-ctat genome lib [/tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.a6P2jx5TIm/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary -sample contains 9022667 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir -J /tmp/nxf.a6P2jx5TIm/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction -O /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.a6P2jx5TIm/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction -building interval tree based on /tmp/nxf.a6P2jx5TIm/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=54545.45/min [30000], rate=64285.71/min [40000], rate=60000.00/min [50000], rate=58823.53/min [60000], rate=54545.45/min [70000], rate=53164.56/min [80000], rate=53932.58/min [90000], rate=52941.18/min [100000], rate=53571.43/min [110000], rate=52800.00/min [120000], rate=53333.33/min [130000], rate=53424.66/min [140000], rate=53503.18/min [150000], rate=46875.00/min [160000], rate=44239.63/min [170000], rate=43589.74/min [180000], rate=43200.00/min [190000], rate=42696.63/min [200000], rate=42105.26/min [210000], rate=42000.00/min [220000], rate=40615.38/min [230000], rate=40350.88/min [240000], rate=40223.46/min -building interval tree based on /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=37500.00/min [20000], rate=48000.00/min [30000], rate=46153.85/min [40000], rate=40000.00/min [50000], rate=36144.58/min [60000], rate=36363.64/min [70000], rate=37168.14/min [80000], rate=37500.00/min [90000], rate=37500.00/min [100000], rate=38461.54/min [110000], rate=38150.29/min [120000], rate=38095.24/min [130000], rate=38235.29/min [140000], rate=38356.16/min [150000], rate=38461.54/min [160000], rate=37795.28/min [170000], rate=37500.00/min [180000], rate=37370.24/min [190000], rate=36893.20/min [200000], rate=36923.08/min [210000], rate=37724.55/min [220000], rate=37288.14/min [230000], rate=37500.00/min [240000], rate=38196.29/min -building interval tree based on /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=70588.24/min [30000], rate=60000.00/min [40000], rate=61538.46/min [50000], rate=53571.43/min [60000], rate=55384.62/min [70000], rate=50602.41/min [80000], rate=45714.29/min [90000], rate=44262.30/min [100000], rate=45112.78/min [110000], rate=45205.48/min [120000], rate=42105.26/min [130000], rate=38235.29/min [140000], rate=36521.74/min [150000], rate=36290.32/min [160000], rate=37209.30/min [170000], rate=34576.27/min [180000], rate=33230.77/min [190000], rate=32664.76/min [200000], rate=31830.24/min [210000], rate=30215.83/min [220000], rate=30626.45/min [230000], rate=31011.24/min [240000], rate=31236.44/min -building interval tree based on /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=70588.24/min [30000], rate=72000.00/min [40000], rate=68571.43/min [50000], rate=71428.57/min [60000], rate=70588.24/min [70000], rate=72413.79/min [80000], rate=68571.43/min [90000], rate=65853.66/min [100000], rate=54545.45/min [110000], rate=42038.22/min [120000], rate=34782.61/min [130000], rate=32098.77/min [140000], rate=31111.11/min [150000], rate=31578.95/min [160000], rate=31270.36/min [170000], rate=31578.95/min [180000], rate=31671.55/min [190000], rate=30978.26/min [200000], rate=30000.00/min [210000], rate=29439.25/min [220000], rate=29729.73/min [230000], rate=29550.32/min [240000], rate=29090.91/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir --filt_file /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 0.00 reads per min processed... 6000000.00 reads per min processed... 3600000.00 reads per min processed... 4000000.00 reads per min processed... 4285714.29 reads per min processed... 4500000.00 reads per min processed... 4200000.00 reads per min processed... 4000000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.a6P2jx5TIm/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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.a6P2jx5TIm/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -13888.687828 EM: Round [1] log likelihood: -13847.920813 EM: Round [2] log likelihood: -13830.027583 EM: Round [3] log likelihood: -13820.846434 EM: Round [4] log likelihood: -13815.834995 EM: Round [5] log likelihood: -13813.000028 EM: Round [6] log likelihood: -13811.339629 EM: Round [7] log likelihood: -13810.327730 EM: Round [8] log likelihood: -13809.684293 EM: Round [9] log likelihood: -13809.257820 EM: Round [10] log likelihood: -13808.964199 EM: Round [11] log likelihood: -13808.755167 EM: Round [12] log likelihood: -13808.602031 EM: Round [13] log likelihood: -13808.487110 EM: Round [14] log likelihood: -13808.399125 EM: Round [15] log likelihood: -13808.330640 EM: Round [16] log likelihood: -13808.276599 EM: Round [17] log likelihood: -13808.233469 EM: Round [18] log likelihood: -13808.198716 EM: Round [19] log likelihood: -13808.170487 EM: Round [20] log likelihood: -13808.147398 EM: Round [21] log likelihood: -13808.128402 EM: Round [22] log likelihood: -13808.112693 EM: Round [23] log likelihood: -13808.099642 EM: Round [24] log likelihood: -13808.088757 EM: Round [25] log likelihood: -13808.079647 EM: Round [26] log likelihood: -13808.071997 EM: Round [27] log likelihood: -13808.065556 EM: Round [28] log likelihood: -13808.060118 EM: Round [29] log likelihood: -13808.055516 EM: Round [30] log likelihood: -13808.051614 EM: Round [31] log likelihood: -13808.048298 EM: Round [32] log likelihood: -13808.045474 EM: Round [33] log likelihood: -13808.043066 EM: Round [34] log likelihood: -13808.041009 EM: Round [35] log likelihood: -13808.039249 EM: Round [36] log likelihood: -13808.037740 EM: Round [37] log likelihood: -13808.036445 EM: Round [38] log likelihood: -13808.035331 EM: Round [39] log likelihood: -13808.034373 EM: Round [40] log likelihood: -13808.033547 EM: Round [41] log likelihood: -13808.032834 EM: Round [42] log likelihood: -13808.032217 EM: Round [43] log likelihood: -13808.031683 EM: Round [44] log likelihood: -13808.031221 EM: Round [45] log likelihood: -13808.030819 EM: Round [46] log likelihood: -13808.030470 EM: Round [47] log likelihood: -13808.030166 EM: Round [48] log likelihood: -13808.029901 EM: Round [49] log likelihood: -13808.029670 EM: Round [50] log likelihood: -13808.029468 EM: Round [51] log likelihood: -13808.029291 EM: Round [52] log likelihood: -13808.029136 EM: Round [53] log likelihood: -13808.029000 EM: Round [54] log likelihood: -13808.028880 EM: Round [55] log likelihood: -13808.028774 EM: Round [56] log likelihood: -13808.028681 EM: Stopping iterations at round 56 due to insufficient improvement in likelihood. EM: Starting log likelihood: -13879.529658 EM: Round [1] log likelihood: -13842.984914 EM: Round [2] log likelihood: -13827.261309 EM: Round [3] log likelihood: -13819.261221 EM: Round [4] log likelihood: -13814.902222 EM: Round [5] log likelihood: -13812.433585 EM: Round [6] log likelihood: -13810.983285 EM: Round [7] log likelihood: -13810.095432 EM: Round [8] log likelihood: -13809.527774 EM: Round [9] log likelihood: -13809.149211 EM: Round [10] log likelihood: -13808.886854 EM: Round [11] log likelihood: -13808.698815 EM: Round [12] log likelihood: -13808.560140 EM: Round [13] log likelihood: -13808.455413 EM: Round [14] log likelihood: -13808.374764 EM: Round [15] log likelihood: -13808.311654 EM: Round [16] log likelihood: -13808.261614 EM: Round [17] log likelihood: -13808.221503 EM: Round [18] log likelihood: -13808.189057 EM: Round [19] log likelihood: -13808.162611 EM: Round [20] log likelihood: -13808.140914 EM: Round [21] log likelihood: -13808.123014 EM: Round [22] log likelihood: -13808.108177 EM: Round [23] log likelihood: -13808.095826 EM: Round [24] log likelihood: -13808.085508 EM: Round [25] log likelihood: -13808.076860 EM: Round [26] log likelihood: -13808.069592 EM: Round [27] log likelihood: -13808.063467 EM: Round [28] log likelihood: -13808.058294 EM: Round [29] log likelihood: -13808.053915 EM: Round [30] log likelihood: -13808.050202 EM: Round [31] log likelihood: -13808.047048 EM: Round [32] log likelihood: -13808.044364 EM: Round [33] log likelihood: -13808.042077 EM: Round [34] log likelihood: -13808.040125 EM: Round [35] log likelihood: -13808.038457 EM: Round [36] log likelihood: -13808.037029 EM: Round [37] log likelihood: -13808.035806 EM: Round [38] log likelihood: -13808.034756 EM: Round [39] log likelihood: -13808.033854 EM: Round [40] log likelihood: -13808.033079 EM: Round [41] log likelihood: -13808.032411 EM: Round [42] log likelihood: -13808.031835 EM: Round [43] log likelihood: -13808.031338 EM: Round [44] log likelihood: -13808.030908 EM: Round [45] log likelihood: -13808.030536 EM: Round [46] log likelihood: -13808.030213 EM: Round [47] log likelihood: -13808.029934 EM: Round [48] log likelihood: -13808.029691 EM: Round [49] log likelihood: -13808.029479 EM: Round [50] log likelihood: -13808.029295 EM: Round [51] log likelihood: -13808.029134 EM: Round [52] log likelihood: -13808.028994 EM: Round [53] log likelihood: -13808.028871 EM: Round [54] log likelihood: -13808.028764 EM: Round [55] log likelihood: -13808.028669 EM: Stopping iterations at round 55 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9022667 > /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir > /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir --annotate /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir -done, see /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.a6P2jx5TIm/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 82, filtered: 1386) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.a6P2jx5TIm/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.a6P2jx5TIm/./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.a6P2jx5TIm/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv 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 [ENSG00000260231.2] 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 [ENSG00000229807.12] WARNING, no entry stored in dbm for [ENSG00000259021.2] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000274727.1] WARNING, no entry stored in dbm for [ENSG00000266088.6] WARNING, no entry stored in dbm for [ENSG00000241081.1] WARNING, no entry stored in dbm for [ENSG00000225483.1] WARNING, no entry stored in dbm for [ENSG00000203993.6] WARNING, no entry stored in dbm for [ENSG00000181577.16] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000231437.3] WARNING, no entry stored in dbm for [ENSG00000239921.6] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000239921.6] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000237296.9] 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 [ENSG00000281383.1] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000280800.1] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000281181.1] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000280614.1] 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 [ENSG00000214548.18] WARNING, no entry stored in dbm for [ENSG00000279141.3] WARNING, no entry stored in dbm for [ENSG00000236333.4] WARNING, no entry stored in dbm for [ENSG00000234975.6] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000259098.1] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000259098.1] WARNING, no entry stored in dbm for [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000279694.1] WARNING, no entry stored in dbm for [ENSG00000286335.1] WARNING, no entry stored in dbm for [ENSG00000243224.1] * STAR-Fusion complete. See output: /tmp/nxf.a6P2jx5TIm/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)