-ctat genome lib [/tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.0kmkuWaYEo/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary -sample contains 1433549 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir -J /tmp/nxf.0kmkuWaYEo/OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.0kmkuWaYEo/OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=75000.00/min [30000], rate=72000.00/min [40000], rate=70588.24/min [50000], rate=69767.44/min [60000], rate=70588.24/min [70000], rate=72413.79/min [80000], rate=71641.79/min [90000], rate=72000.00/min [100000], rate=71428.57/min [110000], rate=67346.94/min [120000], rate=66666.67/min [130000], rate=66666.67/min [140000], rate=66141.73/min [150000], rate=67164.18/min -building interval tree based on /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=60000.00/min [20000], rate=60000.00/min [30000], rate=66666.67/min [40000], rate=61538.46/min [50000], rate=63829.79/min [60000], rate=66666.67/min [70000], rate=62686.57/min [80000], rate=62337.66/min [90000], rate=62790.70/min [100000], rate=63157.89/min [110000], rate=62857.14/min [120000], rate=63716.81/min [130000], rate=65000.00/min [140000], rate=65625.00/min [150000], rate=66176.47/min -building interval tree based on /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=100000.00/min [30000], rate=85714.29/min [40000], rate=82758.62/min [50000], rate=85714.29/min [60000], rate=85714.29/min [70000], rate=73684.21/min [80000], rate=64864.86/min [90000], rate=62068.97/min [100000], rate=63829.79/min [110000], rate=63461.54/min [120000], rate=64285.71/min [130000], rate=62903.23/min [140000], rate=62686.57/min [150000], rate=63829.79/min -building interval tree based on /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=50000.00/min [20000], rate=57142.86/min [30000], rate=62068.97/min [40000], rate=66666.67/min [50000], rate=69767.44/min [60000], rate=70588.24/min [70000], rate=71186.44/min [80000], rate=68571.43/min [90000], rate=67500.00/min [100000], rate=64516.13/min [110000], rate=66000.00/min [120000], rate=64864.86/min [130000], rate=63934.43/min [140000], rate=61313.87/min [150000], rate=60000.00/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir --filt_file /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... 4000000.00 reads per min processed... 4500000.00 reads per min processed... 4800000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.0kmkuWaYEo/OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction --tmpdir /tmp --min_junction_reads 0 --min_sum_frags 1 --require_LDAS 0 --max_promiscuity 10 --min_pct_dom_promiscuity 20 --min_novel_junction_support 1 --min_alt_pct_junction 10 --aggregate_novel_junction_dist 5 --min_spanning_frags_only 1 --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -6335.803757 EM: Round [1] log likelihood: -6329.184551 EM: Round [2] log likelihood: -6326.005548 EM: Round [3] log likelihood: -6324.152571 EM: Round [4] log likelihood: -6323.058852 EM: Round [5] log likelihood: -6322.414706 EM: Round [6] log likelihood: -6322.031045 EM: Round [7] log likelihood: -6321.797489 EM: Round [8] log likelihood: -6321.651627 EM: Round [9] log likelihood: -6321.558232 EM: Round [10] log likelihood: -6321.497077 EM: Round [11] log likelihood: -6321.456246 EM: Round [12] log likelihood: -6321.428523 EM: Round [13] log likelihood: -6321.409427 EM: Round [14] log likelihood: -6321.396107 EM: Round [15] log likelihood: -6321.386714 EM: Round [16] log likelihood: -6321.380024 EM: Round [17] log likelihood: -6321.375218 EM: Round [18] log likelihood: -6321.371737 EM: Round [19] log likelihood: -6321.369199 EM: Round [20] log likelihood: -6321.367336 EM: Round [21] log likelihood: -6321.365960 EM: Round [22] log likelihood: -6321.364938 EM: Round [23] log likelihood: -6321.364175 EM: Round [24] log likelihood: -6321.363603 EM: Round [25] log likelihood: -6321.363172 EM: Round [26] log likelihood: -6321.362846 EM: Round [27] log likelihood: -6321.362599 EM: Round [28] log likelihood: -6321.362410 EM: Round [29] log likelihood: -6321.362266 EM: Round [30] log likelihood: -6321.362156 EM: Round [31] log likelihood: -6321.362071 EM: Stopping iterations at round 31 due to insufficient improvement in likelihood. EM: Starting log likelihood: -6334.469790 EM: Round [1] log likelihood: -6328.328221 EM: Round [2] log likelihood: -6325.461485 EM: Round [3] log likelihood: -6323.834260 EM: Round [4] log likelihood: -6322.883152 EM: Round [5] log likelihood: -6322.320434 EM: Round [6] log likelihood: -6321.980811 EM: Round [7] log likelihood: -6321.770557 EM: Round [8] log likelihood: -6321.636990 EM: Round [9] log likelihood: -6321.550138 EM: Round [10] log likelihood: -6321.492515 EM: Round [11] log likelihood: -6321.453625 EM: Round [12] log likelihood: -6321.426991 EM: Round [13] log likelihood: -6321.408517 EM: Round [14] log likelihood: -6321.395559 EM: Round [15] log likelihood: -6321.386380 EM: Round [16] log likelihood: -6321.379820 EM: Round [17] log likelihood: -6321.375092 EM: Round [18] log likelihood: -6321.371661 EM: Round [19] log likelihood: -6321.369152 EM: Round [20] log likelihood: -6321.367308 EM: Round [21] log likelihood: -6321.365943 EM: Round [22] log likelihood: -6321.364928 EM: Round [23] log likelihood: -6321.364170 EM: Round [24] log likelihood: -6321.363600 EM: Round [25] log likelihood: -6321.363171 EM: Round [26] log likelihood: -6321.362846 EM: Round [27] log likelihood: -6321.362599 EM: Round [28] log likelihood: -6321.362411 EM: Round [29] log likelihood: -6321.362267 EM: Round [30] log likelihood: -6321.362156 EM: Round [31] log likelihood: -6321.362071 EM: Stopping iterations at round 31 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered * Running CMD: /usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 1433549 > /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM * Running CMD: /usr/local/src/STAR-Fusion/util/append_breakpoint_junction_info.pl /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir > /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir --annotate /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot * Running CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir -done, see /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass * Running CMD: /usr/local/src/STAR-Fusion/util/filter_likely_RT_artifacts.pl --fusions /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 61, filtered: 1013) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.0kmkuWaYEo/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass.minFFPM.0.00001.pass star-fusion.fusion_predictions.tsv * Running CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl star-fusion.fusion_predictions.tsv JunctionReads,SpanningFrags > star-fusion.fusion_predictions.abridged.tsv * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions star-fusion.fusion_predictions.abridged.tsv --genome_lib_dir /tmp/nxf.0kmkuWaYEo/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000213742.7] WARNING, no entry stored in dbm for [ENSG00000197558.13] WARNING, no entry stored in dbm for [ENSG00000286176.2] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000230461.9] WARNING, no entry stored in dbm for [ENSG00000272078.1] WARNING, no entry stored in dbm for [ENSG00000230426.4] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000228422.5] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000226043.2] WARNING, no entry stored in dbm for [ENSG00000287531.1] WARNING, no entry stored in dbm for [ENSG00000260046.1] WARNING, no entry stored in dbm for [ENSG00000255811.1] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000259116.2] WARNING, no entry stored in dbm for [ENSG00000250746.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000260807.7] WARNING, no entry stored in dbm for [ENSG00000284707.2] WARNING, no entry stored in dbm for [ENSG00000286218.2] * STAR-Fusion complete. See output: /tmp/nxf.0kmkuWaYEo/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)