Done.
-parsing GTF file: /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
10:55:04 : INFO : Done.
-parsing GTF file: /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_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]
[590000]
[600000]
[610000]
[620000]
[630000]
[640000] -done parsing /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'excessive soft clipping' => 3313,
'num genes matched < 2' => 10,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 8,
'seq-similar region overlap' => 18,
'low complexity anchor region' => 18,
' ** passed ** ' => 6377,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9,
'small anchor length' => 152,
'per_id < 96' => 2906,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 32
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_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: AC092666.2--ACTR3B
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC2
[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: PCDHA7--PCDHA13
[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: PCDHGA5--PCDHGA8
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000] -fusion SPANNING read extraction for scaff: PCDHGA5--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] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
[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: PCDHGA5--PCDHGA12
[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] -fusion SPANNING read extraction for scaff: PCDHGA5--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] -fusion SPANNING read extraction for scaff: PCDHGA5--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]
[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] -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]
[139000]
[140000] -fusion SPANNING read extraction for scaff: TCEAL4--MTRNR2L12
[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] -fusion SPANNING read extraction for scaff: TLK2--LINC01347
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000] -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] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 968,
'seq similar region alignment' => 5619
};
EM: Starting log likelihood: -3519.248944
EM: Round [1] log likelihood: -3518.563840
EM: Round [2] log likelihood: -3518.472049
EM: Round [3] log likelihood: -3518.406234
EM: Round [4] log likelihood: -3518.341434
EM: Round [5] log likelihood: -3518.276635
EM: Round [6] log likelihood: -3518.211837
EM: Round [7] log likelihood: -3518.147089
EM: Round [8] log likelihood: -3518.082441
EM: Round [9] log likelihood: -3518.017947
EM: Round [10] log likelihood: -3517.953661
EM: Round [11] log likelihood: -3517.889637
EM: Round [12] log likelihood: -3517.825929
EM: Round [13] log likelihood: -3517.762591
EM: Round [14] log likelihood: -3517.699676
EM: Round [15] log likelihood: -3517.637236
EM: Round [16] log likelihood: -3517.575319
EM: Round [17] log likelihood: -3517.513974
EM: Round [18] log likelihood: -3517.453247
EM: Round [19] log likelihood: -3517.393180
EM: Round [20] log likelihood: -3517.333815
EM: Round [21] log likelihood: -3517.275187
EM: Round [22] log likelihood: -3517.217334
EM: Round [23] log likelihood: -3517.160285
EM: Round [24] log likelihood: -3517.104072
EM: Round [25] log likelihood: -3517.048718
EM: Round [26] log likelihood: -3516.994248
EM: Round [27] log likelihood: -3516.940682
EM: Round [28] log likelihood: -3516.888036
EM: Round [29] log likelihood: -3516.836326
EM: Round [30] log likelihood: -3516.785563
EM: Round [31] log likelihood: -3516.735756
EM: Round [32] log likelihood: -3516.686913
EM: Round [33] log likelihood: -3516.639037
EM: Round [34] log likelihood: -3516.592131
EM: Round [35] log likelihood: -3516.546196
EM: Round [36] log likelihood: -3516.501229
EM: Round [37] log likelihood: -3516.457227
EM: Round [38] log likelihood: -3516.414184
EM: Round [39] log likelihood: -3516.372094
EM: Round [40] log likelihood: -3516.330949
EM: Round [41] log likelihood: -3516.290739
EM: Round [42] log likelihood: -3516.251453
EM: Round [43] log likelihood: -3516.213080
EM: Round [44] log likelihood: -3516.175607
EM: Round [45] log likelihood: -3516.139021
EM: Round [46] log likelihood: -3516.103307
EM: Round [47] log likelihood: -3516.068450
EM: Round [48] log likelihood: -3516.034436
EM: Round [49] log likelihood: -3516.001249
EM: Round [50] log likelihood: -3515.968872
EM: Round [51] log likelihood: -3515.937288
EM: Round [52] log likelihood: -3515.906482
EM: Round [53] log likelihood: -3515.876436
EM: Round [54] log likelihood: -3515.847133
EM: Round [55] log likelihood: -3515.818557
EM: Round [56] log likelihood: -3515.790691
EM: Round [57] log likelihood: -3515.763516
EM: Round [58] log likelihood: -3515.737018
EM: Round [59] log likelihood: -3515.711178
EM: Round [60] log likelihood: -3515.685980
EM: Round [61] log likelihood: -3515.661408
EM: Round [62] log likelihood: -3515.637445
EM: Round [63] log likelihood: -3515.614076
EM: Round [64] log likelihood: -3515.591285
EM: Round [65] log likelihood: -3515.569057
EM: Round [66] log likelihood: -3515.547375
EM: Round [67] log likelihood: -3515.526226
EM: Round [68] log likelihood: -3515.505594
EM: Round [69] log likelihood: -3515.485466
EM: Round [70] log likelihood: -3515.465827
EM: Round [71] log likelihood: -3515.446664
EM: Round [72] log likelihood: -3515.427963
EM: Round [73] log likelihood: -3515.409712
EM: Round [74] log likelihood: -3515.391897
EM: Round [75] log likelihood: -3515.374507
EM: Round [76] log likelihood: -3515.357529
EM: Round [77] log likelihood: -3515.340952
EM: Round [78] log likelihood: -3515.324764
EM: Round [79] log likelihood: -3515.308954
EM: Round [80] log likelihood: -3515.293512
EM: Round [81] log likelihood: -3515.278426
EM: Round [82] log likelihood: -3515.263688
EM: Round [83] log likelihood: -3515.249287
EM: Round [84] log likelihood: -3515.235213
EM: Round [85] log likelihood: -3515.221458
EM: Round [86] log likelihood: -3515.208012
EM: Round [87] log likelihood: -3515.194866
EM: Round [88] log likelihood: -3515.182013
EM: Round [89] log likelihood: -3515.169443
EM: Round [90] log likelihood: -3515.157150
EM: Round [91] log likelihood: -3515.145126
EM: Round [92] log likelihood: -3515.133362
EM: Round [93] log likelihood: -3515.121852
EM: Round [94] log likelihood: -3515.110589
EM: Round [95] log likelihood: -3515.099566
EM: Round [96] log likelihood: -3515.088777
EM: Round [97] log likelihood: -3515.078215
EM: Round [98] log likelihood: -3515.067875
EM: Round [99] log likelihood: -3515.057749
EM: Round [100] log likelihood: -3515.047833
EM: Round [101] log likelihood: -3515.038121
EM: Round [102] log likelihood: -3515.028608
EM: Round [103] log likelihood: -3515.019288
EM: Round [104] log likelihood: -3515.010157
EM: Round [105] log likelihood: -3515.001209
EM: Round [106] log likelihood: -3514.992440
EM: Round [107] log likelihood: -3514.983845
EM: Round [108] log likelihood: -3514.975420
EM: Round [109] log likelihood: -3514.967161
EM: Round [110] log likelihood: -3514.959063
EM: Round [111] log likelihood: -3514.951123
EM: Round [112] log likelihood: -3514.943336
EM: Round [113] log likelihood: -3514.935699
EM: Round [114] log likelihood: -3514.928207
EM: Round [115] log likelihood: -3514.920859
EM: Round [116] log likelihood: -3514.913650
EM: Round [117] log likelihood: -3514.906576
EM: Round [118] log likelihood: -3514.899635
EM: Round [119] log likelihood: -3514.892824
EM: Round [120] log likelihood: -3514.886139
EM: Round [121] log likelihood: -3514.879577
EM: Round [122] log likelihood: -3514.873136
EM: Round [123] log likelihood: -3514.866813
EM: Round [124] log likelihood: -3514.860606
EM: Round [125] log likelihood: -3514.854511
EM: Round [126] log likelihood: -3514.848526
EM: Round [127] log likelihood: -3514.842649
EM: Round [128] log likelihood: -3514.836877
EM: Round [129] log likelihood: -3514.831207
EM: Round [130] log likelihood: -3514.825639
EM: Round [131] log likelihood: -3514.820169
EM: Round [132] log likelihood: -3514.814796
EM: Round [133] log likelihood: -3514.809517
EM: Round [134] log likelihood: -3514.804330
EM: Round [135] log likelihood: -3514.799233
EM: Round [136] log likelihood: -3514.794225
EM: Round [137] log likelihood: -3514.789304
EM: Round [138] log likelihood: -3514.784468
EM: Round [139] log likelihood: -3514.779714
EM: Round [140] log likelihood: -3514.775042
EM: Round [141] log likelihood: -3514.770450
EM: Round [142] log likelihood: -3514.765936
EM: Round [143] log likelihood: -3514.761498
EM: Round [144] log likelihood: -3514.757136
EM: Round [145] log likelihood: -3514.752847
EM: Round [146] log likelihood: -3514.748630
EM: Round [147] log likelihood: -3514.744483
EM: Round [148] log likelihood: -3514.740406
EM: Round [149] log likelihood: -3514.736397
EM: Round [150] log likelihood: -3514.732455
EM: Round [151] log likelihood: -3514.728577
EM: Round [152] log likelihood: -3514.724764
EM: Round [153] log likelihood: -3514.721014
EM: Round [154] log likelihood: -3514.717326
EM: Round [155] log likelihood: -3514.713698
EM: Round [156] log likelihood: -3514.710129
EM: Round [157] log likelihood: -3514.706618
EM: Round [158] log likelihood: -3514.703165
EM: Round [159] log likelihood: -3514.699768
EM: Round [160] log likelihood: -3514.696426
EM: Round [161] log likelihood: -3514.693138
EM: Round [162] log likelihood: -3514.689904
EM: Round [163] log likelihood: -3514.686721
EM: Round [164] log likelihood: -3514.683589
EM: Round [165] log likelihood: -3514.680508
EM: Round [166] log likelihood: -3514.677476
EM: Round [167] log likelihood: -3514.674493
EM: Round [168] log likelihood: -3514.671557
EM: Round [169] log likelihood: -3514.668668
EM: Round [170] log likelihood: -3514.665825
EM: Round [171] log likelihood: -3514.663028
EM: Round [172] log likelihood: -3514.660274
EM: Round [173] log likelihood: -3514.657564
EM: Round [174] log likelihood: -3514.654897
EM: Round [175] log likelihood: -3514.652272
EM: Round [176] log likelihood: -3514.649688
EM: Round [177] log likelihood: -3514.647145
EM: Round [178] log likelihood: -3514.644642
EM: Round [179] log likelihood: -3514.642178
EM: Round [180] log likelihood: -3514.639753
EM: Round [181] log likelihood: -3514.637366
EM: Round [182] log likelihood: -3514.635016
EM: Round [183] log likelihood: -3514.632702
EM: Round [184] log likelihood: -3514.630425
EM: Round [185] log likelihood: -3514.628183
EM: Round [186] log likelihood: -3514.625976
EM: Round [187] log likelihood: -3514.623803
EM: Round [188] log likelihood: -3514.621664
EM: Round [189] log likelihood: -3514.619557
EM: Round [190] log likelihood: -3514.617484
EM: Round [191] log likelihood: -3514.615442
EM: Round [192] log likelihood: -3514.613432
EM: Round [193] log likelihood: -3514.611453
EM: Round [194] log likelihood: -3514.609505
EM: Round [195] log likelihood: -3514.607586
EM: Round [196] log likelihood: -3514.605697
EM: Round [197] log likelihood: -3514.603837
EM: Round [198] log likelihood: -3514.602005
EM: Round [199] log likelihood: -3514.600202
EM: Round [200] log likelihood: -3514.598426
EM: Round [201] log likelihood: -3514.596677
EM: Round [202] log likelihood: -3514.594955
EM: Round [203] log likelihood: -3514.593259
EM: Round [204] log likelihood: -3514.591589
EM: Round [205] log likelihood: -3514.589945
EM: Round [206] log likelihood: -3514.588325
EM: Round [207] log likelihood: -3514.586731
EM: Round [208] log likelihood: -3514.585160
EM: Round [209] log likelihood: -3514.583613
EM: Round [210] log likelihood: -3514.582090
EM: Round [211] log likelihood: -3514.580590
EM: Round [212] log likelihood: -3514.579112
EM: Round [213] log likelihood: -3514.577657
EM: Round [214] log likelihood: -3514.576224
EM: Round [215] log likelihood: -3514.574813
EM: Round [216] log likelihood: -3514.573423
EM: Round [217] log likelihood: -3514.572054
EM: Round [218] log likelihood: -3514.570706
EM: Round [219] log likelihood: -3514.569378
EM: Round [220] log likelihood: -3514.568070
EM: Round [221] log likelihood: -3514.566781
EM: Round [222] log likelihood: -3514.565512
EM: Round [223] log likelihood: -3514.564262
EM: Round [224] log likelihood: -3514.563031
EM: Round [225] log likelihood: -3514.561819
EM: Round [226] log likelihood: -3514.560624
EM: Round [227] log likelihood: -3514.559448
EM: Round [228] log likelihood: -3514.558289
EM: Round [229] log likelihood: -3514.557148
EM: Round [230] log likelihood: -3514.556023
EM: Round [231] log likelihood: -3514.554916
EM: Round [232] log likelihood: -3514.553825
EM: Round [233] log likelihood: -3514.552751
EM: Round [234] log likelihood: -3514.551692
EM: Round [235] log likelihood: -3514.550649
EM: Round [236] log likelihood: -3514.549622
EM: Round [237] log likelihood: -3514.548610
EM: Round [238] log likelihood: -3514.547614
EM: Round [239] log likelihood: -3514.546632
EM: Round [240] log likelihood: -3514.545665
EM: Round [241] log likelihood: -3514.544712
EM: Round [242] log likelihood: -3514.543774
EM: Round [243] log likelihood: -3514.542849
EM: Round [244] log likelihood: -3514.541938
EM: Round [245] log likelihood: -3514.541041
EM: Round [246] log likelihood: -3514.540157
EM: Round [247] log likelihood: -3514.539286
EM: Round [248] log likelihood: -3514.538428
EM: Round [249] log likelihood: -3514.537583
EM: Round [250] log likelihood: -3514.536751
EM: Round [251] log likelihood: -3514.535931
EM: Round [252] log likelihood: -3514.535123
EM: Round [253] log likelihood: -3514.534327
EM: Round [254] log likelihood: -3514.533542
EM: Round [255] log likelihood: -3514.532770
EM: Round [256] log likelihood: -3514.532009
EM: Round [257] log likelihood: -3514.531259
EM: Round [258] log likelihood: -3514.530520
EM: Round [259] log likelihood: -3514.529792
EM: Round [260] log likelihood: -3514.529075
EM: Round [261] log likelihood: -3514.528369
EM: Round [262] log likelihood: -3514.527673
EM: Round [263] log likelihood: -3514.526987
EM: Round [264] log likelihood: -3514.526311
EM: Round [265] log likelihood: -3514.525646
EM: Round [266] log likelihood: -3514.524990
EM: Round [267] log likelihood: -3514.524344
EM: Round [268] log likelihood: -3514.523707
EM: Round [269] log likelihood: -3514.523080
EM: Round [270] log likelihood: -3514.522462
EM: Round [271] log likelihood: -3514.521854
EM: Round [272] log likelihood: -3514.521254
EM: Round [273] log likelihood: -3514.520663
EM: Round [274] log likelihood: -3514.520081
EM: Round [275] log likelihood: -3514.519507
EM: Round [276] log likelihood: -3514.518942
EM: Round [277] log likelihood: -3514.518385
EM: Round [278] log likelihood: -3514.517836
EM: Round [279] log likelihood: -3514.517296
EM: Round [280] log likelihood: -3514.516763
EM: Round [281] log likelihood: -3514.516238
EM: Round [282] log likelihood: -3514.515721
EM: Round [283] log likelihood: -3514.515212
EM: Round [284] log likelihood: -3514.514710
EM: Round [285] log likelihood: -3514.514215
EM: Round [286] log likelihood: -3514.513728
EM: Round [287] log likelihood: -3514.513247
EM: Round [288] log likelihood: -3514.512774
EM: Round [289] log likelihood: -3514.512308
EM: Round [290] log likelihood: -3514.511849
EM: Round [291] log likelihood: -3514.511396
EM: Round [292] log likelihood: -3514.510950
EM: Round [293] log likelihood: -3514.510511
EM: Round [294] log likelihood: -3514.510078
EM: Round [295] log likelihood: -3514.509651
EM: Round [296] log likelihood: -3514.509231
EM: Round [297] log likelihood: -3514.508817
EM: Round [298] log likelihood: -3514.508409
EM: Round [299] log likelihood: -3514.508007
EM: Round [300] log likelihood: -3514.507610
EM: Round [301] log likelihood: -3514.507220
EM: Round [302] log likelihood: -3514.506835
EM: Round [303] log likelihood: -3514.506456
EM: Round [304] log likelihood: -3514.506083
EM: Round [305] log likelihood: -3514.505715
EM: Round [306] log likelihood: -3514.505352
EM: Round [307] log likelihood: -3514.504995
EM: Round [308] log likelihood: -3514.504643
EM: Round [309] log likelihood: -3514.504296
EM: Round [310] log likelihood: -3514.503954
EM: Round [311] log likelihood: -3514.503617
EM: Round [312] log likelihood: -3514.503285
EM: Round [313] log likelihood: -3514.502958
EM: Round [314] log likelihood: -3514.502636
EM: Round [315] log likelihood: -3514.502318
EM: Round [316] log likelihood: -3514.502005
EM: Round [317] log likelihood: -3514.501697
EM: Round [318] log likelihood: -3514.501393
EM: Round [319] log likelihood: -3514.501094
EM: Round [320] log likelihood: -3514.500799
EM: Round [321] log likelihood: -3514.500508
EM: Round [322] log likelihood: -3514.500222
EM: Round [323] log likelihood: -3514.499939
EM: Round [324] log likelihood: -3514.499661
EM: Round [325] log likelihood: -3514.499387
EM: Round [326] log likelihood: -3514.499117
EM: Round [327] log likelihood: -3514.498851
EM: Round [328] log likelihood: -3514.498589
EM: Round [329] log likelihood: -3514.498330
EM: Round [330] log likelihood: -3514.498075
EM: Round [331] log likelihood: -3514.497825
EM: Round [332] log likelihood: -3514.497577
EM: Round [333] log likelihood: -3514.497334
EM: Round [334] log likelihood: -3514.497093
EM: Round [335] log likelihood: -3514.496857
EM: Round [336] log likelihood: -3514.496624
EM: Round [337] log likelihood: -3514.496394
EM: Round [338] log likelihood: -3514.496168
EM: Round [339] log likelihood: -3514.495944
EM: Round [340] log likelihood: -3514.495725
EM: Round [341] log likelihood: -3514.495508
EM: Round [342] log likelihood: -3514.495294
EM: Round [343] log likelihood: -3514.495084
EM: Round [344] log likelihood: -3514.494877
EM: Round [345] log likelihood: -3514.494673
EM: Round [346] log likelihood: -3514.494471
EM: Round [347] log likelihood: -3514.494273
EM: Round [348] log likelihood: -3514.494077
EM: Round [349] log likelihood: -3514.493885
EM: Round [350] log likelihood: -3514.493695
EM: Round [351] log likelihood: -3514.493508
EM: Round [352] log likelihood: -3514.493324
EM: Round [353] log likelihood: -3514.493142
EM: Round [354] log likelihood: -3514.492963
EM: Round [355] log likelihood: -3514.492787
EM: Round [356] log likelihood: -3514.492613
EM: Round [357] log likelihood: -3514.492441
EM: Round [358] log likelihood: -3514.492273
EM: Round [359] log likelihood: -3514.492106
EM: Round [360] log likelihood: -3514.491942
EM: Round [361] log likelihood: -3514.491781
EM: Round [362] log likelihood: -3514.491622
EM: Round [363] log likelihood: -3514.491465
EM: Round [364] log likelihood: -3514.491310
EM: Round [365] log likelihood: -3514.491158
EM: Round [366] log likelihood: -3514.491008
EM: Round [367] log likelihood: -3514.490860
EM: Round [368] log likelihood: -3514.490714
EM: Round [369] log likelihood: -3514.490571
EM: Round [370] log likelihood: -3514.490429
EM: Round [371] log likelihood: -3514.490290
EM: Round [372] log likelihood: -3514.490152
EM: Round [373] log likelihood: -3514.490017
EM: Round [374] log likelihood: -3514.489883
EM: Round [375] log likelihood: -3514.489752
EM: Round [376] log likelihood: -3514.489622
EM: Round [377] log likelihood: -3514.489494
EM: Round [378] log likelihood: -3514.489368
EM: Round [379] log likelihood: -3514.489244
EM: Round [380] log likelihood: -3514.489122
EM: Round [381] log likelihood: -3514.489001
EM: Round [382] log likelihood: -3514.488883
EM: Round [383] log likelihood: -3514.488766
EM: Round [384] log likelihood: -3514.488650
EM: Round [385] log likelihood: -3514.488537
EM: Round [386] log likelihood: -3514.488425
EM: Round [387] log likelihood: -3514.488314
EM: Round [388] log likelihood: -3514.488206
EM: Round [389] log likelihood: -3514.488099
EM: Round [390] log likelihood: -3514.487993
EM: Round [391] log likelihood: -3514.487889
EM: Round [392] log likelihood: -3514.487786
EM: Round [393] log likelihood: -3514.487685
EM: Round [394] log likelihood: -3514.487586
EM: Stopping iterations at round 394 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_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.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_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.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2768.914917
EM: Round [1] log likelihood: -2768.294182
EM: Round [2] log likelihood: -2768.266923
EM: Round [3] log likelihood: -2768.265768
EM: Round [4] log likelihood: -2768.265720
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 233665214
Warning - not locating file: /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000276538.1]
WARNING, no entry stored in dbm for [ENSG00000276538.1]
WARNING, no entry stored in dbm for [ENSG00000276538.1]
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 [ENSG00000214837.8]
ls: cannot access 'IGV_inputs': No such file or directory