Hi all - I’m going nuts trying to determine why a monetdb SQL query does not work. I am trying to pull data from 2 tables. These tables are in the DB as shown here: sql>\d TABLE maizefullgenome.fullgenomegff TABLE maizefullgenome.fullgenomestable TABLE maizefullgenome.gene_from_gff TABLE maizefullgenome.ranges_from_gff sql> If I join only on the “pos” field, the query executes. Here is that query:
delChrPosGene_fullGenome <-dbGetQuery(conn,
"SELECT fg.chr,fg.pos,gt.gene_name FROM maizeFullGenome.fullgenomestable fg join maizeFullGenome.gene_from_gff gt on (fg.pos >= gt.start_pos AND fg.pos <= gt.end_pos) where gerp_score> 2 AND gerp_neutral_tree_length > 2 AND ((sift_score_a < 0.05 AND sift_score_a >= -1) OR (sift_score_c < 0.05 AND sift_score_c >=-1) OR (sift_score_g < 0.05 AND sift_score_g >=-1) OR (sift_score_t < 0.05 AND sift_score_t >=-1))") If I add the “chr” field, it fails with the message below. Can anyone tell me what is wrong with this second query?
delChrPosGene_fullGenome <-dbGetQuery(conn,
"SELECT fg.chr,fg.pos,gt.gene_name FROM maizeFullGenome.fullgenomestable fg join maizeFullGenome.gene_from_gff gt on (fg.chr = gt.chr AND fg.pos >= gt.start_pos AND fg.pos <= gt.end_pos) where gerp_score> 2 AND gerp_neutral_tree_length > 2 AND ((sift_score_a < 0.05 AND sift_score_a >= -1) OR (sift_score_c < 0.05 AND sift_score_c >=-1) OR (sift_score_g < 0.05 AND sift_score_g >=-1) OR (sift_score_t < 0.05 AND sift_score_t >=-1))") Error in .local(conn, statement, ...) : Unable to execute statement 'SELECT fg.chr,fg.pos,gt.gene_name FROM maizeFullGenome.fullgenomestable fg join maizeFullGenome.gene...'. Server says '!Object not found'. Here are the fields in the gene_from_gff table: sql>\d maizefullgenome.gene_from_gff CREATE TABLE "maizefullgenome"."gene_from_gff" ( "chr" INTEGER, "start_pos" INTEGER, "end_pos" INTEGER, "gene_name" CHARACTER LARGE OBJECT ); sql> Here are the fields in the fullgenomestable table: sql>\d maizefullgenome.fullgenomestable CREATE TABLE "maizefullgenome"."fullgenomestable" ( "chr" INTEGER, "pos" INTEGER, "ref_allele" TINYINT, "two_bp_upstream" INTEGER, "two_bp_downstream" INTEGER, "three_bp_upstream" INTEGER, "three_bp_center" INTEGER, "three_bp_downstream" INTEGER, "four_bp_upstream" INTEGER, "four_bp_downstream" INTEGER, "five_bp_upstream" INTEGER, "five_bp_center" INTEGER, "five_bp_downstream" INTEGER, "gc_content" TINYINT, "gerp_neutral_tree_length" REAL, "gerp_score" REAL, "gerp_conserved" BOOLEAN, "cmethylation" REAL, "cpg_methylation_1bk_moving_average" REAL, "chg_methylation_1bk_moving_average" REAL, "chh_methylation_1bk_moving_average" REAL, "mnase_low_minus_high_rpm_shoots" REAL, "mnase_bayes_factor_shoots" REAL, "mnase_hotspot_shoots" BOOLEAN, "mnase_low_minus_high_rpm_roots" REAL, "mnase_bayes_factor_roots" REAL, "mnase_hotspot_roots" BOOLEAN, "allele_total_depth" INTEGER, "site_presence" INTEGER, "conservedgene_presence" BOOLEAN, "minor_allele" INTEGER, "maf" REAL, "combined_site_uniqueness_score" REAL, "site_uniqueness_score_sd" REAL, "expected_invariant_site" BOOLEAN, "codon_position" TINYINT, "within_cds" BOOLEAN, "within_gene" BOOLEAN, "within_transcript" BOOLEAN, "within_exon" BOOLEAN, "within_five_prime_utr" BOOLEAN, "within_three_prime_utr" BOOLEAN, "within_mirna" BOOLEAN, "line_family" INTEGER, "sine_family" INTEGER, "ltr_family" INTEGER, "helitron" BOOLEAN, "carot_common_support_interval" TINYINT, "toco_common_support_interval" TINYINT, "orig_amino_acid_a" TINYINT, "new_amino_acid_a" TINYINT, "amino_acid_substitute_pos_a" INTEGER, "sift_score_a" REAL, "sift_median_seq_info_a" REAL, "number_seqs_at_pos_a" INTEGER, "orig_amino_acid_c" TINYINT, "new_amino_acid_c" TINYINT, "amino_acid_substitute_pos_c" INTEGER, "sift_score_c" REAL, "sift_median_seq_info_c" REAL, "number_seqs_at_pos_c" INTEGER, "orig_amino_acid_g" TINYINT, "new_amino_acid_g" TINYINT, "amino_acid_substitute_pos_g" INTEGER, "sift_score_g" REAL, "sift_median_seq_info_g" REAL, "number_seqs_at_pos_g" INTEGER, "orig_amino_acid_t" TINYINT, "new_amino_acid_t" TINYINT, "amino_acid_substitute_pos_t" INTEGER, "sift_score_t" REAL, "sift_median_seq_info_t" REAL, "number_seqs_at_pos_t" INTEGER, "b73_uniqueness_score" REAL, "cml247_uniqueness_score" REAL, "ph207_uniqueness_score" REAL, "w22_uniqueness_score" REAL, "coelorachis_anc" TINYINT, "vossia_anc" TINYINT, "sorghum_anc" TINYINT, "oryza_anc" TINYINT, "setaria_anc" TINYINT, "brachypodium_anc" TINYINT, "hordeum_anc" TINYINT, "musa_anc" TINYINT, "populus_anc" TINYINT, "vitis_anc" TINYINT, "arabidopsis_anc" TINYINT, "panicum_anc" TINYINT ); sql> Any hints are greatly appreciated! Thanks - Lynn