=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =cut =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =head1 NAME Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf =head1 DESCRIPTION The PipeConfig file for ProteinTrees pipeline that should automate most of the pre-execution tasks. =head1 SYNOPSIS #1. update ensembl-hive, ensembl and ensembl-compara GIT repositories before each new release #3. make sure that all default_options are set correctly #4. Run init_pipeline.pl script: init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf -password -mlss_id #5. Sync and loop the beekeeper.pl as shown in init_pipeline.pl's output =head1 AUTHORSHIP Ensembl Team. Individual contributions can be found in the GIT log. =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore (_) =cut package Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf; use strict; use warnings; use Bio::EnsEMBL::Hive::Version 2.5; use Bio::EnsEMBL::Compara::PipeConfig::Parts::CAFE; use Bio::EnsEMBL::Compara::PipeConfig::Parts::GOC; use Bio::EnsEMBL::Compara::PipeConfig::Parts::GeneSetQC; use Bio::EnsEMBL::Compara::PipeConfig::Parts::GeneMemberHomologyStats; use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf; use base ('Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf'); sub default_options { my ($self) = @_; return { %{$self->SUPER::default_options}, # inherit the generic ones # User details #'email' => 'john.smith@example.com', # parameters inherited from EnsemblGeneric_conf and very unlikely to be redefined: # It defaults to Bio::EnsEMBL::ApiVersion::software_version() #'ensembl_release' => 88, # parameters that are likely to change from execution to another: # It is very important to check that this value is current (commented out to make it obligatory to specify) #'mlss_id' => 40077, # Change this one to allow multiple runs #'rel_suffix' => 'b', #production run or test/development run 'test_mode' => 1, # names of species we don't want to reuse this time 'do_not_reuse_list' => [ ], # where to find the list of Compara methods. Unlikely to be changed 'method_link_dump_file' => $self->check_file_in_ensembl('ensembl-compara/sql/method_link.txt'), # Parameters to allow merging different runs of the pipeline 'dbID_range_index' => undef, 'collection' => undef, 'label_prefix' => undef, #default parameters for the geneset qc 'coverage_threshold' => 50, #percent 'missing_sequence_threshold' => 0.05, 'species_threshold' => '#expr(#species_count#/2)expr#', #half of ensembl species # data directories: 'work_dir' => $self->o('pipeline_dir'), 'fasta_dir' => $self->o('work_dir') . '/blast_db', # affects 'dump_subset_create_blastdb' and 'blastp' 'cluster_dir' => $self->o('work_dir') . '/cluster', 'dump_dir' => $self->o('work_dir') . '/dumps', 'dump_pafs_dir' => $self->o('dump_dir') . '/pafs', 'examl_dir' => $self->o('work_dir') . '/examl', 'plots_dir' => $self->o('work_dir') . '/plots', # Directory used to store plots and their input files # "Member" parameters: 'allow_ambiguity_codes' => 0, 'allow_missing_coordinates' => 0, 'allow_missing_cds_seqs' => 0, # blast parameters: # Amount of sequences to be included in each blast job 'num_sequences_per_blast_job' => 500, # define blast parameters and evalues for ranges of sequence-length # Important note: -max_hsps parameter is only available on ncbi-blast-2.3.0 or higher. 'all_blast_params' => [ [ 0, 35, '-seg no -max_hsps 1 -use_sw_tback -num_threads 1 -matrix PAM30 -word_size 2', '1e-4' ], [ 35, 50, '-seg no -max_hsps 1 -use_sw_tback -num_threads 1 -matrix PAM70 -word_size 2', '1e-6' ], [ 50, 100, '-seg no -max_hsps 1 -use_sw_tback -num_threads 1 -matrix BLOSUM80 -word_size 2', '1e-8' ], [ 100, 10000000, '-seg no -max_hsps 1 -use_sw_tback -num_threads 1 -matrix BLOSUM62 -word_size 3', '1e-10' ], # should really be infinity, but ten million should be big enough ], # clustering parameters: # affects 'hcluster_dump_input_per_genome' 'outgroups' => {}, # (half of the previously used 'clutering_max_gene_count=1500) affects 'hcluster_run' 'clustering_max_gene_halfcount' => 750, # File with gene / peptide names that must be excluded from the clusters (e.g. know to disturb the trees) 'gene_blacklist_file' => '/dev/null', # tree building parameters: 'use_raxml' => 0, 'use_notung' => 0, 'use_treerecs' => 0, 'do_model_selection' => 0, 'use_quick_tree_break' => 1, 'treebreak_gene_count' => 1500, 'split_genes_gene_count' => 5000, 'mcoffee_short_gene_count' => 20, 'mcoffee_himem_gene_count' => 250, 'mafft_gene_count' => 300, 'mafft_himem_gene_count' => 400, 'mafft_runtime' => 7200, 'raxml_threshold_n_genes' => 500, 'raxml_threshold_aln_len' => 150, 'examl_ptiles' => 16, 'treebest_threshold_n_residues' => 10000, 'treebest_threshold_n_genes' => 400, 'update_threshold_trees' => 0.2, # sequence type used on the phylogenetic inferences # It has to be set to 1 for the strains 'use_dna_for_phylogeny' => 0, # alignment filtering options 'threshold_n_genes' => 20, 'threshold_aln_len' => 1000, 'threshold_n_genes_large' => 2000, 'threshold_aln_len_large' => 15000, 'noisy_cutoff' => 0.4, 'noisy_cutoff_large' => 1, # species tree reconciliation # you can define your own species_tree for 'treebest'. It can contain multifurcations 'species_tree_input_file' => undef, # When automatically binarizing the tree, should we assume timetree tags to be there ? 'use_timetree_times' => 0, # you can define your own species_tree for 'notung' or 'CAFE'. It *has* to be binary 'binary_species_tree_input_file' => undef, # homology_dnds parameters: # used by 'homology_dNdS' 'codeml_parameters_file' => $self->check_file_in_ensembl('ensembl-compara/scripts/pipeline/protein_trees.codeml.ctl.hash'), 'taxlevels' => [], # threshold used by per_genome_qc in order to check if the amount of orphan genes are acceptable # values were infered by checking previous releases, values that are out of these ranges may be caused by assembly and/or gene annotation problems. # SELECT stn1.node_id, stn1.left_index, stn1.right_index, stn1.node_name, stn1.taxon_id, COUNT(*), MIN(ratio), AVG(ratio), MAX(ratio) # FROM species_tree_node stn1 # JOIN (SELECT node_id, root_id, left_index, right_index, taxon_id, genome_db_id, node_name, nb_genes, nb_genes_in_tree/nb_genes AS ratio FROM species_tree_node JOIN species_tree_node_attr USING (node_id) WHERE genome_db_id IS NOT NULL) stn2 # ON stn1.root_id = stn2.root_id AND stn1.left_index < stn2.left_index AND stn1.right_index > stn2.right_index # WHERE stn1.root_id = 40140000 # GROUP BY stn1.node_id # ORDER BY stn1.left_index; 'mapped_gene_ratio_per_taxon' => { '2759' => 0.5, #eukaryotes }, # mapping parameters: 'do_stable_id_mapping' => 0, 'do_treefam_xref' => 0, # The TreeFam release to map to 'tf_release' => undef, # plots #compute Jaccard Index 'do_jaccard_index' => 1, 'jaccard_index_script' => $self->check_exe_in_ensembl('ensembl-compara/scripts/homology/plotJaccardIndex.r'), #Compute Gini coefficient (Lorenz curve) 'do_gini_coefficient' => 1, 'lorentz_curve_script' => $self->check_exe_in_ensembl('ensembl-compara/scripts/homology/plotLorentzCurve.r'), # HMM specific parameters (mostly set in the ENV file) # Dumps coming from InterPro 'panther_annotation_file' => '/dev/null', #'panther_annotation_file' => '/nfs/nobackup2/ensemblgenomes/ckong/workspace/buildhmmprofiles/panther_Interpro_annot_v8_1/loose_dummy.txt', # A file that holds additional tags we want to add to the HMM clusters (for instance: Best-fit models) 'extra_model_tags_file' => undef, # hive_capacity values for some analyses: 'reuse_capacity' => 3, 'blast_factory_capacity' => 50, 'blastp_capacity' => 900, 'blastpu_capacity' => 1000, 'mcoffee_short_capacity' => 600, 'mafft_capacity' => 2500, 'mafft_himem_capacity' => 1200, 'split_genes_capacity' => 600, 'alignment_filtering_capacity' => 400, 'cluster_tagging_capacity' => 200, 'prottest_capacity' => 400, 'treebest_capacity' => 400, 'raxml_capacity' => 400, 'examl_capacity' => 400, 'copy_tree_capacity' => 100, 'notung_capacity' => 400, 'ortho_tree_capacity' => 50, 'quick_tree_break_capacity' => 100, 'build_hmm_capacity' => 200, 'ktreedist_capacity' => 150, 'goc_capacity' => 30, 'goc_stats_capacity' => 5, 'genesetQC_capacity' => 100, 'other_paralogs_capacity' => 100, 'homology_dNdS_capacity' => 1500, 'copy_homology_dNdS_capacity' => 100, 'homology_dNdS_factory_capacity' => 10, 'hc_capacity' => 4, 'decision_capacity' => 4, 'hc_post_tree_capacity' => 100, 'HMMer_classify_capacity' => 400, 'loadmembers_capacity' => 30, 'HMMer_classifyPantherScore_capacity' => 1500, 'HMMer_search_capacity' => 8000, 'copy_trees_capacity' => 50, 'copy_alignments_capacity' => 50, 'mafft_update_capacity' => 50, 'raxml_update_capacity' => 50, 'ortho_stats_capacity' => 10, # hive priority values for some analyses: 'hc_priority' => -10, 'mcoffee_himem_priority' => 40, 'mafft_himem_priority' => 35, 'mafft_priority' => 30, 'mcoffee_priority' => 20, 'treebest_long_himem_priority' => 20, #default maximum retry count: 'hive_default_max_retry_count' => 1, # connection parameters to various databases: # Uncomment and update the database locations # the master database for synchronization of various ids (use undef if you don't have a master database) #'master_db' => 'mysql://ensro@compara1:3306/mm14_ensembl_compara_master', 'master_db' => undef, 'ncbi_db' => $self->o('master_db'), # Add the database location of the previous Compara release. Use "undef" if running the pipeline without reuse #'prev_rel_db' => 'mysql://ensro@compara3:3306/mm14_compara_homology_67' 'prev_rel_db' => undef, # By default, the stable ID mapping is done on the previous release database 'mapping_db' => $self->o('prev_rel_db'), # Where the members come from (as loaded by the LoadMembers pipeline) #'member_db' => 'mysql://....', # Configuration of the pipeline worklow # How will the pipeline create clusters (families) ? # Possible values: 'blastp' (default), 'hmm', 'hybrid' # 'blastp' means that the pipeline will run a all-vs-all blastp comparison of the proteins and run hcluster to create clusters. This can take a *lot* of compute # 'ortholog' means that the pipeline will use previously inferred orthologs to perform a cluster projection # 'hmm' means that the pipeline will run an HMM classification # 'hybrid' is like "hmm" except that the unclustered proteins go to a all-vs-all blastp + hcluster stage # 'topup' means that the HMM classification is reused from prev_rel_db, and topped-up with the updated / new species >> UNIMPLEMENTED << 'clustering_mode' => 'blastp', # How much the pipeline will try to reuse from "prev_rel_db" # Possible values: 'clusters' (default), 'members' # 'members' means that only the members are copied over, and the rest will be re-computed # 'hmms' is like 'members', but also copies the HMM profiles. It requires that the clustering mode is not 'blastp' >> UNIMPLEMENTED << # 'hmm_hits' is like 'hmms', but also copies the HMM hits >> UNIMPLEMENTED << # 'blastp' is like 'members', but also copies the blastp hits. It requires that the clustering mode is 'blastp' >> UNIMPLEMENTED << # 'ortholog' the orthologs will be copied from the reuse db >> UNIMPLEMENTED << # 'clusters' is like 'hmm_hits' or 'blastp' (depending on the clustering mode), but also copies the clusters # 'alignments' is like 'clusters', but also copies the alignments >> UNIMPLEMENTED << # 'trees' is like 'alignments', but also copies the trees >> UNIMPLEMENTED << # 'homologies is like 'trees', but also copies the homologies >> UNIMPLEMENTED << 'reuse_level' => 'members', # Ortholog-clustering parameters 'ref_ortholog_db' => undef, # CAFE parameters # Do we want to initialise the CAFE part now ? 'initialise_cafe_pipeline' => undef, 'cafe_lambdas' => '', # For now, we don't supply lambdas 'cafe_struct_tree_str' => '', # Not set by default 'full_species_tree_label' => 'default', 'per_family_table' => 1, 'cafe_species' => [], #Use Timetree divergence times for the GeneTree internal nodes 'use_timetree_times' => 0, # GOC parameters 'goc_reuse_db' => undef, 'goc_taxlevels' => [], 'goc_threshold' => undef, 'calculate_goc_distribution' => 1, # Extra analyses # Export HMMs ? 'do_hmm_export' => 0, # Do we want the Gene QC part to run ? 'do_gene_qc' => 0, # Do we extract overall statistics for each pair of species ? 'do_homology_stats' => 0, # Do we need a mapping between homology_ids of this database to another database ? # This parameter is automatically set to 1 when the GOC pipeline is going to run with a reuse database 'do_homology_id_mapping' => 0, }; } sub pipeline_checks_pre_init { my ($self) = @_; # The master db must be defined to allow mapping stable_ids and checking species for reuse die "The master dabase must be defined with a mlss_id" if $self->o('master_db') and not $self->o('mlss_id'); die "mlss_id can not be defined in the absence of a master dabase" if $self->o('mlss_id') and not $self->o('master_db'); die "Mapping of stable_id is only possible with a master database" if $self->o('do_stable_id_mapping') and not $self->o('master_db'); die "Species reuse is only possible with a master database" if $self->o('prev_rel_db') and not $self->o('master_db'); # Without a master database, we must provide other parameters die if not $self->o('master_db') and not $self->o('ncbi_db'); my %reuse_modes = (clusters => 1, members => 1); die "'reuse_level' must be set to one of: ".join(", ", keys %reuse_modes) unless $self->o('reuse_level') and $reuse_modes{$self->o('reuse_level')}; my %clustering_modes = (blastp => 1, ortholog => 1, hmm => 1, hybrid => 1, topup => 1); die "'clustering_mode' must be set to one of: ".join(", ", keys %clustering_modes) unless $self->o('clustering_mode') and $clustering_modes{$self->o('clustering_mode')}; # In HMM mode the library must exist if (($self->o('clustering_mode') ne 'blastp') and ($self->o('clustering_mode') ne 'ortholog')) { my $lib = $self->o('hmm_library_basedir'); if ($self->o('hmm_library_version') == 2){ die "'$lib' does not seem to be a valid HMM library (Panther-style)\n" unless ((-d $lib) && (-d "$lib/books") && (-d "$lib/globals") && (-s "$lib/globals/con.Fasta")); } elsif($self->o('hmm_library_version') == 3){ die "$lib does not seem to be a valid HMM library (Panther-style)\n" unless ((-d $lib) && (-s "$lib/compara_hmm_".$self->o('ensembl_release').".hmm3") && (-s "$lib/compara_hmm_".$self->o('ensembl_release').".hmm3.h3f") && (-s "$lib/compara_hmm_".$self->o('ensembl_release').".hmm3.h3i") && (-s "$lib/compara_hmm_".$self->o('ensembl_release').".hmm3.h3m") && (-s "$lib/compara_hmm_".$self->o('ensembl_release').".hmm3.h3p")); } } } sub pipeline_create_commands { my ($self) = @_; return [ @{$self->SUPER::pipeline_create_commands}, # here we inherit creation of database, hive tables and compara tables $self->pipeline_create_commands_rm_mkdir(['work_dir', 'cluster_dir', 'dump_dir', 'dump_pafs_dir', 'examl_dir', 'fasta_dir', 'plots_dir']), $self->pipeline_create_commands_lfs_setstripe('fasta_dir'), ]; } sub pipeline_wide_parameters { # these parameter values are visible to all analyses, can be overridden by parameters{} and input_id{} my ($self) = @_; return { %{$self->SUPER::pipeline_wide_parameters}, # here we inherit anything from the base class 'master_db' => $self->o('master_db'), 'ncbi_db' => $self->o('ncbi_db'), 'member_db' => $self->o('member_db'), 'reuse_db' => $self->o('prev_rel_db'), 'mapping_db' => $self->o('mapping_db'), 'reg_conf' => $self->o('reg_conf'), 'cluster_dir' => $self->o('cluster_dir'), 'fasta_dir' => $self->o('fasta_dir'), 'examl_dir' => $self->o('examl_dir'), 'dump_dir' => $self->o('dump_dir'), 'plots_dir' => $self->o('plots_dir'), 'dump_pafs_dir' => $self->o('dump_pafs_dir'), 'hmm_library_basedir' => $self->o('hmm_library_basedir'), 'hmm_library_version' => $self->o('hmm_library_version'), 'clustering_mode' => $self->o('clustering_mode'), 'reuse_level' => $self->o('reuse_level'), 'goc_threshold' => $self->o('goc_threshold'), 'goc_reuse_db' => $self->o('goc_reuse_db'), 'calculate_goc_distribution' => $self->o('calculate_goc_distribution'), 'do_homology_id_mapping' => $self->o('do_homology_id_mapping'), 'do_jaccard_index' => $self->o('do_jaccard_index'), 'binary_species_tree_input_file' => $self->o('binary_species_tree_input_file'), 'all_blast_params' => $self->o('all_blast_params'), 'use_quick_tree_break' => $self->o('use_quick_tree_break'), 'use_notung' => $self->o('use_notung'), 'use_treerecs' => $self->o('use_treerecs'), 'use_raxml' => $self->o('use_raxml'), 'initialise_cafe_pipeline' => $self->o('initialise_cafe_pipeline'), 'do_stable_id_mapping' => $self->o('do_stable_id_mapping'), 'do_treefam_xref' => $self->o('do_treefam_xref'), 'do_homology_stats' => $self->o('do_homology_stats'), 'do_hmm_export' => $self->o('do_hmm_export'), 'do_gene_qc' => $self->o('do_gene_qc'), 'dbID_range_index' => $self->o('dbID_range_index'), 'mapped_gene_ratio_per_taxon' => $self->o('mapped_gene_ratio_per_taxon'), }; } sub core_pipeline_analyses { my ($self) = @_; my %hc_analysis_params = ( -analysis_capacity => $self->o('hc_capacity'), -priority => $self->o('hc_priority'), -batch_size => 20, ); my %decision_analysis_params = ( -analysis_capacity => $self->o('decision_capacity'), -priority => $self->o('hc_priority'), -batch_size => 20, ); my %raxml_parsimony_parameters = ( 'raxml_pthread_exe_sse3' => $self->o('raxml_pthread_exe_sse3'), 'raxml_pthread_exe_avx' => $self->o('raxml_pthread_exe_avx'), 'raxml_exe_sse3' => $self->o('raxml_exe_sse3'), 'raxml_exe_avx' => $self->o('raxml_exe_avx'), 'treebest_exe' => $self->o('treebest_exe'), 'input_clusterset_id' => 'default', 'output_clusterset_id' => 'raxml_parsimony', ); my %examl_parameters = ( 'examl_exe_sse3' => $self->o('examl_exe_sse3'), 'examl_exe_avx' => $self->o('examl_exe_avx'), 'parse_examl_exe' => $self->o('parse_examl_exe'), 'treebest_exe' => $self->o('treebest_exe'), 'mpirun_exe' => $self->o('mpirun_exe'), 'output_clusterset_id' => $self->o('use_notung') ? 'raxml' : 'default', 'input_clusterset_id' => 'raxml_parsimony', ); my %raxml_parameters = ( 'raxml_pthread_exe_sse3' => $self->o('raxml_pthread_exe_sse3'), 'raxml_pthread_exe_avx' => $self->o('raxml_pthread_exe_avx'), 'raxml_exe_sse3' => $self->o('raxml_exe_sse3'), 'raxml_exe_avx' => $self->o('raxml_exe_avx'), 'treebest_exe' => $self->o('treebest_exe'), 'output_clusterset_id' => $self->o('use_notung') ? 'raxml' : 'default', 'input_clusterset_id' => 'raxml_parsimony', ); my %raxml_update_parameters = ( 'raxml_pthread_exe_sse3' => $self->o('raxml_pthread_exe_sse3'), 'raxml_pthread_exe_avx' => $self->o('raxml_pthread_exe_avx'), 'raxml_exe_sse3' => $self->o('raxml_exe_sse3'), 'raxml_exe_avx' => $self->o('raxml_exe_avx'), 'treebest_exe' => $self->o('treebest_exe'), 'input_clusterset_id' => 'copy', 'output_clusterset_id' => 'raxml_update', ); my %raxml_bl_parameters = ( 'raxml_pthread_exe_sse3' => $self->o('raxml_pthread_exe_sse3'), 'raxml_pthread_exe_avx' => $self->o('raxml_pthread_exe_avx'), 'raxml_exe_sse3' => $self->o('raxml_exe_sse3'), 'raxml_exe_avx' => $self->o('raxml_exe_avx'), 'treebest_exe' => $self->o('treebest_exe'), 'input_clusterset_id' => 'notung', 'output_clusterset_id' => 'raxml_bl', ); my %notung_parameters = ( 'notung_jar' => $self->o('notung_jar'), 'treebest_exe' => $self->o('treebest_exe'), 'java_exe' => $self->o('java_exe'), 'label' => 'binary', 'input_clusterset_id' => $self->o('use_raxml') ? 'raxml' : 'default', 'output_clusterset_id' => 'notung', ); my %blastp_parameters = ( 'blast_bin_dir' => $self->o('blast_bin_dir'), 'blast_params' => "#expr( #all_blast_params#->[#param_index#]->[2])expr#", 'evalue_limit' => "#expr( #all_blast_params#->[#param_index#]->[3])expr#", ); return [ # ---------------------------------------------[backbone]-------------------------------------------------------------------------------- { -logic_name => 'backbone_fire_db_prepare', -module => 'Bio::EnsEMBL::Compara::RunnableDB::AssertMatchingVersions', -input_ids => [ { } ], -flow_into => { '1->A' => [ 'copy_ncbi_tables_factory' ], 'A->1' => [ 'backbone_fire_clustering' ], }, }, { -logic_name => 'backbone_fire_clustering', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper', -parameters => { 'output_file' => '#dump_dir#/snapshot_1_before_clustering.sql.gz', }, -rc_name => '1Gb_job', -flow_into => { '1->A' => WHEN( '#are_all_species_reused# and (#reuse_level# eq "clusters")' => 'copy_clusters', ELSE 'clustering_method_decision', ), 'A->1' => [ 'backbone_fire_tree_building' ], }, }, { -logic_name => 'backbone_fire_tree_building', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper', -parameters => { 'table_list' => 'peptide_align_feature%', 'exclude_list' => 1, 'output_file' => '#dump_dir#/snapshot_2_before_tree_building.sql.gz', }, -flow_into => { '1->A' => [ 'cluster_factory' ], 'A->1' => [ 'backbone_fire_posttree' ], }, }, { -logic_name => 'backbone_fire_posttree', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper', -parameters => { 'table_list' => 'peptide_align_feature%', 'exclude_list' => 1, 'output_file' => '#dump_dir#/snapshot_3_after_tree_building.sql.gz', }, -flow_into => { '1->A' => [ 'rib_fire_gene_qc' ], 'A->1' => [ 'backbone_pipeline_finished' ], }, }, { -logic_name => 'backbone_pipeline_finished', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper', -parameters => { 'table_list' => 'peptide_align_feature%', 'exclude_list' => 1, 'output_file' => '#dump_dir#/snapshot_4_pipeline_finished.sql.gz', }, -rc_name => '500Mb_job', -flow_into => [ 'notify_pipeline_completed' ], }, { -logic_name => 'notify_pipeline_completed', -module => 'Bio::EnsEMBL::Compara::RunnableDB::NotifyByEmail', -parameters => { 'text' => 'The pipeline has completed.', 'email' => $self->o('email'), }, -flow_into => [ 'register_pipeline_url' ], }, { -logic_name => 'register_pipeline_url', -module => 'Bio::EnsEMBL::Compara::RunnableDB::RegisterMLSS', -parameters => { 'test_mode' => $self->o('test_mode'), } }, # ---------------------------------------------[copy tables from master]----------------------------------------------------------------- { -logic_name => 'copy_ncbi_tables_factory', -module => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory', -parameters => { 'inputlist' => [ 'ncbi_taxa_node', 'ncbi_taxa_name' ], 'column_names' => [ 'table' ], }, -flow_into => { '2->A' => [ 'copy_ncbi_table' ], 'A->1' => [ 'check_member_db_is_same_version' ], }, }, { -logic_name => 'copy_ncbi_table', -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer', -parameters => { 'src_db_conn' => '#ncbi_db#', 'mode' => 'overwrite', 'filter_cmd' => 'sed "s/ENGINE=MyISAM/ENGINE=InnoDB/"', }, }, { -logic_name => 'populate_method_links_from_db', -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer', -parameters => { 'src_db_conn' => '#master_db#', 'mode' => 'overwrite', 'filter_cmd' => 'sed "s/ENGINE=MyISAM/ENGINE=InnoDB/"', 'table' => 'method_link', }, -flow_into => [ 'offset_tables' ], }, # CreateReuseSpeciesSets/PrepareSpeciesSetsMLSS may want to create new # entries. We need to make sure they don't collide with the master database { -logic_name => 'offset_tables', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => [ 'ALTER TABLE species_set_header AUTO_INCREMENT=10000001', 'ALTER TABLE method_link_species_set AUTO_INCREMENT=10000001', ], }, -flow_into => [ 'load_genomedb_factory' ], }, # ---------------------------------------------[load GenomeDB entries from member_db]--------------------------------------------- { -logic_name => 'load_genomedb_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -parameters => { 'compara_db' => '#master_db#', # that's where genome_db_ids come from 'mlss_id' => $self->o('mlss_id'), # Add the locators coming from member_db 'extra_parameters' => [ 'locator' ], 'genome_db_data_source' => '#member_db#', }, -rc_name => '4Gb_job', -flow_into => { '2->A' => { 'load_genomedb' => { 'master_dbID' => '#genome_db_id#', 'locator' => '#locator#' }, }, 'A->1' => [ 'member_copy_factory' ], }, }, { -logic_name => 'load_genomedb', -module => 'Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB', -batch_size => 10, -hive_capacity => 30, -max_retry_count => 2, }, { -logic_name => 'populate_method_links_from_file', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DbCmd', -parameters => { 'method_link_dump_file' => $self->o('method_link_dump_file'), 'executable' => 'mysqlimport', 'append' => [ '#method_link_dump_file#' ], }, -flow_into => { 1 => { 'load_genomedb_factory' => INPUT_PLUS( { 'master_db' => '#member_db#', } ), } }, }, # ---------------------------------------------[filter genome_db entries into reusable and non-reusable ones]------------------------ { -logic_name => 'check_reusability', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CheckBlastReusability', -parameters => { 'do_not_reuse_list' => $self->o('do_not_reuse_list'), }, -batch_size => 5, -hive_capacity => 30, -flow_into => { 2 => '?accu_name=reused_gdb_ids&accu_address=[]&accu_input_variable=genome_db_id', 3 => '?accu_name=nonreused_gdb_ids&accu_address=[]&accu_input_variable=genome_db_id', }, }, { -logic_name => 'create_mlss_ss', -module => 'Bio::EnsEMBL::Compara::RunnableDB::PrepareSpeciesSetsMLSS', -parameters => { 'whole_method_links' => [ 'PROTEIN_TREES' ], 'singleton_method_links' => [ 'ENSEMBL_PARALOGUES', 'ENSEMBL_HOMOEOLOGUES' ], 'pairwise_method_links' => [ 'ENSEMBL_ORTHOLOGUES' ], }, -rc_name => '2Gb_job', -flow_into => { 1 => [ 'make_treebest_species_tree', 'hc_members_globally' ], }, }, { -logic_name => 'check_member_db_is_same_version', -module => 'Bio::EnsEMBL::Compara::RunnableDB::AssertMatchingVersions', -parameters => { 'db_conn' => '#member_db#', }, -flow_into => WHEN( '#master_db#' => 'populate_method_links_from_db', ELSE 'populate_method_links_from_file', ), }, # ---------------------------------------------[load species tree]------------------------------------------------------------------- { -logic_name => 'make_treebest_species_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::MakeSpeciesTree', -parameters => { 'species_tree_input_file' => $self->o('species_tree_input_file'), # empty by default, but if nonempty this file will be used instead of tree generation from genome_db }, -flow_into => { 2 => [ 'hc_species_tree' ], } }, { -logic_name => 'hc_species_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'species_tree', binary => 0, n_missing_species_in_tree => 0, }, -flow_into => WHEN( '#use_notung# and #binary_species_tree_input_file#' => 'load_binary_species_tree', '#use_notung# and !#binary_species_tree_input_file#' => 'make_binary_species_tree', '#use_treerecs# and #binary_species_tree_input_file#' => 'load_binary_species_tree', '#use_treerecs# and !#binary_species_tree_input_file#' => 'make_binary_species_tree', ), %hc_analysis_params, }, { -logic_name => 'load_binary_species_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::MakeSpeciesTree', -parameters => { 'label' => 'binary', 'species_tree_input_file' => '#binary_species_tree_input_file#', }, -flow_into => { 2 => [ 'hc_binary_species_tree' ], } }, { -logic_name => 'make_binary_species_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::CAFESpeciesTree', -parameters => { 'new_label' => 'binary', 'label' => 'default', 'use_timetree_times' => $self->o('use_timetree_times'), }, -flow_into => { 2 => [ 'hc_binary_species_tree' ], } }, { -logic_name => 'hc_binary_species_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'species_tree', binary => 1, n_missing_species_in_tree => 0, }, %hc_analysis_params, }, { -logic_name => 'copy_trees_from_previous_release', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::CopyTreesFromDB', -parameters => { 'input_clusterset_id' => 'default', 'output_clusterset_id' => 'copy', 'branch_for_new_tree' => '3', 'branch_for_wiped_out_trees' => '4', 'branch_for_update_threshold_trees' => '5', 'update_threshold_trees' => $self->o('update_threshold_trees'), }, -flow_into => { 1 => [ 'copy_alignments_from_previous_release' ], 3 => [ 'alignment_entry_point' ], 4 => [ 'alignment_entry_point' ], 5 => [ 'alignment_entry_point' ], }, -hive_capacity => $self->o('copy_trees_capacity'), -rc_name => '8Gb_job', }, { -logic_name => 'copy_alignments_from_previous_release', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CopyAlignmentsFromDB', -parameters => { 'input_clusterset_id' => 'default', }, -flow_into => [ 'mafft_update' ], -hive_capacity => $self->o('copy_alignments_capacity'), -rc_name => '8Gb_job', }, # ---------------------------------------------[reuse members]----------------------------------------------------------------------- { -logic_name => 'member_copy_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -parameters => { 'extra_parameters' => [ 'is_polyploid' ], }, -rc_name => '4Gb_job', -flow_into => { '2->A' => [ 'genome_member_copy' ], 'A->1' => [ 'create_mlss_ss' ], }, }, { -logic_name => 'genome_member_copy', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::CopyCanonRefMembersByGenomeDB', -parameters => { 'reuse_db' => '#member_db#', 'biotype_filter' => 'biotype_group = "coding"', }, -hive_capacity => $self->o('reuse_capacity'), -flow_into => WHEN( '#is_polyploid#' => 'check_reusability', ELSE 'hc_members_per_genome' ), }, { -logic_name => 'hc_members_per_genome', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'members_per_genome', allow_ambiguity_codes => $self->o('allow_ambiguity_codes'), allow_missing_coordinates => $self->o('allow_missing_coordinates'), allow_missing_cds_seqs => $self->o('allow_missing_cds_seqs'), only_canonical => 1, }, -flow_into => [ 'check_reusability' ], %hc_analysis_params, }, { -logic_name => 'hc_members_globally', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'members_globally', }, -flow_into => [ 'insert_member_projections' ], %hc_analysis_params, }, { -logic_name => 'insert_member_projections', -module => 'Bio::EnsEMBL::Compara::RunnableDB::InsertMemberProjections', -parameters => { 'source_species_names' => [ 'homo_sapiens', 'mus_musculus', ], }, -flow_into => WHEN('#dbID_range_index#' => 'offset_homology_tables' ), }, { -logic_name => 'offset_homology_tables', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OffsetTables', -parameters => { 'range_index' => '#dbID_range_index#', }, }, # ---------------------------------------------[create and populate blast analyses]-------------------------------------------------- { -logic_name => 'blastp_controller', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => { '1->A' => [ 'reusedspecies_factory', 'nonreusedspecies_factory' ], 'A->1' => [ 'hcluster_dump_factory' ], }, }, { -logic_name => 'reusedspecies_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -parameters => { 'polyploid_genomes' => 0, 'component_genomes' => '#expr( (#reuse_level# eq "members") ? 0 : 1 )expr#', 'normal_genomes' => '#expr( (#reuse_level# eq "members") ? 0 : 1 )expr#', 'species_set_id' => '#reuse_ss_id#', }, -flow_into => { 2 => [ 'paf_table_reuse' ], }, }, { -logic_name => 'nonreusedspecies_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -parameters => { 'polyploid_genomes' => 0, 'species_set_id' => '#expr( (#reuse_level# eq "members") ? undef : #nonreuse_ss_id# )expr#', }, -flow_into => { 2 => [ 'paf_create_empty_table' ], }, }, { -logic_name => 'paf_table_reuse', -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer', -parameters => { 'src_db_conn' => '#reuse_db#', 'table' => 'peptide_align_feature_#genome_db_id#', 'filter_cmd' => 'sed "s/ENGINE=MyISAM/ENGINE=InnoDB/"', 'where' => 'hgenome_db_id IN (#reuse_ss_csv#)', }, -flow_into => [ 'members_against_nonreusedspecies_factory' ], -hive_capacity => $self->o('reuse_capacity'), }, { -logic_name => 'paf_create_empty_table', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => [ 'CREATE TABLE IF NOT EXISTS peptide_align_feature_#genome_db_id# LIKE peptide_align_feature', 'ALTER TABLE peptide_align_feature_#genome_db_id# DISABLE KEYS, AUTO_INCREMENT=#genome_db_id#00000000', ], }, -flow_into => [ 'members_against_allspecies_factory' ], -analysis_capacity => 1, }, #----------------------------------------------[classify canonical members based on HMM searches]----------------------------------- { -logic_name => 'load_InterproAnnotation', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'panther_annotation_file' => $self->o('panther_annotation_file'), 'sql' => "LOAD DATA LOCAL INFILE '#panther_annotation_file#' INTO TABLE panther_annot FIELDS TERMINATED BY '\\t' LINES TERMINATED BY '\\n' (upi, ensembl_id, ensembl_div, panther_family_id, start, end, score, evalue)", }, -flow_into => [ 'HMMer_classifyCurated' ], }, { -logic_name => 'HMMer_classifyCurated', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => 'INSERT INTO hmm_annot SELECT seq_member_id, model_id, NULL FROM hmm_curated_annot hca JOIN seq_member sm ON sm.stable_id = hca.seq_member_stable_id', }, -flow_into => [ 'HMMer_classifyInterpro' ], }, { -logic_name => 'HMMer_classifyInterpro', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => 'INSERT IGNORE INTO hmm_annot SELECT seq_member_id, panther_family_id, evalue FROM panther_annot pa JOIN seq_member sm ON sm.stable_id = pa.ensembl_id', }, -flow_into => [ 'HMMer_remove_projection_hits' ], }, { -logic_name => 'HMMer_remove_projection_hits', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => 'DELETE hmm_annot FROM hmm_annot JOIN seq_member_projection ON seq_member_id = target_seq_member_id', }, -flow_into => [ 'HMMer_classify_factory' ], }, { -logic_name => 'HMMer_classify_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::FactoryUnannotatedMembers', -rc_name => '4Gb_job', -hive_capacity => $self->o('blast_factory_capacity'), -flow_into => { '2->A' => WHEN( '#hmm_library_version# == 3' => 'HMMer_search', '#hmm_library_version# == 2' => 'HMMer_classifyPantherScore', ), 'A->1' => [ 'HMM_clusterize' ], }, }, { -logic_name => 'HMMer_classifyPantherScore', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::HMMClassifyPantherScore', -parameters => { 'blast_bin_dir' => $self->o('blast_bin_dir'), 'pantherScore_path' => $self->o('pantherScore_path'), 'hmmer_path' => $self->o('hmmer2_home'), }, -hive_capacity => $self->o('HMMer_classifyPantherScore_capacity'), -rc_name => '4Gb_job', -flow_into => { -1 => [ 'HMMer_classifyPantherScore_himem' ], # MEMLIMIT }, }, { -logic_name => 'HMMer_classifyPantherScore_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::HMMClassifyPantherScore', -parameters => { 'blast_bin_dir' => $self->o('blast_bin_dir'), 'pantherScore_path' => $self->o('pantherScore_path'), 'hmmer_path' => $self->o('hmmer2_home'), }, -hive_capacity => $self->o('HMMer_classifyPantherScore_capacity'), -rc_name => '8Gb_job', }, { -logic_name => 'HMMer_search', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::HMMerSearch', -parameters => { 'hmmer_home' => $self->o('hmmer3_home'), 'library_name' => $self->o('hmm_library_name'), 'library_basedir' => $self->o('hmm_library_basedir'), 'hmmer_cutoff' => $self->o('hmmer_search_cutoff'), }, -hive_capacity => $self->o('HMMer_search_capacity'), -rc_name => '2Gb_job', -flow_into => { -1 => [ 'HMMer_search_himem' ], # MEMLIMIT }, }, { -logic_name => 'HMMer_search_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::HMMerSearch', -parameters => { 'hmmer_home' => $self->o('hmmer3_home'), 'library_name' => $self->o('hmm_library_name'), 'library_basedir' => $self->o('hmm_library_basedir'), 'hmmer_cutoff' => $self->o('hmmer_search_cutoff'), }, -hive_capacity => $self->o('HMMer_search_capacity'), -rc_name => '4Gb_job', -priority=> 20, -flow_into => { -1 => [ 'HMMer_search_super_himem' ], # MEMLIMIT }, }, { -logic_name => 'HMMer_search_super_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::HMMerSearch', -parameters => { 'hmmer_home' => $self->o('hmmer3_home'), 'library_name' => $self->o('hmm_library_name'), 'library_basedir' => $self->o('hmm_library_basedir'), 'hmmer_cutoff' => $self->o('hmmer_search_cutoff'), }, -hive_capacity => $self->o('HMMer_search_capacity'), -rc_name => '64Gb_job', -priority=> 25, }, { -logic_name => 'HMM_clusterize', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::HMMClusterize', -parameters => { 'division' => $self->o('division'), 'extra_tags_file' => $self->o('extra_model_tags_file'), }, -rc_name => '8Gb_job', -flow_into => { 1 => WHEN( '#clustering_mode# eq "hybrid"' => 'dump_unannotated_members', ), } }, { -logic_name => 'flag_update_clusters', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::FlagUpdateClusters', -parameters => { 'update_threshold_trees' => $self->o('update_threshold_trees'), }, -rc_name => '16Gb_job', }, # -------------------------------------------------[BuildHMMprofiles pipeline]------------------------------------------------------- { -logic_name => 'dump_unannotated_members', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::DumpUnannotatedMembersIntoFasta', -parameters => { 'fasta_file' => '#fasta_dir#/unannotated.fasta', }, -rc_name => '4Gb_job', -hive_capacity => $self->o('reuse_capacity'), -flow_into => [ 'make_blastdb_unannotated' ], }, { -logic_name => 'make_blastdb_unannotated', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { 'blast_bin_dir' => $self->o('blast_bin_dir'), 'cmd' => '#blast_bin_dir#/makeblastdb -dbtype prot -parse_seqids -logfile #fasta_name#.blastdb_log -in #fasta_name#', }, -flow_into => { -1 => [ 'make_blastdb_unannotated_himem' ], 1 => [ 'unannotated_all_vs_all_factory' ], } }, { -logic_name => 'make_blastdb_unannotated_himem', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { 'blast_bin_dir' => $self->o('blast_bin_dir'), 'cmd' => '#blast_bin_dir#/makeblastdb -dbtype prot -parse_seqids -logfile #fasta_name#.blastdb_log -in #fasta_name#', }, -rc_name => '1Gb_job', -flow_into => [ 'unannotated_all_vs_all_factory' ], }, { -logic_name => 'unannotated_all_vs_all_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::BlastFactoryUnannotatedMembers', -parameters => { 'step' => $self->o('num_sequences_per_blast_job'), }, -rc_name => '8Gb_job', -hive_capacity => $self->o('blast_factory_capacity'), -flow_into => { '2->A' => [ 'blastp_unannotated' ], 'A->1' => [ 'hcluster_dump_input_all_pafs' ] }, }, { -logic_name => 'blastp_unannotated', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::BlastpUnannotated', -parameters => { 'blast_db' => '#fasta_dir#/unannotated.fasta', %blastp_parameters, }, -rc_name => '250Mb_6_hour_job', -flow_into => { -1 => [ 'blastp_unannotated_himem' ], # MEMLIMIT -2 => 'break_batch_unannotated', }, -hive_capacity => $self->o('blastpu_capacity'), }, { -logic_name => 'blastp_unannotated_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::BlastpUnannotated', -parameters => { 'blast_db' => '#fasta_dir#/unannotated.fasta', %blastp_parameters, }, -rc_name => '2Gb_6_hour_job', -flow_into => { -2 => 'break_batch_unannotated', }, -priority => 20, -hive_capacity => $self->o('blastpu_capacity'), }, { -logic_name => 'blastp_unannotated_no_runlimit', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::BlastpUnannotated', -parameters => { 'blast_db' => '#fasta_dir#/unannotated.fasta', %blastp_parameters, }, -flow_into => { -1 => [ 'blastp_unannotated_himem_no_runlimit' ], # MEMLIMIT }, -hive_capacity => $self->o('blastpu_capacity'), }, { -logic_name => 'blastp_unannotated_himem_no_runlimit', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::BlastpUnannotated', -parameters => { 'blast_db' => '#fasta_dir#/unannotated.fasta', %blastp_parameters, }, -rc_name => '2Gb_job', -priority => 20, -hive_capacity => $self->o('blastpu_capacity'), }, { -logic_name => 'break_batch_unannotated', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::BreakUnannotatedBlast', -flow_into => { 2 => 'blastp_unannotated_no_runlimit', } }, { -logic_name => 'hcluster_dump_input_all_pafs', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HclusterPrepareSingleTable', -parameters => { 'outgroups' => $self->o('outgroups'), }, -rc_name => '4Gb_job', -hive_capacity => $self->o('reuse_capacity'), -flow_into => [ 'hcluster_run', 'backup_single_paf' ], }, { -logic_name => 'backup_single_paf', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper', -parameters => { 'table_list' => 'peptide_align_feature', 'output_file' => '#dump_pafs_dir#/peptide_align_feature.sql.gz', 'exclude_ehive' => 1, }, -analysis_capacity => $self->o('reuse_capacity'), }, # ---------------------------------------------[create and populate blast analyses]-------------------------------------------------- { -logic_name => 'prepare_blastdb', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => { '1->A' => [ 'blastdb_factory' ], 'A->1' => [ 'blastp_controller' ], }, }, { -logic_name => 'blastdb_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -parameters => { 'polyploid_genomes' => 0, 'arrayref_branch' => 1, }, -flow_into => { '2->A' => [ 'dump_canonical_members' ], 'A->1' => [ 'cdhit' ], }, }, { -logic_name => 'dump_canonical_members', -module => 'Bio::EnsEMBL::Compara::RunnableDB::DumpMembersIntoFasta', # Gets fasta_dir from pipeline_wide_parameters -rc_name => '500Mb_job', -hive_capacity => $self->o('reuse_capacity'), #-flow_into => [ 'cdhit' ], }, { -logic_name => 'cdhit', -module => 'Bio::EnsEMBL::Compara::RunnableDB::CDHit', -parameters => { 'cdhit_exe' => $self->o('cdhit_exe'), 'cdhit_identity_threshold' => $self->o('cdhit_identity_threshold'), 'cdhit_num_threads' => 4, 'cdhit_memory_in_mb' => 8000, }, -flow_into => { 2 => [ 'dump_representative_members' ], 3 => [ '?table_name=seq_member_projection' ], }, -rc_name => '8Gb_4c_job', -hive_capacity => $self->o('reuse_capacity'), }, { -logic_name => 'dump_representative_members', -module => 'Bio::EnsEMBL::Compara::RunnableDB::DumpMembersIntoFasta', -rc_name => '500Mb_job', -parameters => { 'only_canonical' => 0, 'only_representative' => 1, }, -hive_capacity => $self->o('reuse_capacity'), -flow_into => [ 'make_blastdb' ], }, { -logic_name => 'make_blastdb', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { 'blast_bin_dir' => $self->o('blast_bin_dir'), 'cmd' => '#blast_bin_dir#/makeblastdb -dbtype prot -parse_seqids -logfile #fasta_name#.blastdb_log -in #fasta_name#', }, -hive_capacity => $self->o('reuse_capacity'), }, { -logic_name => 'members_against_allspecies_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BlastFactory', -parameters => { 'step' => $self->o('num_sequences_per_blast_job'), }, -rc_name => '500Mb_job', -hive_capacity => $self->o('blast_factory_capacity'), -flow_into => { '2->A' => { 'blastp' => INPUT_PLUS() }, 'A->1' => [ 'hc_pafs' ], }, }, { -logic_name => 'members_against_nonreusedspecies_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BlastFactory', -parameters => { 'species_set_id' => '#nonreuse_ss_id#', 'step' => $self->o('num_sequences_per_blast_job'), }, -rc_name => '500Mb_job', -hive_capacity => $self->o('blast_factory_capacity'), -flow_into => { '2->A' => { 'blastp' => INPUT_PLUS() }, 'A->1' => [ 'hc_pafs' ], }, }, { -logic_name => 'blastp', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BlastpWithReuse', -parameters => { 'allow_same_species_hits' => 1, %blastp_parameters, }, -batch_size => 25, -rc_name => '250Mb_6_hour_job', -flow_into => { -1 => [ 'blastp_himem' ], # MEMLIMIT -2 => [ 'break_batch' ], # RUNLIMIT }, -hive_capacity => $self->o('blastp_capacity'), }, { -logic_name => 'blastp_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BlastpWithReuse', -parameters => { 'allow_same_species_hits' => 1, %blastp_parameters, }, -batch_size => 25, -rc_name => '1Gb_job', -hive_capacity => $self->o('blastp_capacity'), }, { -logic_name => 'break_batch', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::BreakUnannotatedBlast', -flow_into => { 2 => 'blastp_no_runlimit', } }, { -logic_name => 'blastp_no_runlimit', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BlastpWithReuse', -parameters => { 'allow_same_species_hits' => 1, %blastp_parameters, }, -flow_into => { -1 => [ 'blastp_himem' ], # MEMLIMIT }, -hive_capacity => $self->o('blastp_capacity'), }, { -logic_name => 'hc_pafs', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'peptide_align_features', }, -flow_into => 'backup_paf', %hc_analysis_params, }, { -logic_name => 'backup_paf', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper', -parameters => { 'table_list' => 'peptide_align_feature_#genome_db_id#', 'output_file' => '#dump_pafs_dir#/peptide_align_feature_#genome_db_id#.sql.gz', 'exclude_ehive' => 1, }, -analysis_capacity => $self->o('reuse_capacity'), }, # ---------------------------------------------[clustering step]--------------------------------------------------------------------- { -logic_name => 'clustering_method_decision', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => { '1->A' => WHEN( '#clustering_mode# eq "blastp"' => 'prepare_blastdb', '#clustering_mode# eq "ortholog"' => 'ortholog_cluster', ELSE 'load_InterproAnnotation', # hmm, hybrid, topup ), 'A->1' => [ 'expand_clusters_with_projections' ], }, }, { -logic_name => 'hcluster_dump_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -parameters => { 'polyploid_genomes' => 0, }, -flow_into => { '2->A' => [ 'hcluster_dump_input_per_genome' ], 'A->1' => [ 'hcluster_merge_factory' ], }, }, { -logic_name => 'ortholog_cluster', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthologClusters', -parameters => { 'sort_clusters' => 1, }, -rc_name => '4Gb_job', -hive_capacity => $self->o('reuse_capacity'), }, { -logic_name => 'hcluster_dump_input_per_genome', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HclusterPrepare', -parameters => { 'outgroups' => $self->o('outgroups'), }, -hive_capacity => $self->o('reuse_capacity'), }, { -logic_name => 'hcluster_merge_factory', -module => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory', -parameters => { 'inputlist' => [ ['txt'], ['cat'], ], 'column_names' => [ 'ext' ], }, -flow_into => { '2->A' => [ 'hcluster_merge_inputs' ], 'A->1' => [ 'hcluster_run' ], }, }, { -logic_name => 'hcluster_merge_inputs', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { 'cmd' => 'cat #cluster_dir#/*.hcluster.#ext# > #cluster_dir#/hcluster.#ext#', }, }, { -logic_name => 'hcluster_run', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd', -parameters => { 'clustering_max_gene_halfcount' => $self->o('clustering_max_gene_halfcount'), 'hcluster_exe' => $self->o('hcluster_exe'), 'cmd' => '#hcluster_exe# -m #clustering_max_gene_halfcount# -w 0 -s 0.34 -O -C #cluster_dir#/hcluster.cat -o #cluster_dir#/hcluster.out #cluster_dir#/hcluster.txt; sleep 30', }, -flow_into => { 1 => [ 'hcluster_parse_output' ], }, -rc_name => '32Gb_job', }, { -logic_name => 'hcluster_parse_output', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HclusterParseOutput', -parameters => { 'division' => $self->o('division'), }, -rc_name => '4Gb_job', }, { -logic_name => 'cluster_tagging', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ClusterTagging', -hive_capacity => $self->o('cluster_tagging_capacity'), -rc_name => '4Gb_job', -batch_size => 50, }, { -logic_name => 'copy_clusters', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::CopyClusters', -parameters => { 'tags_to_copy' => [ 'division' ], }, -flow_into => [ 'remove_blacklisted_genes' ], -rc_name => '4Gb_job', }, { -logic_name => 'expand_clusters_with_projections', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ExpandClustersWithProjections', -flow_into => [ 'remove_blacklisted_genes' ], }, { -logic_name => 'remove_blacklisted_genes', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::RemoveBlacklistedGenes', -parameters => { blacklist_file => $self->o('gene_blacklist_file'), }, -flow_into => [ 'hc_clusters' ], -rc_name => '500Mb_job', }, { -logic_name => 'hc_clusters', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'global_tree_set', }, -flow_into => [ 'run_qc_tests' ], %hc_analysis_params, }, { -logic_name => 'create_additional_clustersets', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::CreateClustersets', -parameters => { member_type => 'protein', 'additional_clustersets' => [qw(treebest phyml-aa phyml-nt nj-dn nj-ds nj-mm raxml raxml_parsimony raxml_bl notung treerecs copy raxml_update )], }, }, # ---------------------------------------------[Pluggable QC step]---------------------------------------------------------- { -logic_name => 'run_qc_tests', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -parameters => { 'polyploid_genomes' => 0, }, -flow_into => { '2->A' => [ 'per_genome_qc' ], '1->A' => [ 'overall_qc' ], 'A->1' => [ 'clusterset_backup' ], }, }, { -logic_name => 'overall_qc', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OverallGroupsetQC', -parameters => { 'reuse_db' => '#mapping_db#', }, -hive_capacity => $self->o('reuse_capacity'), -rc_name => '4Gb_job', }, { -logic_name => 'per_genome_qc', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::PerGenomeGroupsetQC', -parameters => { 'reuse_db' => '#mapping_db#', }, -hive_capacity => $self->o('reuse_capacity'), -rc_name => '4Gb_job', }, { -logic_name => 'clusterset_backup', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => 'INSERT IGNORE INTO gene_tree_backup (seq_member_id, root_id) SELECT seq_member_id, root_id FROM gene_tree_node WHERE seq_member_id IS NOT NULL', }, -flow_into => { 1 => [ 'create_additional_clustersets', 'cluster_tagging_factory', WHEN( '#clustering_mode# eq "topup"' => 'flag_update_clusters', ), ], }, }, { -logic_name => 'cluster_tagging_factory', -module => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory', -parameters => { 'inputquery' => 'SELECT root_id AS gene_tree_id FROM gene_tree_root WHERE tree_type = "tree" AND clusterset_id="default"', }, -flow_into => { 2 => 'cluster_tagging', }, -rc_name => '1Gb_job', }, # ---------------------------------------------[main tree fan]------------------------------------------------------------- { -logic_name => 'cluster_factory', -module => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory', -parameters => { 'inputquery' => 'SELECT root_id AS gene_tree_id, COUNT(seq_member_id) AS tree_num_genes FROM gene_tree_root JOIN gene_tree_node USING (root_id) WHERE tree_type = "tree" AND clusterset_id="default" GROUP BY root_id', }, -flow_into => { '2->A' => WHEN( '#clustering_mode# eq "topup"' => 'copy_trees_from_previous_release', ELSE 'alignment_entry_point', ), '1->A' => [ 'join_panther_subfam' ], 'A->1' => [ 'hc_global_tree_set' ], }, -rc_name => '2Gb_job', }, { -logic_name => 'alignment_entry_point', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'tags' => { 'gene_count' => 0, 'reuse_aln_runtime' => 0, }, 'mcoffee_short_gene_count' => $self->o('mcoffee_short_gene_count'), 'mcoffee_himem_gene_count' => $self->o('mcoffee_himem_gene_count'), 'mafft_gene_count' => $self->o('mafft_gene_count'), 'mafft_himem_gene_count' => $self->o('mafft_himem_gene_count'), 'mafft_runtime' => $self->o('mafft_runtime'), }, -flow_into => { '1->A' => WHEN ( '(#tree_gene_count# < #mcoffee_short_gene_count#) and (#tree_reuse_aln_runtime#/1000 < #mafft_runtime#)' => 'mcoffee_short', '(#tree_gene_count# >= #mcoffee_short_gene_count# and #tree_gene_count# < #mcoffee_himem_gene_count#) and (#tree_reuse_aln_runtime#/1000 < #mafft_runtime#)' => 'mcoffee', '(#tree_gene_count# >= #mcoffee_himem_gene_count# and #tree_gene_count# < #mafft_gene_count#) and (#tree_reuse_aln_runtime#/1000 < #mafft_runtime#)' => 'mcoffee_himem', '(#tree_gene_count# >= #mafft_gene_count# and #tree_gene_count# < #mafft_himem_gene_count#) or (#tree_reuse_aln_runtime#/1000 >= #mafft_runtime#)' => 'mafft', '(#tree_gene_count# >= #mafft_himem_gene_count#) or (#tree_reuse_aln_runtime#/1000 >= #mafft_runtime#)' => 'mafft_himem', ), 'A->1' => 'exon_boundaries_prep', }, %decision_analysis_params, }, { -logic_name => 'hc_global_tree_set', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'global_tree_set', }, -flow_into => [ 'compute_statistics' ], %hc_analysis_params, }, { -logic_name => 'compute_statistics', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::ComputeStatistics', -parameters => { member_type => 'protein', homology_id_threshold => '100000000', }, -rc_name => '500Mb_job', -flow_into => [ 'write_stn_tags', WHEN('#do_stable_id_mapping#' => 'stable_id_mapping'), WHEN('#do_treefam_xref#' => 'treefam_xref_idmap'), WHEN('#clustering_mode# eq "ortholog"' => 'remove_overlapping_homologies'), ], }, { -logic_name => 'compute_jaccard_index', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::ComputeJaccardIndex', -parameters => { 'jaccard_index_script' => $self->o('jaccard_index_script'), 'lorentz_curve_script' => $self->o('lorentz_curve_script'), 'output_jaccard_file' => '#plots_dir#/jaccard_index.out', 'output_jaccard_pdf' => '#plots_dir#/jaccard_index.pdf', 'output_gini_file' => '#plots_dir#/gini_coefficient.out', 'output_gini_pdf' => '#plots_dir#/gini_coefficient.pdf', }, -rc_name => '500Mb_job', }, { -logic_name => 'write_stn_tags', -module => 'Bio::EnsEMBL::Hive::RunnableDB::DbCmd', -parameters => { 'input_file' => $self->o('tree_stats_sql'), }, -flow_into => [ 'email_tree_stats_report' ], }, { -logic_name => 'email_tree_stats_report', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::HTMLReport', -parameters => { 'email' => $self->o('email'), }, }, # ---------------------------------------------[Pluggable MSA steps]---------------------------------------------------------- { -logic_name => 'mcoffee_short', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee', -parameters => { 'cmd_max_runtime' => '21600', # 6 hours 'method' => 'cmcoffee', 'mcoffee_home' => $self->o('mcoffee_home'), 'extaligners_exe_dir' => $self->o('extaligners_exe_dir'), 'escape_branch' => -1, }, -hive_capacity => $self->o('mcoffee_short_capacity'), -batch_size => 20, -rc_name => '1Gb_job', -flow_into => { -1 => [ 'mcoffee' ], # MEMLIMIT -2 => [ 'mafft' ], }, }, { -logic_name => 'mcoffee', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee', -parameters => { 'cmd_max_runtime' => '43200', # 12 hours 'method' => 'cmcoffee', 'mcoffee_home' => $self->o('mcoffee_home'), 'extaligners_exe_dir' => $self->o('extaligners_exe_dir'), 'escape_branch' => -1, }, -rc_name => '2Gb_job', -priority => $self->o('mcoffee_priority'), -flow_into => { -1 => [ 'mcoffee_himem' ], # MEMLIMIT -2 => [ 'mafft' ], }, }, { -logic_name => 'mafft', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Mafft', -parameters => { 'mafft_home' => $self->o('mafft_home'), 'escape_branch' => -1, }, -hive_capacity => $self->o('mafft_capacity'), -rc_name => '2Gb_job', -priority => $self->o('mafft_priority'), -flow_into => { -1 => [ 'mafft_himem' ], # MEMLIMIT }, }, { -logic_name => 'mafft_update', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Mafft_update', -parameters => { 'mafft_home' => $self->o('mafft_home'), }, -hive_capacity => $self->o('mafft_update_capacity'), -rc_name => '2Gb_job', -flow_into => [ 'raxml_update_decision' ], }, { -logic_name => 'mcoffee_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee', -parameters => { 'cmd_max_runtime' => '43200', 'method' => 'cmcoffee', 'mcoffee_home' => $self->o('mcoffee_home'), 'extaligners_exe_dir' => $self->o('extaligners_exe_dir'), 'escape_branch' => -2, }, -rc_name => '8Gb_job', -priority => $self->o('mcoffee_himem_priority'), -flow_into => { -1 => [ 'mafft_himem' ], -2 => [ 'mafft_himem' ], }, }, { -logic_name => 'mafft_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Mafft', -parameters => { 'mafft_home' => $self->o('mafft_home'), }, -hive_capacity => $self->o('mafft_himem_capacity'), -rc_name => '8Gb_job', -priority => $self->o('mafft_himem_priority'), -flow_into => { -1 => [ 'mafft_huge' ], }, }, { -logic_name => 'mafft_huge', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Mafft', -parameters => { 'mafft_home' => $self->o('mafft_home'), 'mafft_threads' => 16, }, -hive_capacity => $self->o('mafft_himem_capacity'), -rc_name => '64Gb_16c_job', -priority => $self->o('mafft_himem_priority'), }, { -logic_name => 'exon_boundaries_prep', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ObjectStore::GeneTreeAlnExonBoundaries', -parameters => { 'treebreak_gene_count' => $self->o('treebreak_gene_count'), }, -flow_into => { -1 => 'exon_boundaries_prep_himem', 1 => WHEN( '#is_already_supertree#' => 'panther_paralogs', '!#is_already_supertree# and #use_quick_tree_break# and (#tree_num_genes# > #treebreak_gene_count#)' => 'quick_tree_break', ELSE 'aln_filtering_tagging', ), }, -rc_name => '500Mb_job', -hive_capacity => $self->o('split_genes_capacity'), -batch_size => 20, }, { -logic_name => 'exon_boundaries_prep_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ObjectStore::GeneTreeAlnExonBoundaries', -parameters => { 'treebreak_gene_count' => $self->o('treebreak_gene_count'), }, -flow_into => WHEN( '#is_already_supertree#' => 'panther_paralogs', '!#is_already_supertree# and #use_quick_tree_break# and (#tree_num_genes# > #treebreak_gene_count#)' => 'quick_tree_break', ELSE 'aln_filtering_tagging', ), -rc_name => '1Gb_job', -hive_capacity => $self->o('split_genes_capacity'), -batch_size => 20, }, # ---------------------------------------------[main tree creation loop]------------------------------------------------------------- { -logic_name => 'split_genes', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::FindContiguousSplitGenes', -parameters => { split_genes_gene_count => $self->o('split_genes_gene_count'), }, -hive_capacity => $self->o('split_genes_capacity'), -rc_name => '500Mb_job', -batch_size => 20, -flow_into => { '2->A' => 'split_genes_per_species', 'A->1' => 'tree_building_entry_point', -1 => 'split_genes_himem', }, }, { -logic_name => 'split_genes_per_species', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::FindContiguousSplitGenes', -hive_capacity => $self->o('split_genes_capacity'), -rc_name => '500Mb_job', }, { -logic_name => 'split_genes_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::FindContiguousSplitGenes', -hive_capacity => $self->o('split_genes_capacity'), -rc_name => '4Gb_job', -flow_into => [ 'tree_building_entry_point' ], }, { -logic_name => 'tree_building_entry_point', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => { '1->A' => WHEN( '#use_raxml#' => 'filter_decision', ELSE 'treebest_decision', ), 'A->1' => WHEN( '#use_notung#' => 'notung_decision', '#use_treerecs#' => 'treerecs', ELSE 'hc_post_tree', ), }, %decision_analysis_params, }, # ---------------------------------------------[alignment filtering]------------------------------------------------------------- { -logic_name => 'filter_decision', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'tags' => { 'gene_count' => 0, 'aln_length' => 0, }, 'threshold_n_genes' => $self->o('threshold_n_genes'), 'threshold_aln_len' => $self->o('threshold_aln_len'), 'threshold_n_genes_large' => $self->o('threshold_n_genes_large'), 'threshold_aln_len_large' => $self->o('threshold_aln_len_large'), }, -flow_into => { 1 => WHEN( '(#tree_gene_count# <= #threshold_n_genes#) || (#tree_aln_length# <= #threshold_aln_len#)' => 'get_num_of_patterns', '(#tree_gene_count# >= #threshold_n_genes_large# and #tree_aln_length# > #threshold_aln_len#) || (#tree_aln_length# >= #threshold_aln_len_large# and #tree_gene_count# > #threshold_n_genes#)' => 'noisy_large', #'' => 'trimal', # Not actually used ELSE 'noisy', ), }, %decision_analysis_params, }, { -logic_name => 'noisy', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Noisy', -parameters => { 'noisy_exe' => $self->o('noisy_exe'), 'noisy_cutoff' => $self->o('noisy_cutoff'), }, -hive_capacity => $self->o('alignment_filtering_capacity'), -rc_name => '4Gb_job', -batch_size => 5, -flow_into => [ 'get_num_of_patterns' ], }, { -logic_name => 'noisy_large', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Noisy', -parameters => { 'noisy_exe' => $self->o('noisy_exe'), 'noisy_cutoff' => $self->o('noisy_cutoff_large'), }, -hive_capacity => $self->o('alignment_filtering_capacity'), -rc_name => '16Gb_job', -batch_size => 5, -flow_into => [ 'get_num_of_patterns' ], }, #{ -logic_name => 'trimal', #-module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::TrimAl', #-parameters => { #'trimal_exe' => $self->o('trimal_exe'), #}, #-hive_capacity => $self->o('alignment_filtering_capacity'), #-rc_name => '500Mb_job', #-batch_size => 5, #-flow_into => [ 'get_num_of_patterns' ], #}, { -logic_name => 'aln_filtering_tagging', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::AlignmentFilteringTagging', -hive_capacity => $self->o('alignment_filtering_capacity'), -rc_name => '2Gb_job', -batch_size => 50, -flow_into => [ 'split_genes' ], }, # ---------------------------------------------[small trees decision]------------------------------------------------------------- { -logic_name => 'small_trees_go_to_treebest', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'tags' => { 'aln_num_of_patterns' => 0, 'num_distinct_sequences' => 0, }, }, -flow_into => { 1 => WHEN ( '(#tree_num_distinct_sequences# >=4) && (#tree_aln_num_of_patterns# >= 4) && #do_model_selection#' => 'prottest_decision', '#tree_num_distinct_sequences# < 4' => 'treebest_small_families', '#tree_aln_num_of_patterns# < 4' => 'treebest_small_families', ELSE 'raxml_parsimony_decision', ), }, %decision_analysis_params, }, # ---------------------------------------------[model test]------------------------------------------------------------- { -logic_name => 'prottest_decision', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'tags' => { #The default value matches the default dataflow we want: _8_cores analysis. 'aln_length' => 200, 'gene_count' => 0, }, }, %decision_analysis_params, -flow_into => { 1 => WHEN ( '(#tree_aln_length# <= 150) && (#tree_gene_count# <= 500)' => 'prottest', '(#tree_aln_length# <= 150) && (#tree_gene_count# > 500)' => 'prottest', '(#tree_aln_length# > 150) && (#tree_aln_length# <= 1200) && (#tree_gene_count# <= 500)' => 'prottest_8_cores', '(#tree_aln_length# > 150) && (#tree_aln_length# <= 1200) && (#tree_gene_count# > 500)' => 'prottest_8_cores', '(#tree_aln_length# > 1200) && (#tree_aln_length# <= 2400) && (#tree_gene_count# <= 500)' => 'prottest_8_cores', '(#tree_aln_length# > 1200) && (#tree_aln_length# <= 2400) && (#tree_gene_count# > 500)' => 'prottest_16_cores', '(#tree_aln_length# > 2400) && (#tree_aln_length# <= 8000) && (#tree_gene_count# <= 500)' => 'prottest_16_cores', '(#tree_aln_length# > 2400) && (#tree_aln_length# <= 8000) && (#tree_gene_count# > 500)' => 'prottest_16_cores', '(#tree_aln_length# > 8000) && (#tree_aln_length# <= 16000) && (#tree_gene_count# <= 500)' => 'prottest_32_cores', '(#tree_aln_length# > 8000) && (#tree_aln_length# <= 16000) && (#tree_gene_count# > 500)' => 'prottest_32_cores', '(#tree_aln_length# > 16000) && (#tree_aln_length# <= 32000) && (#tree_gene_count# <= 500)' => 'prottest_32_cores', '(#tree_aln_length# > 16000) && (#tree_aln_length# <= 32000) && (#tree_gene_count# > 500)' => 'raxml_parsimony_decision', '(#tree_aln_length# > 32000)' => 'raxml_parsimony_decision', ), }, }, { -logic_name => 'prottest', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ProtTest', -parameters => { 'prottest_jar' => $self->o('prottest_jar'), 'java_exe' => $self->o('java_exe'), 'prottest_memory' => 3500, 'n_cores' => 1, }, -hive_capacity => $self->o('prottest_capacity'), -rc_name => '2Gb_job', -flow_into => { -1 => [ 'prottest_himem' ], 1 => [ 'raxml_parsimony_decision' ], } }, { -logic_name => 'prottest_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ProtTest', -parameters => { 'prottest_jar' => $self->o('prottest_jar'), 'java_exe' => $self->o('java_exe'), 'prottest_memory' => 7000, #'escape_branch' => -1, # RAxML will use a default model, anyway 'n_cores' => 1, }, -hive_capacity => $self->o('prottest_capacity'), -rc_name => '4Gb_job', -flow_into => { #-1 => [ 'raxml_parsimony_decision' ], 1 => [ 'raxml_parsimony_decision' ], } }, { -logic_name => 'prottest_8_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ProtTest', -parameters => { 'prottest_jar' => $self->o('prottest_jar'), 'java_exe' => $self->o('java_exe'), 'prottest_memory' => 3500, #'escape_branch' => -1, 'n_cores' => 8, }, -hive_capacity => $self->o('prottest_capacity'), -rc_name => '8Gb_8c_job', -flow_into => { 1 => [ 'raxml_parsimony_decision' ], } }, { -logic_name => 'prottest_16_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ProtTest', -parameters => { 'prottest_jar' => $self->o('prottest_jar'), 'java_exe' => $self->o('java_exe'), 'prottest_memory' => 3500, #'escape_branch' => -1, 'n_cores' => 16, }, -hive_capacity => $self->o('prottest_capacity'), -rc_name => '16Gb_16c_job', -flow_into => { 1 => [ 'raxml_parsimony_decision' ], } }, { -logic_name => 'prottest_32_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ProtTest', -parameters => { 'prottest_jar' => $self->o('prottest_jar'), 'java_exe' => $self->o('java_exe'), 'prottest_memory' => 3500, #'escape_branch' => -1, 'n_cores' => 32, }, -hive_capacity => $self->o('prottest_capacity'), -rc_name => '16Gb_32c_job', -flow_into => { 1 => [ 'raxml_parsimony_decision' ], } }, # ---------------------------------------------[tree building with treebest]------------------------------------------------------------- { -logic_name => 'treebest_decision', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'tags' => { 'aln_num_residues' => 200, 'gene_count' => 0, }, 'treebest_threshold_n_residues' => $self->o('treebest_threshold_n_residues'), 'treebest_threshold_n_genes' => $self->o('treebest_threshold_n_genes'), }, -flow_into => { 1 => WHEN ( '(#tree_aln_num_residues# < #treebest_threshold_n_residues#)' => 'treebest_short', '(#tree_gene_count# >= #treebest_threshold_n_genes#)' => 'treebest_long_himem', ELSE 'treebest', ), }, %decision_analysis_params, }, { -logic_name => 'treebest_short', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML', -parameters => { 'cdna' => 1, 'store_intermediate_trees' => 1, 'store_filtered_align' => 1, 'treebest_exe' => $self->o('treebest_exe'), }, -hive_capacity => $self->o('treebest_capacity'), -rc_name => '500Mb_job', -batch_size => 10, -flow_into => { -1 => 'treebest', -2 => 'treebest_long_himem', } }, { -logic_name => 'treebest', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML', -parameters => { 'cdna' => 1, 'store_intermediate_trees' => 1, 'store_filtered_align' => 1, 'treebest_exe' => $self->o('treebest_exe'), }, -hive_capacity => $self->o('treebest_capacity'), -rc_name => '2Gb_job', -flow_into => { -1 => 'treebest_long_himem', -2 => 'treebest_long_himem', } }, { -logic_name => 'treebest_long_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML', -parameters => { 'cdna' => 1, 'store_intermediate_trees' => 1, 'store_filtered_align' => 1, 'treebest_exe' => $self->o('treebest_exe'), }, -hive_capacity => $self->o('treebest_capacity'), -priority => $self->o('treebest_long_himem_priority'), -rc_name => '8Gb_job', }, # ---------------------------------------------[tree building with raxml]------------------------------------------------------------- { -logic_name => 'get_num_of_patterns', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::GetPatterns', -parameters => { 'getPatterns_exe' => $self->o('getPatterns_exe'), }, -hive_capacity => $self->o('prottest_capacity'), -batch_size => 100, -rc_name => '4Gb_job', -flow_into => { -1 => [ 'get_num_of_patterns_himem' ], 2 => [ 'treebest_small_families' ], 1 => [ 'small_trees_go_to_treebest' ], } }, { -logic_name => 'get_num_of_patterns_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::GetPatterns', -parameters => { 'getPatterns_exe' => $self->o('getPatterns_exe'), }, -hive_capacity => $self->o('prottest_capacity'), -batch_size => 100, -rc_name => '16Gb_job', -flow_into => { 1 => [ 'small_trees_go_to_treebest' ], } }, { -logic_name => 'raxml_parsimony_decision', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'raxml_patterns_per_core' => $self->o('use_dna_for_phylogeny') ? '500' : '150', 'raxml_cores' => '#expr(#tree_aln_num_of_patterns# / #raxml_patterns_per_core# )expr#', 'tags' => { #The default value matches the default dataflow we want: _8_cores analysis. 'aln_num_of_patterns' => 200, 'gene_count' => 0, }, }, %decision_analysis_params, #------------------------------------------------------------------------------- # This boundaries are based on RAxML and ExaML manuals. # Which suggest the following number of cores: # # ExaML: DNA: 3.5K patterns/core # AAs: 1K patterns/core # # RAxML: DNA: 500 patterns/core # AAs: 150 patterns/core # #------------------------------------------------------------------------------- -flow_into => { '1->A' => WHEN ( '( #raxml_cores# <= 1 ) && (#tree_gene_count# <= 500)' => 'raxml_parsimony', '( #raxml_cores# <= 1 ) && (#tree_gene_count# > 500)' => 'raxml_parsimony', '( #raxml_cores# > 1 ) && ( #raxml_cores# <= 8 ) && (#tree_gene_count# <= 500)' => 'raxml_parsimony_8_cores', '( #raxml_cores# > 1 ) && ( #raxml_cores# <= 8 ) && (#tree_gene_count# > 500)' => 'raxml_parsimony_8_cores', '( #raxml_cores# > 8) && (#raxml_cores# <= 16 ) && (#tree_gene_count# <= 500)' => 'raxml_parsimony_8_cores', '( #raxml_cores# > 8) && (#raxml_cores# <= 16 ) && (#tree_gene_count# > 500)' => 'raxml_parsimony_16_cores', '( #raxml_cores# > 16) && (#raxml_cores# <= 32 ) && (#tree_gene_count# <= 500)' => 'raxml_parsimony_16_cores', '( #raxml_cores# > 16) && (#raxml_cores# <= 32 ) && (#tree_gene_count# > 500)' => 'raxml_parsimony_32_cores', '( #raxml_cores# > 32) ' => 'raxml_parsimony_64_cores', ), 'A->1' => 'raxml_decision', }, }, { -logic_name => 'raxml_parsimony', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_parsimony', -parameters => { %raxml_parsimony_parameters, 'escape_branch' => -1, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '1Gb_job', -flow_into => { -1 => [ 'raxml_parsimony_himem' ], } }, { -logic_name => 'raxml_parsimony_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_parsimony', -parameters => { %raxml_parsimony_parameters, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '4Gb_job', }, { -logic_name => 'raxml_parsimony_8_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_parsimony', -parameters => { %raxml_parsimony_parameters, 'raxml_number_of_cores' => 8, 'escape_branch' => -1, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '16Gb_8c_job', -flow_into => { -1 => [ 'raxml_parsimony_8_cores_himem' ], } }, { -logic_name => 'raxml_parsimony_8_cores_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_parsimony', -parameters => { %raxml_parsimony_parameters, 'raxml_number_of_cores' => 8, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '32Gb_8c_job', }, { -logic_name => 'raxml_parsimony_16_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_parsimony', -parameters => { %raxml_parsimony_parameters, 'raxml_number_of_cores' => 16, 'escape_branch' => -1, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '16Gb_16c_job', -flow_into => { -1 => [ 'raxml_parsimony_16_cores_himem' ], } }, { -logic_name => 'raxml_parsimony_16_cores_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_parsimony', -parameters => { %raxml_parsimony_parameters, 'raxml_number_of_cores' => 16, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '32Gb_16c_job', }, { -logic_name => 'raxml_parsimony_32_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_parsimony', -parameters => { %raxml_parsimony_parameters, 'raxml_number_of_cores' => 32, 'escape_branch' => -1, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '16Gb_32c_job', -flow_into => { -1 => [ 'raxml_parsimony_32_cores_himem' ], } }, { -logic_name => 'raxml_parsimony_32_cores_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_parsimony', -parameters => { %raxml_parsimony_parameters, 'raxml_number_of_cores' => 32, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '32Gb_32c_job', }, { -logic_name => 'raxml_parsimony_64_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_parsimony', -parameters => { %raxml_parsimony_parameters, 'raxml_number_of_cores' => 64, 'cmd_max_runtime' => '518400', 'escape_branch' => -1, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '16Gb_64c_job', -flow_into => { -1 => [ 'raxml_parsimony_64_cores_himem' ], -2 => [ 'fasttree' ], } }, { -logic_name => 'raxml_parsimony_64_cores_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_parsimony', -parameters => { %raxml_parsimony_parameters, 'raxml_number_of_cores' => 64, 'cmd_max_runtime' => '518400', }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '32Gb_64c_job', -flow_into => { -2 => [ 'fasttree' ], } }, { -logic_name => 'fasttree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::FastTree', -parameters => { 'fasttree_exe' => $self->o('fasttree_exe'), 'treebest_exe' => $self->o('treebest_exe'), 'output_clusterset_id' => $self->o('use_notung') ? 'raxml' : 'default', 'input_clusterset_id' => 'default', }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '32Gb_32c_job', }, { -logic_name => 'raxml_decision', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'examl_patterns_per_core' => $self->o('use_dna_for_phylogeny') ? '3500' : '1000', 'raxml_patterns_per_core' => $self->o('use_dna_for_phylogeny') ? '500' : '150', 'examl_cores' => '#expr(#tree_aln_num_of_patterns# / #examl_patterns_per_core# )expr#', 'raxml_cores' => '#expr(#tree_aln_num_of_patterns# / #raxml_patterns_per_core# )expr#', 'tags' => { #The default value matches the default dataflow we want: _8_cores analysis. 'aln_num_of_patterns' => 200, 'gene_count' => 0, }, }, %decision_analysis_params, #------------------------------------------------------------------------------- # This boundaries are based on RAxML and ExaML manuals. # Which suggest the following number of cores: # # ExaML: DNA: 3.5K patterns/core # AAs: 1K patterns/core # # RAxML: DNA: 500 patterns/core # AAs: 150 patterns/core # #------------------------------------------------------------------------------- -flow_into => { 1 => WHEN ( '( #raxml_cores# <= 1 ) && (#tree_gene_count# <= 500)' => 'raxml', '( #raxml_cores# <= 1 ) && (#tree_gene_count# > 500)' => 'raxml_8_cores', '( #raxml_cores# > 1 ) && ( #raxml_cores# <= 8 ) && (#tree_gene_count# <= 500)' => 'raxml_8_cores', '( #raxml_cores# > 1 ) && ( #raxml_cores# <= 8 ) && (#tree_gene_count# > 500)' => 'raxml_16_cores', '( #raxml_cores# > 8) && (#raxml_cores# <= 16 ) && (#tree_gene_count# <= 500)' => 'raxml_16_cores', '( #raxml_cores# > 8) && (#raxml_cores# <= 16 ) && (#tree_gene_count# > 500)' => 'examl_8_cores', '( #raxml_cores# > 16) && (#examl_cores# <= 8 ) && (#tree_gene_count# <= 500)' => 'examl_8_cores', '( #raxml_cores# > 16) && (#examl_cores# <= 8 ) && (#tree_gene_count# > 500)' => 'examl_16_cores', '( #raxml_cores# > 16) && ( #examl_cores# > 8 ) && (#examl_cores# <= 16 ) && (#tree_gene_count# <= 500)' => 'examl_16_cores', '( #raxml_cores# > 16) && ( #examl_cores# > 8 ) && (#examl_cores# <= 16 ) && (#tree_gene_count# > 500)' => 'examl_32_cores', '( #raxml_cores# > 16) && ( #examl_cores# > 16 ) && (#examl_cores# <= 32 ) && (#tree_gene_count# <= 500)' => 'examl_32_cores', '( #raxml_cores# > 16) && ( #examl_cores# > 16 ) && (#examl_cores# <= 32 ) && (#tree_gene_count# > 500)' => 'examl_64_cores', '( #examl_cores# > 32 )' => 'examl_64_cores', ), }, }, { -logic_name => 'examl_8_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ExaML', -parameters => { %examl_parameters, 'cmd_max_runtime' => '518400', }, -hive_capacity => $self->o('examl_capacity'), -rc_name => '8Gb_8c_mpi', -flow_into => { -1 => [ 'examl_8_cores_himem' ], # MEMLIMIT -2 => [ 'examl_16_cores' ], # RUNTIME } }, { -logic_name => 'examl_8_cores_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ExaML', -parameters => { %examl_parameters, 'cmd_max_runtime' => '518400', }, -hive_capacity => $self->o('examl_capacity'), -rc_name => '32Gb_8c_mpi', }, { -logic_name => 'examl_16_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ExaML', -parameters => { %examl_parameters, 'cmd_max_runtime' => '518400', }, -hive_capacity => $self->o('examl_capacity'), -rc_name => '8Gb_16c_mpi', -flow_into => { -1 => [ 'examl_16_cores_himem' ], # MEMLIMIT -2 => [ 'examl_32_cores' ], # RUNTIME } }, { -logic_name => 'examl_16_cores_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ExaML', -parameters => { %examl_parameters, 'cmd_max_runtime' => '518400', }, -hive_capacity => $self->o('examl_capacity'), -rc_name => '32Gb_16c_mpi', }, { -logic_name => 'examl_32_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ExaML', -parameters => { %examl_parameters, 'cmd_max_runtime' => '518400', }, -hive_capacity => $self->o('examl_capacity'), -rc_name => '8Gb_32c_mpi', -flow_into => { -1 => [ 'examl_32_cores_himem' ], # MEMLIMIT -2 => [ 'examl_64_cores' ], # RUNTIME } }, { -logic_name => 'examl_32_cores_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ExaML', -parameters => { %examl_parameters, 'cmd_max_runtime' => '518400', }, -hive_capacity => $self->o('examl_capacity'), -rc_name => '32Gb_32c_mpi', }, { -logic_name => 'examl_64_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ExaML', -parameters => { %examl_parameters, 'cmd_max_runtime' => '518400', 'escape_branch' => -2, }, -hive_capacity => $self->o('examl_capacity'), -rc_name => '8Gb_64c_mpi', -max_retry_count => 3, #We restart this jobs 3 times then they will run in FastTree. After 18 days (3*518400) of ExaML 64 cores. It will probably not converge. -flow_into => { -1 => [ 'examl_64_cores_himem' ], # MEMLIMIT -2 => [ 'fasttree' ], # RUNLIMIT } }, { -logic_name => 'examl_64_cores_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::ExaML', -parameters => { %examl_parameters, 'cmd_max_runtime' => '518400', 'escape_branch' => -2, }, -hive_capacity => $self->o('examl_capacity'), -rc_name => '32Gb_64c_mpi', -max_retry_count => 3, #We restart this jobs 3 times then they will run in FastTree. After 18 days (3*518400) of ExaML 64 cores. It will probably not converge. -flow_into => { -2 => [ 'fasttree' ], # RUNLIMIT } }, { -logic_name => 'raxml', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML', -parameters => { %raxml_parameters, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '1Gb_job', -flow_into => { -1 => [ 'raxml_8_cores_himem' ], -2 => [ 'raxml_8_cores' ], } }, { -logic_name => 'raxml_update_decision', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'tags' => { #The default value matches the default dataflow we want: _8_cores analysis. 'gene_count' => 0, }, }, -flow_into => { 1 => WHEN( '(#tree_gene_count# <= 500)' => 'raxml_update', '(#tree_gene_count# > 500) && (#tree_gene_count# <= 1000)' => 'raxml_update_8', '(#tree_gene_count# > 1000) && (#tree_gene_count# <= 2000)' => 'raxml_update_16', '(#tree_gene_count# > 3000)' => 'raxml_update_32', ), }, %decision_analysis_params, }, { -logic_name => 'raxml_update', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_update', -parameters => { %raxml_update_parameters, }, -hive_capacity => $self->o('raxml_update_capacity'), -rc_name => '8Gb_job', }, { -logic_name => 'raxml_update_8', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_update', -parameters => { %raxml_update_parameters, 'raxml_number_of_cores' => 8, }, -hive_capacity => $self->o('raxml_update_capacity'), -rc_name => '16Gb_8c_job', }, { -logic_name => 'raxml_update_16', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_update', -parameters => { %raxml_update_parameters, 'raxml_number_of_cores' => 16, }, -hive_capacity => $self->o('raxml_update_capacity'), -rc_name => '16Gb_16c_job', }, { -logic_name => 'raxml_update_32', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_update', -parameters => { %raxml_update_parameters, 'raxml_number_of_cores' => 32, }, -hive_capacity => $self->o('raxml_update_capacity'), -rc_name => '32Gb_32c_job', }, { -logic_name => 'treebest_small_families', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML', -parameters => { 'cdna' => 1, 'store_intermediate_trees' => 1, 'extra_args' => ' -F 0 ', 'treebest_exe' => $self->o('treebest_exe'), 'output_clusterset_id' => $self->o('use_notung') ? 'raxml' : 'default', }, -hive_capacity => $self->o('treebest_capacity'), -rc_name => '1Gb_job', }, { -logic_name => 'raxml_8_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML', -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 8, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '16Gb_8c_job', -flow_into => { -1 => [ 'raxml_8_cores_himem' ], -2 => [ 'examl_16_cores' ], } }, { -logic_name => 'raxml_8_cores_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML', -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 8, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '32Gb_8c_job', }, { -logic_name => 'raxml_16_cores', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML', -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 16, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '16Gb_16c_job', -flow_into => { -1 => [ 'raxml_16_cores_himem' ], -2 => [ 'examl_32_cores' ], } }, { -logic_name => 'raxml_16_cores_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML', -parameters => { %raxml_parameters, 'raxml_number_of_cores' => 16, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '32Gb_16c_job', }, # ---------------------------------------------[tree reconciliation / rearrangements]------------------------------------------------------------- { -logic_name => 'treerecs', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Treerecs', -parameters => { 'input_clusterset_id' => 'default', 'output_clusterset_id' => 'treerecs', 'treebest_exe' => $self->o('treebest_exe'), 'treerecs_exe' => $self->o('treerecs_exe'), }, -hive_capacity => $self->o('notung_capacity'), -batch_size => 2, -rc_name => '2Gb_job', -flow_into => { 1 => [ 'copy_treerecs_bl_tree_2_default_tree' ], }, }, { -logic_name => 'notung_decision', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'tags' => { #The default value matches the default dataflow we want: _8_cores analysis. 'gene_count' => 0, }, }, -flow_into => { 1 => WHEN( '(#tree_gene_count# <= 500)' => 'notung', '(#tree_gene_count# > 500) && (#tree_gene_count# <= 1000)' => 'notung_8gb', '(#tree_gene_count# > 1000) && (#tree_gene_count# <= 2000)' => 'notung_16gb', '(#tree_gene_count# > 3000) && (#tree_gene_count# <= 6000)' => 'notung_32gb', '(#tree_gene_count# > 6000) && (#tree_gene_count# <= 10000)' => 'notung_64gb', '(#tree_gene_count# > 10000)' => 'notung_512gb', ), }, %decision_analysis_params, }, { -logic_name => 'notung', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Notung', -parameters => { %notung_parameters, 'notung_memory' => 1500, }, -hive_capacity => $self->o('notung_capacity'), -batch_size => 2, -priority => 1, -rc_name => '2Gb_job', -flow_into => { 1 => [ 'raxml_bl_decision' ], }, }, { -logic_name => 'notung_8gb', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Notung', -parameters => { %notung_parameters, 'notung_memory' => 7000, }, -hive_capacity => $self->o('notung_capacity'), -priority => 10, -rc_name => '8Gb_job', -flow_into => [ 'raxml_bl_decision' ], }, { -logic_name => 'notung_16gb', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Notung', -parameters => { %notung_parameters, 'notung_memory' => 14000, }, -hive_capacity => $self->o('notung_capacity'), -priority => 15, -rc_name => '16Gb_job', -flow_into => [ 'raxml_bl_decision' ], }, { -logic_name => 'notung_32gb', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Notung', -parameters => { %notung_parameters, 'notung_memory' => 28000, }, -hive_capacity => $self->o('notung_capacity'), -priority => 20, -rc_name => '32Gb_job', -flow_into => [ 'raxml_bl_decision' ], }, { -logic_name => 'notung_64gb', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Notung', -parameters => { %notung_parameters, 'notung_memory' => 56000, }, -hive_capacity => $self->o('notung_capacity'), -priority => 25, -rc_name => '64Gb_job', -flow_into => [ 'raxml_bl_decision' ], }, { -logic_name => 'notung_512gb', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Notung', -parameters => { %notung_parameters, 'notung_memory' => 448000, }, -hive_capacity => $self->o('notung_capacity'), -priority => 30, -rc_name => '512Gb_job', -flow_into => [ 'raxml_bl_decision' ], }, { -logic_name => 'raxml_bl_decision', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'tags' => { #The default value matches the default dataflow we want: _8_cores analysis. 'gene_count' => 0, }, }, -flow_into => { 1 => WHEN( '(#tree_gene_count# <= 500)' => 'raxml_bl', '(#tree_gene_count# > 500) && (#tree_gene_count# <= 1000)' => 'raxml_bl_8', '(#tree_gene_count# > 1000) && (#tree_gene_count# <= 2000)' => 'raxml_bl_16', '(#tree_gene_count# > 3000) && (#tree_gene_count# <= 10000)' => 'raxml_bl_32', '(#tree_gene_count# > 10000)' => 'raxml_bl_64', ), }, %decision_analysis_params, }, { -logic_name => 'raxml_bl', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_bl', -parameters => { %raxml_bl_parameters, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '8Gb_job', -flow_into => { 1 => [ 'copy_raxml_bl_tree_2_default_tree' ], 2 => [ 'copy_treebest_tree_2_raxml_bl_tree' ], } }, { -logic_name => 'raxml_bl_8', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_bl', -parameters => { %raxml_bl_parameters, 'raxml_number_of_cores' => 8, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '16Gb_8c_job', -flow_into => { 1 => [ 'copy_raxml_bl_tree_2_default_tree' ], 2 => [ 'copy_treebest_tree_2_raxml_bl_tree' ], } }, { -logic_name => 'raxml_bl_16', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_bl', -parameters => { %raxml_bl_parameters, 'raxml_number_of_cores' => 16, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '16Gb_16c_job', -flow_into => { 1 => [ 'copy_raxml_bl_tree_2_default_tree' ], 2 => [ 'copy_treebest_tree_2_raxml_bl_tree' ], } }, { -logic_name => 'raxml_bl_32', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_bl', -parameters => { %raxml_bl_parameters, 'raxml_number_of_cores' => 32, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '32Gb_32c_job', -flow_into => { 1 => [ 'copy_raxml_bl_tree_2_default_tree' ], 2 => [ 'copy_treebest_tree_2_raxml_bl_tree' ], } }, { -logic_name => 'raxml_bl_64', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::RAxML_bl', -parameters => { %raxml_bl_parameters, 'raxml_number_of_cores' => 64, }, -hive_capacity => $self->o('raxml_capacity'), -rc_name => '256Gb_64c_job', -flow_into => { 1 => [ 'copy_raxml_bl_tree_2_default_tree' ], 2 => [ 'copy_treebest_tree_2_raxml_bl_tree' ], } }, # At this point, we are currently storing the treebest trees as raxml and raxml_bl. # if we need to reduce the storage footprint we may skip this, and copy direct to default. { -logic_name => 'copy_treebest_tree_2_raxml_bl_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::CopyLocalTree', -parameters => { 'treebest_exe' => $self->o('treebest_exe'), 'input_clusterset_id' => 'notung', 'output_clusterset_id' => 'raxml_bl', }, -hive_capacity => $self->o('copy_tree_capacity'), -rc_name => '2Gb_job', -flow_into => { 1 => [ 'copy_raxml_bl_tree_2_default_tree' ], } }, { -logic_name => 'copy_raxml_bl_tree_2_default_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::CopyLocalTree', -parameters => { 'treebest_exe' => $self->o('treebest_exe'), 'input_clusterset_id' => 'raxml_bl', 'output_clusterset_id' => 'default', }, -hive_capacity => $self->o('copy_tree_capacity'), -rc_name => '2Gb_job', -flow_into => [ 'hc_post_tree' ], }, { -logic_name => 'copy_treerecs_bl_tree_2_default_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::CopyLocalTree', -parameters => { 'treebest_exe' => $self->o('treebest_exe'), 'input_clusterset_id' => 'treerecs', 'output_clusterset_id' => 'default', }, -hive_capacity => $self->o('copy_tree_capacity'), -rc_name => '2Gb_job', -flow_into => [ 'hc_post_tree' ], }, # ---------------------------------------------[orthologies]------------------------------------------------------------- { -logic_name => 'hc_post_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::HCOneTree', -flow_into => [ 'ortho_tree_decision' ], -hive_capacity => $self->o('hc_post_tree_capacity'), %hc_analysis_params, }, { -logic_name => 'ortho_tree_decision', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::LoadTags', -parameters => { 'tags' => { #The default value matches the default dataflow we want: ortho_tree analysis. 'gene_count' => 0, }, }, -flow_into => { 1 => WHEN( '(#tree_gene_count# <= 400)' => 'ortho_tree', ELSE 'ortho_tree_himem', ), }, %decision_analysis_params, }, { -logic_name => 'ortho_tree', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OrthoTree', -parameters => { 'tag_split_genes' => 1, 'input_clusterset_id' => $self->o('use_notung') ? 'raxml_bl' : 'default', }, -hive_capacity => $self->o('ortho_tree_capacity'), -priority => -10, -rc_name => '1Gb_job', -flow_into => { 1 => [ 'hc_tree_homologies' ], -1 => 'ortho_tree_himem', }, }, { -logic_name => 'ortho_tree_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OrthoTree', -parameters => { 'tag_split_genes' => 1, 'input_clusterset_id' => $self->o('use_notung') ? 'raxml_bl' : 'default', }, -hive_capacity => $self->o('ortho_tree_capacity'), -priority => 20, -rc_name => '4Gb_job', -flow_into => [ 'hc_tree_homologies' ], }, { -logic_name => 'hc_tree_homologies', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'tree_homologies', }, -flow_into => [ 'ktreedist', 'consensus_cigar_line_prep' ], %hc_analysis_params, }, { -logic_name => 'ktreedist', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::Ktreedist', -parameters => { 'treebest_exe' => $self->o('treebest_exe'), 'ktreedist_exe' => $self->o('ktreedist_exe'), }, -hive_capacity => $self->o('ktreedist_capacity'), -batch_size => 5, -rc_name => '500Mb_job', -flow_into => { -1 => [ 'ktreedist_himem' ], }, }, { -logic_name => 'ktreedist_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::Ktreedist', -parameters => { 'treebest_exe' => $self->o('treebest_exe'), 'ktreedist_exe' => $self->o('ktreedist_exe'), }, -hive_capacity => $self->o('ktreedist_capacity'), -rc_name => '4Gb_job', }, { -logic_name => 'consensus_cigar_line_prep', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ObjectStore::GeneTreeAlnConsensusCigarLine', -rc_name => '500Mb_job', -hive_capacity => $self->o('ktreedist_capacity'), -batch_size => 20, -flow_into => { -1 => [ 'consensus_cigar_line_prep_himem' ], }, }, { -logic_name => 'consensus_cigar_line_prep_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ObjectStore::GeneTreeAlnConsensusCigarLine', -rc_name => '4Gb_job', -hive_capacity => $self->o('ktreedist_capacity'), -batch_size => 20, }, { -logic_name => 'build_HMM_aa_v3', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BuildHMM', -parameters => { 'hmmer_home' => $self->o('hmmer3_home'), 'hmmer_version' => 3, }, -hive_capacity => $self->o('build_hmm_capacity'), -batch_size => 5, -flow_into => { -1 => 'build_HMM_aa_v3_himem' }, }, { -logic_name => 'build_HMM_aa_v3_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BuildHMM', -parameters => { 'hmmer_home' => $self->o('hmmer3_home'), 'hmmer_version' => 3, }, -hive_capacity => $self->o('build_hmm_capacity'), -rc_name => '1Gb_job', }, { -logic_name => 'build_HMM_cds_v3', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BuildHMM', -parameters => { 'cdna' => 1, 'hmmer_home' => $self->o('hmmer3_home'), 'hmmer_version' => 3, }, -hive_capacity => $self->o('build_hmm_capacity'), -batch_size => 5, -rc_name => '500Mb_job', -flow_into => { -1 => 'build_HMM_cds_v3_himem' }, }, { -logic_name => 'build_HMM_cds_v3_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BuildHMM', -parameters => { 'cdna' => 1, 'hmmer_home' => $self->o('hmmer3_home'), 'hmmer_version' => 3, }, -hive_capacity => $self->o('build_hmm_capacity'), -rc_name => '2Gb_job', }, # ---------------------------------------------[Quick tree break steps]----------------------------------------------------------------------- { -logic_name => 'quick_tree_break', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::QuickTreeBreak', -parameters => { 'quicktree_exe' => $self->o('quicktree_exe'), 'treebreak_gene_count' => $self->o('treebreak_gene_count'), }, -hive_capacity => $self->o('quick_tree_break_capacity'), -rc_name => '2Gb_job', -flow_into => { 1 => 'other_paralogs', -1 => 'quick_tree_break_himem', }, }, { -logic_name => 'quick_tree_break_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::QuickTreeBreak', -parameters => { 'quicktree_exe' => $self->o('quicktree_exe'), 'treebreak_gene_count' => $self->o('treebreak_gene_count'), }, -hive_capacity => $self->o('quick_tree_break_capacity'), -rc_name => '4Gb_job', -flow_into => [ 'other_paralogs_himem' ], }, { -logic_name => 'other_paralogs', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OtherParalogs', -parameters => { 'dataflow_subclusters' => 1, }, -hive_capacity => $self->o('other_paralogs_capacity'), -flow_into => { -1 => [ 'other_paralogs_himem', ], 2 => [ 'tree_backup' ], 3 => { 'other_paralogs' => INPUT_PLUS }, } }, { -logic_name => 'other_paralogs_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OtherParalogs', -parameters => { 'dataflow_subclusters' => 1, }, -hive_capacity => $self->o('other_paralogs_capacity'), -rc_name => '500Mb_job', -flow_into => { 2 => [ 'tree_backup' ], 3 => { 'other_paralogs_himem' => INPUT_PLUS }, } }, { -logic_name => 'tree_backup', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => 'INSERT INTO gene_tree_backup (seq_member_id, root_id) SELECT seq_member_id, root_id FROM gene_tree_node WHERE seq_member_id IS NOT NULL AND root_id = #gene_tree_id#', }, -flow_into => [ 'alignment_entry_point' ], }, { -logic_name => 'join_panther_subfam', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ComparaHMM::MakePantherSuperTrees', -rc_name => '1Gb_job', -flow_into => { 2 => 'panther_backup', }, }, { -logic_name => 'panther_backup', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => 'INSERT INTO gene_tree_backup (seq_member_id, root_id) SELECT gtn3.seq_member_id, gtn1.root_id FROM gene_tree_node gtn1 JOIN gene_tree_node gtn2 ON gtn1.node_id = gtn2.parent_id JOIN gene_tree_node gtn3 ON gtn2.root_id = gtn3.root_id WHERE gtn3.seq_member_id IS NOT NULL AND gtn1.root_id = #gene_tree_id#', }, -flow_into => { 1 => { 'alignment_entry_point' => INPUT_PLUS({ 'is_already_supertree' => 1 }) }, }, }, { -logic_name => 'panther_paralogs', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::PantherParalogs', -hive_capacity => $self->o('other_paralogs_capacity'), -rc_name => '1Gb_job', -flow_into => { -1 => [ 'panther_paralogs_himem', ], 3 => { 'panther_paralogs' => INPUT_PLUS }, } }, { -logic_name => 'panther_paralogs_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::PantherParalogs', -hive_capacity => $self->o('other_paralogs_capacity'), -rc_name => '4Gb_job', -flow_into => { 3 => { 'panther_paralogs_himem' => INPUT_PLUS }, } }, # -------------------------------------------[name mapping step]--------------------------------------------------------------------- { -logic_name => 'stable_id_mapping', -module => 'Bio::EnsEMBL::Compara::RunnableDB::StableIdMapper', -parameters => { 'prev_rel_db' => '#mapping_db#', 'type' => 't', }, -flow_into => [ 'hc_stable_id_mapping' ], -rc_name => '2Gb_job', }, { -logic_name => 'hc_stable_id_mapping', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'stable_id_mapping', }, -flow_into => [ WHEN('#do_jaccard_index# && #reuse_db#' => 'compute_jaccard_index'), ], %hc_analysis_params, }, { -logic_name => 'treefam_xref_idmap', -module => 'Bio::EnsEMBL::Compara::RunnableDB::TreefamXrefMapper', -parameters => { 'tf_release' => $self->o('tf_release'), 'tag_prefix' => '', }, -rc_name => '2Gb_job', }, { -logic_name => 'build_HMM_factory', -module => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory', -parameters => { 'inputquery' => 'SELECT root_id AS gene_tree_id FROM gene_tree_root WHERE tree_type = "tree" AND clusterset_id="default"', }, -flow_into => { # We don't use build_HMM_aa_v2 because hmmcalibrate takes ages 2 => [ 'build_HMM_aa_v3', 'build_HMM_cds_v3' ], }, -rc_name => '1Gb_job', }, # ---------------------------------------------[homology step]----------------------------------------------------------------------- { -logic_name => 'polyploid_move_back_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GenomeDBFactory', -parameters => { 'component_genomes' => 0, 'normal_genomes' => 0, }, -flow_into => { '2->A' => [ 'component_genome_dbs_move_back_factory' ], 'A->1' => [ 'floating_rib' ], }, }, { -logic_name => 'component_genome_dbs_move_back_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::ComponentGenomeDBFactory', -flow_into => { 2 => { 'move_back_component_genes' => { 'source_gdb_id' => '#component_genome_db_id#', 'target_gdb_id' => '#principal_genome_db_id#'}, }, }, }, { -logic_name => 'move_back_component_genes', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MoveComponentGenes', -hive_capacity => $self->o('reuse_capacity'), }, { -logic_name => 'rib_fire_gene_qc', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => { '1->A' => WHEN('#do_gene_qc#' => 'get_species_set'), 'A->1' => 'rib_fire_homology_id_mapping', }, }, { -logic_name => 'rib_fire_cafe', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => { '1->A' => WHEN('#initialise_cafe_pipeline#' => 'CAFE_species_tree'), 'A->1' => 'rib_fire_homology_stats', }, }, { -logic_name => 'rib_fire_homology_stats', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => { '1->A' => [ WHEN('#do_homology_stats#' => 'homology_stats_factory'), 'set_default_values', ], 'A->1' => 'rib_fire_hmm_build', }, }, { -logic_name => 'rib_fire_hmm_build', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -flow_into => { '1->A' => WHEN('#do_hmm_export#' => 'build_HMM_factory'), 'A->1' => 'rib_fire_rename_labels', }, }, { -logic_name => 'rib_fire_homology_id_mapping', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -parameters => { 'goc_taxlevels' => $self->o('goc_taxlevels'), }, -flow_into => { '1->A' => WHEN('(scalar(@{#goc_taxlevels#}) && #goc_reuse_db#) || #do_homology_id_mapping#' => 'id_map_mlss_factory'), 'A->1' => 'group_genomes_under_taxa', }, }, { -logic_name => 'rib_fire_rename_labels', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -parameters => { 'label_prefix' => $self->o('label_prefix'), }, -flow_into => { # FIXME this assumes that label_prefix is set iff the collection is not "default" '1->A' => WHEN('#label_prefix#' => 'rename_labels'), 'A->1' => 'rib_fire_goc', }, }, { -logic_name => 'floating_rib', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', }, { -logic_name => 'group_genomes_under_taxa', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::GroupGenomesUnderTaxa', -parameters => { 'taxlevels' => $self->o('taxlevels'), }, -flow_into => { '2->A' => [ 'mlss_factory' ], 'A->1' => [ 'rib_fire_cafe' ], }, }, { -logic_name => 'id_map_mlss_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::MLSSIDFactory', -parameters => { 'methods' => { 'ENSEMBL_ORTHOLOGUES' => 2, }, }, -rc_name => '500Mb_job', -flow_into => { 2 => [ 'mlss_id_mapping' ], }, }, { -logic_name => 'mlss_id_mapping', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MLSSIDMapping', -parameters => { 'prev_rel_db' => '#mapping_db#', }, -hive_capacity => $self->o('homology_dNdS_capacity'), -rc_name => '500Mb_job', -flow_into => { -1 => [ 'mlss_id_mapping_himem' ], 1 => { 'homology_id_mapping' => INPUT_PLUS() }, }, }, { -logic_name => 'mlss_id_mapping_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MLSSIDMapping', -parameters => { 'prev_rel_db' => '#mapping_db#', }, -hive_capacity => $self->o('homology_dNdS_capacity'), -rc_name => '1Gb_job', -flow_into => { 1 => { 'homology_id_mapping' => INPUT_PLUS() } }, }, { -logic_name => 'mlss_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MLSSIDFactory', -flow_into => { 2 => [ 'homology_factory' ], }, }, { -logic_name => 'homology_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HomologyGroupingFactory', -hive_capacity => $self->o('homology_dNdS_factory_capacity'), -rc_name => '500Mb_job', -flow_into => { 'A->1' => [ 'hc_dnds' ], '2->A' => [ 'homology_dNdS' ], '3->A' => [ 'copy_homology_dNdS' ], }, }, { -logic_name => 'homology_id_mapping', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HomologyIDMapping', -parameters => { 'prev_rel_db' => '#mapping_db#', }, -rc_name => '1Gb_job', -flow_into => { -1 => [ 'homology_id_mapping_himem' ], }, -analysis_capacity => 100, }, { -logic_name => 'homology_id_mapping_himem', -parameters => { 'prev_rel_db' => '#mapping_db#', }, -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HomologyIDMapping', -flow_into => { -1 => [ 'homology_id_mapping_hugemem' ], }, -analysis_capacity => 20, -rc_name => '8Gb_job', }, { -logic_name => 'homology_id_mapping_hugemem', -parameters => { 'prev_rel_db' => '#mapping_db#', }, -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HomologyIDMapping', -analysis_capacity => 20, -rc_name => '16Gb_job', }, { -logic_name => 'homology_dNdS', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Homology_dNdS', -parameters => { 'codeml_parameters_file' => $self->o('codeml_parameters_file'), 'codeml_exe' => $self->o('codeml_exe'), 'force_rerunning' => 0, }, -hive_capacity => $self->o('homology_dNdS_capacity'), -priority=> 20, -rc_name => '500Mb_job', }, { -logic_name => 'copy_homology_dNdS', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CopyHomology_dNdS', -parameters => { }, -hive_capacity => $self->o('copy_homology_dNdS_capacity'), -rc_name => '500Mb_job', -batch_size => 5, -flow_into => { 2 => [ 'homology_dNdS' ], }, }, { -logic_name => 'hc_dnds', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::SqlHealthChecks', -parameters => { mode => 'homology_dnds', }, -flow_into => [ 'threshold_on_dS' ], %hc_analysis_params, }, { -logic_name => 'threshold_on_dS', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Threshold_on_dS', -hive_capacity => $self->o('homology_dNdS_capacity'), -flow_into => { -1 => 'threshold_on_dS_himem', }, }, { -logic_name => 'threshold_on_dS_himem', -module => 'Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Threshold_on_dS', -hive_capacity => $self->o('homology_dNdS_capacity'), -rc_name => '500Mb_job', }, { -logic_name => 'rib_fire_goc', -module => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy', -parameters => { 'taxlevels' => $self->o('goc_taxlevels'), }, -flow_into => { '1->A' => WHEN( 'scalar(@{#taxlevels#})' => 'goc_entry_point' ), 'A->1' => ['polyploid_move_back_factory'], }, }, { -logic_name => 'homology_stats_factory', -module => 'Bio::EnsEMBL::Compara::RunnableDB::MLSSIDFactory', -parameters => { 'methods' => { 'ENSEMBL_ORTHOLOGUES' => 2, 'ENSEMBL_PARALOGUES' => 3, }, }, -rc_name => '500Mb_job', -flow_into => { 2 => { 'orthology_stats' => { 'homo_mlss_id' => '#mlss_id#' }, }, 3 => { 'paralogy_stats' => { 'homo_mlss_id' => '#mlss_id#' }, }, }, }, { -logic_name => 'orthology_stats', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::OrthologyStats', -parameters => { 'member_type' => 'protein', }, -rc_name => '500Mb_job', -hive_capacity => $self->o('ortho_stats_capacity'), }, { -logic_name => 'paralogy_stats', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::ParalogyStats', -parameters => { 'member_type' => 'protein', 'species_tree_label' => $self->o('use_notung') ? 'binary' : 'default', }, -rc_name => '500Mb_job', -hive_capacity => $self->o('ortho_stats_capacity'), }, { -logic_name => 'rename_labels', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::RenameLabelsBeforMerge', -parameters => { 'clusterset_id'=> $self->o('collection'), 'label_prefix' => $self->o('label_prefix'), }, }, { -logic_name => 'remove_overlapping_homologies', -module => 'Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::RemoveOverlappingHomologies', }, @{ Bio::EnsEMBL::Compara::PipeConfig::Parts::CAFE::pipeline_analyses_cafe($self) }, @{ Bio::EnsEMBL::Compara::PipeConfig::Parts::GOC::pipeline_analyses_goc($self) }, @{ Bio::EnsEMBL::Compara::PipeConfig::Parts::GeneSetQC::pipeline_analyses_GeneSetQC($self) }, @{ Bio::EnsEMBL::Compara::PipeConfig::Parts::GeneMemberHomologyStats::pipeline_analyses_hom_stats($self) }, ]; } 1;