-ctat genome lib [/tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.9F9wSOHPJX/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary -sample contains 7383040 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir -J /tmp/nxf.9F9wSOHPJX/dna_s739.Chimeric.out.junction -O /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.9F9wSOHPJX/dna_s739.Chimeric.out.junction -building interval tree based on /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=50000.00/min [20000], rate=52173.91/min [30000], rate=58064.52/min [40000], rate=54545.45/min [50000], rate=50847.46/min [60000], rate=49315.07/min [70000], rate=48275.86/min [80000], rate=46153.85/min [90000], rate=45000.00/min [100000], rate=45112.78/min [110000], rate=45833.33/min [120000], rate=45283.02/min [130000], rate=45086.71/min [140000], rate=44680.85/min [150000], rate=43478.26/min [160000], rate=43049.33/min [170000], rate=43220.34/min [180000], rate=43724.70/min -building interval tree based on /tmp/nxf.9F9wSOHPJX/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=63157.89/min [30000], rate=62068.97/min [40000], rate=70588.24/min [50000], rate=69767.44/min [60000], rate=59016.39/min [70000], rate=48837.21/min [80000], rate=44859.81/min [90000], rate=44628.10/min [100000], rate=45112.78/min [110000], rate=42857.14/min [120000], rate=41860.47/min [130000], rate=41489.36/min [140000], rate=42211.06/min [150000], rate=39823.01/min [160000], rate=38709.68/min [170000], rate=38636.36/min [180000], rate=38434.16/min -building interval tree based on /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=54545.45/min [20000], rate=46153.85/min [30000], rate=43902.44/min [40000], rate=45283.02/min [50000], rate=44776.12/min [60000], rate=42857.14/min [70000], rate=42424.24/min [80000], rate=40000.00/min [90000], rate=39416.06/min [100000], rate=40268.46/min [110000], rate=41250.00/min [120000], rate=38918.92/min [130000], rate=38048.78/min [140000], rate=35443.04/min [150000], rate=32374.10/min [160000], rate=31578.95/min [170000], rate=31677.02/min [180000], rate=31858.41/min -building interval tree based on /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=120000.00/min [20000], rate=23529.41/min [30000], rate=22784.81/min [40000], rate=22222.22/min [50000], rate=23622.05/min [60000], rate=25352.11/min [70000], rate=27272.73/min [80000], rate=27906.98/min [90000], rate=28421.05/min [100000], rate=29556.65/min [110000], rate=28205.13/min [120000], rate=28015.56/min [130000], rate=28782.29/min [140000], rate=28865.98/min [150000], rate=28571.43/min [160000], rate=29003.02/min [170000], rate=29737.61/min [180000], rate=30422.54/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir --filt_file /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 2000000.00 reads per min processed... 2400000.00 reads per min processed... 2571428.57 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.9F9wSOHPJX/dna_s739.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.9F9wSOHPJX/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -19923.093750 EM: Round [1] log likelihood: -19918.497089 EM: Round [2] log likelihood: -19916.693581 EM: Round [3] log likelihood: -19915.823110 EM: Round [4] log likelihood: -19915.366059 EM: Round [5] log likelihood: -19915.120841 EM: Round [6] log likelihood: -19914.988729 EM: Round [7] log likelihood: -19914.917125 EM: Round [8] log likelihood: -19914.877859 EM: Round [9] log likelihood: -19914.855969 EM: Round [10] log likelihood: -19914.843530 EM: Round [11] log likelihood: -19914.836314 EM: Round [12] log likelihood: -19914.832041 EM: Round [13] log likelihood: -19914.829460 EM: Round [14] log likelihood: -19914.827874 EM: Round [15] log likelihood: -19914.826884 EM: Round [16] log likelihood: -19914.826257 EM: Round [17] log likelihood: -19914.825856 EM: Round [18] log likelihood: -19914.825596 EM: Round [19] log likelihood: -19914.825428 EM: Round [20] log likelihood: -19914.825318 EM: Round [21] log likelihood: -19914.825245 EM: Stopping iterations at round 21 due to insufficient improvement in likelihood. EM: Starting log likelihood: -19922.336064 EM: Round [1] log likelihood: -19917.837620 EM: Round [2] log likelihood: -19916.219848 EM: Round [3] log likelihood: -19915.525456 EM: Round [4] log likelihood: -19915.195939 EM: Round [5] log likelihood: -19915.029294 EM: Round [6] log likelihood: -19914.941148 EM: Round [7] log likelihood: -19914.892857 EM: Round [8] log likelihood: -19914.865601 EM: Round [9] log likelihood: -19914.849810 EM: Round [10] log likelihood: -19914.840442 EM: Round [11] log likelihood: -19914.834768 EM: Round [12] log likelihood: -19914.831267 EM: Round [13] log likelihood: -19914.829074 EM: Round [14] log likelihood: -19914.827681 EM: Round [15] log likelihood: -19914.826787 EM: Round [16] log likelihood: -19914.826208 EM: Round [17] log likelihood: -19914.825831 EM: Round [18] log likelihood: -19914.825584 EM: Round [19] log likelihood: -19914.825422 EM: Round [20] log likelihood: -19914.825315 EM: Round [21] log likelihood: -19914.825244 EM: Stopping iterations at round 21 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 7383040 > /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir > /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir --annotate /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir -done, see /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.9F9wSOHPJX/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 204, filtered: 2570) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.9F9wSOHPJX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.9F9wSOHPJX/./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.9F9wSOHPJX/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000276088.1] WARNING, no entry stored in dbm for [ENSG00000282458.1] WARNING, no entry stored in dbm for [ENSG00000245248.8] WARNING, no entry stored in dbm for [ENSG00000265345.1] WARNING, no entry stored in dbm for [ENSG00000175061.18] WARNING, no entry stored in dbm for [ENSG00000233907.1] WARNING, no entry stored in dbm for [ENSG00000233907.1] WARNING, no entry stored in dbm for [ENSG00000233907.1] WARNING, no entry stored in dbm for [ENSG00000233907.1] WARNING, no entry stored in dbm for [ENSG00000205822.10] WARNING, no entry stored in dbm for [ENSG00000287837.1] WARNING, no entry stored in dbm for [ENSG00000234405.2] WARNING, no entry stored in dbm for [ENSG00000279652.1] WARNING, no entry stored in dbm for [ENSG00000135502.19] WARNING, no entry stored in dbm for [ENSG00000260402.1] WARNING, no entry stored in dbm for [ENSG00000260179.1] WARNING, no entry stored in dbm for [ENSG00000278935.1] WARNING, no entry stored in dbm for [ENSG00000167798.17] WARNING, no entry stored in dbm for [ENSG00000251474.6] WARNING, no entry stored in dbm for [ENSG00000260808.1] WARNING, no entry stored in dbm for [ENSG00000243199.1] WARNING, no entry stored in dbm for [ENSG00000267270.6] WARNING, no entry stored in dbm for [ENSG00000224714.3] WARNING, no entry stored in dbm for [ENSG00000126952.18] WARNING, no entry stored in dbm for [ENSG00000235997.3] WARNING, no entry stored in dbm for [ENSG00000235997.3] WARNING, no entry stored in dbm for [ENSG00000235997.3] WARNING, no entry stored in dbm for [ENSG00000266978.1] WARNING, no entry stored in dbm for [ENSG00000186301.8] WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [ENSG00000260144.1] WARNING, no entry stored in dbm for [ENSG00000227195.11] WARNING, no entry stored in dbm for [ENSG00000255248.9] WARNING, no entry stored in dbm for [ENSG00000234948.2] WARNING, no entry stored in dbm for [ENSG00000229950.1] WARNING, no entry stored in dbm for [ENSG00000275711.1] WARNING, no entry stored in dbm for [ENSG00000235137.2] WARNING, no entry stored in dbm for [ENSG00000260689.2] WARNING, no entry stored in dbm for [ENSG00000198786.2] WARNING, no entry stored in dbm for [ENSG00000232385.2] WARNING, no entry stored in dbm for [ENSG00000231527.7] WARNING, no entry stored in dbm for [ENSG00000248844.6] WARNING, no entry stored in dbm for [ENSG00000214821.4] WARNING, no entry stored in dbm for [ENSG00000257185.2] WARNING, no entry stored in dbm for [ENSG00000229385.2] WARNING, no entry stored in dbm for [ENSG00000255920.3] WARNING, no entry stored in dbm for [ENSG00000286698.1] WARNING, no entry stored in dbm for [ENSG00000243302.3] WARNING, no entry stored in dbm for [ENSG00000199241.1] WARNING, no entry stored in dbm for [ENSG00000242561.1] WARNING, no entry stored in dbm for [ENSG00000282917.2] WARNING, no entry stored in dbm for [ENSG00000234261.4] WARNING, no entry stored in dbm for [ENSG00000287892.1] WARNING, no entry stored in dbm for [ENSG00000230676.1] WARNING, no entry stored in dbm for [ENSG00000204790.9] WARNING, no entry stored in dbm for [ENSG00000176320.2] WARNING, no entry stored in dbm for [ENSG00000287914.1] WARNING, no entry stored in dbm for [ENSG00000279110.1] WARNING, no entry stored in dbm for [ENSG00000260427.1] WARNING, no entry stored in dbm for [ENSG00000281344.1] WARNING, no entry stored in dbm for [ENSG00000257563.1] WARNING, no entry stored in dbm for [ENSG00000279528.1] WARNING, no entry stored in dbm for [ENSG00000250284.3] WARNING, no entry stored in dbm for [ENSG00000145063.15] WARNING, no entry stored in dbm for [ENSG00000287677.2] WARNING, no entry stored in dbm for [ENSG00000240919.1] WARNING, no entry stored in dbm for [ENSG00000272702.1] WARNING, no entry stored in dbm for [ENSG00000279404.1] WARNING, no entry stored in dbm for [ENSG00000279249.3] WARNING, no entry stored in dbm for [ENSG00000242593.7] * STAR-Fusion complete. See output: /tmp/nxf.9F9wSOHPJX/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)