Done.
-parsing GTF file: /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.VlOYCGRWmh/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.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.VlOYCGRWmh/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.VlOYCGRWmh/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00146_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00146_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:37:30 : INFO : Done.
-parsing GTF file: /tmp/nxf.VlOYCGRWmh/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.VlOYCGRWmh/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_1.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] -done parsing /tmp/nxf.VlOYCGRWmh/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'small anchor length' => 1,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
'num genes matched < 2' => 42,
' ** passed ** ' => 3506,
'per_id < 96' => 2192,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 66,
'excessive soft clipping' => 5387
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.VlOYCGRWmh/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: AC011037.1--CPA6
[1000]
[2000]
[3000]
[4000]
[5000]
[6000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180
[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] -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1
[1000]
[2000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
[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] -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC2
[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] -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC1
[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] -fusion SPANNING read extraction for scaff: PCDHA5--PCDHA13
[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] -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]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
[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: PCDHA6--PCDHAC1
[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] -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] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
[1000]
[2000]
[3000]
[4000] -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] -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]
[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] -fusion SPANNING read extraction for scaff: ZFHX3--LINC01572
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 24961
};
EM: Starting log likelihood: -3336.759151
EM: Round [1] log likelihood: -3335.235254
EM: Round [2] log likelihood: -3335.201202
EM: Round [3] log likelihood: -3335.181225
EM: Round [4] log likelihood: -3335.162016
EM: Round [5] log likelihood: -3335.143204
EM: Round [6] log likelihood: -3335.124771
EM: Round [7] log likelihood: -3335.106705
EM: Round [8] log likelihood: -3335.088996
EM: Round [9] log likelihood: -3335.071637
EM: Round [10] log likelihood: -3335.054618
EM: Round [11] log likelihood: -3335.037930
EM: Round [12] log likelihood: -3335.021565
EM: Round [13] log likelihood: -3335.005516
EM: Round [14] log likelihood: -3334.989774
EM: Round [15] log likelihood: -3334.974332
EM: Round [16] log likelihood: -3334.959184
EM: Round [17] log likelihood: -3334.944321
EM: Round [18] log likelihood: -3334.929737
EM: Round [19] log likelihood: -3334.915426
EM: Round [20] log likelihood: -3334.901381
EM: Round [21] log likelihood: -3334.887596
EM: Round [22] log likelihood: -3334.874065
EM: Round [23] log likelihood: -3334.860783
EM: Round [24] log likelihood: -3334.847743
EM: Round [25] log likelihood: -3334.834940
EM: Round [26] log likelihood: -3334.822370
EM: Round [27] log likelihood: -3334.810026
EM: Round [28] log likelihood: -3334.797904
EM: Round [29] log likelihood: -3334.785998
EM: Round [30] log likelihood: -3334.774305
EM: Round [31] log likelihood: -3334.762820
EM: Round [32] log likelihood: -3334.751538
EM: Round [33] log likelihood: -3334.740454
EM: Round [34] log likelihood: -3334.729565
EM: Round [35] log likelihood: -3334.718867
EM: Round [36] log likelihood: -3334.708355
EM: Round [37] log likelihood: -3334.698026
EM: Round [38] log likelihood: -3334.687876
EM: Round [39] log likelihood: -3334.677900
EM: Round [40] log likelihood: -3334.668097
EM: Round [41] log likelihood: -3334.658461
EM: Round [42] log likelihood: -3334.648990
EM: Round [43] log likelihood: -3334.639681
EM: Round [44] log likelihood: -3334.630529
EM: Round [45] log likelihood: -3334.621533
EM: Round [46] log likelihood: -3334.612688
EM: Round [47] log likelihood: -3334.603992
EM: Round [48] log likelihood: -3334.595442
EM: Round [49] log likelihood: -3334.587035
EM: Round [50] log likelihood: -3334.578769
EM: Round [51] log likelihood: -3334.570640
EM: Round [52] log likelihood: -3334.562646
EM: Round [53] log likelihood: -3334.554784
EM: Round [54] log likelihood: -3334.547053
EM: Round [55] log likelihood: -3334.539448
EM: Round [56] log likelihood: -3334.531969
EM: Round [57] log likelihood: -3334.524612
EM: Round [58] log likelihood: -3334.517375
EM: Round [59] log likelihood: -3334.510257
EM: Round [60] log likelihood: -3334.503254
EM: Round [61] log likelihood: -3334.496365
EM: Round [62] log likelihood: -3334.489587
EM: Round [63] log likelihood: -3334.482919
EM: Round [64] log likelihood: -3334.476359
EM: Round [65] log likelihood: -3334.469904
EM: Round [66] log likelihood: -3334.463552
EM: Round [67] log likelihood: -3334.457303
EM: Round [68] log likelihood: -3334.451153
EM: Round [69] log likelihood: -3334.445102
EM: Round [70] log likelihood: -3334.439147
EM: Round [71] log likelihood: -3334.433286
EM: Round [72] log likelihood: -3334.427519
EM: Round [73] log likelihood: -3334.421843
EM: Round [74] log likelihood: -3334.416256
EM: Round [75] log likelihood: -3334.410758
EM: Round [76] log likelihood: -3334.405346
EM: Round [77] log likelihood: -3334.400019
EM: Round [78] log likelihood: -3334.394776
EM: Round [79] log likelihood: -3334.389615
EM: Round [80] log likelihood: -3334.384535
EM: Round [81] log likelihood: -3334.379534
EM: Round [82] log likelihood: -3334.374611
EM: Round [83] log likelihood: -3334.369764
EM: Round [84] log likelihood: -3334.364993
EM: Round [85] log likelihood: -3334.360296
EM: Round [86] log likelihood: -3334.355671
EM: Round [87] log likelihood: -3334.351118
EM: Round [88] log likelihood: -3334.346635
EM: Round [89] log likelihood: -3334.342222
EM: Round [90] log likelihood: -3334.337876
EM: Round [91] log likelihood: -3334.333597
EM: Round [92] log likelihood: -3334.329384
EM: Round [93] log likelihood: -3334.325235
EM: Round [94] log likelihood: -3334.321150
EM: Round [95] log likelihood: -3334.317127
EM: Round [96] log likelihood: -3334.313166
EM: Round [97] log likelihood: -3334.309265
EM: Round [98] log likelihood: -3334.305424
EM: Round [99] log likelihood: -3334.301640
EM: Round [100] log likelihood: -3334.297915
EM: Round [101] log likelihood: -3334.294246
EM: Round [102] log likelihood: -3334.290632
EM: Round [103] log likelihood: -3334.287073
EM: Round [104] log likelihood: -3334.283568
EM: Round [105] log likelihood: -3334.280116
EM: Round [106] log likelihood: -3334.276716
EM: Round [107] log likelihood: -3334.273367
EM: Round [108] log likelihood: -3334.270068
EM: Round [109] log likelihood: -3334.266819
EM: Round [110] log likelihood: -3334.263619
EM: Round [111] log likelihood: -3334.260467
EM: Round [112] log likelihood: -3334.257362
EM: Round [113] log likelihood: -3334.254303
EM: Round [114] log likelihood: -3334.251291
EM: Round [115] log likelihood: -3334.248323
EM: Round [116] log likelihood: -3334.245399
EM: Round [117] log likelihood: -3334.242520
EM: Round [118] log likelihood: -3334.239683
EM: Round [119] log likelihood: -3334.236888
EM: Round [120] log likelihood: -3334.234134
EM: Round [121] log likelihood: -3334.231422
EM: Round [122] log likelihood: -3334.228750
EM: Round [123] log likelihood: -3334.226117
EM: Round [124] log likelihood: -3334.223524
EM: Round [125] log likelihood: -3334.220969
EM: Round [126] log likelihood: -3334.218451
EM: Round [127] log likelihood: -3334.215971
EM: Round [128] log likelihood: -3334.213528
EM: Round [129] log likelihood: -3334.211120
EM: Round [130] log likelihood: -3334.208748
EM: Round [131] log likelihood: -3334.206411
EM: Round [132] log likelihood: -3334.204108
EM: Round [133] log likelihood: -3334.201839
EM: Round [134] log likelihood: -3334.199604
EM: Round [135] log likelihood: -3334.197401
EM: Round [136] log likelihood: -3334.195231
EM: Round [137] log likelihood: -3334.193092
EM: Round [138] log likelihood: -3334.190985
EM: Round [139] log likelihood: -3334.188909
EM: Round [140] log likelihood: -3334.186863
EM: Round [141] log likelihood: -3334.184847
EM: Round [142] log likelihood: -3334.182860
EM: Round [143] log likelihood: -3334.180903
EM: Round [144] log likelihood: -3334.178973
EM: Round [145] log likelihood: -3334.177073
EM: Round [146] log likelihood: -3334.175199
EM: Round [147] log likelihood: -3334.173353
EM: Round [148] log likelihood: -3334.171534
EM: Round [149] log likelihood: -3334.169742
EM: Round [150] log likelihood: -3334.167975
EM: Round [151] log likelihood: -3334.166234
EM: Round [152] log likelihood: -3334.164519
EM: Round [153] log likelihood: -3334.162828
EM: Round [154] log likelihood: -3334.161162
EM: Round [155] log likelihood: -3334.159520
EM: Round [156] log likelihood: -3334.157902
EM: Round [157] log likelihood: -3334.156307
EM: Round [158] log likelihood: -3334.154735
EM: Round [159] log likelihood: -3334.153186
EM: Round [160] log likelihood: -3334.151660
EM: Round [161] log likelihood: -3334.150155
EM: Round [162] log likelihood: -3334.148672
EM: Round [163] log likelihood: -3334.147211
EM: Round [164] log likelihood: -3334.145771
EM: Round [165] log likelihood: -3334.144351
EM: Round [166] log likelihood: -3334.142952
EM: Round [167] log likelihood: -3334.141573
EM: Round [168] log likelihood: -3334.140214
EM: Round [169] log likelihood: -3334.138875
EM: Round [170] log likelihood: -3334.137555
EM: Round [171] log likelihood: -3334.136254
EM: Round [172] log likelihood: -3334.134971
EM: Round [173] log likelihood: -3334.133707
EM: Round [174] log likelihood: -3334.132461
EM: Round [175] log likelihood: -3334.131233
EM: Round [176] log likelihood: -3334.130023
EM: Round [177] log likelihood: -3334.128830
EM: Round [178] log likelihood: -3334.127654
EM: Round [179] log likelihood: -3334.126495
EM: Round [180] log likelihood: -3334.125352
EM: Round [181] log likelihood: -3334.124226
EM: Round [182] log likelihood: -3334.123116
EM: Round [183] log likelihood: -3334.122022
EM: Round [184] log likelihood: -3334.120944
EM: Round [185] log likelihood: -3334.119881
EM: Round [186] log likelihood: -3334.118833
EM: Round [187] log likelihood: -3334.117800
EM: Round [188] log likelihood: -3334.116782
EM: Round [189] log likelihood: -3334.115779
EM: Round [190] log likelihood: -3334.114790
EM: Round [191] log likelihood: -3334.113815
EM: Round [192] log likelihood: -3334.112854
EM: Round [193] log likelihood: -3334.111906
EM: Round [194] log likelihood: -3334.110972
EM: Round [195] log likelihood: -3334.110052
EM: Round [196] log likelihood: -3334.109144
EM: Round [197] log likelihood: -3334.108250
EM: Round [198] log likelihood: -3334.107368
EM: Round [199] log likelihood: -3334.106499
EM: Round [200] log likelihood: -3334.105642
EM: Round [201] log likelihood: -3334.104797
EM: Round [202] log likelihood: -3334.103965
EM: Round [203] log likelihood: -3334.103144
EM: Round [204] log likelihood: -3334.102335
EM: Round [205] log likelihood: -3334.101537
EM: Round [206] log likelihood: -3334.100751
EM: Round [207] log likelihood: -3334.099976
EM: Round [208] log likelihood: -3334.099212
EM: Round [209] log likelihood: -3334.098458
EM: Round [210] log likelihood: -3334.097716
EM: Round [211] log likelihood: -3334.096984
EM: Round [212] log likelihood: -3334.096262
EM: Round [213] log likelihood: -3334.095551
EM: Round [214] log likelihood: -3334.094850
EM: Round [215] log likelihood: -3334.094158
EM: Round [216] log likelihood: -3334.093477
EM: Round [217] log likelihood: -3334.092805
EM: Round [218] log likelihood: -3334.092143
EM: Round [219] log likelihood: -3334.091490
EM: Round [220] log likelihood: -3334.090846
EM: Round [221] log likelihood: -3334.090211
EM: Round [222] log likelihood: -3334.089586
EM: Round [223] log likelihood: -3334.088969
EM: Round [224] log likelihood: -3334.088361
EM: Round [225] log likelihood: -3334.087762
EM: Round [226] log likelihood: -3334.087171
EM: Round [227] log likelihood: -3334.086588
EM: Round [228] log likelihood: -3334.086014
EM: Round [229] log likelihood: -3334.085447
EM: Round [230] log likelihood: -3334.084889
EM: Round [231] log likelihood: -3334.084339
EM: Round [232] log likelihood: -3334.083796
EM: Round [233] log likelihood: -3334.083261
EM: Round [234] log likelihood: -3334.082734
EM: Round [235] log likelihood: -3334.082214
EM: Round [236] log likelihood: -3334.081702
EM: Round [237] log likelihood: -3334.081196
EM: Round [238] log likelihood: -3334.080698
EM: Round [239] log likelihood: -3334.080207
EM: Round [240] log likelihood: -3334.079723
EM: Round [241] log likelihood: -3334.079246
EM: Round [242] log likelihood: -3334.078775
EM: Round [243] log likelihood: -3334.078311
EM: Round [244] log likelihood: -3334.077854
EM: Round [245] log likelihood: -3334.077403
EM: Round [246] log likelihood: -3334.076958
EM: Round [247] log likelihood: -3334.076520
EM: Round [248] log likelihood: -3334.076087
EM: Round [249] log likelihood: -3334.075661
EM: Round [250] log likelihood: -3334.075241
EM: Round [251] log likelihood: -3334.074827
EM: Round [252] log likelihood: -3334.074419
EM: Round [253] log likelihood: -3334.074016
EM: Round [254] log likelihood: -3334.073619
EM: Round [255] log likelihood: -3334.073228
EM: Round [256] log likelihood: -3334.072842
EM: Round [257] log likelihood: -3334.072462
EM: Round [258] log likelihood: -3334.072087
EM: Round [259] log likelihood: -3334.071717
EM: Round [260] log likelihood: -3334.071352
EM: Round [261] log likelihood: -3334.070993
EM: Round [262] log likelihood: -3334.070639
EM: Round [263] log likelihood: -3334.070289
EM: Round [264] log likelihood: -3334.069945
EM: Round [265] log likelihood: -3334.069605
EM: Round [266] log likelihood: -3334.069270
EM: Round [267] log likelihood: -3334.068940
EM: Round [268] log likelihood: -3334.068615
EM: Round [269] log likelihood: -3334.068294
EM: Round [270] log likelihood: -3334.067977
EM: Round [271] log likelihood: -3334.067666
EM: Round [272] log likelihood: -3334.067358
EM: Round [273] log likelihood: -3334.067055
EM: Round [274] log likelihood: -3334.066756
EM: Round [275] log likelihood: -3334.066461
EM: Round [276] log likelihood: -3334.066170
EM: Round [277] log likelihood: -3334.065884
EM: Round [278] log likelihood: -3334.065601
EM: Round [279] log likelihood: -3334.065323
EM: Round [280] log likelihood: -3334.065048
EM: Round [281] log likelihood: -3334.064777
EM: Round [282] log likelihood: -3334.064510
EM: Round [283] log likelihood: -3334.064247
EM: Round [284] log likelihood: -3334.063987
EM: Round [285] log likelihood: -3334.063732
EM: Round [286] log likelihood: -3334.063479
EM: Round [287] log likelihood: -3334.063231
EM: Round [288] log likelihood: -3334.062985
EM: Round [289] log likelihood: -3334.062743
EM: Round [290] log likelihood: -3334.062505
EM: Round [291] log likelihood: -3334.062270
EM: Round [292] log likelihood: -3334.062038
EM: Round [293] log likelihood: -3334.061810
EM: Round [294] log likelihood: -3334.061584
EM: Round [295] log likelihood: -3334.061362
EM: Round [296] log likelihood: -3334.061143
EM: Round [297] log likelihood: -3334.060927
EM: Round [298] log likelihood: -3334.060714
EM: Round [299] log likelihood: -3334.060504
EM: Round [300] log likelihood: -3334.060297
EM: Round [301] log likelihood: -3334.060093
EM: Round [302] log likelihood: -3334.059892
EM: Round [303] log likelihood: -3334.059693
EM: Round [304] log likelihood: -3334.059498
EM: Round [305] log likelihood: -3334.059305
EM: Round [306] log likelihood: -3334.059114
EM: Round [307] log likelihood: -3334.058927
EM: Round [308] log likelihood: -3334.058742
EM: Round [309] log likelihood: -3334.058560
EM: Round [310] log likelihood: -3334.058380
EM: Round [311] log likelihood: -3334.058203
EM: Round [312] log likelihood: -3334.058028
EM: Round [313] log likelihood: -3334.057855
EM: Round [314] log likelihood: -3334.057686
EM: Round [315] log likelihood: -3334.057518
EM: Round [316] log likelihood: -3334.057353
EM: Round [317] log likelihood: -3334.057190
EM: Round [318] log likelihood: -3334.057029
EM: Round [319] log likelihood: -3334.056871
EM: Round [320] log likelihood: -3334.056715
EM: Round [321] log likelihood: -3334.056561
EM: Round [322] log likelihood: -3334.056409
EM: Round [323] log likelihood: -3334.056260
EM: Round [324] log likelihood: -3334.056112
EM: Round [325] log likelihood: -3334.055967
EM: Round [326] log likelihood: -3334.055823
EM: Round [327] log likelihood: -3334.055682
EM: Round [328] log likelihood: -3334.055542
EM: Round [329] log likelihood: -3334.055405
EM: Round [330] log likelihood: -3334.055269
EM: Round [331] log likelihood: -3334.055135
EM: Round [332] log likelihood: -3334.055004
EM: Round [333] log likelihood: -3334.054874
EM: Round [334] log likelihood: -3334.054745
EM: Round [335] log likelihood: -3334.054619
EM: Round [336] log likelihood: -3334.054494
EM: Round [337] log likelihood: -3334.054372
EM: Round [338] log likelihood: -3334.054251
EM: Round [339] log likelihood: -3334.054131
EM: Round [340] log likelihood: -3334.054013
EM: Round [341] log likelihood: -3334.053897
EM: Round [342] log likelihood: -3334.053783
EM: Round [343] log likelihood: -3334.053670
EM: Round [344] log likelihood: -3334.053559
EM: Round [345] log likelihood: -3334.053449
EM: Round [346] log likelihood: -3334.053341
EM: Round [347] log likelihood: -3334.053234
EM: Round [348] log likelihood: -3334.053129
EM: Round [349] log likelihood: -3334.053025
EM: Round [350] log likelihood: -3334.052923
EM: Round [351] log likelihood: -3334.052822
EM: Round [352] log likelihood: -3334.052722
EM: Stopping iterations at round 352 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.VlOYCGRWmh/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_1.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.VlOYCGRWmh/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_1.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.VlOYCGRWmh/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2950.550017
EM: Round [1] log likelihood: -2949.990312
EM: Round [2] log likelihood: -2949.973937
EM: Round [3] log likelihood: -2949.973381
EM: Round [4] log likelihood: -2949.973364
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1_1.fastp.fastq.gz: 295931232
Warning - not locating file: /tmp/nxf.VlOYCGRWmh/tih_rna_sample_00146_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000236438.7]
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 [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
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 [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 [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
ls: cannot access 'IGV_inputs': No such file or directory