Done.
-parsing GTF file: /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.MytSv7bv3H/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.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:59:05 : INFO : Done.
-parsing GTF file: /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

[10000]   
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[720000]   -done parsing /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'seq-similar region overlap' => 110,
          'low complexity anchor region' => 10,
          'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 21,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
          ' ** passed ** ' => 8866,
          'per_id < 96' => 2418,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
          'small anchor length' => 46,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2,
          'excessive soft clipping' => 3593,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 36,
          'num genes matched < 2' => 15,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 8
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
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[6000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: AP001347.1--ANKRD20A11P

[1000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
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[8000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

[1000]   
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[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
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[3000]   
[4000]   
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[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

[1000]   
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[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

[1000]   
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[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

[1000]   
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[6000]   
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[11000]   
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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[24000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

[1000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

[1000]   
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[6000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4

[1000]   
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[13000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

[1000]   
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[3000]   
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[7000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5

[1000]   
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[10000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

[1000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

[1000]   
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[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3

[1000]   
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[12000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

[1000]   
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[3000]   
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[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7

[1000]   
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[16000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12

[1000]   
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[3000]   
[4000]   
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[6000]   
[7000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
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[6000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
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[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[44000]   
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[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[11000]   
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[13000]   
[14000]   
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[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
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[30000]   
[31000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
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[56000]   
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[62000]   
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[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
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[73000]   
[74000]   
[75000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[8000]   
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[16000]   
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[18000]   
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[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
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[14000]   
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[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 2703,
          'seq similar region alignment' => 33639
        };
EM: Starting log likelihood: -3749.389101
EM: Round [1] log likelihood: -3748.252192
EM: Round [2] log likelihood: -3747.477766
EM: Round [3] log likelihood: -3746.809832
EM: Round [4] log likelihood: -3746.227212
EM: Round [5] log likelihood: -3745.713703
EM: Round [6] log likelihood: -3745.256683
EM: Round [7] log likelihood: -3744.846208
EM: Round [8] log likelihood: -3744.474372
EM: Round [9] log likelihood: -3744.134843
EM: Round [10] log likelihood: -3743.822519
EM: Round [11] log likelihood: -3743.533264
EM: Round [12] log likelihood: -3743.263715
EM: Round [13] log likelihood: -3743.011123
EM: Round [14] log likelihood: -3742.773236
EM: Round [15] log likelihood: -3742.548201
EM: Round [16] log likelihood: -3742.334490
EM: Round [17] log likelihood: -3742.130838
EM: Round [18] log likelihood: -3741.936197
EM: Round [19] log likelihood: -3741.749691
EM: Round [20] log likelihood: -3741.570590
EM: Round [21] log likelihood: -3741.398281
EM: Round [22] log likelihood: -3741.232247
EM: Round [23] log likelihood: -3741.072051
EM: Round [24] log likelihood: -3740.917319
EM: Round [25] log likelihood: -3740.767731
EM: Round [26] log likelihood: -3740.623011
EM: Round [27] log likelihood: -3740.482919
EM: Round [28] log likelihood: -3740.347243
EM: Round [29] log likelihood: -3740.215797
EM: Round [30] log likelihood: -3740.088414
EM: Round [31] log likelihood: -3739.964942
EM: Round [32] log likelihood: -3739.845245
EM: Round [33] log likelihood: -3739.729197
EM: Round [34] log likelihood: -3739.616679
EM: Round [35] log likelihood: -3739.507584
EM: Round [36] log likelihood: -3739.401807
EM: Round [37] log likelihood: -3739.299252
EM: Round [38] log likelihood: -3739.199824
EM: Round [39] log likelihood: -3739.103434
EM: Round [40] log likelihood: -3739.009996
EM: Round [41] log likelihood: -3738.919426
EM: Round [42] log likelihood: -3738.831644
EM: Round [43] log likelihood: -3738.746571
EM: Round [44] log likelihood: -3738.664131
EM: Round [45] log likelihood: -3738.584248
EM: Round [46] log likelihood: -3738.506851
EM: Round [47] log likelihood: -3738.431866
EM: Round [48] log likelihood: -3738.359226
EM: Round [49] log likelihood: -3738.288862
EM: Round [50] log likelihood: -3738.220706
EM: Round [51] log likelihood: -3738.154695
EM: Round [52] log likelihood: -3738.090764
EM: Round [53] log likelihood: -3738.028851
EM: Round [54] log likelihood: -3737.968895
EM: Round [55] log likelihood: -3737.910837
EM: Round [56] log likelihood: -3737.854618
EM: Round [57] log likelihood: -3737.800182
EM: Round [58] log likelihood: -3737.747474
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EM: Round [66] log likelihood: -3737.381817
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EM: Round [69] log likelihood: -3737.267247
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EM: Round [75] log likelihood: -3737.068648
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EM: Round [82] log likelihood: -3736.880005
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EM: Round [90] log likelihood: -3736.709163
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EM: Round [95] log likelihood: -3736.621635
EM: Round [96] log likelihood: -3736.605637
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EM: Round [136] log likelihood: -3736.222780
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EM: Round [177] log likelihood: -3736.067135
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EM: Round [181] log likelihood: -3736.057124
EM: Round [182] log likelihood: -3736.054715
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EM: Round [184] log likelihood: -3736.050003
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EM: Round [201] log likelihood: -3736.014919
EM: Round [202] log likelihood: -3736.013095
EM: Round [203] log likelihood: -3736.011294
EM: Round [204] log likelihood: -3736.009517
EM: Round [205] log likelihood: -3736.007762
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EM: Round [207] log likelihood: -3736.004318
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EM: Round [213] log likelihood: -3735.994483
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EM: Round [215] log likelihood: -3735.991361
EM: Round [216] log likelihood: -3735.989827
EM: Round [217] log likelihood: -3735.988312
EM: Round [218] log likelihood: -3735.986814
EM: Round [219] log likelihood: -3735.985334
EM: Round [220] log likelihood: -3735.983871
EM: Round [221] log likelihood: -3735.982425
EM: Round [222] log likelihood: -3735.980995
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EM: Round [228] log likelihood: -3735.972752
EM: Round [229] log likelihood: -3735.971431
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EM: Round [231] log likelihood: -3735.968833
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EM: Round [234] log likelihood: -3735.965041
EM: Round [235] log likelihood: -3735.963805
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EM: Round [512] log likelihood: -3735.843304
EM: Round [513] log likelihood: -3735.843202
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EM: Round [515] log likelihood: -3735.843000
EM: Round [516] log likelihood: -3735.842901
EM: Stopping iterations at round 516 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-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.MytSv7bv3H/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2520.458624
EM: Round [1] log likelihood: -2520.234213
EM: Round [2] log likelihood: -2520.234136
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296655419
Warning - not locating file: /tmp/nxf.MytSv7bv3H/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [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 [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
ls: cannot access 'IGV_inputs': No such file or directory