-ctat genome lib [/tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.7fFu7tgbmw/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary -sample contains 14304435 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir -J /tmp/nxf.7fFu7tgbmw/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_3.Chimeric.out.junction -O /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.7fFu7tgbmw/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_3.Chimeric.out.junction -building interval tree based on /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=54545.45/min [30000], rate=52941.18/min [40000], rate=53333.33/min [50000], rate=55555.56/min [60000], rate=53731.34/min [70000], rate=52500.00/min [80000], rate=54545.45/min [90000], rate=55102.04/min [100000], rate=54054.05/min [110000], rate=54098.36/min [120000], rate=55384.62/min [130000], rate=57352.94/min [140000], rate=57931.03/min [150000], rate=59210.53/min [160000], rate=60000.00/min [170000], rate=60000.00/min [180000], rate=61016.95/min [190000], rate=60317.46/min [200000], rate=60913.71/min -building interval tree based on /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=40000.00/min [20000], rate=46153.85/min [30000], rate=51428.57/min [40000], rate=55813.95/min [50000], rate=55555.56/min [60000], rate=58064.52/min [70000], rate=62686.57/min [80000], rate=67605.63/min [90000], rate=65060.24/min [100000], rate=65934.07/min [110000], rate=62857.14/min [120000], rate=61016.95/min [130000], rate=60937.50/min [140000], rate=60869.57/min [150000], rate=61643.84/min [160000], rate=61935.48/min [170000], rate=60355.03/min [180000], rate=59340.66/min [190000], rate=59375.00/min [200000], rate=60301.51/min -building interval tree based on /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=37500.00/min [20000], rate=40000.00/min [30000], rate=45000.00/min [40000], rate=47058.82/min [50000], rate=43478.26/min [60000], rate=41379.31/min [70000], rate=40776.70/min [80000], rate=42105.26/min [90000], rate=43902.44/min [100000], rate=46153.85/min [110000], rate=48175.18/min [120000], rate=50349.65/min [130000], rate=52348.99/min [140000], rate=53846.15/min [150000], rate=54878.05/min [160000], rate=53932.58/min [170000], rate=52307.69/min [180000], rate=52427.18/min [190000], rate=53271.03/min [200000], rate=53333.33/min -building interval tree based on /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=120000.00/min [20000], rate=100000.00/min [30000], rate=46153.85/min [40000], rate=40677.97/min [50000], rate=39473.68/min [60000], rate=39560.44/min [70000], rate=40000.00/min [80000], rate=41025.64/min [90000], rate=42857.14/min [100000], rate=44776.12/min [110000], rate=46153.85/min [120000], rate=47368.42/min [130000], rate=49367.09/min [140000], rate=48554.91/min [150000], rate=47120.42/min [160000], rate=46601.94/min [170000], rate=46363.64/min [180000], rate=46351.93/min [190000], rate=46530.61/min [200000], rate=46875.00/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir --filt_file /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 3000000.00 reads per min processed... 2400000.00 reads per min processed... 2250000.00 reads per min processed... 2400000.00 reads per min processed... 2500000.00 reads per min processed... 2571428.57 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.7fFu7tgbmw/BVT_FFPE_TRNA_utn_01_A23WKFTLT4_3.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.7fFu7tgbmw/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -15095.165852 EM: Round [1] log likelihood: -15085.949395 EM: Round [2] log likelihood: -15081.588263 EM: Round [3] log likelihood: -15079.198125 EM: Round [4] log likelihood: -15077.846422 EM: Round [5] log likelihood: -15077.075442 EM: Round [6] log likelihood: -15076.626803 EM: Round [7] log likelihood: -15076.356110 EM: Round [8] log likelihood: -15076.184985 EM: Round [9] log likelihood: -15076.071238 EM: Round [10] log likelihood: -15075.991872 EM: Round [11] log likelihood: -15075.934014 EM: Round [12] log likelihood: -15075.890206 EM: Round [13] log likelihood: -15075.855967 EM: Round [14] log likelihood: -15075.828501 EM: Round [15] log likelihood: -15075.805999 EM: Round [16] log likelihood: -15075.787248 EM: Round [17] log likelihood: -15075.771411 EM: Round [18] log likelihood: -15075.757889 EM: Round [19] log likelihood: -15075.746245 EM: Round [20] log likelihood: -15075.736148 EM: Round [21] log likelihood: -15075.727346 EM: Round [22] log likelihood: -15075.719639 EM: Round [23] log likelihood: -15075.712868 EM: Round [24] log likelihood: -15075.706903 EM: Round [25] log likelihood: -15075.701636 EM: Round [26] log likelihood: -15075.696977 EM: Round [27] log likelihood: -15075.692850 EM: Round [28] log likelihood: -15075.689190 EM: Round [29] log likelihood: -15075.685942 EM: Round [30] log likelihood: -15075.683056 EM: Round [31] log likelihood: -15075.680491 EM: Round [32] log likelihood: -15075.678210 EM: Round [33] log likelihood: -15075.676180 EM: Round [34] log likelihood: -15075.674373 EM: Round [35] log likelihood: -15075.672763 EM: Round [36] log likelihood: -15075.671330 EM: Round [37] log likelihood: -15075.670052 EM: Round [38] log likelihood: -15075.668914 EM: Round [39] log likelihood: -15075.667899 EM: Round [40] log likelihood: -15075.666993 EM: Round [41] log likelihood: -15075.666186 EM: Round [42] log likelihood: -15075.665465 EM: Round [43] log likelihood: -15075.664822 EM: Round [44] log likelihood: -15075.664248 EM: Round [45] log likelihood: -15075.663735 EM: Round [46] log likelihood: -15075.663277 EM: Round [47] log likelihood: -15075.662868 EM: Round [48] log likelihood: -15075.662502 EM: Round [49] log likelihood: -15075.662175 EM: Round [50] log likelihood: -15075.661883 EM: Round [51] log likelihood: -15075.661622 EM: Round [52] log likelihood: -15075.661388 EM: Round [53] log likelihood: -15075.661178 EM: Round [54] log likelihood: -15075.660991 EM: Round [55] log likelihood: -15075.660823 EM: Round [56] log likelihood: -15075.660673 EM: Round [57] log likelihood: -15075.660539 EM: Round [58] log likelihood: -15075.660418 EM: Round [59] log likelihood: -15075.660310 EM: Round [60] log likelihood: -15075.660213 EM: Stopping iterations at round 60 due to insufficient improvement in likelihood. EM: Starting log likelihood: -15091.459083 EM: Round [1] log likelihood: -15083.592997 EM: Round [2] log likelihood: -15080.063050 EM: Round [3] log likelihood: -15078.246122 EM: Round [4] log likelihood: -15077.265033 EM: Round [5] log likelihood: -15076.720830 EM: Round [6] log likelihood: -15076.407558 EM: Round [7] log likelihood: -15076.217459 EM: Round [8] log likelihood: -15076.094805 EM: Round [9] log likelihood: -15076.010701 EM: Round [10] log likelihood: -15075.949826 EM: Round [11] log likelihood: -15075.903746 EM: Round [12] log likelihood: -15075.867607 EM: Round [13] log likelihood: -15075.838475 EM: Round [14] log likelihood: -15075.814490 EM: Round [15] log likelihood: -15075.794422 EM: Round [16] log likelihood: -15075.777422 EM: Round [17] log likelihood: -15075.762882 EM: Round [18] log likelihood: -15075.750353 EM: Round [19] log likelihood: -15075.739494 EM: Round [20] log likelihood: -15075.730039 EM: Round [21] log likelihood: -15075.721778 EM: Round [22] log likelihood: -15075.714537 EM: Round [23] log likelihood: -15075.708178 EM: Round [24] log likelihood: -15075.702582 EM: Round [25] log likelihood: -15075.697651 EM: Round [26] log likelihood: -15075.693300 EM: Round [27] log likelihood: -15075.689458 EM: Round [28] log likelihood: -15075.686061 EM: Round [29] log likelihood: -15075.683057 EM: Round [30] log likelihood: -15075.680399 EM: Round [31] log likelihood: -15075.678045 EM: Round [32] log likelihood: -15075.675959 EM: Round [33] log likelihood: -15075.674111 EM: Round [34] log likelihood: -15075.672473 EM: Round [35] log likelihood: -15075.671020 EM: Round [36] log likelihood: -15075.669731 EM: Round [37] log likelihood: -15075.668587 EM: Round [38] log likelihood: -15075.667572 EM: Round [39] log likelihood: -15075.666670 EM: Round [40] log likelihood: -15075.665870 EM: Round [41] log likelihood: -15075.665158 EM: Round [42] log likelihood: -15075.664526 EM: Round [43] log likelihood: -15075.663964 EM: Round [44] log likelihood: -15075.663465 EM: Round [45] log likelihood: -15075.663020 EM: Round [46] log likelihood: -15075.662625 EM: Round [47] log likelihood: -15075.662273 EM: Round [48] log likelihood: -15075.661960 EM: Round [49] log likelihood: -15075.661681 EM: Round [50] log likelihood: -15075.661432 EM: Round [51] log likelihood: -15075.661211 EM: Round [52] log likelihood: -15075.661014 EM: Round [53] log likelihood: -15075.660838 EM: Round [54] log likelihood: -15075.660681 EM: Round [55] log likelihood: -15075.660541 EM: Round [56] log likelihood: -15075.660416 EM: Round [57] log likelihood: -15075.660305 EM: Round [58] log likelihood: -15075.660205 EM: Stopping iterations at round 58 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 14304435 > /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir > /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir --annotate /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir -done, see /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.7fFu7tgbmw/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 193, filtered: 1896) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.7fFu7tgbmw/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.7fFu7tgbmw/./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.7fFu7tgbmw/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 [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 [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 [ENSG00000285410.1] WARNING, no entry stored in dbm for [ENSG00000216824.2] WARNING, no entry stored in dbm for [ENSG00000257495.5] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000248994.2] WARNING, no entry stored in dbm for [ENSG00000250307.2] WARNING, no entry stored in dbm for [ENSG00000256817.1] WARNING, no entry stored in dbm for [ENSG00000234782.3] WARNING, no entry stored in dbm for [ENSG00000224533.4] WARNING, no entry stored in dbm for [ENSG00000215296.10] WARNING, no entry stored in dbm for [ENSG00000240549.2] WARNING, no entry stored in dbm for [ENSG00000287338.1] WARNING, no entry stored in dbm for [ENSG00000128438.10] WARNING, no entry stored in dbm for [ENSG00000248660.1] WARNING, no entry stored in dbm for [ENSG00000206983.1] WARNING, no entry stored in dbm for [ENSG00000242986.2] WARNING, no entry stored in dbm for [ENSG00000230559.1] WARNING, no entry stored in dbm for [ENSG00000286847.1] WARNING, no entry stored in dbm for [ENSG00000257634.1] WARNING, no entry stored in dbm for [ENSG00000270793.1] WARNING, no entry stored in dbm for [ENSG00000253642.6] WARNING, no entry stored in dbm for [ENSG00000260278.1] WARNING, no entry stored in dbm for [ENSG00000223704.2] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000233237.8] WARNING, no entry stored in dbm for [ENSG00000245067.7] WARNING, no entry stored in dbm for [ENSG00000279620.1] WARNING, no entry stored in dbm for [ENSG00000225465.10] WARNING, no entry stored in dbm for [ENSG00000185684.15] WARNING, no entry stored in dbm for [ENSG00000251562.8] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000225539.7] WARNING, no entry stored in dbm for [ENSG00000232000.3] WARNING, no entry stored in dbm for [ENSG00000230773.9] WARNING, no entry stored in dbm for [ENSG00000223966.1] WARNING, no entry stored in dbm for [ENSG00000230805.8] WARNING, no entry stored in dbm for [ENSG00000226645.1] WARNING, no entry stored in dbm for [ENSG00000265179.7] WARNING, no entry stored in dbm for [ENSG00000254924.2] WARNING, no entry stored in dbm for [ENSG00000285799.1] WARNING, no entry stored in dbm for [ENSG00000254741.1] WARNING, no entry stored in dbm for [ENSG00000230869.1] WARNING, no entry stored in dbm for [ENSG00000272140.2] WARNING, no entry stored in dbm for [ENSG00000242586.1] WARNING, no entry stored in dbm for [ENSG00000227733.10] WARNING, no entry stored in dbm for [ENSG00000205976.4] WARNING, no entry stored in dbm for [ENSG00000258320.1] WARNING, no entry stored in dbm for [ENSG00000264151.6] WARNING, no entry stored in dbm for [ENSG00000287232.1] WARNING, no entry stored in dbm for [ENSG00000285329.1] WARNING, no entry stored in dbm for [ENSG00000177359.20] WARNING, no entry stored in dbm for [ENSG00000272140.2] WARNING, no entry stored in dbm for [ENSG00000275734.2] WARNING, no entry stored in dbm for [ENSG00000262420.3] WARNING, no entry stored in dbm for [ENSG00000228113.7] * STAR-Fusion complete. See output: /tmp/nxf.7fFu7tgbmw/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)