Done.
-parsing GTF file: /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.UbMrnt2Om7/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.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.UbMrnt2Om7/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.UbMrnt2Om7/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
21:59:01 : INFO : Done.
-parsing GTF file: /tmp/nxf.UbMrnt2Om7/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.UbMrnt2Om7/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[1690000]   -done parsing /tmp/nxf.UbMrnt2Om7/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 9520,
          'small anchor length' => 19,
          'exons hit < 2' => 1,
          'num genes matched < 2' => 22,
          'seq-similar region overlap' => 380,
          'per_id < 96' => 8255,
          ' ** passed ** ' => 4132,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 94,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 62,
          'low complexity anchor region' => 6,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 44
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.UbMrnt2Om7/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[129000]   -fusion SPANNING read extraction for scaff: AC060809.1--ERBB4

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[53000]   -fusion SPANNING read extraction for scaff: ARSG--DPH1

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[59000]   -fusion SPANNING read extraction for scaff: BMP2K--PTPRT

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[21000]   -fusion SPANNING read extraction for scaff: CDK19--ROS1

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[9000]   -fusion SPANNING read extraction for scaff: DECR1--DPYS

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[9000]   -fusion SPANNING read extraction for scaff: DECR1--AP002847.1

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[57000]   -fusion SPANNING read extraction for scaff: DPH1--PIK3R6

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[35000]   -fusion SPANNING read extraction for scaff: EXOC4--TMEM212-AS1

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[77000]   -fusion SPANNING read extraction for scaff: EXOC4--NUP205

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[3000]   -fusion SPANNING read extraction for scaff: FAM227B--SEMA3D

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[39000]   -fusion SPANNING read extraction for scaff: HSPD1--AC068489.1

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[39000]   -fusion SPANNING read extraction for scaff: HSPD1--LLPHP3

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[179000]   -fusion SPANNING read extraction for scaff: KIAA1109--SPATA5

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[15000]   -fusion SPANNING read extraction for scaff: MEIS2--SEMA3D

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[14000]   -fusion SPANNING read extraction for scaff: MEIS2--LINC02490

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[14000]   -fusion SPANNING read extraction for scaff: MEIS2--AC066614.1

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[16000]   -fusion SPANNING read extraction for scaff: MEIS2--FAM227B

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[45000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[42000]   
[43000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[37000]   
[38000]   
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[41000]   
[42000]   
[43000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[151000]   
[152000]   
[153000]   -fusion SPANNING read extraction for scaff: PIK3CA--TBC1D32

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[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: RDH10--SPAG1

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[87000]   
[88000]   
[89000]   -fusion SPANNING read extraction for scaff: SHANK2--AC104042.1

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[87000]   
[88000]   
[89000]   -fusion SPANNING read extraction for scaff: SHANK2--AC061997.1

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[153000]   
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[158000]   
[159000]   -fusion SPANNING read extraction for scaff: SKIL--NCEH1

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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: SPATA5--DCHS2

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[46000]   
[47000]   -fusion SPANNING read extraction for scaff: SPIDR--ZNF595

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[40000]   
[41000]   -fusion SPANNING read extraction for scaff: TUBGCP2--AC104640.2

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[41000]   -fusion SPANNING read extraction for scaff: TUBGCP2--AC117434.1

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[20000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[76000]   -fusion SPANNING read extraction for scaff: UAP1--INO80
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 37114,
          'lacks exon overlap' => 18004
        };
EM: Starting log likelihood: -3900.571544
EM: Round [1] log likelihood: -3900.542356
EM: Round [2] log likelihood: -3900.513813
EM: Round [3] log likelihood: -3900.485895
EM: Round [4] log likelihood: -3900.458584
EM: Round [5] log likelihood: -3900.431863
EM: Round [6] log likelihood: -3900.405716
EM: Round [7] log likelihood: -3900.380127
EM: Round [8] log likelihood: -3900.355081
EM: Round [9] log likelihood: -3900.330562
EM: Round [10] log likelihood: -3900.306556
EM: Round [11] log likelihood: -3900.283050
EM: Round [12] log likelihood: -3900.260030
EM: Round [13] log likelihood: -3900.237484
EM: Round [14] log likelihood: -3900.215400
EM: Round [15] log likelihood: -3900.193764
EM: Round [16] log likelihood: -3900.172567
EM: Round [17] log likelihood: -3900.151796
EM: Round [18] log likelihood: -3900.131442
EM: Round [19] log likelihood: -3900.111493
EM: Round [20] log likelihood: -3900.091940
EM: Round [21] log likelihood: -3900.072773
EM: Round [22] log likelihood: -3900.053982
EM: Round [23] log likelihood: -3900.035559
EM: Round [24] log likelihood: -3900.017494
EM: Round [25] log likelihood: -3899.999780
EM: Round [26] log likelihood: -3899.982407
EM: Round [27] log likelihood: -3899.965367
EM: Round [28] log likelihood: -3899.948654
EM: Round [29] log likelihood: -3899.932259
EM: Round [30] log likelihood: -3899.916176
EM: Round [31] log likelihood: -3899.900396
EM: Round [32] log likelihood: -3899.884913
EM: Round [33] log likelihood: -3899.869720
EM: Round [34] log likelihood: -3899.854811
EM: Round [35] log likelihood: -3899.840180
EM: Round [36] log likelihood: -3899.825820
EM: Round [37] log likelihood: -3899.811726
EM: Round [38] log likelihood: -3899.797891
EM: Round [39] log likelihood: -3899.784309
EM: Round [40] log likelihood: -3899.770977
EM: Round [41] log likelihood: -3899.757887
EM: Round [42] log likelihood: -3899.745035
EM: Round [43] log likelihood: -3899.732416
EM: Round [44] log likelihood: -3899.720025
EM: Round [45] log likelihood: -3899.707857
EM: Round [46] log likelihood: -3899.695907
EM: Round [47] log likelihood: -3899.684171
EM: Round [48] log likelihood: -3899.672644
EM: Round [49] log likelihood: -3899.661323
EM: Round [50] log likelihood: -3899.650202
EM: Round [51] log likelihood: -3899.639278
EM: Round [52] log likelihood: -3899.628547
EM: Round [53] log likelihood: -3899.618004
EM: Round [54] log likelihood: -3899.607647
EM: Round [55] log likelihood: -3899.597471
EM: Round [56] log likelihood: -3899.587473
EM: Round [57] log likelihood: -3899.577648
EM: Round [58] log likelihood: -3899.567995
EM: Round [59] log likelihood: -3899.558509
EM: Round [60] log likelihood: -3899.549187
EM: Round [61] log likelihood: -3899.540026
EM: Round [62] log likelihood: -3899.531022
EM: Round [63] log likelihood: -3899.522173
EM: Round [64] log likelihood: -3899.513476
EM: Round [65] log likelihood: -3899.504928
EM: Round [66] log likelihood: -3899.496525
EM: Round [67] log likelihood: -3899.488266
EM: Round [68] log likelihood: -3899.480146
EM: Round [69] log likelihood: -3899.472165
EM: Round [70] log likelihood: -3899.464319
EM: Round [71] log likelihood: -3899.456605
EM: Round [72] log likelihood: -3899.449022
EM: Round [73] log likelihood: -3899.441566
EM: Round [74] log likelihood: -3899.434235
EM: Round [75] log likelihood: -3899.427027
EM: Round [76] log likelihood: -3899.419940
EM: Round [77] log likelihood: -3899.412971
EM: Round [78] log likelihood: -3899.406119
EM: Round [79] log likelihood: -3899.399381
EM: Round [80] log likelihood: -3899.392754
EM: Round [81] log likelihood: -3899.386238
EM: Round [82] log likelihood: -3899.379830
EM: Round [83] log likelihood: -3899.373527
EM: Round [84] log likelihood: -3899.367329
EM: Round [85] log likelihood: -3899.361233
EM: Round [86] log likelihood: -3899.355238
EM: Round [87] log likelihood: -3899.349341
EM: Round [88] log likelihood: -3899.343540
EM: Round [89] log likelihood: -3899.337835
EM: Round [90] log likelihood: -3899.332224
EM: Round [91] log likelihood: -3899.326704
EM: Round [92] log likelihood: -3899.321274
EM: Round [93] log likelihood: -3899.315933
EM: Round [94] log likelihood: -3899.310679
EM: Round [95] log likelihood: -3899.305510
EM: Round [96] log likelihood: -3899.300425
EM: Round [97] log likelihood: -3899.295423
EM: Round [98] log likelihood: -3899.290502
EM: Round [99] log likelihood: -3899.285660
EM: Round [100] log likelihood: -3899.280897
EM: Round [101] log likelihood: -3899.276210
EM: Round [102] log likelihood: -3899.271599
EM: Round [103] log likelihood: -3899.267063
EM: Round [104] log likelihood: -3899.262599
EM: Round [105] log likelihood: -3899.258207
EM: Round [106] log likelihood: -3899.253886
EM: Round [107] log likelihood: -3899.249634
EM: Round [108] log likelihood: -3899.245450
EM: Round [109] log likelihood: -3899.241333
EM: Round [110] log likelihood: -3899.237281
EM: Round [111] log likelihood: -3899.233295
EM: Round [112] log likelihood: -3899.229372
EM: Round [113] log likelihood: -3899.225511
EM: Round [114] log likelihood: -3899.221713
EM: Round [115] log likelihood: -3899.217974
EM: Round [116] log likelihood: -3899.214295
EM: Round [117] log likelihood: -3899.210674
EM: Round [118] log likelihood: -3899.207111
EM: Round [119] log likelihood: -3899.203604
EM: Round [120] log likelihood: -3899.200153
EM: Round [121] log likelihood: -3899.196757
EM: Round [122] log likelihood: -3899.193414
EM: Round [123] log likelihood: -3899.190124
EM: Round [124] log likelihood: -3899.186886
EM: Round [125] log likelihood: -3899.183699
EM: Round [126] log likelihood: -3899.180562
EM: Round [127] log likelihood: -3899.177474
EM: Round [128] log likelihood: -3899.174436
EM: Round [129] log likelihood: -3899.171445
EM: Round [130] log likelihood: -3899.168500
EM: Round [131] log likelihood: -3899.165603
EM: Round [132] log likelihood: -3899.162750
EM: Round [133] log likelihood: -3899.159943
EM: Round [134] log likelihood: -3899.157179
EM: Round [135] log likelihood: -3899.154459
EM: Round [136] log likelihood: -3899.151781
EM: Round [137] log likelihood: -3899.149145
EM: Round [138] log likelihood: -3899.146550
EM: Round [139] log likelihood: -3899.143996
EM: Round [140] log likelihood: -3899.141481
EM: Round [141] log likelihood: -3899.139006
EM: Round [142] log likelihood: -3899.136569
EM: Round [143] log likelihood: -3899.134171
EM: Round [144] log likelihood: -3899.131809
EM: Round [145] log likelihood: -3899.129485
EM: Round [146] log likelihood: -3899.127196
EM: Round [147] log likelihood: -3899.124944
EM: Round [148] log likelihood: -3899.122726
EM: Round [149] log likelihood: -3899.120542
EM: Round [150] log likelihood: -3899.118393
EM: Round [151] log likelihood: -3899.116276
EM: Round [152] log likelihood: -3899.114193
EM: Round [153] log likelihood: -3899.112142
EM: Round [154] log likelihood: -3899.110122
EM: Round [155] log likelihood: -3899.108134
EM: Round [156] log likelihood: -3899.106177
EM: Round [157] log likelihood: -3899.104250
EM: Round [158] log likelihood: -3899.102352
EM: Round [159] log likelihood: -3899.100484
EM: Round [160] log likelihood: -3899.098645
EM: Round [161] log likelihood: -3899.096834
EM: Round [162] log likelihood: -3899.095051
EM: Round [163] log likelihood: -3899.093296
EM: Round [164] log likelihood: -3899.091567
EM: Round [165] log likelihood: -3899.089866
EM: Round [166] log likelihood: -3899.088190
EM: Round [167] log likelihood: -3899.086540
EM: Round [168] log likelihood: -3899.084916
EM: Round [169] log likelihood: -3899.083316
EM: Round [170] log likelihood: -3899.081742
EM: Round [171] log likelihood: -3899.080191
EM: Round [172] log likelihood: -3899.078664
EM: Round [173] log likelihood: -3899.077161
EM: Round [174] log likelihood: -3899.075680
EM: Round [175] log likelihood: -3899.074223
EM: Round [176] log likelihood: -3899.072788
EM: Round [177] log likelihood: -3899.071374
EM: Round [178] log likelihood: -3899.069983
EM: Round [179] log likelihood: -3899.068613
EM: Round [180] log likelihood: -3899.067263
EM: Round [181] log likelihood: -3899.065935
EM: Round [182] log likelihood: -3899.064627
EM: Round [183] log likelihood: -3899.063338
EM: Round [184] log likelihood: -3899.062070
EM: Round [185] log likelihood: -3899.060821
EM: Round [186] log likelihood: -3899.059591
EM: Round [187] log likelihood: -3899.058379
EM: Round [188] log likelihood: -3899.057187
EM: Round [189] log likelihood: -3899.056012
EM: Round [190] log likelihood: -3899.054855
EM: Round [191] log likelihood: -3899.053717
EM: Round [192] log likelihood: -3899.052595
EM: Round [193] log likelihood: -3899.051491
EM: Round [194] log likelihood: -3899.050403
EM: Round [195] log likelihood: -3899.049332
EM: Round [196] log likelihood: -3899.048277
EM: Round [197] log likelihood: -3899.047239
EM: Round [198] log likelihood: -3899.046216
EM: Round [199] log likelihood: -3899.045209
EM: Round [200] log likelihood: -3899.044217
EM: Round [201] log likelihood: -3899.043240
EM: Round [202] log likelihood: -3899.042278
EM: Round [203] log likelihood: -3899.041331
EM: Round [204] log likelihood: -3899.040398
EM: Round [205] log likelihood: -3899.039479
EM: Round [206] log likelihood: -3899.038574
EM: Round [207] log likelihood: -3899.037683
EM: Round [208] log likelihood: -3899.036806
EM: Round [209] log likelihood: -3899.035942
EM: Round [210] log likelihood: -3899.035091
EM: Round [211] log likelihood: -3899.034253
EM: Round [212] log likelihood: -3899.033428
EM: Round [213] log likelihood: -3899.032615
EM: Round [214] log likelihood: -3899.031814
EM: Round [215] log likelihood: -3899.031026
EM: Round [216] log likelihood: -3899.030250
EM: Round [217] log likelihood: -3899.029485
EM: Round [218] log likelihood: -3899.028732
EM: Round [219] log likelihood: -3899.027991
EM: Round [220] log likelihood: -3899.027261
EM: Round [221] log likelihood: -3899.026541
EM: Round [222] log likelihood: -3899.025833
EM: Round [223] log likelihood: -3899.025135
EM: Round [224] log likelihood: -3899.024448
EM: Round [225] log likelihood: -3899.023772
EM: Round [226] log likelihood: -3899.023105
EM: Round [227] log likelihood: -3899.022449
EM: Round [228] log likelihood: -3899.021803
EM: Round [229] log likelihood: -3899.021166
EM: Round [230] log likelihood: -3899.020539
EM: Round [231] log likelihood: -3899.019922
EM: Round [232] log likelihood: -3899.019314
EM: Round [233] log likelihood: -3899.018715
EM: Round [234] log likelihood: -3899.018125
EM: Round [235] log likelihood: -3899.017544
EM: Round [236] log likelihood: -3899.016972
EM: Round [237] log likelihood: -3899.016409
EM: Round [238] log likelihood: -3899.015854
EM: Round [239] log likelihood: -3899.015307
EM: Round [240] log likelihood: -3899.014769
EM: Round [241] log likelihood: -3899.014239
EM: Round [242] log likelihood: -3899.013717
EM: Round [243] log likelihood: -3899.013202
EM: Round [244] log likelihood: -3899.012696
EM: Round [245] log likelihood: -3899.012197
EM: Round [246] log likelihood: -3899.011706
EM: Round [247] log likelihood: -3899.011222
EM: Round [248] log likelihood: -3899.010745
EM: Round [249] log likelihood: -3899.010276
EM: Round [250] log likelihood: -3899.009814
EM: Round [251] log likelihood: -3899.009358
EM: Round [252] log likelihood: -3899.008910
EM: Round [253] log likelihood: -3899.008468
EM: Round [254] log likelihood: -3899.008033
EM: Round [255] log likelihood: -3899.007605
EM: Round [256] log likelihood: -3899.007183
EM: Round [257] log likelihood: -3899.006767
EM: Round [258] log likelihood: -3899.006358
EM: Round [259] log likelihood: -3899.005954
EM: Round [260] log likelihood: -3899.005557
EM: Round [261] log likelihood: -3899.005166
EM: Round [262] log likelihood: -3899.004781
EM: Round [263] log likelihood: -3899.004402
EM: Round [264] log likelihood: -3899.004028
EM: Round [265] log likelihood: -3899.003660
EM: Round [266] log likelihood: -3899.003297
EM: Round [267] log likelihood: -3899.002940
EM: Round [268] log likelihood: -3899.002589
EM: Round [269] log likelihood: -3899.002242
EM: Round [270] log likelihood: -3899.001901
EM: Round [271] log likelihood: -3899.001565
EM: Round [272] log likelihood: -3899.001234
EM: Round [273] log likelihood: -3899.000908
EM: Round [274] log likelihood: -3899.000587
EM: Round [275] log likelihood: -3899.000271
EM: Round [276] log likelihood: -3898.999959
EM: Round [277] log likelihood: -3898.999653
EM: Round [278] log likelihood: -3898.999351
EM: Round [279] log likelihood: -3898.999053
EM: Round [280] log likelihood: -3898.998760
EM: Round [281] log likelihood: -3898.998471
EM: Round [282] log likelihood: -3898.998187
EM: Round [283] log likelihood: -3898.997907
EM: Round [284] log likelihood: -3898.997631
EM: Round [285] log likelihood: -3898.997359
EM: Round [286] log likelihood: -3898.997091
EM: Round [287] log likelihood: -3898.996828
EM: Round [288] log likelihood: -3898.996568
EM: Round [289] log likelihood: -3898.996312
EM: Round [290] log likelihood: -3898.996061
EM: Round [291] log likelihood: -3898.995813
EM: Round [292] log likelihood: -3898.995568
EM: Round [293] log likelihood: -3898.995327
EM: Round [294] log likelihood: -3898.995090
EM: Round [295] log likelihood: -3898.994857
EM: Round [296] log likelihood: -3898.994627
EM: Round [297] log likelihood: -3898.994400
EM: Round [298] log likelihood: -3898.994177
EM: Round [299] log likelihood: -3898.993957
EM: Round [300] log likelihood: -3898.993741
EM: Round [301] log likelihood: -3898.993528
EM: Round [302] log likelihood: -3898.993318
EM: Round [303] log likelihood: -3898.993111
EM: Round [304] log likelihood: -3898.992907
EM: Round [305] log likelihood: -3898.992707
EM: Round [306] log likelihood: -3898.992509
EM: Round [307] log likelihood: -3898.992314
EM: Round [308] log likelihood: -3898.992122
EM: Round [309] log likelihood: -3898.991934
EM: Round [310] log likelihood: -3898.991748
EM: Round [311] log likelihood: -3898.991564
EM: Round [312] log likelihood: -3898.991384
EM: Round [313] log likelihood: -3898.991206
EM: Round [314] log likelihood: -3898.991031
EM: Round [315] log likelihood: -3898.990858
EM: Round [316] log likelihood: -3898.990689
EM: Round [317] log likelihood: -3898.990521
EM: Round [318] log likelihood: -3898.990356
EM: Round [319] log likelihood: -3898.990194
EM: Round [320] log likelihood: -3898.990034
EM: Round [321] log likelihood: -3898.989877
EM: Round [322] log likelihood: -3898.989721
EM: Round [323] log likelihood: -3898.989569
EM: Round [324] log likelihood: -3898.989418
EM: Round [325] log likelihood: -3898.989270
EM: Round [326] log likelihood: -3898.989124
EM: Round [327] log likelihood: -3898.988980
EM: Round [328] log likelihood: -3898.988838
EM: Round [329] log likelihood: -3898.988699
EM: Round [330] log likelihood: -3898.988561
EM: Round [331] log likelihood: -3898.988426
EM: Round [332] log likelihood: -3898.988293
EM: Round [333] log likelihood: -3898.988161
EM: Round [334] log likelihood: -3898.988032
EM: Round [335] log likelihood: -3898.987904
EM: Round [336] log likelihood: -3898.987779
EM: Round [337] log likelihood: -3898.987655
EM: Round [338] log likelihood: -3898.987533
EM: Round [339] log likelihood: -3898.987413
EM: Round [340] log likelihood: -3898.987295
EM: Round [341] log likelihood: -3898.987179
EM: Round [342] log likelihood: -3898.987064
EM: Round [343] log likelihood: -3898.986951
EM: Round [344] log likelihood: -3898.986840
EM: Round [345] log likelihood: -3898.986731
EM: Round [346] log likelihood: -3898.986623
EM: Round [347] log likelihood: -3898.986516
EM: Round [348] log likelihood: -3898.986412
EM: Round [349] log likelihood: -3898.986309
EM: Round [350] log likelihood: -3898.986207
EM: Round [351] log likelihood: -3898.986107
EM: Round [352] log likelihood: -3898.986008
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.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.UbMrnt2Om7/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_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.UbMrnt2Om7/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_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.UbMrnt2Om7/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3755.283441
EM: Round [1] log likelihood: -3755.283441
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 219597035
Warning - not locating file: /tmp/nxf.UbMrnt2Om7/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000259543.1]
WARNING, no entry stored in dbm for [ENSG00000234717.2]
ls: cannot access 'IGV_inputs': No such file or directory