Done.
-parsing GTF file: /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.Zp1BtusVJM/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.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.Zp1BtusVJM/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.Zp1BtusVJM/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
09:33:04 : INFO : Done.
-parsing GTF file: /tmp/nxf.Zp1BtusVJM/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.Zp1BtusVJM/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[4360000]   -done parsing /tmp/nxf.Zp1BtusVJM/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 25131,
          'per_id < 96' => 14912,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 40,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
          ' ** passed ** ' => 8686,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 24,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 18,
          'small anchor length' => 17,
          'low complexity anchor region' => 43,
          'exons hit < 2' => 13,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 189,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 441,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 36,
          'seq-similar region overlap' => 299,
          'num genes matched < 2' => 75,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 70
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.Zp1BtusVJM/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
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[4000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

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[23000]   -fusion SPANNING read extraction for scaff: AC026412.1--SDHAP1

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[63000]   -fusion SPANNING read extraction for scaff: AC084809.1--SELENBP1

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[3000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[4000]   -fusion SPANNING read extraction for scaff: AC242842.2--KCNN3

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[343000]   -fusion SPANNING read extraction for scaff: ACACA--ETV2

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[93000]   -fusion SPANNING read extraction for scaff: AGO2--TRAPPC9

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[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: BCAS3--CASC17

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[589000]   
[590000]   
[591000]   
[592000]   
[593000]   
[594000]   -fusion SPANNING read extraction for scaff: BRD4--NOTCH3

[1000]   
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[6000]   
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[8000]   
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[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   -fusion SPANNING read extraction for scaff: C1orf112--F5

[1000]   
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[6000]   
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[8000]   
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[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   -fusion SPANNING read extraction for scaff: CERCAM--VDAC3

[1000]   
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[6000]   
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[8000]   
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[33000]   
[34000]   -fusion SPANNING read extraction for scaff: CERCAM--SLC20A2

[1000]   
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[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   -fusion SPANNING read extraction for scaff: CNPPD1--GAPDHP49

[1000]   
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[108000]   
[109000]   
[110000]   -fusion SPANNING read extraction for scaff: DIAPH1--PCDH1

[1000]   
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[6000]   
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[8000]   
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[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: ELK1--SYN1

[1000]   
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[6000]   
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[8000]   
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[29000]   
[30000]   
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[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: FBXL20--PAMR1

[1000]   
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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: FBXL20--SH3RF3

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[296000]   
[297000]   -fusion SPANNING read extraction for scaff: GSK3A--CIC

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[23000]   
[24000]   
[25000]   
[26000]   -fusion SPANNING read extraction for scaff: IGF1R--TRIM37

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: ING5--FP236383.3

[1000]   
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[8000]   
[9000]   
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[75000]   
[76000]   
[77000]   -fusion SPANNING read extraction for scaff: INPPL1--GHSR

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[6000]   
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[8000]   
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[84000]   
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[87000]   
[88000]   
[89000]   -fusion SPANNING read extraction for scaff: INPPL1--TNFSF10

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[21000]   -fusion SPANNING read extraction for scaff: INTS10--AC018541.1

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[22000]   
[23000]   -fusion SPANNING read extraction for scaff: INTS2--BCAS3

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[6000]   
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[8000]   
[9000]   -fusion SPANNING read extraction for scaff: INTS9--DLGAP2

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: KLF15--ALG1L2

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: LINC00937--AC083906.5

[1000]   -fusion SPANNING read extraction for scaff: LINC00937--AC083906.2

[1000]   
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[35000]   
[36000]   -fusion SPANNING read extraction for scaff: MAD1L1--SDK1

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[34000]   
[35000]   -fusion SPANNING read extraction for scaff: MARK2--AC019211.1

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[23000]   -fusion SPANNING read extraction for scaff: NEK6--AC092958.4

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[22000]   
[23000]   -fusion SPANNING read extraction for scaff: NEK8--EPHA6

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[96000]   
[97000]   -fusion SPANNING read extraction for scaff: NF1--AL353742.1

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[96000]   
[97000]   -fusion SPANNING read extraction for scaff: NF1--AL669983.1

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[44000]   
[45000]   -fusion SPANNING read extraction for scaff: PARG--BMS1

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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[6000]   
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[9000]   
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[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[6000]   
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[8000]   
[9000]   
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[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[6000]   
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[9000]   
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[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

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[8000]   
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[16000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

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[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

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[42000]   
[43000]   -fusion SPANNING read extraction for scaff: PHF21A--KIT

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[218000]   
[219000]   -fusion SPANNING read extraction for scaff: PIGS--SPAG5

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[15000]   -fusion SPANNING read extraction for scaff: PSMD14--AC005040.2

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[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PSMD14--LINC01789

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[117000]   
[118000]   -fusion SPANNING read extraction for scaff: PTK2--AGO2

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[232000]   -fusion SPANNING read extraction for scaff: PTPRF--AC099671.1

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[78000]   
[79000]   -fusion SPANNING read extraction for scaff: QKI--AL449043.2

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[108000]   
[109000]   -fusion SPANNING read extraction for scaff: QKI--WASHC1

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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: RFC1--WDR19

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[168000]   
[169000]   -fusion SPANNING read extraction for scaff: RRM2B--UBR5

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[5000]   -fusion SPANNING read extraction for scaff: RSRC1--IL12A-AS1

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[56000]   
[57000]   -fusion SPANNING read extraction for scaff: SCARB1--DHX37

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[90000]   
[91000]   -fusion SPANNING read extraction for scaff: SDHA--PLEKHG4B

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[30000]   
[31000]   -fusion SPANNING read extraction for scaff: SRP68--ZMAT3

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[8000]   
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[70000]   
[71000]   -fusion SPANNING read extraction for scaff: TBC1D8--AGFG1

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[21000]   
[22000]   -fusion SPANNING read extraction for scaff: TERF1--KCNB2

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[45000]   
[46000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[7000]   
[8000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[15000]   -fusion SPANNING read extraction for scaff: TRIM37--AC022523.1

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[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[26000]   
[27000]   -fusion SPANNING read extraction for scaff: USP37--AC008281.1

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[6000]   
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[26000]   
[27000]   -fusion SPANNING read extraction for scaff: USP37--AC009310.1

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[23000]   -fusion SPANNING read extraction for scaff: UXS1--NHEJ1

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[31000]   -fusion SPANNING read extraction for scaff: VMP1--PINX1

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[38000]   -fusion SPANNING read extraction for scaff: VPS72--AC137761.1

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[28000]   -fusion SPANNING read extraction for scaff: WT1--AC006504.5

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[27000]   -fusion SPANNING read extraction for scaff: WT1--AC006504.2

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[27000]   -fusion SPANNING read extraction for scaff: WT1--AC005357.2

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[190000]   -fusion SPANNING read extraction for scaff: XPO1--USP34

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[13000]   -fusion SPANNING read extraction for scaff: ZFP3--TM4SF5

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[7000]   -fusion SPANNING read extraction for scaff: ZNF528--ZNF610

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[9000]   -fusion SPANNING read extraction for scaff: ZNF528--ZNF880
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 59399,
          'seq similar region alignment' => 32227
        };
EM: Starting log likelihood: -15817.089297
EM: Round [1] log likelihood: -15811.193564
EM: Round [2] log likelihood: -15810.145538
EM: Round [3] log likelihood: -15809.267083
EM: Round [4] log likelihood: -15808.513129
EM: Round [5] log likelihood: -15807.860997
EM: Round [6] log likelihood: -15807.293106
EM: Round [7] log likelihood: -15806.795555
EM: Round [8] log likelihood: -15806.357199
EM: Round [9] log likelihood: -15805.968998
EM: Round [10] log likelihood: -15805.623542
EM: Round [11] log likelihood: -15805.314710
EM: Round [12] log likelihood: -15805.037403
EM: Round [13] log likelihood: -15804.787354
EM: Round [14] log likelihood: -15804.560966
EM: Round [15] log likelihood: -15804.355196
EM: Round [16] log likelihood: -15804.167456
EM: Round [17] log likelihood: -15803.995540
EM: Round [18] log likelihood: -15803.837558
EM: Round [19] log likelihood: -15803.691886
EM: Round [20] log likelihood: -15803.557128
EM: Round [21] log likelihood: -15803.432075
EM: Round [22] log likelihood: -15803.315682
EM: Round [23] log likelihood: -15803.207041
EM: Round [24] log likelihood: -15803.105364
EM: Round [25] log likelihood: -15803.009960
EM: Round [26] log likelihood: -15802.920228
EM: Round [27] log likelihood: -15802.835640
EM: Round [28] log likelihood: -15802.755732
EM: Round [29] log likelihood: -15802.680095
EM: Round [30] log likelihood: -15802.608371
EM: Round [31] log likelihood: -15802.540238
EM: Round [32] log likelihood: -15802.475416
EM: Round [33] log likelihood: -15802.413651
EM: Round [34] log likelihood: -15802.354720
EM: Round [35] log likelihood: -15802.298421
EM: Round [36] log likelihood: -15802.244574
EM: Round [37] log likelihood: -15802.193018
EM: Round [38] log likelihood: -15802.143606
EM: Round [39] log likelihood: -15802.096207
EM: Round [40] log likelihood: -15802.050699
EM: Round [41] log likelihood: -15802.006974
EM: Round [42] log likelihood: -15801.964932
EM: Round [43] log likelihood: -15801.924483
EM: Round [44] log likelihood: -15801.885542
EM: Round [45] log likelihood: -15801.848032
EM: Round [46] log likelihood: -15801.811882
EM: Round [47] log likelihood: -15801.777028
EM: Round [48] log likelihood: -15801.743406
EM: Round [49] log likelihood: -15801.710962
EM: Round [50] log likelihood: -15801.679641
EM: Round [51] log likelihood: -15801.649394
EM: Round [52] log likelihood: -15801.620175
EM: Round [53] log likelihood: -15801.591941
EM: Round [54] log likelihood: -15801.564651
EM: Round [55] log likelihood: -15801.538265
EM: Round [56] log likelihood: -15801.512748
EM: Round [57] log likelihood: -15801.488066
EM: Round [58] log likelihood: -15801.464185
EM: Round [59] log likelihood: -15801.441076
EM: Round [60] log likelihood: -15801.418708
EM: Round [61] log likelihood: -15801.397053
EM: Round [62] log likelihood: -15801.376086
EM: Round [63] log likelihood: -15801.355781
EM: Round [64] log likelihood: -15801.336114
EM: Round [65] log likelihood: -15801.317061
EM: Round [66] log likelihood: -15801.298602
EM: Round [67] log likelihood: -15801.280714
EM: Round [68] log likelihood: -15801.263378
EM: Round [69] log likelihood: -15801.246574
EM: Round [70] log likelihood: -15801.230285
EM: Round [71] log likelihood: -15801.214491
EM: Round [72] log likelihood: -15801.199177
EM: Round [73] log likelihood: -15801.184326
EM: Round [74] log likelihood: -15801.169921
EM: Round [75] log likelihood: -15801.155949
EM: Round [76] log likelihood: -15801.142395
EM: Round [77] log likelihood: -15801.129244
EM: Round [78] log likelihood: -15801.116483
EM: Round [79] log likelihood: -15801.104100
EM: Round [80] log likelihood: -15801.092082
EM: Round [81] log likelihood: -15801.080417
EM: Round [82] log likelihood: -15801.069093
EM: Round [83] log likelihood: -15801.058099
EM: Round [84] log likelihood: -15801.047426
EM: Round [85] log likelihood: -15801.037061
EM: Round [86] log likelihood: -15801.026996
EM: Round [87] log likelihood: -15801.017220
EM: Round [88] log likelihood: -15801.007725
EM: Round [89] log likelihood: -15800.998502
EM: Round [90] log likelihood: -15800.989541
EM: Round [91] log likelihood: -15800.980835
EM: Round [92] log likelihood: -15800.972376
EM: Round [93] log likelihood: -15800.964155
EM: Round [94] log likelihood: -15800.956166
EM: Round [95] log likelihood: -15800.948400
EM: Round [96] log likelihood: -15800.940852
EM: Round [97] log likelihood: -15800.933514
EM: Round [98] log likelihood: -15800.926380
EM: Round [99] log likelihood: -15800.919443
EM: Round [100] log likelihood: -15800.912697
EM: Round [101] log likelihood: -15800.906137
EM: Round [102] log likelihood: -15800.899757
EM: Round [103] log likelihood: -15800.893550
EM: Round [104] log likelihood: -15800.887513
EM: Round [105] log likelihood: -15800.881639
EM: Round [106] log likelihood: -15800.875925
EM: Round [107] log likelihood: -15800.870364
EM: Round [108] log likelihood: -15800.864952
EM: Round [109] log likelihood: -15800.859685
EM: Round [110] log likelihood: -15800.854559
EM: Round [111] log likelihood: -15800.849569
EM: Round [112] log likelihood: -15800.844711
EM: Round [113] log likelihood: -15800.839980
EM: Round [114] log likelihood: -15800.835375
EM: Round [115] log likelihood: -15800.830890
EM: Round [116] log likelihood: -15800.826521
EM: Round [117] log likelihood: -15800.822267
EM: Round [118] log likelihood: -15800.818122
EM: Round [119] log likelihood: -15800.814085
EM: Round [120] log likelihood: -15800.810151
EM: Round [121] log likelihood: -15800.806318
EM: Round [122] log likelihood: -15800.802583
EM: Round [123] log likelihood: -15800.798943
EM: Round [124] log likelihood: -15800.795394
EM: Round [125] log likelihood: -15800.791936
EM: Round [126] log likelihood: -15800.788564
EM: Round [127] log likelihood: -15800.785276
EM: Round [128] log likelihood: -15800.782071
EM: Round [129] log likelihood: -15800.778944
EM: Round [130] log likelihood: -15800.775896
EM: Round [131] log likelihood: -15800.772922
EM: Round [132] log likelihood: -15800.770021
EM: Round [133] log likelihood: -15800.767191
EM: Round [134] log likelihood: -15800.764429
EM: Round [135] log likelihood: -15800.761735
EM: Round [136] log likelihood: -15800.759105
EM: Round [137] log likelihood: -15800.756538
EM: Round [138] log likelihood: -15800.754033
EM: Round [139] log likelihood: -15800.751587
EM: Round [140] log likelihood: -15800.749199
EM: Round [141] log likelihood: -15800.746868
EM: Round [142] log likelihood: -15800.744591
EM: Round [143] log likelihood: -15800.742367
EM: Round [144] log likelihood: -15800.740196
EM: Round [145] log likelihood: -15800.738074
EM: Round [146] log likelihood: -15800.736001
EM: Round [147] log likelihood: -15800.733976
EM: Round [148] log likelihood: -15800.731997
EM: Round [149] log likelihood: -15800.730063
EM: Round [150] log likelihood: -15800.728172
EM: Round [151] log likelihood: -15800.726324
EM: Round [152] log likelihood: -15800.724518
EM: Round [153] log likelihood: -15800.722752
EM: Round [154] log likelihood: -15800.721024
EM: Round [155] log likelihood: -15800.719335
EM: Round [156] log likelihood: -15800.717684
EM: Round [157] log likelihood: -15800.716068
EM: Round [158] log likelihood: -15800.714487
EM: Round [159] log likelihood: -15800.712940
EM: Round [160] log likelihood: -15800.711427
EM: Round [161] log likelihood: -15800.709946
EM: Round [162] log likelihood: -15800.708497
EM: Round [163] log likelihood: -15800.707078
EM: Round [164] log likelihood: -15800.705690
EM: Round [165] log likelihood: -15800.704330
EM: Round [166] log likelihood: -15800.702999
EM: Round [167] log likelihood: -15800.701695
EM: Round [168] log likelihood: -15800.700418
EM: Round [169] log likelihood: -15800.699168
EM: Round [170] log likelihood: -15800.697942
EM: Round [171] log likelihood: -15800.696742
EM: Round [172] log likelihood: -15800.695566
EM: Round [173] log likelihood: -15800.694414
EM: Round [174] log likelihood: -15800.693285
EM: Round [175] log likelihood: -15800.692178
EM: Round [176] log likelihood: -15800.691093
EM: Round [177] log likelihood: -15800.690029
EM: Round [178] log likelihood: -15800.688986
EM: Round [179] log likelihood: -15800.687964
EM: Round [180] log likelihood: -15800.686961
EM: Round [181] log likelihood: -15800.685977
EM: Round [182] log likelihood: -15800.685012
EM: Round [183] log likelihood: -15800.684066
EM: Round [184] log likelihood: -15800.683137
EM: Round [185] log likelihood: -15800.682226
EM: Round [186] log likelihood: -15800.681332
EM: Round [187] log likelihood: -15800.680455
EM: Round [188] log likelihood: -15800.679593
EM: Round [189] log likelihood: -15800.678748
EM: Round [190] log likelihood: -15800.677918
EM: Round [191] log likelihood: -15800.677103
EM: Round [192] log likelihood: -15800.676303
EM: Round [193] log likelihood: -15800.675517
EM: Round [194] log likelihood: -15800.674745
EM: Round [195] log likelihood: -15800.673987
EM: Round [196] log likelihood: -15800.673243
EM: Round [197] log likelihood: -15800.672511
EM: Round [198] log likelihood: -15800.671792
EM: Round [199] log likelihood: -15800.671086
EM: Round [200] log likelihood: -15800.670392
EM: Round [201] log likelihood: -15800.669709
EM: Round [202] log likelihood: -15800.669039
EM: Round [203] log likelihood: -15800.668380
EM: Round [204] log likelihood: -15800.667732
EM: Round [205] log likelihood: -15800.667094
EM: Round [206] log likelihood: -15800.666468
EM: Round [207] log likelihood: -15800.665852
EM: Round [208] log likelihood: -15800.665246
EM: Round [209] log likelihood: -15800.664650
EM: Round [210] log likelihood: -15800.664064
EM: Round [211] log likelihood: -15800.663487
EM: Round [212] log likelihood: -15800.662919
EM: Round [213] log likelihood: -15800.662361
EM: Round [214] log likelihood: -15800.661812
EM: Round [215] log likelihood: -15800.661271
EM: Round [216] log likelihood: -15800.660739
EM: Round [217] log likelihood: -15800.660215
EM: Round [218] log likelihood: -15800.659699
EM: Round [219] log likelihood: -15800.659192
EM: Round [220] log likelihood: -15800.658692
EM: Round [221] log likelihood: -15800.658200
EM: Round [222] log likelihood: -15800.657716
EM: Round [223] log likelihood: -15800.657238
EM: Round [224] log likelihood: -15800.656769
EM: Round [225] log likelihood: -15800.656306
EM: Round [226] log likelihood: -15800.655850
EM: Round [227] log likelihood: -15800.655401
EM: Round [228] log likelihood: -15800.654958
EM: Round [229] log likelihood: -15800.654522
EM: Round [230] log likelihood: -15800.654093
EM: Round [231] log likelihood: -15800.653670
EM: Round [232] log likelihood: -15800.653253
EM: Round [233] log likelihood: -15800.652842
EM: Round [234] log likelihood: -15800.652437
EM: Round [235] log likelihood: -15800.652037
EM: Round [236] log likelihood: -15800.651644
EM: Round [237] log likelihood: -15800.651256
EM: Round [238] log likelihood: -15800.650873
EM: Round [239] log likelihood: -15800.650496
EM: Round [240] log likelihood: -15800.650124
EM: Round [241] log likelihood: -15800.649757
EM: Round [242] log likelihood: -15800.649396
EM: Round [243] log likelihood: -15800.649039
EM: Round [244] log likelihood: -15800.648687
EM: Round [245] log likelihood: -15800.648340
EM: Round [246] log likelihood: -15800.647998
EM: Round [247] log likelihood: -15800.647661
EM: Round [248] log likelihood: -15800.647328
EM: Round [249] log likelihood: -15800.646999
EM: Round [250] log likelihood: -15800.646675
EM: Round [251] log likelihood: -15800.646355
EM: Round [252] log likelihood: -15800.646040
EM: Round [253] log likelihood: -15800.645728
EM: Round [254] log likelihood: -15800.645421
EM: Round [255] log likelihood: -15800.645118
EM: Round [256] log likelihood: -15800.644818
EM: Round [257] log likelihood: -15800.644523
EM: Round [258] log likelihood: -15800.644231
EM: Round [259] log likelihood: -15800.643943
EM: Round [260] log likelihood: -15800.643659
EM: Round [261] log likelihood: -15800.643379
EM: Round [262] log likelihood: -15800.643102
EM: Round [263] log likelihood: -15800.642828
EM: Round [264] log likelihood: -15800.642558
EM: Round [265] log likelihood: -15800.642292
EM: Round [266] log likelihood: -15800.642028
EM: Round [267] log likelihood: -15800.641769
EM: Round [268] log likelihood: -15800.641512
EM: Round [269] log likelihood: -15800.641258
EM: Round [270] log likelihood: -15800.641008
EM: Round [271] log likelihood: -15800.640761
EM: Round [272] log likelihood: -15800.640517
EM: Round [273] log likelihood: -15800.640275
EM: Round [274] log likelihood: -15800.640037
EM: Round [275] log likelihood: -15800.639802
EM: Round [276] log likelihood: -15800.639569
EM: Round [277] log likelihood: -15800.639339
EM: Round [278] log likelihood: -15800.639113
EM: Round [279] log likelihood: -15800.638888
EM: Round [280] log likelihood: -15800.638667
EM: Round [281] log likelihood: -15800.638448
EM: Round [282] log likelihood: -15800.638232
EM: Round [283] log likelihood: -15800.638018
EM: Round [284] log likelihood: -15800.637807
EM: Round [285] log likelihood: -15800.637598
EM: Round [286] log likelihood: -15800.637392
EM: Round [287] log likelihood: -15800.637188
EM: Round [288] log likelihood: -15800.636987
EM: Round [289] log likelihood: -15800.636788
EM: Round [290] log likelihood: -15800.636591
EM: Round [291] log likelihood: -15800.636397
EM: Round [292] log likelihood: -15800.636205
EM: Round [293] log likelihood: -15800.636015
EM: Round [294] log likelihood: -15800.635827
EM: Round [295] log likelihood: -15800.635641
EM: Round [296] log likelihood: -15800.635458
EM: Round [297] log likelihood: -15800.635276
EM: Round [298] log likelihood: -15800.635097
EM: Round [299] log likelihood: -15800.634920
EM: Round [300] log likelihood: -15800.634745
EM: Round [301] log likelihood: -15800.634571
EM: Round [302] log likelihood: -15800.634400
EM: Round [303] log likelihood: -15800.634231
EM: Round [304] log likelihood: -15800.634063
EM: Round [305] log likelihood: -15800.633898
EM: Round [306] log likelihood: -15800.633734
EM: Round [307] log likelihood: -15800.633572
EM: Round [308] log likelihood: -15800.633412
EM: Round [309] log likelihood: -15800.633254
EM: Round [310] log likelihood: -15800.633098
EM: Round [311] log likelihood: -15800.632943
EM: Round [312] log likelihood: -15800.632790
EM: Round [313] log likelihood: -15800.632638
EM: Round [314] log likelihood: -15800.632489
EM: Round [315] log likelihood: -15800.632341
EM: Round [316] log likelihood: -15800.632194
EM: Round [317] log likelihood: -15800.632050
EM: Round [318] log likelihood: -15800.631906
EM: Round [319] log likelihood: -15800.631765
EM: Round [320] log likelihood: -15800.631625
EM: Round [321] log likelihood: -15800.631486
EM: Round [322] log likelihood: -15800.631349
EM: Round [323] log likelihood: -15800.631214
EM: Round [324] log likelihood: -15800.631079
EM: Round [325] log likelihood: -15800.630947
EM: Round [326] log likelihood: -15800.630816
EM: Round [327] log likelihood: -15800.630686
EM: Round [328] log likelihood: -15800.630558
EM: Round [329] log likelihood: -15800.630431
EM: Round [330] log likelihood: -15800.630305
EM: Round [331] log likelihood: -15800.630181
EM: Round [332] log likelihood: -15800.630058
EM: Round [333] log likelihood: -15800.629936
EM: Round [334] log likelihood: -15800.629816
EM: Round [335] log likelihood: -15800.629697
EM: Round [336] log likelihood: -15800.629579
EM: Round [337] log likelihood: -15800.629463
EM: Round [338] log likelihood: -15800.629347
EM: Round [339] log likelihood: -15800.629233
EM: Round [340] log likelihood: -15800.629121
EM: Round [341] log likelihood: -15800.629009
EM: Round [342] log likelihood: -15800.628899
EM: Round [343] log likelihood: -15800.628789
EM: Round [344] log likelihood: -15800.628681
EM: Round [345] log likelihood: -15800.628574
EM: Round [346] log likelihood: -15800.628468
EM: Round [347] log likelihood: -15800.628364
EM: Round [348] log likelihood: -15800.628260
EM: Round [349] log likelihood: -15800.628158
EM: Round [350] log likelihood: -15800.628056
EM: Round [351] log likelihood: -15800.627956
EM: Round [352] log likelihood: -15800.627856
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.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-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.Zp1BtusVJM/fi_workdir/aih-tih-sc-8e3550-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.Zp1BtusVJM/fi_workdir/aih-tih-sc-8e3550-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.Zp1BtusVJM/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -14252.371454
EM: Round [1] log likelihood: -14250.516883
EM: Round [2] log likelihood: -14250.500733
EM: Round [3] log likelihood: -14250.500647
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 154970419
Warning - not locating file: /tmp/nxf.Zp1BtusVJM/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000267575.7]
WARNING, no entry stored in dbm for [ENSG00000267575.7]
WARNING, no entry stored in dbm for [ENSG00000267575.7]
WARNING, no entry stored in dbm for [ENSG00000267575.7]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000234285.1]
WARNING, no entry stored in dbm for [ENSG00000267623.3]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000188002.10]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000260158.1]
WARNING, no entry stored in dbm for [ENSG00000260785.2]
WARNING, no entry stored in dbm for [ENSG00000239498.1]
WARNING, no entry stored in dbm for [ENSG00000226377.2]
WARNING, no entry stored in dbm for [ENSG00000285409.1]
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 [ENSG00000280441.3]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
ls: cannot access 'IGV_inputs': No such file or directory