Done. -parsing GTF file: /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.gtf * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.FeA4L09rE1/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.FeA4L09rE1/fi_workdir/tih_rna_sample_00087_B23WHTKLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.FeA4L09rE1/fi_workdir/tih_rna_sample_00087_B23WHTKLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' * Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00087_B23WHTKLT4_2.star.sortedByCoord.out.bam * Running CMD: samtools index tih_rna_sample_00087_B23WHTKLT4_2.star.sortedByCoord.out.bam 11:36:01 : INFO : Done. -parsing GTF file: /tmp/nxf.FeA4L09rE1/fi_workdir/tih_rna_sample_00087_B23WHTKLT4_2.gtf -parsing /tmp/nxf.FeA4L09rE1/fi_workdir/tih_rna_sample_00087_B23WHTKLT4_2.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [770000] [780000] [790000] [800000] [810000] [820000] [830000] [840000] [850000] [860000] [870000] [880000] [890000] [900000] [910000] [920000] [930000] -done parsing /tmp/nxf.FeA4L09rE1/fi_workdir/tih_rna_sample_00087_B23WHTKLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { ' ** passed ** ' => 26021, 'excessive soft clipping' => 6695, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 85, 'per_id < 96' => 4555, 'seq-similar region overlap' => 12, 'small anchor length' => 152, 'exons hit < 2' => 4, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 36, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 20, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 80, 'low complexity anchor region' => 31, 'num genes matched < 2' => 15 }; -writing fusion junction support info. -outputting the spanning read info: /tmp/nxf.FeA4L09rE1/fi_workdir/tih_rna_sample_00087_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. -fusion SPANNING read extraction for scaff: AC004923.1--AC127526.2 [1000] -fusion SPANNING read extraction for scaff: AC026341.1--GAP43 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: AC079781.4--ASNS [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: AC090572.2--CNBD1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: AP006294.2--ENPP7P3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] -fusion SPANNING read extraction for scaff: B4GALT4--IGSF11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: C1QTNF7-AS1--LINC00504 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: GTF2A1L--STON1-GTF2A1L [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] -fusion SPANNING read extraction for scaff: THRAP3P2--SLCO3A1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] -fusion SPANNING read extraction for scaff: UPK1B--IGSF11 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 7356, 'seq similar region alignment' => 13347 }; EM: Starting log likelihood: -10288.397010 EM: Round [1] log likelihood: -10285.494918 EM: Round [2] log likelihood: -10285.471954 EM: Round [3] log likelihood: -10285.471223 EM: Round [4] log likelihood: -10285.471002 EM: Round [5] log likelihood: -10285.470792 EM: Round [6] log likelihood: -10285.470583 EM: Round [7] log likelihood: -10285.470373 EM: Round [8] log likelihood: -10285.470165 EM: Round [9] log likelihood: -10285.469956 EM: Round [10] log likelihood: -10285.469747 EM: Round [11] log likelihood: -10285.469539 EM: Round [12] log likelihood: -10285.469331 EM: Round [13] log likelihood: -10285.469123 EM: Round [14] log likelihood: -10285.468916 EM: Round [15] log likelihood: -10285.468708 EM: Round [16] log likelihood: -10285.468501 EM: Round [17] log likelihood: -10285.468294 EM: Round [18] log likelihood: -10285.468088 EM: Round [19] log likelihood: -10285.467881 EM: Round [20] log likelihood: -10285.467675 EM: Round [21] log likelihood: -10285.467469 EM: Round [22] log likelihood: -10285.467263 EM: Round [23] log likelihood: -10285.467057 EM: Round [24] log likelihood: -10285.466852 EM: Round [25] log likelihood: -10285.466647 EM: Round [26] log likelihood: -10285.466442 EM: Round [27] log likelihood: -10285.466237 EM: Round [28] log likelihood: -10285.466032 EM: Round [29] log likelihood: -10285.465828 EM: Round [30] log likelihood: -10285.465624 EM: Round [31] log likelihood: -10285.465420 EM: Round [32] log likelihood: -10285.465216 EM: Round [33] log likelihood: -10285.465013 EM: Round [34] log likelihood: -10285.464809 EM: Round [35] log likelihood: -10285.464606 EM: Round [36] log likelihood: -10285.464404 EM: Round [37] log likelihood: -10285.464201 EM: Round [38] log likelihood: -10285.463998 EM: Round [39] log likelihood: -10285.463796 EM: Round [40] log likelihood: -10285.463594 EM: Round [41] log likelihood: -10285.463392 EM: Round [42] log likelihood: -10285.463191 EM: Round [43] log likelihood: -10285.462989 EM: Round [44] log likelihood: -10285.462788 EM: Round [45] log likelihood: -10285.462587 EM: Round [46] log likelihood: -10285.462387 EM: Round [47] log likelihood: -10285.462186 EM: Round [48] log likelihood: -10285.461986 EM: Round [49] log likelihood: -10285.461786 EM: Round [50] log likelihood: -10285.461586 EM: Round [51] log likelihood: -10285.461386 EM: Round [52] log likelihood: -10285.461187 EM: Round [53] log likelihood: -10285.460987 EM: Round [54] log likelihood: -10285.460788 EM: Round [55] log likelihood: -10285.460589 EM: Round [56] log likelihood: -10285.460391 EM: Round [57] log likelihood: -10285.460192 EM: Round [58] log likelihood: -10285.459994 EM: Round [59] log likelihood: -10285.459796 EM: Round [60] log likelihood: -10285.459598 EM: Round [61] log likelihood: -10285.459400 EM: Round [62] log likelihood: -10285.459203 EM: Round [63] log likelihood: -10285.459006 EM: Round [64] log likelihood: -10285.458809 EM: Round [65] log likelihood: -10285.458612 EM: Round [66] log likelihood: -10285.458415 EM: Round [67] log likelihood: -10285.458219 EM: Round [68] log likelihood: -10285.458023 EM: Round [69] log likelihood: -10285.457827 EM: Round [70] log likelihood: -10285.457631 EM: Round [71] log likelihood: -10285.457435 EM: Round [72] log likelihood: -10285.457240 EM: Round [73] log likelihood: -10285.457045 EM: Round [74] log likelihood: -10285.456850 EM: Round [75] log likelihood: -10285.456655 EM: Round [76] log likelihood: -10285.456460 EM: Round [77] log likelihood: -10285.456266 EM: Round [78] log likelihood: -10285.456072 EM: Round [79] log likelihood: -10285.455878 EM: Round [80] log likelihood: -10285.455684 EM: Round [81] log likelihood: -10285.455491 EM: Round [82] log likelihood: -10285.455297 EM: Round [83] log likelihood: -10285.455104 EM: Round [84] log likelihood: -10285.454911 EM: Round [85] log likelihood: -10285.454718 EM: Round [86] log likelihood: -10285.454526 EM: Round [87] log likelihood: -10285.454333 EM: Round [88] log likelihood: -10285.454141 EM: Round [89] log likelihood: -10285.453949 EM: Round [90] log likelihood: -10285.453757 EM: Round [91] log likelihood: -10285.453566 EM: Round [92] log likelihood: -10285.453374 EM: Round [93] log likelihood: -10285.453183 EM: Round [94] log likelihood: -10285.452992 EM: Round [95] log likelihood: -10285.452801 EM: Round [96] log likelihood: -10285.452611 EM: Round [97] log likelihood: -10285.452421 EM: Round [98] log likelihood: -10285.452230 EM: Round [99] log likelihood: -10285.452040 EM: Round [100] log likelihood: -10285.451851 EM: Round [101] log likelihood: -10285.451661 EM: Round [102] log likelihood: -10285.451471 EM: Round [103] log likelihood: -10285.451282 EM: Round [104] log likelihood: -10285.451093 EM: Round [105] log likelihood: -10285.450904 EM: Round [106] log likelihood: -10285.450716 EM: Round [107] log likelihood: -10285.450527 EM: Round [108] log likelihood: -10285.450339 EM: Round [109] log likelihood: -10285.450151 EM: Round [110] log likelihood: -10285.449963 EM: Round [111] log likelihood: -10285.449776 EM: Round [112] log likelihood: -10285.449588 EM: Round [113] log likelihood: -10285.449401 EM: Round [114] log likelihood: -10285.449214 EM: Round [115] log likelihood: -10285.449027 EM: Round [116] log likelihood: -10285.448840 EM: Round [117] log likelihood: -10285.448654 EM: Round [118] log likelihood: -10285.448467 EM: Round [119] log likelihood: -10285.448281 EM: Round [120] log likelihood: -10285.448095 EM: Round [121] log likelihood: -10285.447910 EM: Round [122] log likelihood: -10285.447724 EM: Round [123] log likelihood: -10285.447539 EM: Round [124] log likelihood: -10285.447353 EM: Round [125] log likelihood: -10285.447168 EM: Round [126] log likelihood: -10285.446984 EM: Round [127] log likelihood: -10285.446799 EM: Round [128] log likelihood: -10285.446615 EM: Round [129] log likelihood: -10285.446430 EM: Round [130] log likelihood: -10285.446246 EM: Round [131] log likelihood: -10285.446063 EM: Round [132] log likelihood: -10285.445879 EM: Round [133] log likelihood: -10285.445695 EM: Round [134] log likelihood: -10285.445512 EM: Round [135] log likelihood: -10285.445329 EM: Round [136] log likelihood: -10285.445146 EM: Round [137] log likelihood: -10285.444963 EM: Round [138] log likelihood: -10285.444781 EM: Round [139] log likelihood: -10285.444599 EM: Round [140] log likelihood: -10285.444416 EM: Round [141] log likelihood: -10285.444235 EM: Round [142] log likelihood: -10285.444053 EM: Round [143] log likelihood: -10285.443871 EM: Round [144] log likelihood: -10285.443690 EM: Round [145] log likelihood: -10285.443509 EM: Round [146] log likelihood: -10285.443327 EM: Round [147] log likelihood: 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Round [581] log likelihood: -10285.379513 EM: Round [582] log likelihood: -10285.379396 EM: Round [583] log likelihood: -10285.379278 EM: Round [584] log likelihood: -10285.379161 EM: Round [585] log likelihood: -10285.379044 EM: Round [586] log likelihood: -10285.378926 EM: Round [587] log likelihood: -10285.378809 EM: Round [588] log likelihood: -10285.378693 EM: Round [589] log likelihood: -10285.378576 EM: Round [590] log likelihood: -10285.378459 EM: Round [591] log likelihood: -10285.378342 EM: Round [592] log likelihood: -10285.378226 EM: Round [593] log likelihood: -10285.378110 EM: Round [594] log likelihood: -10285.377993 EM: Round [595] log likelihood: -10285.377877 EM: Round [596] log likelihood: -10285.377761 EM: Round [597] log likelihood: -10285.377645 EM: Round [598] log likelihood: -10285.377529 EM: Round [599] log likelihood: -10285.377414 EM: Round [600] log likelihood: -10285.377298 EM: Round [601] log likelihood: -10285.377183 EM: Round [602] log likelihood: -10285.377067 EM: Round [603] log likelihood: -10285.376952 EM: Round [604] log likelihood: -10285.376837 EM: Round [605] log likelihood: -10285.376722 EM: Round [606] log likelihood: -10285.376607 EM: Round [607] log likelihood: -10285.376492 EM: Round [608] log likelihood: -10285.376377 EM: Round [609] log likelihood: -10285.376263 EM: Round [610] log likelihood: -10285.376148 EM: Round [611] log likelihood: -10285.376034 EM: Round [612] log likelihood: -10285.375920 EM: Round [613] log likelihood: -10285.375806 EM: Round [614] log likelihood: -10285.375692 EM: Round [615] log likelihood: -10285.375578 EM: Round [616] log likelihood: -10285.375464 EM: Round [617] log likelihood: -10285.375350 EM: Round [618] log likelihood: -10285.375237 EM: Round [619] log likelihood: -10285.375123 EM: Round [620] log likelihood: -10285.375010 EM: Round [621] log likelihood: -10285.374896 EM: Round [622] log likelihood: -10285.374783 EM: Round [623] log likelihood: -10285.374670 EM: Round [624] log likelihood: -10285.374557 EM: Round [625] log likelihood: -10285.374444 EM: Round [626] log likelihood: -10285.374332 EM: Round [627] log likelihood: -10285.374219 EM: Round [628] log likelihood: -10285.374106 EM: Round [629] log likelihood: -10285.373994 EM: Round [630] log likelihood: -10285.373882 EM: Round [631] log likelihood: -10285.373769 EM: Round [632] log likelihood: -10285.373657 EM: Round [633] log likelihood: -10285.373545 EM: Round [634] log likelihood: -10285.373433 EM: Round [635] log likelihood: -10285.373322 EM: Round [636] log likelihood: -10285.373210 EM: Round [637] log likelihood: -10285.373098 EM: Round [638] log likelihood: -10285.372987 EM: Round [639] log likelihood: -10285.372876 EM: Round [640] log likelihood: -10285.372764 EM: Round [641] log likelihood: -10285.372653 EM: Round [642] log likelihood: -10285.372542 EM: Round [643] log likelihood: -10285.372431 EM: Round [644] log likelihood: -10285.372320 EM: Round [645] log likelihood: -10285.372210 EM: Round [646] log likelihood: -10285.372099 EM: Round [647] log likelihood: -10285.371989 EM: Round [648] log likelihood: -10285.371878 EM: Round [649] log likelihood: -10285.371768 EM: Round [650] log likelihood: -10285.371658 EM: Round [651] log likelihood: -10285.371548 EM: Round [652] log likelihood: -10285.371438 EM: Round [653] log likelihood: -10285.371328 EM: Round [654] log likelihood: -10285.371218 EM: Round [655] log likelihood: -10285.371108 EM: Round [656] log likelihood: -10285.370999 EM: Round [657] log likelihood: -10285.370889 EM: Round [658] log likelihood: -10285.370780 EM: Round [659] log likelihood: -10285.370671 EM: Round [660] log likelihood: -10285.370562 EM: Round [661] log likelihood: -10285.370453 EM: Round [662] log likelihood: -10285.370344 EM: Round [663] log likelihood: -10285.370235 EM: Round [664] log likelihood: -10285.370126 EM: Round [665] log likelihood: -10285.370017 EM: Round [666] log likelihood: -10285.369909 EM: Round [667] log likelihood: -10285.369800 EM: Round [668] log likelihood: -10285.369692 EM: Round [669] log likelihood: -10285.369584 EM: Round [670] log likelihood: -10285.369476 EM: Round [671] log likelihood: -10285.369368 EM: Round [672] log likelihood: -10285.369260 EM: Round [673] log likelihood: -10285.369152 EM: Round [674] log likelihood: -10285.369044 EM: Round [675] log likelihood: -10285.368937 EM: Round [676] log likelihood: -10285.368829 EM: Round [677] log likelihood: -10285.368722 EM: Round [678] log likelihood: -10285.368615 EM: Round [679] log likelihood: -10285.368507 EM: Round [680] log likelihood: -10285.368400 EM: Round [681] log likelihood: -10285.368293 EM: Round [682] log likelihood: -10285.368186 EM: Round [683] log likelihood: -10285.368080 EM: Round [684] log likelihood: -10285.367973 EM: Round [685] log likelihood: -10285.367866 EM: Round [686] log likelihood: -10285.367760 EM: Round [687] log likelihood: -10285.367654 EM: Round [688] log likelihood: -10285.367547 EM: Round [689] log likelihood: -10285.367441 EM: Round [690] log likelihood: -10285.367335 EM: Round [691] log likelihood: -10285.367229 EM: Round [692] log likelihood: -10285.367123 EM: Round [693] log likelihood: -10285.367017 EM: Round [694] log likelihood: -10285.366912 EM: Round [695] log likelihood: -10285.366806 EM: Round [696] log likelihood: -10285.366701 EM: Round [697] log likelihood: -10285.366595 EM: Round [698] log likelihood: -10285.366490 EM: Round [699] log likelihood: -10285.366385 EM: Round [700] log likelihood: -10285.366280 EM: Round [701] log likelihood: -10285.366175 EM: Round [702] log likelihood: -10285.366070 EM: Round [703] log likelihood: -10285.365965 EM: Round [704] log likelihood: -10285.365860 EM: Round [705] log likelihood: -10285.365756 EM: Round [706] log likelihood: -10285.365651 EM: Round [707] log likelihood: -10285.365547 EM: Round [708] log likelihood: -10285.365443 EM: Round [709] log likelihood: -10285.365339 EM: Round [710] log likelihood: -10285.365234 EM: Round [711] log likelihood: -10285.365131 EM: Round [712] log likelihood: -10285.365027 EM: Round [713] log likelihood: -10285.364923 EM: Round [714] log likelihood: -10285.364819 EM: Round [715] log likelihood: -10285.364716 EM: Round [716] log likelihood: -10285.364612 EM: Round [717] log likelihood: -10285.364509 EM: Round [718] log likelihood: -10285.364405 EM: Round [719] log likelihood: -10285.364302 EM: Round [720] log likelihood: -10285.364199 EM: Round [721] log likelihood: -10285.364096 EM: Round [722] log likelihood: -10285.363993 EM: Round [723] log likelihood: -10285.363890 EM: Round [724] log likelihood: -10285.363788 EM: Round [725] log likelihood: -10285.363685 EM: Round [726] log likelihood: -10285.363582 EM: Round [727] log likelihood: -10285.363480 EM: Round [728] log likelihood: -10285.363378 EM: Round [729] log likelihood: -10285.363275 EM: Round [730] log likelihood: -10285.363173 EM: Round [731] log likelihood: -10285.363071 EM: Round [732] log likelihood: -10285.362969 EM: Round [733] log likelihood: -10285.362868 EM: Round [734] log likelihood: -10285.362766 EM: Round [735] log likelihood: -10285.362664 EM: Round [736] log likelihood: -10285.362563 EM: Round [737] log likelihood: -10285.362461 EM: Round [738] log likelihood: -10285.362360 EM: Round [739] log likelihood: -10285.362258 EM: Round [740] log likelihood: -10285.362157 EM: Round [741] log likelihood: -10285.362056 EM: Round [742] log likelihood: -10285.361955 EM: Round [743] log likelihood: -10285.361854 EM: Round [744] log likelihood: -10285.361754 EM: Round [745] log likelihood: -10285.361653 EM: Round [746] log likelihood: -10285.361552 EM: Round [747] log likelihood: -10285.361452 EM: Round [748] log likelihood: -10285.361351 EM: Round [749] log likelihood: -10285.361251 EM: Round [750] log likelihood: -10285.361151 EM: Round [751] log likelihood: -10285.361051 EM: Round [752] log likelihood: -10285.360951 EM: Round [753] log likelihood: -10285.360851 EM: Stopping iterations at round 753 due to insufficient improvement in likelihood. [bam_sort_core] merging from 0 files and 8 in-memory blocks... -extracting read coordinates from /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.consolidated.bam.read_coords CMD: touch /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.FeA4L09rE1/fi_workdir/tih_rna_sample_00087_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.FeA4L09rE1/fi_workdir/tih_rna_sample_00087_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: cp /tmp/nxf.FeA4L09rE1/fi_workdir/tih_rna_sample_00087_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.post_blast_and_promiscuity_filter -done, see /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass EM: Starting log likelihood: -9653.333868 EM: Round [1] log likelihood: -9652.351161 EM: Round [2] log likelihood: -9652.349565 EM: Round [3] log likelihood: -9652.349561 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. -total frags in /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2_1.fastp.fastq.gz: 296062230 Warning - not locating file: /tmp/nxf.FeA4L09rE1/tih_rna_sample_00087_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed WARNING, no entry stored in dbm for [ENSG00000284627.1] WARNING, no entry stored in dbm for [ENSG00000284627.1] WARNING, no entry stored in dbm for [ENSG00000284627.1] WARNING, no entry stored in dbm for [ENSG00000284627.1] WARNING, no entry stored in dbm for [ENSG00000254610.3] WARNING, no entry stored in dbm for [ENSG00000255367.3] WARNING, no entry stored in dbm for [ENSG00000254610.3] WARNING, no entry stored in dbm for [ENSG00000255367.3] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000284639.1] WARNING, no entry stored in dbm for [ENSG00000248618.1] WARNING, no entry stored in dbm for [ENSG00000253778.1] WARNING, no entry stored in dbm for [ENSG00000253778.1] WARNING, no entry stored in dbm for [ENSG00000253778.1] WARNING, no entry stored in dbm for [ENSG00000253778.1] WARNING, no entry stored in dbm for [ENSG00000253778.1] WARNING, no entry stored in dbm for [ENSG00000253778.1] WARNING, no entry stored in dbm for [ENSG00000253778.1] WARNING, no entry stored in dbm for [ENSG00000253778.1] 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 [ENSG00000068781.21] WARNING, no entry stored in dbm for [ENSG00000068781.21] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000242880.2] WARNING, no entry stored in dbm for [ENSG00000242880.2] WARNING, no entry stored in dbm for [ENSG00000249252.5] WARNING, no entry stored in dbm for [ENSG00000248360.7] WARNING, no entry stored in dbm for [ENSG00000249252.5] WARNING, no entry stored in dbm for [ENSG00000248360.7] WARNING, no entry stored in dbm for [ENSG00000249252.5] WARNING, no entry stored in dbm for [ENSG00000248360.7] ls: cannot access 'IGV_inputs': No such file or directory