Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/4d236ec70a548a0aeba345f9e0e72c/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/a7f3e07c3c224e166d137e41d57cc2/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/a7f3e07c3c224e166d137e41d57cc2/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/61bb27d0c7cb8f64214780eb2c6dc5/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/61bb27d0c7cb8f64214780eb2c6dc5/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.ApftGg0uOS/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary -sample contains 4362646 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir -J /tmp/nxf.ApftGg0uOS/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction -O /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.ApftGg0uOS/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=42857.14/min [20000], rate=44444.44/min [30000], rate=50000.00/min [40000], rate=52173.91/min [50000], rate=50847.46/min -building interval tree based on /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=54545.45/min [30000], rate=51428.57/min [40000], rate=51063.83/min [50000], rate=50847.46/min -building interval tree based on /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=50000.00/min [20000], rate=50000.00/min [30000], rate=47368.42/min [40000], rate=47058.82/min [50000], rate=46875.00/min -building interval tree based on /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=57142.86/min [30000], rate=46153.85/min [40000], rate=43636.36/min [50000], rate=44117.65/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir --filt_file /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 3000000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.ApftGg0uOS/1173_OHF_T1_RNA_SLD_01_A23T55JLT4_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.ApftGg0uOS/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -9780.615024 EM: Round [1] log likelihood: -9775.588806 EM: Round [2] log likelihood: -9773.274349 EM: Round [3] log likelihood: -9772.070101 EM: Round [4] log likelihood: -9771.412894 EM: Round [5] log likelihood: -9771.043899 EM: Round [6] log likelihood: -9770.831238 EM: Round [7] log likelihood: -9770.705320 EM: Round [8] log likelihood: -9770.628774 EM: Round [9] log likelihood: -9770.581119 EM: Round [10] log likelihood: -9770.550836 EM: Round [11] log likelihood: -9770.531262 EM: Round [12] log likelihood: -9770.518433 EM: Round [13] log likelihood: -9770.509926 EM: Round [14] log likelihood: -9770.504233 EM: Round [15] log likelihood: -9770.500392 EM: Round [16] log likelihood: -9770.497784 EM: Round [17] log likelihood: -9770.496002 EM: Round [18] log likelihood: -9770.494778 EM: Round [19] log likelihood: -9770.493934 EM: Round [20] log likelihood: -9770.493349 EM: Round [21] log likelihood: -9770.492942 EM: Round [22] log likelihood: -9770.492657 EM: Round [23] log likelihood: -9770.492458 EM: Round [24] log likelihood: -9770.492317 EM: Round [25] log likelihood: -9770.492218 EM: Stopping iterations at round 25 due to insufficient improvement in likelihood. EM: Starting log likelihood: -9780.209559 EM: Round [1] log likelihood: -9775.406485 EM: Round [2] log likelihood: -9773.187337 EM: Round [3] log likelihood: -9772.027541 EM: Round [4] log likelihood: -9771.391840 EM: Round [5] log likelihood: -9771.033428 EM: Round [6] log likelihood: -9770.826016 EM: Round [7] log likelihood: -9770.702713 EM: Round [8] log likelihood: -9770.627471 EM: Round [9] log likelihood: -9770.580468 EM: Round [10] log likelihood: -9770.550511 EM: Round [11] log likelihood: -9770.531100 EM: Round [12] log likelihood: -9770.518351 EM: Round [13] log likelihood: -9770.509886 EM: Round [14] log likelihood: -9770.504213 EM: Round [15] log likelihood: -9770.500382 EM: Round [16] log likelihood: -9770.497779 EM: Round [17] log likelihood: -9770.496000 EM: Round [18] log likelihood: -9770.494777 EM: Round [19] log likelihood: -9770.493934 EM: Round [20] log likelihood: -9770.493349 EM: Round [21] log likelihood: -9770.492942 EM: Round [22] log likelihood: -9770.492657 EM: Round [23] log likelihood: -9770.492458 EM: Round [24] log likelihood: -9770.492317 EM: Round [25] log likelihood: -9770.492218 EM: Stopping iterations at round 25 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 4362646 > /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir > /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir --annotate /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir -done, see /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.ApftGg0uOS/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 190, filtered: 1157) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.ApftGg0uOS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.ApftGg0uOS/./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.ApftGg0uOS/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000231252.3] WARNING, no entry stored in dbm for [ENSG00000275374.1] WARNING, no entry stored in dbm for [ENSG00000226472.8] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000100181.22] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000281896.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000228376.3] WARNING, no entry stored in dbm for [ENSG00000181984.11] WARNING, no entry stored in dbm for [ENSG00000286694.1] WARNING, no entry stored in dbm for [ENSG00000253925.1] WARNING, no entry stored in dbm for [ENSG00000278733.1] WARNING, no entry stored in dbm for [ENSG00000230556.1] WARNING, no entry stored in dbm for [ENSG00000285269.2] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000224049.1] WARNING, no entry stored in dbm for [ENSG00000233006.8] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000238042.5] WARNING, no entry stored in dbm for [ENSG00000238241.2] WARNING, no entry stored in dbm for [ENSG00000279232.2] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] 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 [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 [ENSG00000271218.1] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000181126.13] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000259768.6] WARNING, no entry stored in dbm for [ENSG00000235257.9] WARNING, no entry stored in dbm for [ENSG00000231231.5] WARNING, no entry stored in dbm for [ENSG00000257167.2] WARNING, no entry stored in dbm for [ENSG00000227195.11] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000249072.1] WARNING, no entry stored in dbm for [ENSG00000168405.17] WARNING, no entry stored in dbm for [ENSG00000260750.7] WARNING, no entry stored in dbm for [ENSG00000230558.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000215302.8] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000284675.1] WARNING, no entry stored in dbm for [ENSG00000254485.5] WARNING, no entry stored in dbm for [ENSG00000284649.1] WARNING, no entry stored in dbm for [ENSG00000280152.1] WARNING, no entry stored in dbm for [ENSG00000261240.1] WARNING, no entry stored in dbm for [ENSG00000270823.1] WARNING, no entry stored in dbm for [ENSG00000280054.1] * STAR-Fusion complete. See output: /tmp/nxf.ApftGg0uOS/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)