Done.
-parsing GTF file: /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.LWz6SM2kxe/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.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
11:27:59 : INFO : Done.
-parsing GTF file: /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam

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[2710000]   -done parsing /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'small anchor length' => 33,
          'num genes matched < 2' => 30,
          'low complexity anchor region' => 10,
          'seq-similar region overlap' => 884,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 180,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 41,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 15,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2252,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 8,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
          'per_id < 96' => 32732,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
          'exons hit < 2' => 6,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
          ' ** passed ** ' => 18180,
          'excessive soft clipping' => 16568,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 1286
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[9000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[471000]   -fusion SPANNING read extraction for scaff: MEOX2--CRPPA

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[464000]   
[465000]   -fusion SPANNING read extraction for scaff: MEOX2--AC006041.1

[1000]   
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[55000]   
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[58000]   
[59000]   
[60000]   
[61000]   -fusion SPANNING read extraction for scaff: NPHP3--ACAD11

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: OR8D1--OR8A1

[1000]   
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[4000]   
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[6000]   
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[8000]   
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[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
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[6000]   
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[8000]   
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[127000]   
[128000]   
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[130000]   
[131000]   
[132000]   
[133000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[103000]   
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[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[12000]   
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[20000]   
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[40000]   
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[65000]   
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[68000]   
[69000]   
[70000]   
[71000]   
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[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[20000]   
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[25000]   
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[27000]   
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[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   -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]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

[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--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -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]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
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[18000]   
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[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

[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]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
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[20000]   
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[32000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[138000]   
[139000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

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[36000]   
[37000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[21000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[24000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[25000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[31000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[138000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[6000]   -fusion SPANNING read extraction for scaff: SLC5A4P1--OR8A1

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[108000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[49000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[14000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[15000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[64000]   
[65000]   -fusion SPANNING read extraction for scaff: WASH3P--LINC01237

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[65000]   -fusion SPANNING read extraction for scaff: WASH3P--LINC01880
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 5464,
          'seq similar region alignment' => 107850
        };
EM: Starting log likelihood: -6034.275448
EM: Round [1] log likelihood: -6033.845861
EM: Round [2] log likelihood: -6033.515176
EM: Round [3] log likelihood: -6033.198294
EM: Round [4] log likelihood: -6032.891806
EM: Round [5] log likelihood: -6032.594629
EM: Round [6] log likelihood: -6032.305925
EM: Round [7] log likelihood: -6032.025018
EM: Round [8] log likelihood: -6031.751366
EM: Round [9] log likelihood: -6031.484539
EM: Round [10] log likelihood: -6031.224197
EM: Round [11] log likelihood: -6030.970074
EM: Round [12] log likelihood: -6030.721961
EM: Round [13] log likelihood: -6030.479696
EM: Round [14] log likelihood: -6030.243149
EM: Round [15] log likelihood: -6030.012218
EM: Round [16] log likelihood: -6029.786818
EM: Round [17] log likelihood: -6029.566875
EM: Round [18] log likelihood: -6029.352322
EM: Round [19] log likelihood: -6029.143097
EM: Round [20] log likelihood: -6028.939134
EM: Round [21] log likelihood: -6028.740370
EM: Round [22] log likelihood: -6028.546734
EM: Round [23] log likelihood: -6028.358152
EM: Round [24] log likelihood: -6028.174545
EM: Round [25] log likelihood: -6027.995828
EM: Round [26] log likelihood: -6027.821911
EM: Round [27] log likelihood: -6027.652699
EM: Round [28] log likelihood: -6027.488090
EM: Round [29] log likelihood: -6027.327982
EM: Round [30] log likelihood: -6027.172265
EM: Round [31] log likelihood: -6027.020828
EM: Round [32] log likelihood: -6026.873558
EM: Round [33] log likelihood: -6026.730338
EM: Round [34] log likelihood: -6026.591053
EM: Round [35] log likelihood: -6026.455585
EM: Round [36] log likelihood: -6026.323816
EM: Round [37] log likelihood: -6026.195631
EM: Round [38] log likelihood: -6026.070911
EM: Round [39] log likelihood: -6025.949544
EM: Round [40] log likelihood: -6025.831415
EM: Round [41] log likelihood: -6025.716413
EM: Round [42] log likelihood: -6025.604431
EM: Round [43] log likelihood: -6025.495361
EM: Round [44] log likelihood: -6025.389099
EM: Round [45] log likelihood: -6025.285545
EM: Round [46] log likelihood: -6025.184600
EM: Round [47] log likelihood: -6025.086170
EM: Round [48] log likelihood: -6024.990163
EM: Round [49] log likelihood: -6024.896489
EM: Round [50] log likelihood: -6024.805064
EM: Round [51] log likelihood: -6024.715804
EM: Round [52] log likelihood: -6024.628630
EM: Round [53] log likelihood: -6024.543465
EM: Round [54] log likelihood: -6024.460236
EM: Round [55] log likelihood: -6024.378874
EM: Round [56] log likelihood: -6024.299309
EM: Round [57] log likelihood: -6024.221477
EM: Round [58] log likelihood: -6024.145316
EM: Round [59] log likelihood: -6024.070768
EM: Round [60] log likelihood: -6023.997774
EM: Round [61] log likelihood: -6023.926280
EM: Round [62] log likelihood: -6023.856235
EM: Round [63] log likelihood: -6023.787589
EM: Round [64] log likelihood: -6023.720294
EM: Round [65] log likelihood: -6023.654306
EM: Round [66] log likelihood: -6023.589579
EM: Round [67] log likelihood: -6023.526074
EM: Round [68] log likelihood: -6023.463750
EM: Round [69] log likelihood: -6023.402571
EM: Round [70] log likelihood: -6023.342498
EM: Round [71] log likelihood: -6023.283499
EM: Round [72] log likelihood: -6023.225540
EM: Round [73] log likelihood: -6023.168590
EM: Round [74] log likelihood: -6023.112618
EM: Round [75] log likelihood: -6023.057596
EM: Round [76] log likelihood: -6023.003495
EM: Round [77] log likelihood: -6022.950291
EM: Round [78] log likelihood: -6022.897957
EM: Round [79] log likelihood: -6022.846470
EM: Round [80] log likelihood: -6022.795806
EM: Round [81] log likelihood: -6022.745943
EM: Round [82] log likelihood: -6022.696860
EM: Round [83] log likelihood: -6022.648536
EM: Round [84] log likelihood: -6022.600953
EM: Round [85] log likelihood: -6022.554091
EM: Round [86] log likelihood: -6022.507932
EM: Round [87] log likelihood: -6022.462459
EM: Round [88] log likelihood: -6022.417656
EM: Round [89] log likelihood: -6022.373506
EM: Round [90] log likelihood: -6022.329995
EM: Round [91] log likelihood: -6022.287107
EM: Round [92] log likelihood: -6022.244828
EM: Round [93] log likelihood: -6022.203145
EM: Round [94] log likelihood: -6022.162044
EM: Round [95] log likelihood: -6022.121513
EM: Round [96] log likelihood: -6022.081539
EM: Round [97] log likelihood: -6022.042110
EM: Round [98] log likelihood: -6022.003216
EM: Round [99] log likelihood: -6021.964844
EM: Round [100] log likelihood: -6021.926985
EM: Round [101] log likelihood: -6021.889628
EM: Round [102] log likelihood: -6021.852763
EM: Round [103] log likelihood: -6021.816380
EM: Round [104] log likelihood: -6021.780470
EM: Round [105] log likelihood: -6021.745024
EM: Round [106] log likelihood: -6021.710033
EM: Round [107] log likelihood: -6021.675488
EM: Round [108] log likelihood: -6021.641381
EM: Round [109] log likelihood: -6021.607705
EM: Round [110] log likelihood: -6021.574451
EM: Round [111] log likelihood: -6021.541611
EM: Round [112] log likelihood: -6021.509179
EM: Round [113] log likelihood: -6021.477147
EM: Round [114] log likelihood: -6021.445508
EM: Round [115] log likelihood: -6021.414255
EM: Round [116] log likelihood: -6021.383382
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EM: Round [577] log likelihood: -6018.245218
EM: Round [578] log likelihood: -6018.244488
EM: Round [579] log likelihood: -6018.243763
EM: Round [580] log likelihood: -6018.243042
EM: Round [581] log likelihood: -6018.242326
EM: Round [582] log likelihood: -6018.241615
EM: Round [583] log likelihood: -6018.240909
EM: Round [584] log likelihood: -6018.240208
EM: Round [585] log likelihood: -6018.239511
EM: Round [586] log likelihood: -6018.238818
EM: Round [587] log likelihood: -6018.238130
EM: Round [588] log likelihood: -6018.237447
EM: Round [589] log likelihood: -6018.236768
EM: Round [590] log likelihood: -6018.236094
EM: Round [591] log likelihood: -6018.235424
EM: Round [592] log likelihood: -6018.234758
EM: Round [593] log likelihood: -6018.234097
EM: Round [594] log likelihood: -6018.233440
EM: Round [595] log likelihood: -6018.232788
EM: Round [596] log likelihood: -6018.232140
EM: Round [597] log likelihood: -6018.231496
EM: Round [598] log likelihood: -6018.230856
EM: Round [599] log likelihood: -6018.230220
EM: Round [600] log likelihood: -6018.229589
EM: Round [601] log likelihood: -6018.228962
EM: Round [602] log likelihood: -6018.228339
EM: Round [603] log likelihood: -6018.227720
EM: Round [604] log likelihood: -6018.227105
EM: Round [605] log likelihood: -6018.226494
EM: Round [606] log likelihood: -6018.225887
EM: Round [607] log likelihood: -6018.225284
EM: Round [608] log likelihood: -6018.224685
EM: Round [609] log likelihood: -6018.224090
EM: Round [610] log likelihood: -6018.223498
EM: Round [611] log likelihood: -6018.222911
EM: Round [612] log likelihood: -6018.222328
EM: Round [613] log likelihood: -6018.221748
EM: Round [614] log likelihood: -6018.221172
EM: Round [615] log likelihood: -6018.220600
EM: Round [616] log likelihood: -6018.220031
EM: Round [617] log likelihood: -6018.219467
EM: Round [618] log likelihood: -6018.218905
EM: Round [619] log likelihood: -6018.218348
EM: Round [620] log likelihood: -6018.217794
EM: Round [621] log likelihood: -6018.217244
EM: Round [622] log likelihood: -6018.216698
EM: Round [623] log likelihood: -6018.216154
EM: Round [624] log likelihood: -6018.215615
EM: Round [625] log likelihood: -6018.215079
EM: Round [626] log likelihood: -6018.214546
EM: Round [627] log likelihood: -6018.214017
EM: Round [628] log likelihood: -6018.213492
EM: Round [629] log likelihood: -6018.212970
EM: Round [630] log likelihood: -6018.212451
EM: Round [631] log likelihood: -6018.211935
EM: Round [632] log likelihood: -6018.211423
EM: Round [633] log likelihood: -6018.210914
EM: Round [634] log likelihood: -6018.210409
EM: Round [635] log likelihood: -6018.209907
EM: Round [636] log likelihood: -6018.209408
EM: Round [637] log likelihood: -6018.208912
EM: Round [638] log likelihood: -6018.208419
EM: Round [639] log likelihood: -6018.207930
EM: Round [640] log likelihood: -6018.207444
EM: Round [641] log likelihood: -6018.206961
EM: Round [642] log likelihood: -6018.206481
EM: Round [643] log likelihood: -6018.206004
EM: Round [644] log likelihood: -6018.205530
EM: Round [645] log likelihood: -6018.205060
EM: Round [646] log likelihood: -6018.204592
EM: Round [647] log likelihood: -6018.204127
EM: Round [648] log likelihood: -6018.203666
EM: Round [649] log likelihood: -6018.203207
EM: Round [650] log likelihood: -6018.202752
EM: Round [651] log likelihood: -6018.202299
EM: Round [652] log likelihood: -6018.201849
EM: Round [653] log likelihood: -6018.201402
EM: Round [654] log likelihood: -6018.200958
EM: Round [655] log likelihood: -6018.200517
EM: Round [656] log likelihood: -6018.200078
EM: Round [657] log likelihood: -6018.199643
EM: Round [658] log likelihood: -6018.199210
EM: Round [659] log likelihood: -6018.198780
EM: Round [660] log likelihood: -6018.198353
EM: Round [661] log likelihood: -6018.197928
EM: Round [662] log likelihood: -6018.197507
EM: Round [663] log likelihood: -6018.197088
EM: Round [664] log likelihood: -6018.196671
EM: Round [665] log likelihood: -6018.196258
EM: Round [666] log likelihood: -6018.195847
EM: Round [667] log likelihood: -6018.195438
EM: Round [668] log likelihood: -6018.195032
EM: Round [669] log likelihood: -6018.194629
EM: Round [670] log likelihood: -6018.194229
EM: Round [671] log likelihood: -6018.193831
EM: Round [672] log likelihood: -6018.193435
EM: Round [673] log likelihood: -6018.193042
EM: Round [674] log likelihood: -6018.192652
EM: Round [675] log likelihood: -6018.192264
EM: Round [676] log likelihood: -6018.191878
EM: Round [677] log likelihood: -6018.191495
EM: Round [678] log likelihood: -6018.191115
EM: Round [679] log likelihood: -6018.190737
EM: Round [680] log likelihood: -6018.190361
EM: Round [681] log likelihood: -6018.189988
EM: Round [682] log likelihood: -6018.189617
EM: Round [683] log likelihood: -6018.189248
EM: Round [684] log likelihood: -6018.188882
EM: Round [685] log likelihood: -6018.188518
EM: Round [686] log likelihood: -6018.188157
EM: Round [687] log likelihood: -6018.187797
EM: Round [688] log likelihood: -6018.187440
EM: Round [689] log likelihood: -6018.187086
EM: Round [690] log likelihood: -6018.186733
EM: Round [691] log likelihood: -6018.186383
EM: Round [692] log likelihood: -6018.186035
EM: Round [693] log likelihood: -6018.185689
EM: Round [694] log likelihood: -6018.185346
EM: Round [695] log likelihood: -6018.185004
EM: Round [696] log likelihood: -6018.184665
EM: Round [697] log likelihood: -6018.184328
EM: Round [698] log likelihood: -6018.183993
EM: Round [699] log likelihood: -6018.183660
EM: Round [700] log likelihood: -6018.183330
EM: Round [701] log likelihood: -6018.183001
EM: Round [702] log likelihood: -6018.182675
EM: Round [703] log likelihood: -6018.182350
EM: Round [704] log likelihood: -6018.182028
EM: Round [705] log likelihood: -6018.181708
EM: Round [706] log likelihood: -6018.181389
EM: Round [707] log likelihood: -6018.181073
EM: Round [708] log likelihood: -6018.180759
EM: Round [709] log likelihood: -6018.180446
EM: Round [710] log likelihood: -6018.180136
EM: Round [711] log likelihood: -6018.179828
EM: Round [712] log likelihood: -6018.179521
EM: Round [713] log likelihood: -6018.179217
EM: Round [714] log likelihood: -6018.178914
EM: Round [715] log likelihood: -6018.178613
EM: Round [716] log likelihood: -6018.178315
EM: Round [717] log likelihood: -6018.178018
EM: Round [718] log likelihood: -6018.177723
EM: Round [719] log likelihood: -6018.177430
EM: Round [720] log likelihood: -6018.177138
EM: Round [721] log likelihood: -6018.176849
EM: Round [722] log likelihood: -6018.176561
EM: Round [723] log likelihood: -6018.176276
EM: Round [724] log likelihood: -6018.175991
EM: Round [725] log likelihood: -6018.175709
EM: Round [726] log likelihood: -6018.175429
EM: Round [727] log likelihood: -6018.175150
EM: Round [728] log likelihood: -6018.174873
EM: Round [729] log likelihood: -6018.174598
EM: Round [730] log likelihood: -6018.174324
EM: Round [731] log likelihood: -6018.174053
EM: Round [732] log likelihood: -6018.173783
EM: Round [733] log likelihood: -6018.173514
EM: Round [734] log likelihood: -6018.173248
EM: Round [735] log likelihood: -6018.172983
EM: Round [736] log likelihood: -6018.172719
EM: Round [737] log likelihood: -6018.172458
EM: Round [738] log likelihood: -6018.172198
EM: Round [739] log likelihood: -6018.171939
EM: Round [740] log likelihood: -6018.171682
EM: Round [741] log likelihood: -6018.171427
EM: Round [742] log likelihood: -6018.171174
EM: Round [743] log likelihood: -6018.170922
EM: Round [744] log likelihood: -6018.170671
EM: Round [745] log likelihood: -6018.170422
EM: Round [746] log likelihood: -6018.170175
EM: Round [747] log likelihood: -6018.169929
EM: Round [748] log likelihood: -6018.169685
EM: Round [749] log likelihood: -6018.169442
EM: Round [750] log likelihood: -6018.169201
EM: Round [751] log likelihood: -6018.168961
EM: Round [752] log likelihood: -6018.168723
EM: Round [753] log likelihood: -6018.168487
EM: Round [754] log likelihood: -6018.168251
EM: Round [755] log likelihood: -6018.168018
EM: Round [756] log likelihood: -6018.167785
EM: Round [757] log likelihood: -6018.167555
EM: Round [758] log likelihood: -6018.167325
EM: Round [759] log likelihood: -6018.167097
EM: Round [760] log likelihood: -6018.166871
EM: Round [761] log likelihood: -6018.166645
EM: Round [762] log likelihood: -6018.166422
EM: Round [763] log likelihood: -6018.166199
EM: Round [764] log likelihood: -6018.165978
EM: Round [765] log likelihood: -6018.165759
EM: Round [766] log likelihood: -6018.165541
EM: Round [767] log likelihood: -6018.165324
EM: Round [768] log likelihood: -6018.165108
EM: Round [769] log likelihood: -6018.164894
EM: Round [770] log likelihood: -6018.164681
EM: Round [771] log likelihood: -6018.164469
EM: Round [772] log likelihood: -6018.164259
EM: Round [773] log likelihood: -6018.164050
EM: Round [774] log likelihood: -6018.163843
EM: Round [775] log likelihood: -6018.163636
EM: Round [776] log likelihood: -6018.163431
EM: Round [777] log likelihood: -6018.163227
EM: Round [778] log likelihood: -6018.163025
EM: Round [779] log likelihood: -6018.162824
EM: Round [780] log likelihood: -6018.162624
EM: Round [781] log likelihood: -6018.162425
EM: Round [782] log likelihood: -6018.162227
EM: Round [783] log likelihood: -6018.162031
EM: Round [784] log likelihood: -6018.161836
EM: Round [785] log likelihood: -6018.161642
EM: Round [786] log likelihood: -6018.161449
EM: Round [787] log likelihood: -6018.161258
EM: Round [788] log likelihood: -6018.161067
EM: Round [789] log likelihood: -6018.160878
EM: Round [790] log likelihood: -6018.160690
EM: Round [791] log likelihood: -6018.160503
EM: Round [792] log likelihood: -6018.160317
EM: Round [793] log likelihood: -6018.160133
EM: Round [794] log likelihood: -6018.159949
EM: Round [795] log likelihood: -6018.159767
EM: Round [796] log likelihood: -6018.159586
EM: Round [797] log likelihood: -6018.159406
EM: Round [798] log likelihood: -6018.159227
EM: Round [799] log likelihood: -6018.159049
EM: Round [800] log likelihood: -6018.158872
EM: Round [801] log likelihood: -6018.158697
EM: Round [802] log likelihood: -6018.158522
EM: Round [803] log likelihood: -6018.158349
EM: Round [804] log likelihood: -6018.158176
EM: Round [805] log likelihood: -6018.158005
EM: Round [806] log likelihood: -6018.157834
EM: Round [807] log likelihood: -6018.157665
EM: Round [808] log likelihood: -6018.157497
EM: Round [809] log likelihood: -6018.157330
EM: Round [810] log likelihood: -6018.157163
EM: Round [811] log likelihood: -6018.156998
EM: Round [812] log likelihood: -6018.156834
EM: Round [813] log likelihood: -6018.156671
EM: Round [814] log likelihood: -6018.156509
EM: Round [815] log likelihood: -6018.156348
EM: Round [816] log likelihood: -6018.156187
EM: Round [817] log likelihood: -6018.156028
EM: Round [818] log likelihood: -6018.155870
EM: Round [819] log likelihood: -6018.155713
EM: Round [820] log likelihood: -6018.155556
EM: Round [821] log likelihood: -6018.155401
EM: Round [822] log likelihood: -6018.155247
EM: Round [823] log likelihood: -6018.155093
EM: Round [824] log likelihood: -6018.154941
EM: Round [825] log likelihood: -6018.154789
EM: Round [826] log likelihood: -6018.154639
EM: Round [827] log likelihood: -6018.154489
EM: Round [828] log likelihood: -6018.154340
EM: Round [829] log likelihood: -6018.154192
EM: Round [830] log likelihood: -6018.154045
EM: Round [831] log likelihood: -6018.153899
EM: Round [832] log likelihood: -6018.153754
EM: Round [833] log likelihood: -6018.153609
EM: Round [834] log likelihood: -6018.153466
EM: Round [835] log likelihood: -6018.153323
EM: Round [836] log likelihood: -6018.153182
EM: Round [837] log likelihood: -6018.153041
EM: Round [838] log likelihood: -6018.152901
EM: Round [839] log likelihood: -6018.152762
EM: Round [840] log likelihood: -6018.152623
EM: Round [841] log likelihood: -6018.152486
EM: Round [842] log likelihood: -6018.152349
EM: Round [843] log likelihood: -6018.152213
EM: Round [844] log likelihood: -6018.152078
EM: Round [845] log likelihood: -6018.151944
EM: Round [846] log likelihood: -6018.151811
EM: Round [847] log likelihood: -6018.151678
EM: Round [848] log likelihood: -6018.151547
EM: Round [849] log likelihood: -6018.151416
EM: Round [850] log likelihood: -6018.151285
EM: Round [851] log likelihood: -6018.151156
EM: Round [852] log likelihood: -6018.151028
EM: Round [853] log likelihood: -6018.150900
EM: Round [854] log likelihood: -6018.150773
EM: Round [855] log likelihood: -6018.150646
EM: Round [856] log likelihood: -6018.150521
EM: Round [857] log likelihood: -6018.150396
EM: Round [858] log likelihood: -6018.150272
EM: Round [859] log likelihood: -6018.150149
EM: Round [860] log likelihood: -6018.150027
EM: Round [861] log likelihood: -6018.149905
EM: Round [862] log likelihood: -6018.149784
EM: Round [863] log likelihood: -6018.149664
EM: Round [864] log likelihood: -6018.149544
EM: Round [865] log likelihood: -6018.149425
EM: Round [866] log likelihood: -6018.149307
EM: Round [867] log likelihood: -6018.149190
EM: Round [868] log likelihood: -6018.149073
EM: Round [869] log likelihood: -6018.148957
EM: Round [870] log likelihood: -6018.148842
EM: Round [871] log likelihood: -6018.148727
EM: Round [872] log likelihood: -6018.148613
EM: Round [873] log likelihood: -6018.148500
EM: Round [874] log likelihood: -6018.148387
EM: Round [875] log likelihood: -6018.148275
EM: Round [876] log likelihood: -6018.148164
EM: Round [877] log likelihood: -6018.148054
EM: Round [878] log likelihood: -6018.147944
EM: Round [879] log likelihood: -6018.147835
EM: Round [880] log likelihood: -6018.147726
EM: Round [881] log likelihood: -6018.147618
EM: Round [882] log likelihood: -6018.147511
EM: Round [883] log likelihood: -6018.147404
EM: Round [884] log likelihood: -6018.147298
EM: Round [885] log likelihood: -6018.147193
EM: Round [886] log likelihood: -6018.147088
EM: Round [887] log likelihood: -6018.146984
EM: Round [888] log likelihood: -6018.146881
EM: Round [889] log likelihood: -6018.146778
EM: Round [890] log likelihood: -6018.146676
EM: Round [891] log likelihood: -6018.146574
EM: Round [892] log likelihood: -6018.146473
EM: Round [893] log likelihood: -6018.146373
EM: Round [894] log likelihood: -6018.146273
EM: Stopping iterations at round 894 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_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.LWz6SM2kxe/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3926.358573
EM: Round [1] log likelihood: -3926.270518
EM: Round [2] log likelihood: -3926.268251
EM: Round [3] log likelihood: -3926.268193
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 246755598
Warning - not locating file: /tmp/nxf.LWz6SM2kxe/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed
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 [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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000185596.16]
WARNING, no entry stored in dbm for [ENSG00000233806.7]
ls: cannot access 'IGV_inputs': No such file or directory