf28/pacbio - - - - {"adapterFinding":{"disableAdapterFinding":false,"leftAdapter":"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT","rightAdapter":"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT"},"controlFilter":{"disableControlFiltering":false,"leftAdapter":"TAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA","rightAdapter":"TAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA","sequence":"TGTCTAGGTCATCTCAACGTAGCTTTGACATATAACTTATCTAAAGTAATCCCTGCACACCTGTATGCATTATGCTTGCTATACACGCGGACACAGGCATATCATTTATTTTTTGCCATGTCCATTAATTGTTCAATAATTTTACTCACGGTATTTAATTTGATGTTGTGTTATATAGAATTGGAATTAAACTTATAAGGATGCTTAGACGTTGCATTATAAAAGTTTATGTACTAAGTATTTAAGACATTGGCATATGATTATAGCTTGACATTATTAAAAATTAATTAATTAAATCTCACACAATACTTATTCAAGACATTTTTACTAAGATAACCAAAGGAATGCGAACAAAATAATACTTAAAATATAAGACTTAGAAGTAATATGATCCAATAGTTACATATAGTACACTAAGTTCCTAAATTATATAACTTTAAAACAAAGTTACGAAATTTGGAAATAATTTTATTTAATCATATTTTCATAATAATGAAATACTGTTTATTTCAGTGGCGAAAAGAGATAATACGATTTTATAGTGATAGAATATCCTTGAAATATCTAAAGATAAAATTAGAAACTTTCTCTTTTCGCTGTAAAGCTATATGACTTAAAAATAACTTATACGCAAAGTATATTGCAGTGGAAACCCAAGAGTATAGTAGCCATGTAATCTCGGGTTCGAAACTACACGCCGCGCACGTAGTCAGATGGTCTGAAACTTGTCTGGGGCTGTTTGTTGACGGATGGAGACTTCACTAAGTGGCGTCAGGCGATGCGCACACACGGGACTCAATCCCGTAGCATGTTATGTGTCGTTCGAAACTCGTGCGTTCGAGATTTACGCCACATTGCCGGCTGGTCCAAGGACGTTATCTACCAGATGATACGGTCCAATTCGTAAGTTTGACTCACATAGTCGCGAACCGCGGAGCTGGAGAACAATAATTACCGGATGATTAGTTGACCATACGCACTATCATGCTCCGTGACTCAGTTTCCGCCATGGAGTTCTCACAGCCCCGTGTGTACCATAACTGCAGTAAGTAAGGACCTTGTTCGGAGGCCGACTCGTATTTCATATGATCTTAGTCTCGCCACCTTATCGCACGAATTGGGGGTGTCTTTTAGCCGACTCCGGCACGATCCGCCGGGAAGTTACTCGACCAGTTGCGGGACGCCCTAGTATGTTCGTATTACGTTCGATGCGTAAGCACCCCAGAGATTTTTGGCGGACGTTTCGGTAAATCATAGTAGAACCGGAGCGGTAAAGCTATTGATAACACGCAGGGACGAGCCAGTCGTCTAAGCTCCTCAGGGGTACCGTTCGCCGGACTACAGCCTGTCCCCGGCGGCCGCAACTGGGCTGCGATCCAGCCCCCGCTCCAAAAGGATGACTCGACCTTGCGCCTCGCGTACTCTGCTCTCGAGCTGTCTCCGTGGGCAATGCCGGCTCACGCTGTGGGGAACCCTGGACGCCCGGGCCGAGCCGACGTGGCCCCGCCCAGGCCTTTTCGTCGATCGCAGCTATGTACCCTGTGCTGGCCAGCGCTACTGCGCCGGCCATTAGCGGTGCGCTCTCGACTCGGCCCCAACGTAGACGGCGTCGCTGGCCGGATTCAAAGAAGTGAGCTACTACCATCGCGTGACGCCCTGCGGGCCTGAGTAACCGTGCACGAAGGACACCCCGTTCGTGGCGGGGGTTGCCTCCGCGACGGTCGCCAACGTTGGGGGTCGGTGCATTCAGGCGACGAGGGACCGCTGGTTTCCGGAGAGCGGCCTGTGCTCACACAGGTGCGGTCCATGGGGCCTGTGGATCCGGTTCTCCCACGCGTAGCGCCGGCGTTAGCATGGACGCTAAATAAGTATACGCCGGCAAAGGGAGTGTAGGCCGGCCCGAGGGCAATCGCGGTTACCGGGGTGGGGGAGCTCCCCGCACCAGCCTTGATGTGGTGTGCGAGCG"},"hqrf":{"method":"M1"},"inputFilter":{"minSnr":2}} - - DefaultSecondaryAutomationName - - - - 0 - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam.pbi b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam.pbi deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.consensusreadset.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.consensusreadset.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.json b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.json deleted file mode 100644 index 6de5cebd..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "createdAt": "2022-11-06T08:33:31.296Z", - "files": [ - { - "createdAt": "2022-11-06T08:33:31.295Z", - "description": "Split BAM file by lima", - "fileSize": 1231145624, - "fileTypeId": "PacBio.DataSet.ConsensusReadSet", - "isChunked": false, - "modifiedAt": "2022-11-06T08:33:31.296Z", - "name": "Barcodes bc1019_BAK8B_OA--bc1019_BAK8B_OA", - "path": "bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.consensusreadset.xml", - "sourceId": "barcoding.tasks.lima-0", - "uniqueId": "030f5f22-cb34-43d4-b1f4-aeebe58f4535" - } - ], - "updatedAt": "2022-11-06T08:33:31.296Z", - "version": "0.2.2" -} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.counts b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.counts deleted file mode 100644 index ae4a3bea..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.counts +++ /dev/null @@ -1,2 +0,0 @@ -IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore -12 12 bc1019_BAK8B_OA bc1019_BAK8B_OA 2654483 98 diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.guess.txt b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.guess.txt deleted file mode 100644 index 1e002006..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.guess.txt +++ /dev/null @@ -1,2 +0,0 @@ -IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed NumZMWs MeanScore Picked -12 12 bc1019_BAK8B_OA bc1019_BAK8B_OA 46856 98 1 diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.report b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.report deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.summary.txt b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.summary.txt deleted file mode 100644 index 99c7339e..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.summary.txt +++ /dev/null @@ -1,24 +0,0 @@ -ZMWs input (A) : 2732784 -ZMWs above all thresholds (B) : 2654483 (97.13%) -ZMWs below any threshold (C) : 78301 (2.87%) - -ZMW marginals for (C): -Below min length : 1 (0.00%) -Below min score : 78294 (99.99%) -Below min end score : 25219 (32.21%) -Below min passes : 0 (0.00%) -Below min score lead : 523 (0.67%) -Below min ref span : 1919 (2.45%) -Without SMRTbell adapter : 6 (0.01%) - -ZMWs for (B): -With same pair : 2654483 (100.00%) -Coefficient of correlation : 0.00% - -ZMWs for (A): -Allow diff pair : 2634196 (96.39%) -Allow same pair : 2732778 (100.00%) - -Reads for (B): -Above length : 2654483 (100.00%) -Below length : 0 (0.00%) diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam.pbi b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam.pbi deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.unbarcoded.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.unbarcoded.consensusreadset.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/lima_guesses_report.json b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/lima_guesses_report.json deleted file mode 100644 index 653e1e5c..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/lima_guesses_report.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "_comment": "Created by pbcopper v2.0.0", - "attributes": [], - "dataset_uuids": [], - "id": "lima_infer", - "plotGroups": [], - "tables": [ - { - "columns": [ - { - "header": "Barcode Name", - "id": "first_bc_name", - "values": [ - "bc1019_BAK8B_OA--bc1019_BAK8B_OA" - ] - }, - { - "header": "#ZMWs", - "id": "num_zmws", - "values": [ - 46856 - ] - }, - { - "header": "Mean Barcode Score", - "id": "mean_bc_score", - "values": [ - 98 - ] - } - ], - "id": "inferred_barcode_table", - "title": "Inferred Barcodes" - } - ], - "title": "Barcoding Inferred Barcodes Report", - "uuid": "677bf779-91aa-4814-b6b7-2a029205d3ba", - "version": "1.0.1" -} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/merged_analysis_report.json b/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/merged_analysis_report.json deleted file mode 100644 index 51d85232..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/merged_analysis_report.json +++ /dev/null @@ -1 +0,0 @@ -{"__CLASS__":"WTSI::NPG::HTS::PacBio::Sequel::Reportdata","created_at":"2022-11-07T22:07:35","meta_data":{"__CLASS__":"WTSI::NPG::HTS::PacBio::Metadata","ccsreads_uuid":"cc8e3c72-f250-45d5-b9ae-9e92ab538ac1","cell_index":"0","collection_number":"0","execution_mode":"OnInstrument","file_path":"/nfs/pacbio_data/smrtlink/userdata/jobs_root/0000/0000010/0000010313/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml","instrument_name":"64229E","movie_name":"m64229e_221104_164228","results_folder":"r64229e_20221104_163119/1_A01/","run_name":"TRACTION-RUN-327","sample_load_name":"TRAC-2-1786","ts_run_name":"r64229e_20221104_163119","version_info":{"chemistry":"11.0.0.143406","ics":"11.0.0.144466","iui":"11.0.0.144466","pa":"11.0.0.144466","paws":"11.0.0.144466","ppa":"11.0.0.144466","realtime":"11.0.0.144466","smrtimisc":"11.0.0.146107","smrtinub":"11.0.0.146107","smrtlink":"11.0.0.146107","smrtlink-analysisservices-gui":"11.0.0.146107","smrttools":"11.0.0.146107","transfer":"11.0.0.144466"},"well_name":"A01"},"reports":{"demultiplex.lima.counts":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tCounts\tMeanScore\n12\t12\tbc1019_BAK8B_OA\tbc1019_BAK8B_OA\t2654483\t98\n","demultiplex.lima.guess.txt":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tNumZMWs\tMeanScore\tPicked\n12\t12\tbc1019_BAK8B_OA\tbc1019_BAK8B_OA\t46856\t98\t1\n","demultiplex.lima.summary.txt":"ZMWs input (A) : 2732784\nZMWs above all thresholds (B) : 2654483 (97.13%)\nZMWs below any threshold (C) : 78301 (2.87%)\n\nZMW marginals for (C):\nBelow min length : 1 (0.00%)\nBelow min score : 78294 (99.99%)\nBelow min end score : 25219 (32.21%)\nBelow min passes : 0 (0.00%)\nBelow min score lead : 523 (0.67%)\nBelow min ref span : 1919 (2.45%)\nWithout SMRTbell adapter : 6 (0.01%)\n\nZMWs for (B):\nWith same pair : 2654483 (100.00%)\nCoefficient of correlation : 0.00%\n\nZMWs for (A):\nAllow diff pair : 2634196 (96.39%)\nAllow same pair : 2732778 (100.00%)\n\nReads for (B):\nAbove length : 2654483 (100.00%)\nBelow length : 0 (0.00%)\n"}} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000010313/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000010313/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml deleted file mode 100644 index f26fbf36..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml +++ /dev/null @@ -1,156 +0,0 @@ - - - - - - - - - - - - - - - - - - - - 32396527545 - 2732784 - - - - - - - - - - 10312 - - - r64229e_20221104_163119 - TRACTION-RUN-327 - chc - 2022-11-04T14:53:49.285Z - unknown - 0001-01-01T00:00:00 - - - A01 - custom - 0.0 - 138.0 - 9177 - false - false - false - false - false - false - 0 - Sequel® II DNA Internal Control Complex 3.2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0 - 0 - 0 - - - - - - - - - - - - - - - - - SequelAlpha - SqlPoC_SubCrf_2C2A-t2.xml - DefaultPrimarySequencingCondition - - OnInstrument - true - - - r64229e_20221104_163119/1_A01/ - /lustre/scratch120/pacbio/staging/r64229e_20221104_163119/1_A01/ - - Fasta - Bam - - Bases_Without_QVs - Minimal - - srs-scheme-1 - SRS - Sanger SRS - Sanger SRS transfer settings - /lustre/scratch120/pacbio/staging/ - - - - - DefaultSecondaryAutomationName - 0 - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam.pbi b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam.pbi deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.consensusreadset.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.consensusreadset.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.json b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.json deleted file mode 100644 index 6de5cebd..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "createdAt": "2022-11-06T08:33:31.296Z", - "files": [ - { - "createdAt": "2022-11-06T08:33:31.295Z", - "description": "Split BAM file by lima", - "fileSize": 1231145624, - "fileTypeId": "PacBio.DataSet.ConsensusReadSet", - "isChunked": false, - "modifiedAt": "2022-11-06T08:33:31.296Z", - "name": "Barcodes bc1019_BAK8B_OA--bc1019_BAK8B_OA", - "path": "bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.consensusreadset.xml", - "sourceId": "barcoding.tasks.lima-0", - "uniqueId": "030f5f22-cb34-43d4-b1f4-aeebe58f4535" - } - ], - "updatedAt": "2022-11-06T08:33:31.296Z", - "version": "0.2.2" -} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.counts b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.counts deleted file mode 100644 index 96e73b4f..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.counts +++ /dev/null @@ -1,2 +0,0 @@ -IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore -8 8 bc1019_BAK8B_OA bc1019_BAK8B_OA 1 97 diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.guess.txt b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.guess.txt deleted file mode 100644 index 7a49d08e..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.guess.txt +++ /dev/null @@ -1,2 +0,0 @@ -IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed NumZMWs MeanScore Picked -9 9 bc1016_BAK8B_OA bc1016_BAK8B_OA 40317 97 1 diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.report b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.report deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.summary.txt b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.summary.txt deleted file mode 100644 index 31a537a3..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.summary.txt +++ /dev/null @@ -1,24 +0,0 @@ -ZMWs input (A) : 2339805 -ZMWs above all thresholds (B) : 1 (0.00%) -ZMWs below any threshold (C) : 2339804 (100.00%) - -ZMW marginals for (C): -Below min length : 0 (0.00%) -Below min score : 2339804 (100.00%) -Below min end score : 2055465 (87.85%) -Below min passes : 0 (0.00%) -Below min score lead : 2055465 (87.85%) -Below min ref span : 2315153 (98.95%) -Without SMRTbell adapter : 0 (0.00%) - -ZMWs for (B): -With same pair : 1 (100.00%) -Coefficient of correlation : 0.00% - -ZMWs for (A): -Allow diff pair : 2339805 (100.00%) -Allow same pair : 2339805 (100.00%) - -Reads for (B): -Above length : 1 (100.00%) -Below length : 0 (0.00%) diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam.pbi b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam.pbi deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.consensusreadset.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/lima_guesses_report.json b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/lima_guesses_report.json deleted file mode 100644 index 653e1e5c..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/lima_guesses_report.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "_comment": "Created by pbcopper v2.0.0", - "attributes": [], - "dataset_uuids": [], - "id": "lima_infer", - "plotGroups": [], - "tables": [ - { - "columns": [ - { - "header": "Barcode Name", - "id": "first_bc_name", - "values": [ - "bc1019_BAK8B_OA--bc1019_BAK8B_OA" - ] - }, - { - "header": "#ZMWs", - "id": "num_zmws", - "values": [ - 46856 - ] - }, - { - "header": "Mean Barcode Score", - "id": "mean_bc_score", - "values": [ - 98 - ] - } - ], - "id": "inferred_barcode_table", - "title": "Inferred Barcodes" - } - ], - "title": "Barcoding Inferred Barcodes Report", - "uuid": "677bf779-91aa-4814-b6b7-2a029205d3ba", - "version": "1.0.1" -} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/merged_analysis_report.json b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/merged_analysis_report.json deleted file mode 100644 index 708b75eb..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/merged_analysis_report.json +++ /dev/null @@ -1 +0,0 @@ -{"__CLASS__":"WTSI::NPG::HTS::PacBio::Sequel::Reportdata","created_at":"2022-11-07T22:07:35","meta_data":{"__CLASS__":"WTSI::NPG::HTS::PacBio::Metadata","ccsreads_uuid":"cc8e3c72-f250-45d5-b9ae-9e92ab538ac1","cell_index":"0","collection_number":"0","execution_mode":"OnInstrument","file_path":"/nfs/pacbio_data/smrtlink/userdata/jobs_root/0000/0000010/0000010313/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml","instrument_name":"64229E","movie_name":"m64229e_221104_164228","results_folder":"r64229e_20221104_163119/1_A01/","run_name":"TRACTION-RUN-327","sample_load_name":"TRAC-2-1786","ts_run_name":"r64229e_20221104_163119","version_info":{"chemistry":"11.0.0.143406","ics":"11.0.0.144466","iui":"11.0.0.144466","pa":"11.0.0.144466","paws":"11.0.0.144466","ppa":"11.0.0.144466","realtime":"11.0.0.144466","smrtimisc":"11.0.0.146107","smrtinub":"11.0.0.146107","smrtlink":"11.0.0.146107","smrtlink-analysisservices-gui":"11.0.0.146107","smrttools":"11.0.0.146107","transfer":"11.0.0.144466"},"well_name":"A01"},"reports":{"demultiplex.lima.counts":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tCounts\tMeanScore\n8\t8\tbc1019_BAK8B_OA\tbc1019_BAK8B_OA\t1\t97\n","demultiplex.lima.guess.txt":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tNumZMWs\tMeanScore\tPicked\n9\t9\tbc1016_BAK8B_OA\tbc1016_BAK8B_OA\t40317\t97\t1\n","demultiplex.lima.summary.txt":"ZMWs input (A) : 2339805\nZMWs above all thresholds (B) : 1 (0.00%)\nZMWs below any threshold (C) : 2339804 (100.00%)\n\nZMW marginals for (C):\nBelow min length : 0 (0.00%)\nBelow min score : 2339804 (100.00%)\nBelow min end score : 2055465 (87.85%)\nBelow min passes : 0 (0.00%)\nBelow min score lead : 2055465 (87.85%)\nBelow min ref span : 2315153 (98.95%)\nWithout SMRTbell adapter : 0 (0.00%)\n\nZMWs for (B):\nWith same pair : 1 (100.00%)\nCoefficient of correlation : 0.00%\n\nZMWs for (A):\nAllow diff pair : 2339805 (100.00%)\nAllow same pair : 2339805 (100.00%)\n\nReads for (B):\nAbove length : 1 (100.00%)\nBelow length : 0 (0.00%)\n"}} diff --git a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000010313_deplexfail/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml deleted file mode 100644 index f26fbf36..00000000 --- a/t/data/pacbio/sequel_analysis/0000010313_deplexfail/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml +++ /dev/null @@ -1,156 +0,0 @@ - - - - - - - - - - - - - - - - - - - - 32396527545 - 2732784 - - - - - - - - - - 10312 - - - r64229e_20221104_163119 - TRACTION-RUN-327 - chc - 2022-11-04T14:53:49.285Z - unknown - 0001-01-01T00:00:00 - - - A01 - custom - 0.0 - 138.0 - 9177 - false - false - false - false - false - false - 0 - Sequel® II DNA Internal Control Complex 3.2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0 - 0 - 0 - - - - - - - - - - - - - - - - - SequelAlpha - SqlPoC_SubCrf_2C2A-t2.xml - DefaultPrimarySequencingCondition - - OnInstrument - true - - - r64229e_20221104_163119/1_A01/ - /lustre/scratch120/pacbio/staging/r64229e_20221104_163119/1_A01/ - - Fasta - Bam - - Bases_Without_QVs - Minimal - - srs-scheme-1 - SRS - Sanger SRS - Sanger SRS transfer settings - /lustre/scratch120/pacbio/staging/ - - - - - DefaultSecondaryAutomationName - 0 - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/pacbio/sequel_analysis/000226/entry-points/acf46f00-12b8-45e6-bc10-b0790f8d6758.subreadset.xml b/t/data/pacbio/sequel_analysis/000226/entry-points/acf46f00-12b8-45e6-bc10-b0790f8d6758.subreadset.xml deleted file mode 100644 index c807b9af..00000000 --- a/t/data/pacbio/sequel_analysis/000226/entry-points/acf46f00-12b8-45e6-bc10-b0790f8d6758.subreadset.xml +++ /dev/null @@ -1,148 +0,0 @@ - - - - - - - - - - - - - - - - - - - - 169315953679 - 14942488 - - - 0 - - 7.0.0.63984 - 7.0.0.63984 - - r64016_20190607_135045 - 45137 - eb13 - 2019-06-07T13:48:04.084Z - unknown - 0001-01-01T00:00:00 - - - B01 - 0.0 - 50.0 - 13000 - false - true - false - false - false - 0 - Sequel® II DNA Internal Control 1.0 - - - - - - - - - - - - - - - - - - - - - - - 1 - 1 - 0 - - - Spider_1p0_NTO - - - - >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTGTCTAGGTCATCTCAACGTAGCTTTGACATATAACTTATCTAAAGTAATCCCTGCACACCTGTATGCATTATGCTTGCTATACACGCGGACACAGGCATATCATTTATTTTTTGCCATGTCCATTAATTGTTCAATAATTTTACTCACGGTATTTAATTTGATGTTGTGTTATATAGAATTGGAATTAAACTTATAAGGATGCTTAGACGTTGCATTATAAAAGTTTATGTACTAAGTATTTAAGACATTGGCATATGATTATAGCTTGACATTATTAAAAATTAATTAATTAAATCTCACACAATACTTATTCAAGACATTTTTACTAAGATAACCAAAGGAATGCGAACAAAATAATACTTAAAATATAAGACTTAGAAGTAATATGATCCAATAGTTACATATAGTACACTAAGTTCCTAAATTATATAACTTTAAAACAAAGTTACGAAATTTGGAAATAATTTTATTTAATCATATTTTCATAATAATGAAATACTGTTTATTTCAGTGGCGAAAAGAGATAATACGATTTTATAGTGATAGAATATCCTTGAAATATCTAAAGATAAAATTAGAAACTTTCTCTTTTCGCTGTAAAGCTATATGACTTAAAAATAACTTATACGCAAAGTATATTGCAGTGGAAACCCAAGAGTATAGTAGCCATGTAATCTCGGGTTCGAAACTACACGCCGCGCACGTAGTCAGATGGTCTGAAACTTGTCTGGGGCTGTTTGTTGACGGATGGAGACTTCACTAAGTGGCGTCAGGCGATGCGCACACACGGGACTCAATCCCGTAGCATGTTATGTGTCGTTCGAAACTCGTGCGTTCGAGATTTACGCCACATTGCCGGCTGGTCCAAGGACGTTATCTACCAGATGATACGGTCCAATTCGTAAGTTTGACTCACATAGTCGCGAACCGCGGAGCTGGAGAACAATAATTACCGGATGATTAGTTGACCATACGCACTATCATGCTCCGTGACTCAGTTTCCGCCATGGAGTTCTCACAGCCCCGTGTGTACCATAACTGCAGTAAGTAAGGACCTTGTTCGGAGGCCGACTCGTATTTCATATGATCTTAGTCTCGCCACCTTATCGCACGAATTGGGGGTGTCTTTTAGCCGACTCCGGCACGATCCGCCGGGAAGTTACTCGACCAGTTGCGGGACGCCCTAGTATGTTCGTATTACGTTCGATGCGTAAGCACCCCAGAGATTTTTGGCGGACGTTTCGGTAAATCATAGTAGAACCGGAGCGGTAAAGCTATTGATAACACGCAGGGACGAGCCAGTCGTCTAAGCTCCTCAGGGGTACCGTTCGCCGGACTACAGCCTGTCCCCGGCGGCCGCAACTGGGCTGCGATCCAGCCCCCGCTCCAAAAGGATGACTCGACCTTGCGCCTCGCGTACTCTGCTCTCGAGCTGTCTCCGTGGGCAATGCCGGCTCACGCTGTGGGGAACCCTGGACGCCCGGGCCGAGCCGACGTGGCCCCGCCCAGGCCTTTTCGTCGATCGCAGCTATGTACCCTGTGCTGGCCAGCGCTACTGCGCCGGCCATTAGCGGTGCGCTCTCGACTCGGCCCCAACGTAGACGGCGTCGCTGGCCGGATTCAAAGAAGTGAGCTACTACCATCGCGTGACGCCCTGCGGGCCTGAGTAACCGTGCACGAAGGACACCCCGTTCGTGGCGGGGGTTGCCTCCGCGACGGTCGCCAACGTTGGGGGTCGGTGCATTCAGGCGACGAGGGACCGCTGGTTTCCGGAGAGCGGCCTGTGCTCACACAGGTGCGGTCCATGGGGCCTGTGGATCCGGTTCTCCCACGCGTAGCGCCGGCGTTAGCATGGACGCTAAATAAGTATACGCCGGCAAAGGGAGTGTAGGCCGGCCCGAGGGCAATCGCGGTTACCGGGGTGGGGGAGCTCCCCGCACCAGCCTTGATGTGGTGTGCGAGCG - - - - ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT - aacggaggaggagga - ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT - aacggaggaggagga - - - - - - - - - - - - SequelAlpha - SqlPoC_SubCrf_2C2A-t2.xml - DefaultPrimarySequencingCondition - - r64016_20190607_135045/2_B01/ - /nfs/sf28/pacbio/r64016_20190607_135045/2_B01/ - - Fasta - Bam - - Bases - Minimal - - new-resource - RSYNC - Sanger sequel - Sanger transfer settings - /nfs/sf28/pacbio - - - - - DefaultSecondaryAutomationName - - - - 0 - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/m64016_190608_025655.ccs.bam b/t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/m64016_190608_025655.ccs.bam deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/m64016_190608_025655.ccs.bam.pbi b/t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/m64016_190608_025655.ccs.bam.pbi deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/merged_analysis_report.json b/t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/merged_analysis_report.json deleted file mode 100644 index 6beed645..00000000 --- a/t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/merged_analysis_report.json +++ /dev/null @@ -1 +0,0 @@ -{"__CLASS__":"WTSI::NPG::HTS::PacBio::Sequel::Reportdata","created_at":"2020-11-07T22:11:51","meta_data":{"__CLASS__":"WTSI::NPG::HTS::PacBio::Metadata","cell_index":"1","collection_number":"1","file_path":"t/data/pacbio/sequel_analysis/000226/entry-points/acf46f00-12b8-45e6-bc10-b0790f8d6758.subreadset.xml","instrument_name":"64016","is_ccs":"true","movie_name":"m64016_190608_025655","results_folder":"r64016_20190607_135045/2_B01/","run_name":"45137","sample_load_name":"DN555690B-A1","ts_run_name":"r64016_20190607_135045","version_info":{"chemistry":"7.0.0.63978","ics":"7.0.0.63984","iui":"7.0.0.63984","pa":"7.0.0.63984","paws":"7.0.0.63984","ppa":"7.0.0.63984","realtime":"7.0.0.63984","smrtimisc":"7.0.1.66975","smrtinub":"7.0.1.66768","smrtlink":"7.0.1.66975","smrtlink-analysisservices-gui":"7.0.1.66974","smrttools":"7.0.1.66768","smrtview":"7.0.1.66768","transfer":"7.0.0.63984"},"well_name":"B01"},"reports":{}} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/001185/entry-points/2c677e30-8918-4ef1-8649-f44adaac75d3.subreadset.xml b/t/data/pacbio/sequel_analysis/001185/entry-points/2c677e30-8918-4ef1-8649-f44adaac75d3.subreadset.xml deleted file mode 100644 index 484bf933..00000000 --- a/t/data/pacbio/sequel_analysis/001185/entry-points/2c677e30-8918-4ef1-8649-f44adaac75d3.subreadset.xml +++ /dev/null @@ -1,158 +0,0 @@ - - - - - - - - - - - - - - - - - - - - 358133270952 - 30243031 - - - - - - - - - - 0 - 8.0.0.78867 - 8.0.0.78867 - - r64089_20200313_164345 - TRACTION-RUN-28 - chc - 2020-03-13T15:48:22.337Z - unknown - 0001-01-01T00:00:00 - - - B01 - 0.0 - 55.0 - 15589 - false - false - false - false - false - 0 - Sequel® II DNA Internal Control 1.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - 1 - 0 - - - Spider_1p0_NTO - - - - >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTGTCTAGGTCATCTCAACGTAGCTTTGACATATAACTTATCTAAAGTAATCCCTGCACACCTGTATGCATTATGCTTGCTATACACGCGGACACAGGCATATCATTTATTTTTTGCCATGTCCATTAATTGTTCAATAATTTTACTCACGGTATTTAATTTGATGTTGTGTTATATAGAATTGGAATTAAACTTATAAGGATGCTTAGACGTTGCATTATAAAAGTTTATGTACTAAGTATTTAAGACATTGGCATATGATTATAGCTTGACATTATTAAAAATTAATTAATTAAATCTCACACAATACTTATTCAAGACATTTTTACTAAGATAACCAAAGGAATGCGAACAAAATAATACTTAAAATATAAGACTTAGAAGTAATATGATCCAATAGTTACATATAGTACACTAAGTTCCTAAATTATATAACTTTAAAACAAAGTTACGAAATTTGGAAATAATTTTATTTAATCATATTTTCATAATAATGAAATACTGTTTATTTCAGTGGCGAAAAGAGATAATACGATTTTATAGTGATAGAATATCCTTGAAATATCTAAAGATAAAATTAGAAACTTTCTCTTTTCGCTGTAAAGCTATATGACTTAAAAATAACTTATACGCAAAGTATATTGCAGTGGAAACCCAAGAGTATAGTAGCCATGTAATCTCGGGTTCGAAACTACACGCCGCGCACGTAGTCAGATGGTCTGAAACTTGTCTGGGGCTGTTTGTTGACGGATGGAGACTTCACTAAGTGGCGTCAGGCGATGCGCACACACGGGACTCAATCCCGTAGCATGTTATGTGTCGTTCGAAACTCGTGCGTTCGAGATTTACGCCACATTGCCGGCTGGTCCAAGGACGTTATCTACCAGATGATACGGTCCAATTCGTAAGTTTGACTCACATAGTCGCGAACCGCGGAGCTGGAGAACAATAATTACCGGATGATTAGTTGACCATACGCACTATCATGCTCCGTGACTCAGTTTCCGCCATGGAGTTCTCACAGCCCCGTGTGTACCATAACTGCAGTAAGTAAGGACCTTGTTCGGAGGCCGACTCGTATTTCATATGATCTTAGTCTCGCCACCTTATCGCACGAATTGGGGGTGTCTTTTAGCCGACTCCGGCACGATCCGCCGGGAAGTTACTCGACCAGTTGCGGGACGCCCTAGTATGTTCGTATTACGTTCGATGCGTAAGCACCCCAGAGATTTTTGGCGGACGTTTCGGTAAATCATAGTAGAACCGGAGCGGTAAAGCTATTGATAACACGCAGGGACGAGCCAGTCGTCTAAGCTCCTCAGGGGTACCGTTCGCCGGACTACAGCCTGTCCCCGGCGGCCGCAACTGGGCTGCGATCCAGCCCCCGCTCCAAAAGGATGACTCGACCTTGCGCCTCGCGTACTCTGCTCTCGAGCTGTCTCCGTGGGCAATGCCGGCTCACGCTGTGGGGAACCCTGGACGCCCGGGCCGAGCCGACGTGGCCCCGCCCAGGCCTTTTCGTCGATCGCAGCTATGTACCCTGTGCTGGCCAGCGCTACTGCGCCGGCCATTAGCGGTGCGCTCTCGACTCGGCCCCAACGTAGACGGCGTCGCTGGCCGGATTCAAAGAAGTGAGCTACTACCATCGCGTGACGCCCTGCGGGCCTGAGTAACCGTGCACGAAGGACACCCCGTTCGTGGCGGGGGTTGCCTCCGCGACGGTCGCCAACGTTGGGGGTCGGTGCATTCAGGCGACGAGGGACCGCTGGTTTCCGGAGAGCGGCCTGTGCTCACACAGGTGCGGTCCATGGGGCCTGTGGATCCGGTTCTCCCACGCGTAGCGCCGGCGTTAGCATGGACGCTAAATAAGTATACGCCGGCAAAGGGAGTGTAGGCCGGCCCGAGGGCAATCGCGGTTACCGGGGTGGGGGAGCTCCCCGCACCAGCCTTGATGTGGTGTGCGAGCG - - - - ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT - aacggaggaggagga - ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT - aacggaggaggagga - - - - - - - - - - - - SequelAlpha - SqlPoC_SubCrf_2C2A-t2.xml - DefaultPrimarySequencingCondition - - r64089_20200313_164345/2_B01/ - /nfs/sf39/pacbio/r64089_20200313_164345/2_B01/ - - Fasta - Bam - - Bases - Minimal - - new-resource - RSYNC - Sanger sequel - Sanger transfer settings - /nfs/sf39/pacbio - - - - - DefaultSecondaryAutomationName - - - - 0 - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam b/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam.pbi b/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam.pbi deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subreadset.xml b/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subreadset.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.bam b/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.bam deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.bam.pbi b/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.bam.pbi deleted file mode 100644 index e69de29b..00000000 diff --git a/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.subreadset.xml b/t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.subreadset.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/t/fixtures/ml_warehouse/300-PacBioRun.yml b/t/fixtures/ml_warehouse/300-PacBioRun.yml index 90097a4a..64dfb48d 100644 --- a/t/fixtures/ml_warehouse/300-PacBioRun.yml +++ b/t/fixtures/ml_warehouse/300-PacBioRun.yml @@ -2424,3 +2424,34 @@ library_created_at: ~ pac_bio_run_name: TRACTION-RUN-1130 pac_bio_library_tube_barcode: TRAC-2-7582 +- id_pac_bio_tmp: 121170 + last_updated: 2024-04-03 10:10:23 + recorded_at: 2024-04-03 10:10:23 + id_sample_tmp: 8409942 + id_study_tmp: 5735 + id_pac_bio_run_lims: TRACTION-RUN-1200 + pac_bio_run_uuid: 8411a0af-0dbc-4e83-9263-d84b7be5dcaa + cost_code: S10010 + id_lims: Traction + tag_identifier: bc2048 + tag_sequence: TGATGCTAGTGAGTAT + tag_set_id_lims: 9 + tag_set_name: Pacbio_96_barcode_plate_v3 + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag2_identifier: ~ + pipeline_id_lims: Pacbio_HiFi + plate_barcode: ~ + plate_uuid_lims: dbf049a3-34a6-40a9-9fbb-a03198a84a71 + plate_number: 1 + well_label: A1 + well_uuid_lims: 22bd526a-fbaa-4a15-a5af-1869e0484fa9 + pac_bio_library_tube_id_lims: 11527 + pac_bio_library_tube_uuid: 0d09a826-1fb40a9-9fbb-a03198a84a71 + pac_bio_library_tube_name: TOL_ASG14636038 + pac_bio_library_tube_legacy_id: ~ + library_created_at: ~ + pac_bio_run_name: TRACTION-RUN-1200 + pac_bio_library_tube_barcode: TRAC-2-8046 + diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitorTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitorTest.pm index 6c5c5af1..5dac244d 100644 --- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitorTest.pm +++ b/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitorTest.pm @@ -36,24 +36,30 @@ my $db_dir = File::Temp->newdir; my $test_response = [ { - comment => "8pM", - createdAt => "2018-04-23T09:04:08.042Z", - createdBy => "chc", - id => 1612, - jobTypeId => "analysis", - subJobTypeId => "pbsmrtpipe.pipelines.sa3_ds_barcode2", - name => "Demultiplexing of DN505769FNCTCPool4", - parentMultiJobId => 1601, - path => "t/data/pacbio/sequel_analysis/001612", - projectId => 1, - smrtlinkVersion => "5.1.0.26412", - state => "SUCCESSFUL", - updatedAt => "2018-04-24T11:02:04.223Z", - uuid => "3bf09718-58fe-4fb6-a32a-9adbda384b27", - workflow => "{}", - jobStartedAt => "2018-04-25T11:02:04.223Z", - jobCompletedAt => "2018-04-26T11:02:04.223Z", - jobUpdatedAt => "2018-04-26T11:02:04.223Z" + "subJobTypeId" => "cromwell.workflows.pb_demux_ccs", + "name" => "TRAC-2-8046-Cell1_redo_demultiplex", + "updatedAt" => "2024-04-08T16:39:32.434Z", + "workflow" => "{}", + "path" => "t/data/pacbio/sequel_analysis/0000019480", + "state" => "SUCCESSFUL", + "tags" => "", + "uuid" => "41b9c9b0-5621-41d8-a373-e04a641ddb2b", + "externalJobId" => "2a15bfd3-d378-4701-9dea-83d77c67a062", + "jobStartedAt" => "2024-04-08T15:45:35.893Z", + "applicationName" => "Demultiplex Barcodes", + "projectId" => 1, + "childJobsCount" => 0, + "jobCompletedAt" => "2024-04-08T16:39:32.434Z", + "jobTypeId" => "analysis", + "id" => 19480, + "smrtlinkVersion" => "13.0.0.207600", + "comment" => "Description for job Run Analysis Application", + "isNested" => "false", + "createdAt" => "2024-04-08T15:45:34.218Z", + "isActive" => "true", + "isMultiJob" => "false", + "jsonSettings" => "", + "jobUpdatedAt" => "2024-04-08T16:39:32.434Z" } ]; @@ -116,7 +122,10 @@ sub publish_completed_jobs : Test(3) { (api_client => $client, dest_collection => $dest_coll, irods => $irods, - mlwh_schema => $wh_schema); + mlwh_schema => $wh_schema, + pipeline_name => 'cromwell.workflows.pb_demux_ccs', + task_name => 'call-lima/execution', + ); my ($num_jobs, $num_processed, $num_errors) = $monitor->publish_analysed_cells; diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm index bfd9694f..db5968fb 100644 --- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm +++ b/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm @@ -97,7 +97,7 @@ sub list_files : Test(3) { 'lima_output.removed.bam'); is_deeply($pub->list_files('bam$'), \@expected_paths1, - 'Found sequence files for 001612'); + 'Found sequence files for 0000019480'); my @expected_paths2 = map { catfile($runfolder_path, $_) } @@ -106,7 +106,7 @@ sub list_files : Test(3) { 'lima_output.removed.bam.pbi'); is_deeply($pub->list_files('pbi$'), \@expected_paths2, - 'Found sequence index files for 001612'); + 'Found sequence index files for 0000019480'); my @expected_paths3 = map { catfile($runfolder_path, $_) } @@ -115,47 +115,9 @@ sub list_files : Test(3) { 'lima_output.removed.subreadset.xml'); is_deeply($pub->list_files('subreadset.xml$'), \@expected_paths3, - 'Found sequence index files for 001612'); + 'Found xml files for 0000019480'); } -sub publish_files : Test(4) { - my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, - strict_baton_version => 0); - my $analysis_path = "$data_path/001612"; - my $runfolder_path = "$analysis_path/tasks/barcoding.tasks.lima-0"; - my $dest_coll = "$irods_tmp_coll/publish_files"; - my $expected_json = 't/data/mlwh_json/pacbio.json'; - - - my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); - my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new - (restart_file => catfile($tmpdir->dirname, 'published.json'), - dest_collection => $dest_coll, - irods => $irods, - mlwh_schema => $wh_schema, - analysis_path => $analysis_path, - runfolder_path => $runfolder_path); - - my $mlwh_json = $pub->mlwh_locations->path; - unlink $mlwh_json; # A file may have been written to this path during a - # previous test set with a different destination collection - - my ($num_files, $num_processed, $num_errors) = $pub->publish_files; - my $num_expected = 10; - - cmp_ok($num_processed, '==', $num_expected, "Published $num_expected files"); - cmp_ok($num_errors, '==', 0); - - ok(-e $mlwh_json, "mlwh loader json file $mlwh_json was written by publisher"); - is_deeply(WTSI::NPG::HTS::LocationWriterTest::read_json_content($mlwh_json), - WTSI::NPG::HTS::LocationWriterTest::set_destination( - WTSI::NPG::HTS::LocationWriterTest::read_json_content($expected_json), - $irods_tmp_coll), "contents of $mlwh_json are correct"); - - unlink $mlwh_json; -} - - sub publish_xml_files : Test(19) { my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, strict_baton_version => 0); @@ -192,84 +154,6 @@ sub publish_xml_files : Test(19) { check_common_metadata($irods, @observed_paths); } -sub publish_sequence_files : Test(64) { - my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, - strict_baton_version => 0); - my $analysis_path = "$data_path/001612"; - my $runfolder_path = "$analysis_path/tasks/barcoding.tasks.lima-0", - my $dest_coll = "$irods_tmp_coll/publish_sequence_files"; - - my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); - my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new - (restart_file => catfile($tmpdir->dirname, 'published.json'), - dest_collection => $dest_coll, - irods => $irods, - mlwh_schema => $wh_schema, - analysis_path => $analysis_path, - runfolder_path => $runfolder_path); - - my @expected_paths = - map { catfile("$dest_coll/2_B01", $_) } - ('lima_output.lbc12--lbc12.bam', - 'lima_output.lbc5--lbc5.bam', - 'lima_output.removed.bam'); - - my ($num_files, $num_processed, $num_errors) = - $pub->publish_sequence_files('bam$'); - cmp_ok($num_files, '==', scalar @expected_paths); - cmp_ok($num_processed, '==', scalar @expected_paths); - cmp_ok($num_errors, '==', 0); - - my @observed_paths = observed_data_objects($irods, $dest_coll); - is_deeply(\@observed_paths, \@expected_paths, - 'Published correctly named sequence files') or - diag explain \@observed_paths; - - check_primary_metadata($irods, 0, @observed_paths); - check_common_metadata($irods, @observed_paths); - check_secondary_metadata($irods, @observed_paths); - - unlink $pub->restart_file; -} - -sub publish_index_files : Test(19) { - my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, - strict_baton_version => 0); - my $analysis_path = "$data_path/001612"; - my $runfolder_path = "$analysis_path/tasks/barcoding.tasks.lima-0", - my $dest_coll = "$irods_tmp_coll/publish_index_files"; - - my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); - my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new - (restart_file => catfile($tmpdir->dirname, 'published.json'), - dest_collection => $dest_coll, - irods => $irods, - mlwh_schema => $wh_schema, - analysis_path => $analysis_path, - runfolder_path => $runfolder_path); - - my @expected_paths = - map { catfile("$dest_coll/2_B01", $_) } - ('lima_output.lbc12--lbc12.bam.pbi', - 'lima_output.lbc5--lbc5.bam.pbi', - 'lima_output.removed.bam.pbi',); - - my ($num_files, $num_processed, $num_errors) = - $pub->publish_non_sequence_files('pbi$'); - cmp_ok($num_files, '==', scalar @expected_paths); - cmp_ok($num_processed, '==', scalar @expected_paths); - cmp_ok($num_errors, '==', 0); - - my @observed_paths = observed_data_objects($irods, $dest_coll); - is_deeply(\@observed_paths, \@expected_paths, - 'Published correctly named index files') or - diag explain \@observed_paths; - - check_common_metadata($irods, @observed_paths); - - unlink $pub->restart_file; -} - sub observed_data_objects { my ($irods, $dest_collection, $regex) = @_; @@ -355,65 +239,13 @@ sub check_secondary_metadata { } } -sub list_files_2 : Test(2) { - my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, - strict_baton_version => 0); - my $analysis_path = "$data_path/000226"; - my $runfolder_path = "$analysis_path/tasks/pbcoretools.tasks.auto_ccs_outputs-0", - my $dest_coll = $irods_tmp_coll; - - my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new - (dest_collection => $dest_coll, - irods => $irods, - mlwh_schema => $wh_schema, - analysis_path => $analysis_path, - runfolder_path => $runfolder_path); - - my @expected_paths1 = - map { catfile($runfolder_path, $_) } - ('m64016_190608_025655.ccs.bam'); - - is_deeply($pub->list_files('bam$'), \@expected_paths1, - 'Found sequence files for 000226'); - - my @expected_paths2 = - map { catfile($runfolder_path, $_) } - ('m64016_190608_025655.ccs.bam.pbi'); - - is_deeply($pub->list_files('pbi$'), \@expected_paths2, - 'Found sequence index files for 000226'); - -} - -sub publish_files_2 : Test(2) { - my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, - strict_baton_version => 0); - my $analysis_path = "$data_path/000226"; - my $runfolder_path = "$analysis_path/tasks/pbcoretools.tasks.auto_ccs_outputs-0", - my $dest_coll = "$irods_tmp_coll/publish_files_2"; - - my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); - my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new - (restart_file => catfile($tmpdir->dirname, 'published.json'), - dest_collection => $dest_coll, - irods => $irods, - mlwh_schema => $wh_schema, - analysis_path => $analysis_path, - runfolder_path => $runfolder_path); - - my ($num_files, $num_processed, $num_errors) = $pub->publish_files; - my $num_expected = 3; - - cmp_ok($num_processed, '==', $num_expected, "Published $num_expected files"); - cmp_ok($num_errors, '==', 0); -} - +sub publish_sequence_files_3 : Test(4) { +## run 81230 cell B01 - expected deplexing -sub publish_sequence_files_2 : Test(42) { my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, strict_baton_version => 0); - my $analysis_path = "$data_path/001185"; - my $runfolder_path = "$analysis_path/tasks/barcoding.tasks.lima-0", + my $analysis_path = "$data_path/0000003442"; + my $runfolder_path = "$analysis_path/cromwell-job/call-demultiplex_barcodes/call-lima/execution", my $dest_coll = "$irods_tmp_coll/publish_sequence_files"; my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); @@ -427,8 +259,8 @@ sub publish_sequence_files_2 : Test(42) { my @expected_paths = map { catfile("$dest_coll/2_B01", $_) } - ('lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam', - 'lima.removed.bam'); + ('demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam', + 'demultiplex.removed.bam'); my ($num_files, $num_processed, $num_errors) = $pub->publish_sequence_files('bam$'); @@ -441,21 +273,16 @@ sub publish_sequence_files_2 : Test(42) { 'Published correctly named sequence files') or diag explain \@observed_paths; - check_primary_metadata($irods, 1, @observed_paths); - check_common_metadata($irods, @observed_paths); - check_secondary_metadata($irods, @observed_paths); - unlink $pub->restart_file; } - -sub publish_sequence_files_3 : Test(4) { -## run 81230 cell B01 - expected deplexing +sub publish_sequence_files_4 : Test(4) { +## redo demultiplexing in SMRT Link v13 my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, strict_baton_version => 0); - my $analysis_path = "$data_path/0000003442"; - my $runfolder_path = "$analysis_path/cromwell-job/call-demultiplex_barcodes/call-lima/execution", + my $analysis_path = "$data_path/0000019480"; + my $runfolder_path = "$analysis_path/cromwell-job/call-lima/execution", my $dest_coll = "$irods_tmp_coll/publish_sequence_files"; my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); @@ -468,9 +295,9 @@ sub publish_sequence_files_3 : Test(4) { runfolder_path => $runfolder_path); my @expected_paths = - map { catfile("$dest_coll/2_B01", $_) } - ('demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam', - 'demultiplex.removed.bam'); + map { catfile("$dest_coll/1_A01", $_) } + ('m84098_240322_112047_s1.bc2048--bc2048.bam', + 'm84098_240322_112047_s1.unbarcoded.bam',); my ($num_files, $num_processed, $num_errors) = $pub->publish_sequence_files('bam$'); @@ -486,31 +313,6 @@ sub publish_sequence_files_3 : Test(4) { unlink $pub->restart_file; } - -sub publish_sequence_files_4 : Test(1) { -## run 81230 cell B01 - unexpected barcode - - my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, - strict_baton_version => 0); - my $analysis_path = "$data_path/0000003280"; - my $runfolder_path = "$analysis_path/cromwell-job/call-demultiplex_barcodes/call-lima/execution", - my $dest_coll = "$irods_tmp_coll/publish_sequence_files"; - - my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); - my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new - (restart_file => catfile($tmpdir->dirname, 'published.json'), - dest_collection => $dest_coll, - irods => $irods, - mlwh_schema => $wh_schema, - analysis_path => $analysis_path, - runfolder_path => $runfolder_path); - - throws_ok { $pub->publish_sequence_files('bam$'); } qr /Unexpected barcode/, - 'Correctly failed to publish data from unexpected barcode'; - - unlink $pub->restart_file; -} - sub publish_sequence_files_5 : Test(4) { ## run 81876 cell A01 - ccs only analysis creating hifi_reads.bam @@ -590,31 +392,7 @@ sub publish_sequence_files_6 : Test(4) { unlink $pub->restart_file; } -sub publish_files_3 : Test(1) { -## run 81230 cell B01 - qc check failed - - my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, - strict_baton_version => 0); - my $analysis_path = "$data_path/0000003280"; - my $runfolder_path = "$analysis_path/cromwell-job/call-demultiplex_barcodes/call-lima/execution", - my $dest_coll = "$irods_tmp_coll/publish_sequence_files"; - - my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); - my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new - (restart_file => catfile($tmpdir->dirname, 'published.json'), - dest_collection => $dest_coll, - irods => $irods, - mlwh_schema => $wh_schema, - analysis_path => $analysis_path, - runfolder_path => $runfolder_path); - - throws_ok { $pub->publish_files } qr /QC check failed/, - 'Correctly failed to publish qc fail data'; - - unlink $pub->restart_file; -} - -sub publish_files_4 : Test(307) { +sub publish_files_3 : Test(307) { ## run 83472 cell A01 - isoseq analysis my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, strict_baton_version => 0); @@ -653,18 +431,19 @@ sub publish_files_4 : Test(307) { unlink $pub->restart_file; } -sub publish_files_5 : Test(4) { -## run TRACTION-RUN-327 cell A01 - SMRT Link deplex in subdirectories +sub publish_files_4 : Test(6) { +## redo demultiplexing in SMRT Link v13 my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, strict_baton_version => 0); my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); - my $analysis_path = catdir($tmpdir->dirname, '0000010313'); - dircopy("$data_path/0000010313",$analysis_path) or die $!; + my $analysis_path = catdir($tmpdir->dirname, '0000019480'); + dircopy("$data_path/0000019480",$analysis_path) or die $!; chmod (0770, "$analysis_path") or die "Chmod 0770 directory failed : $!"; - + my $runfolder_path = "$analysis_path/cromwell-job/call-lima/execution", my $dest_coll = "$irods_tmp_coll/publish_sequence_files"; + my $expected_json = 't/data/mlwh_json/pacbio.json'; my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new (restart_file => catfile($tmpdir->dirname, 'published.json'), @@ -673,17 +452,24 @@ sub publish_files_5 : Test(4) { mlwh_schema => $wh_schema, analysis_path => $analysis_path, runfolder_path => $runfolder_path, - is_oninstrument => 1); + ); + + my $mlwh_json = $pub->mlwh_locations->path; + unlink $mlwh_json; # A file may have been written to this path during a + # previous test set with a different destination collection + my ($num_files, $num_processed, $num_errors) = $pub->publish_files; my @expected_paths = map { catfile("$dest_coll/1_A01", $_) } - ('demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam', - 'demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam.pbi', - 'demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.consensusreadset.xml', + ('m84098_240322_112047_s1.bc2048--bc2048.bam', + 'm84098_240322_112047_s1.bc2048--bc2048.bam.pbi', + 'm84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml', + 'm84098_240322_112047_s1.consensusreadset.xml', + 'm84098_240322_112047_s1.unbarcoded.bam', + 'm84098_240322_112047_s1.unbarcoded.bam.pbi', + 'm84098_240322_112047_s1.unbarcoded.consensusreadset.xml', 'merged_analysis_report.json'); - my ($num_files, $num_processed, $num_errors) = $pub->publish_files; - cmp_ok($num_files, '==', scalar @expected_paths); cmp_ok($num_processed, '==', scalar @expected_paths); cmp_ok($num_errors, '==', 0); @@ -693,15 +479,21 @@ sub publish_files_5 : Test(4) { 'Published correctly named sequence files') or diag explain \@observed_paths; + ok(-e $mlwh_json, "mlwh loader json file $mlwh_json was written by publisher"); + is_deeply(WTSI::NPG::HTS::LocationWriterTest::read_json_content($mlwh_json), + WTSI::NPG::HTS::LocationWriterTest::set_destination( + WTSI::NPG::HTS::LocationWriterTest::read_json_content($expected_json), + $irods_tmp_coll), "contents of $mlwh_json are correct"); } -sub publish_files_6 : Test(1) { -## run TRACTION-RUN-327 cell A01 - deplex in subdirectories - deplex fail + +sub publish_files_5 : Test(1) { +## redo demultiplexing in SMRT Link v13 - deplexing fail my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, strict_baton_version => 0); my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX"); - my $analysis_path = catdir($tmpdir->dirname, '0000010313_deplexfail'); - dircopy("$data_path/0000010313_deplexfail",$analysis_path) or die $!; + my $analysis_path = catdir($tmpdir->dirname, '0000019480_deplexfail'); + dircopy("$data_path/0000019480_deplexfail",$analysis_path) or die $!; chmod (0770, "$analysis_path") or die "Chmod 0770 directory failed : $!"; my $runfolder_path = "$analysis_path/cromwell-job/call-lima/execution", @@ -714,14 +506,14 @@ sub publish_files_6 : Test(1) { mlwh_schema => $wh_schema, analysis_path => $analysis_path, runfolder_path => $runfolder_path, - is_oninstrument => 1); + ); - throws_ok { $pub->publish_files(); } qr /QC check failed/, + throws_ok { $pub->publish_files(); } qr /QC check failed/, 'Correctly failed to publish data where QC check fails'; } -sub list_files_3 : Test(2) { -# testing finding files in sud-directories for on instrument analysis +sub list_files_2 : Test(2) { +# testing finding files in sub-directories for on instrument analysis my $irods = WTSI::NPG::iRODS->new(environment => \%ENV, strict_baton_version => 0); my $analysis_path = "$rundata_path/r64089e_20220615_171559/1_A01"; From 5df8919ca47609cc4d705ee3ba9b67ef1940e6a8 Mon Sep 17 00:00:00 2001 From: Carol Scott Date: Mon, 15 Apr 2024 12:57:10 +0100 Subject: [PATCH 4/5] fix tests --- MANIFEST | 12 +- .../HTS/PacBio/Sequel/AnalysisPublisher.pm | 2 +- t/data/mlwh_json/pacbio.json | 2 +- t/data/mlwh_json/pacbio2.json | 1 + ...m84098_240322_112047_s1.bc2048--bc2048.bam | 0 ...98_240322_112047_s1.bc2048--bc2048.bam.pbi | 0 ...047_s1.bc2048--bc2048.consensusreadset.xml | 164 ++++++++++++++++ ...s1.bc2048--bc2048.consensusreadset.xml.md5 | 1 + .../execution/lima_guesses.report.json | 42 ++++ ...4098_240322_112047_s1.consensusreadset.xml | 183 ++++++++++++++++++ ..._240322_112047_s1.consensusreadset.xml.md5 | 1 + .../execution/m84098_240322_112047_s1.json | 19 ++ .../m84098_240322_112047_s1.lima.counts | 3 + .../m84098_240322_112047_s1.lima.guess | 2 + .../m84098_240322_112047_s1.lima.guess.txt | 2 + .../m84098_240322_112047_s1.lima.report | 0 .../m84098_240322_112047_s1.lima.summary | 24 +++ .../m84098_240322_112047_s1.lima.summary.txt | 24 +++ .../m84098_240322_112047_s1.unbarcoded.bam | 0 ...m84098_240322_112047_s1.unbarcoded.bam.pbi | 0 ..._112047_s1.unbarcoded.consensusreadset.xml | 161 +++++++++++++++ ...047_s1.unbarcoded.consensusreadset.xml.md5 | 1 + .../m84098_240322_112047_s1.unbarcoded.json | 19 ++ .../execution/merged_analysis_report.json | 1 + .../execution/merged_analysis_report.json.md5 | 1 + .../call-lima/execution/mlwh_locations.json | 1 + ...047_s1.bc2048--bc2048.consensusreadset.xml | 164 ++++++++++++++++ ...4098_240322_112047_s1.consensusreadset.xml | 183 ++++++++++++++++++ ...m84098_240322_112047_s1.bc2048--bc2048.bam | 0 ...98_240322_112047_s1.bc2048--bc2048.bam.pbi | 0 ...047_s1.bc2048--bc2048.consensusreadset.xml | 164 ++++++++++++++++ .../execution/lima_guesses.report.json | 42 ++++ ...4098_240322_112047_s1.consensusreadset.xml | 183 ++++++++++++++++++ .../execution/m84098_240322_112047_s1.json | 19 ++ .../m84098_240322_112047_s1.lima.counts | 3 + .../m84098_240322_112047_s1.lima.guess | 2 + .../m84098_240322_112047_s1.lima.guess.txt | 2 + .../m84098_240322_112047_s1.lima.report | 0 .../m84098_240322_112047_s1.lima.summary | 24 +++ .../m84098_240322_112047_s1.lima.summary.txt | 24 +++ .../m84098_240322_112047_s1.unbarcoded.bam | 0 ...m84098_240322_112047_s1.unbarcoded.bam.pbi | 0 ..._112047_s1.unbarcoded.consensusreadset.xml | 161 +++++++++++++++ .../m84098_240322_112047_s1.unbarcoded.json | 19 ++ ...047_s1.bc2048--bc2048.consensusreadset.xml | 164 ++++++++++++++++ ...4098_240322_112047_s1.consensusreadset.xml | 183 ++++++++++++++++++ .../PacBio/Sequel/AnalysisPublisherTest.pm | 2 +- 47 files changed, 1991 insertions(+), 14 deletions(-) create mode 100644 t/data/mlwh_json/pacbio2.json create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml.md5 create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/lima_guesses.report.json create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml.md5 create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml.md5 create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.json create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/merged_analysis_report.json create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/merged_analysis_report.json.md5 create mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/mlwh_locations.json create mode 100644 t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml create mode 100644 t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.consensusreadset.xml create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/lima_guesses.report.json create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.json create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml create mode 100644 t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.consensusreadset.xml diff --git a/MANIFEST b/MANIFEST index 4ddf52f8..9483dbbd 100644 --- a/MANIFEST +++ b/MANIFEST @@ -16298,6 +16298,7 @@ t/data/log_publisher/outgoing/100818_IL32_10371/RTALogs/20150909-1608_WarningLog t/data/mlwh_json/illumina.json t/data/mlwh_json/illumina_existing.json t/data/mlwh_json/pacbio.json +t/data/mlwh_json/pacbio2.json t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.adapters.fasta t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam.pbi @@ -16591,17 +16592,6 @@ t/data/pacbio/sequel_analysis/0000002152/entry-points/7da072af-387d-49e8-8ee3-b0 t/data/pacbio/sequel_analysis/0000002152/outputs/barcode_ccs.report.json t/data/pacbio/sequel_analysis/0000002152/outputs/ccs_processing.report.json t/data/pacbio/sequel_analysis/0000002152/outputs/ccs.report.json -t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.bam -t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.bam.pbi -t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.consensusreadset.xml -t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.counts -t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.guess.txt -t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.summary.txt -t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam -t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam.pbi -t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.consensusreadset.xml -t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json -t/data/pacbio/sequel_analysis/0000003280/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam.pbi t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.consensusreadset.xml diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm b/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm index 5487ed9c..8141cf6b 100644 --- a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm +++ b/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm @@ -380,7 +380,7 @@ sub _build_metadata{ # well and plate number as no merged cell analysis - so just pick one. my @files = $self->list_directory ($output_path, filter => $METADATA_SET .q[.]. $METADATA_FORMAT . q[$]); - push @metafiles, $files[0]; + push @metafiles, $files[0]; } elsif ($self->is_oninstrument == 1 && ! -d $entry_path && $self->is_smtwelve == 1) { # Revio @metafiles = $self->list_directory diff --git a/t/data/mlwh_json/pacbio.json b/t/data/mlwh_json/pacbio.json index 16817feb..1417dea2 100644 --- a/t/data/mlwh_json/pacbio.json +++ b/t/data/mlwh_json/pacbio.json @@ -1 +1 @@ -{"version":"1.0","products":[{"id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_root_collection":"/testZone/home/irods/RunPublisherTest.XXXXX.0/publish_sequence_files/1_A01/","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","pipeline_name":"npg-prod","seq_platform_name":"pacbio"}]} +{"version":"1.0","products":[{"irods_data_relative_path":"lima_output.lbc5--lbc5.bam","id_product":"6948c60e9ee9117255f1123e2c403013596339eda68b6b8e8867bc132023955d","irods_root_collection":"/testZone/home/irods/RunPublisherTest.XXXXX.0/publish_files/2_B01/","pipeline_name":"npg-prod","seq_platform_name":"pacbio"}, {"irods_data_relative_path":"lima_output.lbc12--lbc12.bam","id_product":"40ff7f2193f3b515a6c69ab284622c935097a63ccbf3eaf09cc39b5ff44468af","irods_root_collection":"/testZone/home/irods/RunPublisherTest.XXXXX.0/publish_files/2_B01/","pipeline_name":"npg-prod","seq_platform_name":"pacbio"}]} diff --git a/t/data/mlwh_json/pacbio2.json b/t/data/mlwh_json/pacbio2.json new file mode 100644 index 00000000..16817feb --- /dev/null +++ b/t/data/mlwh_json/pacbio2.json @@ -0,0 +1 @@ +{"version":"1.0","products":[{"id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_root_collection":"/testZone/home/irods/RunPublisherTest.XXXXX.0/publish_sequence_files/1_A01/","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","pipeline_name":"npg-prod","seq_platform_name":"pacbio"}]} diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml new file mode 100644 index 00000000..869faf2c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml @@ -0,0 +1,164 @@ + + + + 57462851406 + 9122662 + + + 0 + + + r84098_20240322_103351 + TRACTION-RUN-1200 + su3 + 2024-03-22T10:18:41.142Z + unknown + 2024-03-22T10:34:27.863237Z + + + A01 + unspecified + 0 + 252 + 5795 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240322_103351/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240322_103351/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml.md5 b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml.md5 new file mode 100644 index 00000000..fe2c41b2 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml.md5 @@ -0,0 +1 @@ +4cf78cc8dc17cd9146ed63a85138b6b1 diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/lima_guesses.report.json b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/lima_guesses.report.json new file mode 100644 index 00000000..d48b00a3 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/lima_guesses.report.json @@ -0,0 +1,42 @@ +{ + "_comment": "Created by pbcopper v2.4.0", + "attributes": [], + "dataset_uuids": [], + "id": "lima_infer", + "plotGroups": [], + "tables": [ + { + "columns": [ + { + "header": "Barcode", + "id": "first_bc_name", + "values": [ + "bc2048--bc2048", + "unassigned" + ] + }, + { + "header": "Reads, %", + "id": "num_zmws", + "values": [ + 98.6, + 1.4 + ] + }, + { + "header": "Barcode score, mean", + "id": "mean_bc_score", + "values": [ + 97, + 0 + ] + } + ], + "id": "inferred_barcode_table", + "title": "Inferred Barcodes" + } + ], + "title": "Inferred Barcodes", + "uuid": "8b88fc06-4c6d-4375-91c8-34153c70b3da", + "version": "1.0.1" +} diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml new file mode 100644 index 00000000..88ca8348 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml @@ -0,0 +1,183 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 57462851406 + 9122662 + + + 0 + + + r84098_20240322_103351 + TRACTION-RUN-1200 + su3 + 2024-03-22T10:18:41.142Z + unknown + 2024-03-22T10:34:27.863237Z + + + A01 + unspecified + 0 + 252 + 5795 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240322_103351/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240322_103351/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml.md5 b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml.md5 new file mode 100644 index 00000000..39d3c432 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml.md5 @@ -0,0 +1 @@ +823fd7eae8820b01bd2ad29a2750b684 diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json new file mode 100644 index 00000000..8d5b048c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json @@ -0,0 +1,19 @@ +{ + "createdAt": "2024-04-08T15:59:05.947Z", + "files": [ + { + "createdAt": "2024-04-08T15:59:05.946Z", + "description": "Split BAM file by lima", + "fileSize": 300968828, + "fileTypeId": "PacBio.DataSet.ConsensusReadSet", + "isChunked": false, + "modifiedAt": "2024-04-08T15:59:05.947Z", + "name": "Barcodes bc2048--bc2048", + "path": "bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml", + "sourceId": "barcoding.tasks.lima-0", + "uniqueId": "c1a6ffcc-35f8-4372-9e4a-7b5bde18fe31" + } + ], + "updatedAt": "2024-04-08T15:59:05.947Z", + "version": "0.2.2" +} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts new file mode 100644 index 00000000..0acb2763 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts @@ -0,0 +1,3 @@ +IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore +-1 -1 Not Barcoded Not Barcoded 13207 41 +47 47 bc2048 bc2048 9122662 97 diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess new file mode 100644 index 00000000..3e7b1202 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess @@ -0,0 +1,2 @@ +IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed NumZMWs MeanScore Picked +47 47 bc2048 bc2048 49322 97 1 diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt new file mode 100644 index 00000000..3e7b1202 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt @@ -0,0 +1,2 @@ +IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed NumZMWs MeanScore Picked +47 47 bc2048 bc2048 49322 97 1 diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary new file mode 100644 index 00000000..3204613e --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary @@ -0,0 +1,24 @@ +ZMWs input (A) : 9135869 +ZMWs above all thresholds (B) : 9122662 (99.86%) +ZMWs below any threshold (C) : 13207 (0.14%) + +ZMW marginals for (C): +Below min length : 3 (0.02%) +Below min score : 13204 (99.98%) +Below min end score : 13204 (99.98%) +Below min passes : 0 (0.00%) +Below min score lead : 0 (0.00%) +Below min ref span : 7503 (56.81%) +Without SMRTbell adapter : 5 (0.04%) + +ZMWs for (B): +With same pair : 9122662 (100.00%) +Coefficient of correlation : 0.00% + +ZMWs for (A): +Allow diff pair : 9061203 (99.18%) +Allow same pair : 9135864 (100.00%) + +Reads for (B): +Above length : 9122662 (100.00%) +Below length : 0 (0.00%) diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt new file mode 100644 index 00000000..3204613e --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt @@ -0,0 +1,24 @@ +ZMWs input (A) : 9135869 +ZMWs above all thresholds (B) : 9122662 (99.86%) +ZMWs below any threshold (C) : 13207 (0.14%) + +ZMW marginals for (C): +Below min length : 3 (0.02%) +Below min score : 13204 (99.98%) +Below min end score : 13204 (99.98%) +Below min passes : 0 (0.00%) +Below min score lead : 0 (0.00%) +Below min ref span : 7503 (56.81%) +Without SMRTbell adapter : 5 (0.04%) + +ZMWs for (B): +With same pair : 9122662 (100.00%) +Coefficient of correlation : 0.00% + +ZMWs for (A): +Allow diff pair : 9061203 (99.18%) +Allow same pair : 9135864 (100.00%) + +Reads for (B): +Above length : 9122662 (100.00%) +Below length : 0 (0.00%) diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml new file mode 100644 index 00000000..2661b11c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml @@ -0,0 +1,161 @@ + + + + 83805002 + 13207 + + + 0 + + + r84098_20240322_103351 + TRACTION-RUN-1200 + su3 + 2024-03-22T10:18:41.142Z + unknown + 2024-03-22T10:34:27.863237Z + + + A01 + unspecified + 0 + 252 + 5795 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + 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b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.json @@ -0,0 +1,19 @@ +{ + "createdAt": "2024-04-08T15:59:01.602Z", + "files": [ + { + "createdAt": "2024-04-08T15:59:01.602Z", + "description": "Split BAM file by lima", + "fileSize": 49031458, + "fileTypeId": "PacBio.DataSet.ConsensusReadSet", + "isChunked": false, + "modifiedAt": "2024-04-08T15:59:01.602Z", + "name": "Barcodes unassigned", + "path": "m84098_240322_112047_s1.unbarcoded.consensusreadset.xml", + "sourceId": "barcoding.tasks.lima-1", + "uniqueId": "4384a8f0-1ae4-4ebc-b83c-a7f2b97d2f50" + } + ], + "updatedAt": "2024-04-08T15:59:01.602Z", + "version": "0.2.2" +} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/merged_analysis_report.json b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/merged_analysis_report.json new file mode 100644 index 00000000..db46cf9d --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/merged_analysis_report.json @@ -0,0 +1 @@ +{"__CLASS__":"WTSI::NPG::HTS::PacBio::Sequel::Reportdata","created_at":"2024-04-15T10:29:14","meta_data":{"__CLASS__":"WTSI::NPG::HTS::PacBio::Metadata","ccsreads_uuid":"c577c932-2708-4b4d-85a4-941ab553253b","cell_index":"0","collection_number":"0","execution_mode":"OnInstrument","file_path":"t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml","instrument_name":"84098","movie_name":"m84098_240322_112047_s1","plate_number":1,"results_folder":"r84098_20240322_103351/1_A01/","run_name":"TRACTION-RUN-1200","sample_load_name":"TRAC-2-8046","ts_run_name":"r84098_20240322_103351","version_info":{"basecaller":"13.0.0","baz2bam":"release/kestrel-13_002388e6797af47f3ebff3ecb52a2da1e62080c5-dirty","ccs":"ccs 8.0.0 (commit v8.0.0) Using: unanimity : 8.0.0 (commit v8.0.0) pbbam : 2.5.0 (commit v2.5.0) pbcopper : 2.4.0 (commit v2.4.0) pancake : 2.2.0 (commit v2.2.0) pbsparc : 1.1.0 (commit v1.1.0) pbdc : 1.3.1 (commit v1.3.1) boost : 1.81 htslib : 1.17 zlib : 1.2.13","chemistry":"13.0.0.205983","ics":"13.0.0.212033","iui":"Unknown","jasmine":"jasmine 2.2.0 Using: jasmine : 2.2.0 (commit v2.2.0) pbbam : 2.5.0 (commit v2.5.0) pbcopper : 2.4.0 (commit v2.4.0) pbort : 1.0.0 (commit v1.0.0) boost : 1.81 htslib : 1.17 onnxruntime : 1.11.0 zlib : 1.2.13","lima":"lima 2.9.0 Using: lima : 2.9.0 (commit v2.9.0) pbbam : 2.5.0 (commit v2.5.0) pbcopper : 2.4.0 (commit v2.4.0) boost : 1.81 htslib : 1.17 zlib : 1.2.13","pa":"13.0.0.212033","pa-cal":"13.0.0.002388e6797af47f3ebff3ecb52a2da1e62080c5-dirty","pa-wsgo":"13.0.2-0fe811ceb7ddd492390327f845a31332a049119c","pawnee":"pawnee 1.3.8 (commit v1.3.8)","reducestats":"release/kestrel-13_002388e6797af47f3ebff3ecb52a2da1e62080c5-dirty","samtools":"samtools 1.17 Using htslib 1.17 Copyright (C) 2023 Genome Research Ltd. Samtools compilation details: Features: build=configure curses=no CC: gcc CPPFLAGS: -I/var/lib/bamboo/bamboo-agent-home/xml-data/build-dir/RBREVIO-K13REVINST-SAM/software/include CFLAGS: -Wall -g -O2 LDFLAGS: -L/var/lib/bamboo/bamboo-agent-home/xml-data/build-dir/RBREVIO-K13REVINST-SAM/software/lib HTSDIR: htslib-1.17 LIBS: CURSES_LIB: HTSlib compilation details: Features: build=configure libcurl=no S3=no GCS=no libdeflate=no lzma=no bzip2=no plugins=no htscodecs=1.4.0 CC: gcc CPPFLAGS: -I/var/lib/bamboo/bamboo-agent-home/xml-data/build-dir/RBREVIO-K13REVINST-SAM/software/include CFLAGS: -Wall -g -O2 -fvisibility=hidden LDFLAGS: -L/var/lib/bamboo/bamboo-agent-home/xml-data/build-dir/RBREVIO-K13REVINST-SAM/software/lib -fvisibility=hidden HTSlib URL scheme handlers present: built-in: preload, data, file crypt4gh-needed: crypt4gh mem: mem","smrtimisc":"13.0.0.207600","smrtinub":"13.0.0.207600","smrtlink":"13.0.0.207600","smrtlink-analysisservices-gui":"13.0.0.207600","smrttools":"13.0.0.207600"},"well_name":"A01"},"reports":{"m84098_240322_112047_s1.lima.counts":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tCounts\tMeanScore\n-1\t-1\tNot Barcoded\tNot Barcoded\t13207\t41\n47\t47\tbc2048\tbc2048\t9122662\t97\n","m84098_240322_112047_s1.lima.guess.txt":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tNumZMWs\tMeanScore\tPicked\n47\t47\tbc2048\tbc2048\t49322\t97\t1\n","m84098_240322_112047_s1.lima.summary.txt":"ZMWs input (A) : 9135869\nZMWs above all thresholds (B) : 9122662 (99.86%)\nZMWs below any threshold (C) : 13207 (0.14%)\n\nZMW marginals for (C):\nBelow min length : 3 (0.02%)\nBelow min score : 13204 (99.98%)\nBelow min end score : 13204 (99.98%)\nBelow min passes : 0 (0.00%)\nBelow min score lead : 0 (0.00%)\nBelow min ref span : 7503 (56.81%)\nWithout SMRTbell adapter : 5 (0.04%)\n\nZMWs for (B):\nWith same pair : 9122662 (100.00%)\nCoefficient of correlation : 0.00%\n\nZMWs for (A):\nAllow diff pair : 9061203 (99.18%)\nAllow same pair : 9135864 (100.00%)\n\nReads for (B):\nAbove length : 9122662 (100.00%)\nBelow length : 0 (0.00%)\n"}} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/merged_analysis_report.json.md5 b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/merged_analysis_report.json.md5 new file mode 100644 index 00000000..a2a90f85 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/merged_analysis_report.json.md5 @@ -0,0 +1 @@ +a3d773995d186175f6cf8d1f1f69cfe5 diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/mlwh_locations.json b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/mlwh_locations.json new file mode 100644 index 00000000..aed5e2d9 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/mlwh_locations.json @@ -0,0 +1 @@ +{"version":"1.0","products":[{"irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.54890.0/1_A01/","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","seq_platform_name":"pacbio","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","pipeline_name":"npg-prod"},{"irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.8865.0/1_A01/","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","pipeline_name":"npg-prod","seq_platform_name":"pacbio"},{"irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.39705.0/1_A01/","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","pipeline_name":"npg-prod","seq_platform_name":"pacbio"},{"seq_platform_name":"pacbio","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","pipeline_name":"npg-prod","irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.13951.0/1_A01/","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam"}]} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml new file mode 100644 index 00000000..869faf2c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml @@ -0,0 +1,164 @@ + + + + 57462851406 + 9122662 + + + 0 + + + r84098_20240322_103351 + TRACTION-RUN-1200 + su3 + 2024-03-22T10:18:41.142Z + unknown + 2024-03-22T10:34:27.863237Z + + + A01 + unspecified + 0 + 252 + 5795 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240322_103351/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240322_103351/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.consensusreadset.xml new file mode 100644 index 00000000..88ca8348 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.consensusreadset.xml @@ -0,0 +1,183 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 57462851406 + 9122662 + + + 0 + + + r84098_20240322_103351 + TRACTION-RUN-1200 + su3 + 2024-03-22T10:18:41.142Z + unknown + 2024-03-22T10:34:27.863237Z + + + A01 + unspecified + 0 + 252 + 5795 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240322_103351/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240322_103351/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + PmJjMjAwMQpBVENHVEdDR0FDR0FHVEFUCj5iYzIwMDIKVEdDQVRHVENBVEdBR1RBVAo+YmMyMDAzCkFDR0FHVEdDVENHQUdUQVQKPmJjMjAwNApUR0NBR1RHQ1RDR0FHVEFUCj5iYzIwMDUKVEdBQ1RDR0FUQ0dBR1RBVAo+YmMyMDA2CkNBVEdDR0FUQ1RHQUdUQVQKPmJjMjAwNwpBQ1RBR0NBVENUR0FHVEFUCj5iYzIwMDgKQUNHQ1RBR1RDVEdBR1RBVAo+YmMyMDA5CkNHQVRDR0NBQ1RHQUdUQVQKPmJjMjAxMApUQUNHVEFHVEFUR0FHVEFUCj5iYzIwMTEKQ1RHQUNBR1RBQ0dBR1RBVAo+YmMyMDEyClRDR1RBQ1RBQ1RHQUdUQVQKPmJjMjAxMwpDVEdDR1RBR0FDR0FHVEFUCj5iYzIwMTQKQVRBQ0FUR0NBQ0dBR1RBVAo+YmMyMDE1CkNHQUNBVEFHQVRHQUdUQVQKPmJjMjAxNgpBVENUR0NBQ0dUR0FHVEFUCj5iYzIwMTcKQ1RBVEdBVEFHQ0dBR1RBVAo+YmMyMDE4CkNHQVRDQUdUR0NHQUdUQVQKPmJjMjAxOQpDR1RDQVRBR1RDR0FHVEFUCj5iYzIwMjAKQUNUQVRHQ0dUQ0dBR1RBVAo+YmMyMDIxCkNHVEFDQVRHQ1RHQUdUQVQKPmJjMjAyMgpUQ0FUQ0dBQ0dUR0FHVEFUCj5iYzIwMjMKVENHQ0FUR0FDVEdBR1RBVAo+YmMyMDI0CkNBVEdBVENHQUNHQUdUQVQKPmJjMjAyNQpBQ0dDQUNHVEFDR0FHVEFUCj5iYzIwMjYKQ0FHVEFHQ0dUQ0dBR1RBVAo+YmMyMDI3ClRHQUNUR1RBR0NHQUdUQVQKPmJjMjAyOApBQ1RHQ0FHQ0FDR0FHVEFUCj5iYzIwMjkKVEFHQ0FHVEFUQ0dBR1RBVAo+YmMyMDMwCkNBVEFDQUdDQVRHQUdUQVQKPmJjMjAzMQpBVEFHQ0dUQUNUR0FHVEFUCj5iYzIwMzIKQVRBR0FDR0FHVEdBR1RBVAo+YmMyMDMzCkNHQUNUQ0dUQVRHQUdUQVQKPmJjMjAzNApUQUNUQUdUR0FDR0FHVEFUCj5iYzIwMzUKQ0FHQ1RHQUNBVEdBR1RBVAo+YmMyMDM2CkFDR1RDR0NUR0NHQUdUQVQKPmJjMjAzNwpDQUdUQVRHQUdDR0FHVEFUCj5iYzIwMzgKVENBQ0dBQ0dBQ0dBR1RBVAo+YmMyMDM5CkNBVEdUQVRHVENHQUdUQVQKPmJjMjA0MApUR0NUR0NHQUNUR0FHVEFUCj5iYzIwNDEKVEFUR0FUQ0FDVEdBR1RBVAo+YmMyMDQyClRDVEdDQUNUR0NHQUdUQVQKPmJjMjA0MwpBQ0dBVEdBQ0dUR0FHVEFUCj5iYzIwNDQKQ0dBVEdBVEdDVEdBR1RBVAo+YmMyMDQ1ClRBQ0dBQ0FHVENHQUdUQVQKPmJjMjA0NgpBVEFHQ0FUR1RDR0FHVEFUCj5iYzIwNDcKQ0FUQUdUQUNUQ0dBR1RBVAo+YmMyMDQ4ClRHQVRHQ1RBR1RHQUdUQVQKPmJjMjA0OQpUQUdUQ1RHQ0dUR0FHVEFUCj5iYzIwNTAKQ1RDQVRDVEFUQ0dBR1RBVAo+YmMyMDUxClRHQ0FUQUNUR0NHQUdUQVQKPmJjMjA1MgpDQUdBQ1RBR1RDR0FHVEFUCj5iYzIwNTMKQVRDR1RHQVRDVEdBR1RBVAo+YmMyMDU0CkNUR0NHQVRDQUNHQUdUQVQKPmJjMjA1NQpDVENBR0NBVEFDR0FHVEFUCj5iYzIwNTYKVENHQ0FHQ0dUQ0dBR1RBVAo+YmMyMDU3ClRBR0NBQ0dDQVRHQUdUQVQKPmJjMjA1OApUQUNUR0FDR0NUR0FHVEFUCj5iYzIwNTkKQVRDVEdBQ1RBVEdBR1RBVAo+YmMyMDYwCkFUQUNHQUdDVENHQUdUQVQKPmJjMjA2MQpDR0FHQ0FDR0NUR0FHVEFUCj5iYzIwNjIKVENUR0NHVEFUQ0dBR1RBVAo+YmMyMDYzClRDVEdDQVRDQVRHQUdUQVQKPmJjMjA2NApUR0NHVEdBVEdDR0FHVEFUCj5iYzIwNjUKVEdBR0NUQVRHQ0dBR1RBVAo+YmMyMDY2CkNUR1RDR1RBR1RHQUdUQVQKPmJjMjA2NwpBVENHQVRHQ0FUR0FHVEFUCj5iYzIwNjgKQUNUQUNHVEdBVEdBR1RBVAo+YmMyMDY5ClRDVEFUR0FDQVRHQUdUQVQKPmJjMjA3MApUQUNUR0NUQ0FDR0FHVEFUCj5iYzIwNzEKQ0dBR1RDVEFHQ0dBR1RBVAo+YmMyMDcyClRBVENBR1RBR1RHQUdUQVQKPmJjMjA3MwpBVENBQ1RBR1RDR0FHVEFUCj5iYzIwNzQKVEFUQ0FDR0FDVEdBR1RBVAo+YmMyMDc1CkNUQ0dUQ0FHQVRHQUdUQVQKPmJjMjA3NgpDQUdDQUdUR0FDR0FHVEFUCj5iYzIwNzcKVEdDR0FDR1RHQ0dBR1RBVAo+YmMyMDc4CkNUQ0FDVEdBR1RHQUdUQVQKPmJjMjA3OQpDQUNUR0FHQ0dUR0FHVEFUCj5iYzIwODAKQ0FHQ0dUQ1RBQ0dBR1RBVAo+YmMyMDgxCkNUQUNUQVRHVENHQUdUQVQKPmJjMjA4MgpBVEdUQUNBR0FDR0FHVEFUCj5iYzIwODMKQUNUQ0FUQ0FHVEdBR1RBVAo+YmMyMDg0CkNUR0FHQ0FDVENHQUdUQVQKPmJjMjA4NQpBVENBVENUQUNUR0FHVEFUCj5iYzIwODYKVEFDQVRHQ0dBVEdBR1RBVAo+YmMyMDg3ClRDR0NUR1RDQUNHQUdUQVQKPmJjMjA4OApBQ0dDVENBVEdDR0FHVEFUCj5iYzIwODkKVEFDVEFHQ0FHQ0dBR1RBVAo+YmMyMDkwCkNHVEFHQ0FHQVRHQUdUQVQKPmJjMjA5MQpDR1RHQ1RDR1RDR0FHVEFUCj5iYzIwOTIKQUNBR0NUR1RBQ0dBR1RBVAo+YmMyMDkzClRDR0FUR0NUQUNHQUdUQVQKPmJjMjA5NApUQUdBVEFDQUdDR0FHVEFUCj5iYzIwOTUKQ1RBQ1RDQVRBQ0dBR1RBVAo+YmMyMDk2CkFUR1RBQ1RBR1RHQUdUQVQK + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml new file mode 100644 index 00000000..869faf2c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml @@ -0,0 +1,164 @@ + + + + 57462851406 + 9122662 + + + 0 + + + r84098_20240322_103351 + TRACTION-RUN-1200 + su3 + 2024-03-22T10:18:41.142Z + unknown + 2024-03-22T10:34:27.863237Z + + + A01 + unspecified + 0 + 252 + 5795 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240322_103351/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240322_103351/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/lima_guesses.report.json b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/lima_guesses.report.json new file mode 100644 index 00000000..d48b00a3 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/lima_guesses.report.json @@ -0,0 +1,42 @@ +{ + "_comment": "Created by pbcopper v2.4.0", + "attributes": [], + "dataset_uuids": [], + "id": "lima_infer", + "plotGroups": [], + "tables": [ + { + "columns": [ + { + "header": "Barcode", + "id": "first_bc_name", + "values": [ + "bc2048--bc2048", + "unassigned" + ] + }, + { + "header": "Reads, %", + "id": "num_zmws", + "values": [ + 98.6, + 1.4 + ] + }, + { + "header": "Barcode score, mean", + "id": "mean_bc_score", + "values": [ + 97, + 0 + ] + } + ], + "id": "inferred_barcode_table", + "title": "Inferred Barcodes" + } + ], + "title": "Inferred Barcodes", + "uuid": "8b88fc06-4c6d-4375-91c8-34153c70b3da", + "version": "1.0.1" +} diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml new file mode 100644 index 00000000..88ca8348 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml @@ -0,0 +1,183 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 57462851406 + 9122662 + + + 0 + + + r84098_20240322_103351 + TRACTION-RUN-1200 + su3 + 2024-03-22T10:18:41.142Z + unknown + 2024-03-22T10:34:27.863237Z + + + A01 + unspecified + 0 + 252 + 5795 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240322_103351/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240322_103351/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json new file mode 100644 index 00000000..8d5b048c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json @@ -0,0 +1,19 @@ +{ + "createdAt": "2024-04-08T15:59:05.947Z", + "files": [ + { + "createdAt": "2024-04-08T15:59:05.946Z", + "description": "Split BAM file by lima", + "fileSize": 300968828, + "fileTypeId": "PacBio.DataSet.ConsensusReadSet", + "isChunked": false, + "modifiedAt": "2024-04-08T15:59:05.947Z", + "name": "Barcodes bc2048--bc2048", + "path": "bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml", + "sourceId": "barcoding.tasks.lima-0", + "uniqueId": "c1a6ffcc-35f8-4372-9e4a-7b5bde18fe31" + } + ], + "updatedAt": "2024-04-08T15:59:05.947Z", + "version": "0.2.2" +} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts new file mode 100644 index 00000000..0acb2763 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts @@ -0,0 +1,3 @@ +IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore +-1 -1 Not Barcoded Not Barcoded 13207 41 +47 47 bc2048 bc2048 9122662 97 diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess new file mode 100644 index 00000000..3e7b1202 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess @@ -0,0 +1,2 @@ +IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed NumZMWs MeanScore Picked +47 47 bc2048 bc2048 49322 97 1 diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt new file mode 100644 index 00000000..3e7b1202 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt @@ -0,0 +1,2 @@ +IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed NumZMWs MeanScore Picked +47 47 bc2048 bc2048 49322 97 1 diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary new file mode 100644 index 00000000..05881a5c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary @@ -0,0 +1,24 @@ +ZMWs input (A) : 9135869 +ZMWs above all thresholds (B) : 13207 (0.14%) +ZMWs below any threshold (C) : 9122662 (99.86%) + +ZMW marginals for (C): +Below min length : 3 (0.02%) +Below min score : 13204 (99.98%) +Below min end score : 13204 (99.98%) +Below min passes : 0 (0.00%) +Below min score lead : 0 (0.00%) +Below min ref span : 7503 (56.81%) +Without SMRTbell adapter : 5 (0.04%) + +ZMWs for (B): +With same pair : 9122662 (100.00%) +Coefficient of correlation : 0.00% + +ZMWs for (A): +Allow diff pair : 9061203 (99.18%) +Allow same pair : 9135864 (100.00%) + +Reads for (B): +Above length : 9122662 (100.00%) +Below length : 0 (0.00%) diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt new file mode 100644 index 00000000..05881a5c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt @@ -0,0 +1,24 @@ +ZMWs input (A) : 9135869 +ZMWs above all thresholds (B) : 13207 (0.14%) +ZMWs below any threshold (C) : 9122662 (99.86%) + +ZMW marginals for (C): +Below min length : 3 (0.02%) +Below min score : 13204 (99.98%) +Below min end score : 13204 (99.98%) +Below min passes : 0 (0.00%) +Below min score lead : 0 (0.00%) +Below min ref span : 7503 (56.81%) +Without SMRTbell adapter : 5 (0.04%) + +ZMWs for (B): +With same pair : 9122662 (100.00%) +Coefficient of correlation : 0.00% + +ZMWs for (A): +Allow diff pair : 9061203 (99.18%) +Allow same pair : 9135864 (100.00%) + +Reads for (B): +Above length : 9122662 (100.00%) +Below length : 0 (0.00%) diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi new file mode 100644 index 00000000..e69de29b diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml new file mode 100644 index 00000000..2661b11c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml @@ -0,0 +1,161 @@ + + + + 83805002 + 13207 + + + 0 + + + r84098_20240322_103351 + TRACTION-RUN-1200 + su3 + 2024-03-22T10:18:41.142Z + unknown + 2024-03-22T10:34:27.863237Z + + + A01 + unspecified + 0 + 252 + 5795 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240322_103351/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240322_103351/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + PmJjMjAwMQpBVENHVEdDR0FDR0FHVEFUCj5iYzIwMDIKVEdDQVRHVENBVEdBR1RBVAo+YmMyMDAzCkFDR0FHVEdDVENHQUdUQVQKPmJjMjAwNApUR0NBR1RHQ1RDR0FHVEFUCj5iYzIwMDUKVEdBQ1RDR0FUQ0dBR1RBVAo+YmMyMDA2CkNBVEdDR0FUQ1RHQUdUQVQKPmJjMjAwNwpBQ1RBR0NBVENUR0FHVEFUCj5iYzIwMDgKQUNHQ1RBR1RDVEdBR1RBVAo+YmMyMDA5CkNHQVRDR0NBQ1RHQUdUQVQKPmJjMjAxMApUQUNHVEFHVEFUR0FHVEFUCj5iYzIwMTEKQ1RHQUNBR1RBQ0dBR1RBVAo+YmMyMDEyClRDR1RBQ1RBQ1RHQUdUQVQKPmJjMjAxMwpDVEdDR1RBR0FDR0FHVEFUCj5iYzIwMTQKQVRBQ0FUR0NBQ0dBR1RBVAo+YmMyMDE1CkNHQUNBVEFHQVRHQUdUQVQKPmJjMjAxNgpBVENUR0NBQ0dUR0FHVEFUCj5iYzIwMTcKQ1RBVEdBVEFHQ0dBR1RBVAo+YmMyMDE4CkNHQVRDQUdUR0NHQUdUQVQKPmJjMjAxOQpDR1RDQVRBR1RDR0FHVEFUCj5iYzIwMjAKQUNUQVRHQ0dUQ0dBR1RBVAo+YmMyMDIxCkNHVEFDQVRHQ1RHQUdUQVQKPmJjMjAyMgpUQ0FUQ0dBQ0dUR0FHVEFUCj5iYzIwMjMKVENHQ0FUR0FDVEdBR1RBVAo+YmMyMDI0CkNBVEdBVENHQUNHQUdUQVQKPmJjMjAyNQpBQ0dDQUNHVEFDR0FHVEFUCj5iYzIwMjYKQ0FHVEFHQ0dUQ0dBR1RBVAo+YmMyMDI3ClRHQUNUR1RBR0NHQUdUQVQKPmJjMjAyOApBQ1RHQ0FHQ0FDR0FHVEFUCj5iYzIwMjkKVEFHQ0FHVEFUQ0dBR1RBVAo+YmMyMDMwCkNBVEFDQUdDQVRHQUdUQVQKPmJjMjAzMQpBVEFHQ0dUQUNUR0FHVEFUCj5iYzIwMzIKQVRBR0FDR0FHVEdBR1RBVAo+YmMyMDMzCkNHQUNUQ0dUQVRHQUdUQVQKPmJjMjAzNApUQUNUQUdUR0FDR0FHVEFUCj5iYzIwMzUKQ0FHQ1RHQUNBVEdBR1RBVAo+YmMyMDM2CkFDR1RDR0NUR0NHQUdUQVQKPmJjMjAzNwpDQUdUQVRHQUdDR0FHVEFUCj5iYzIwMzgKVENBQ0dBQ0dBQ0dBR1RBVAo+YmMyMDM5CkNBVEdUQVRHVENHQUdUQVQKPmJjMjA0MApUR0NUR0NHQUNUR0FHVEFUCj5iYzIwNDEKVEFUR0FUQ0FDVEdBR1RBVAo+YmMyMDQyClRDVEdDQUNUR0NHQUdUQVQKPmJjMjA0MwpBQ0dBVEdBQ0dUR0FHVEFUCj5iYzIwNDQKQ0dBVEdBVEdDVEdBR1RBVAo+YmMyMDQ1ClRBQ0dBQ0FHVENHQUdUQVQKPmJjMjA0NgpBVEFHQ0FUR1RDR0FHVEFUCj5iYzIwNDcKQ0FUQUdUQUNUQ0dBR1RBVAo+YmMyMDQ4ClRHQVRHQ1RBR1RHQUdUQVQKPmJjMjA0OQpUQUdUQ1RHQ0dUR0FHVEFUCj5iYzIwNTAKQ1RDQVRDVEFUQ0dBR1RBVAo+YmMyMDUxClRHQ0FUQUNUR0NHQUdUQVQKPmJjMjA1MgpDQUdBQ1RBR1RDR0FHVEFUCj5iYzIwNTMKQVRDR1RHQVRDVEdBR1RBVAo+YmMyMDU0CkNUR0NHQVRDQUNHQUdUQVQKPmJjMjA1NQpDVENBR0NBVEFDR0FHVEFUCj5iYzIwNTYKVENHQ0FHQ0dUQ0dBR1RBVAo+YmMyMDU3ClRBR0NBQ0dDQVRHQUdUQVQKPmJjMjA1OApUQUNUR0FDR0NUR0FHVEFUCj5iYzIwNTkKQVRDVEdBQ1RBVEdBR1RBVAo+YmMyMDYwCkFUQUNHQUdDVENHQUdUQVQKPmJjMjA2MQpDR0FHQ0FDR0NUR0FHVEFUCj5iYzIwNjIKVENUR0NHVEFUQ0dBR1RBVAo+YmMyMDYzClRDVEdDQVRDQVRHQUdUQVQKPmJjMjA2NApUR0NHVEdBVEdDR0FHVEFUCj5iYzIwNjUKVEdBR0NUQVRHQ0dBR1RBVAo+YmMyMDY2CkNUR1RDR1RBR1RHQUdUQVQKPmJjMjA2NwpBVENHQVRHQ0FUR0FHVEFUCj5iYzIwNjgKQUNUQUNHVEdBVEdBR1RBVAo+YmMyMDY5ClRDVEFUR0FDQVRHQUdUQVQKPmJjMjA3MApUQUNUR0NUQ0FDR0FHVEFUCj5iYzIwNzEKQ0dBR1RDVEFHQ0dBR1RBVAo+YmMyMDcyClRBVENBR1RBR1RHQUdUQVQKPmJjMjA3MwpBVENBQ1RBR1RDR0FHVEFUCj5iYzIwNzQKVEFUQ0FDR0FDVEdBR1RBVAo+YmMyMDc1CkNUQ0dUQ0FHQVRHQUdUQVQKPmJjMjA3NgpDQUdDQUdUR0FDR0FHVEFUCj5iYzIwNzcKVEdDR0FDR1RHQ0dBR1RBVAo+YmMyMDc4CkNUQ0FDVEdBR1RHQUdUQVQKPmJjMjA3OQpDQUNUR0FHQ0dUR0FHVEFUCj5iYzIwODAKQ0FHQ0dUQ1RBQ0dBR1RBVAo+YmMyMDgxCkNUQUNUQVRHVENHQUdUQVQKPmJjMjA4MgpBVEdUQUNBR0FDR0FHVEFUCj5iYzIwODMKQUNUQ0FUQ0FHVEdBR1RBVAo+YmMyMDg0CkNUR0FHQ0FDVENHQUdUQVQKPmJjMjA4NQpBVENBVENUQUNUR0FHVEFUCj5iYzIwODYKVEFDQVRHQ0dBVEdBR1RBVAo+YmMyMDg3ClRDR0NUR1RDQUNHQUdUQVQKPmJjMjA4OApBQ0dDVENBVEdDR0FHVEFUCj5iYzIwODkKVEFDVEFHQ0FHQ0dBR1RBVAo+YmMyMDkwCkNHVEFHQ0FHQVRHQUdUQVQKPmJjMjA5MQpDR1RHQ1RDR1RDR0FHVEFUCj5iYzIwOTIKQUNBR0NUR1RBQ0dBR1RBVAo+YmMyMDkzClRDR0FUR0NUQUNHQUdUQVQKPmJjMjA5NApUQUdBVEFDQUdDR0FHVEFUCj5iYzIwOTUKQ1RBQ1RDQVRBQ0dBR1RBVAo+YmMyMDk2CkFUR1RBQ1RBR1RHQUdUQVQK + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.json b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.json new file mode 100644 index 00000000..b356445c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.json @@ -0,0 +1,19 @@ +{ + "createdAt": "2024-04-08T15:59:01.602Z", + "files": [ + { + "createdAt": "2024-04-08T15:59:01.602Z", + "description": "Split BAM file by lima", + "fileSize": 49031458, + "fileTypeId": "PacBio.DataSet.ConsensusReadSet", + "isChunked": false, + "modifiedAt": "2024-04-08T15:59:01.602Z", + "name": "Barcodes unassigned", + "path": "m84098_240322_112047_s1.unbarcoded.consensusreadset.xml", + "sourceId": "barcoding.tasks.lima-1", + "uniqueId": "4384a8f0-1ae4-4ebc-b83c-a7f2b97d2f50" + } + ], + "updatedAt": "2024-04-08T15:59:01.602Z", + "version": "0.2.2" +} \ No newline at end of file diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml new file mode 100644 index 00000000..869faf2c --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml @@ -0,0 +1,164 @@ + + + + 57462851406 + 9122662 + + + 0 + + + r84098_20240322_103351 + TRACTION-RUN-1200 + su3 + 2024-03-22T10:18:41.142Z + unknown + 2024-03-22T10:34:27.863237Z + + + A01 + unspecified + 0 + 252 + 5795 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240322_103351/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240322_103351/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.consensusreadset.xml b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.consensusreadset.xml new file mode 100644 index 00000000..88ca8348 --- /dev/null +++ b/t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.consensusreadset.xml @@ -0,0 +1,183 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 57462851406 + 9122662 + + + 0 + + + r84098_20240322_103351 + TRACTION-RUN-1200 + su3 + 2024-03-22T10:18:41.142Z + unknown + 2024-03-22T10:34:27.863237Z + + + A01 + unspecified + 0 + 252 + 5795 + false + true + false + false + false + 0 + Revio sequencing control + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + 0 + 0 + + KestrelRTO2 + + + >left_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>right_adapter\nTAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA\n>custom_sequence\nTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA + + + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + CAACAACAACAACGGAGGAGGAGGAAAAG + aacggaggaggagga + + + + + SequelAlpha + SqlPoC_SubCrf_2C2A-t2.xml + DefaultPrimarySequencingCondition + + OnInstrument + false + + + r84098_20240322_103351/1_A01/ + /lustre/scratch120/pacbio/staging/r84098_20240322_103351/1_A01/ + + Bam + Fasta + + Bases_Without_QVs + Minimal + + 76b3ab89-686d-483b-99f9-cb348bd596ab + SRS + srs-scheme-2 + Sanger srs + /lustre/scratch120/pacbio/staging + + + + + SMRTLinkRunDesign + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm index db5968fb..626afa2a 100644 --- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm +++ b/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm @@ -443,7 +443,7 @@ sub publish_files_4 : Test(6) { my $runfolder_path = "$analysis_path/cromwell-job/call-lima/execution", my $dest_coll = "$irods_tmp_coll/publish_sequence_files"; - my $expected_json = 't/data/mlwh_json/pacbio.json'; + my $expected_json = 't/data/mlwh_json/pacbio2.json'; my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new (restart_file => catfile($tmpdir->dirname, 'published.json'), From c29b6b4869db5bda8d9c2bd3af4c19256f698d6e Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Fri, 19 Apr 2024 15:48:10 +0100 Subject: [PATCH 5/5] prepare relase 2.49.0 --- Changes | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/Changes b/Changes index 58edc3aa..fe537549 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,13 @@ Unreleased +Release 2.49.0 + - PacBio iRODS data - set QC state metadata when it is safe to do so. + - Allow non deplexed Revio cells to publish now + - Analysis loading changes post SMRT Link v13 + Remove very old test data and update some tests. Add new test data and minor + code change to support loading of data from deplexing jobs in SMRT Link v13+ + (very rare as only done when deplexing on instrument is incorrect). + Release 2.48.0 - Add sequencing_control.subreads.bam and index file to PacBio run archiving. These files can be used to regenerate QC metrics.