Done.
-parsing GTF file: /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.2j0AlTEFrB/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.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.2j0AlTEFrB/fi_workdir/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.2j0AlTEFrB/fi_workdir/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:31:42 : INFO : Done.
-parsing GTF file: /tmp/nxf.2j0AlTEFrB/fi_workdir/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.2j0AlTEFrB/fi_workdir/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[4950000]   -done parsing /tmp/nxf.2j0AlTEFrB/fi_workdir/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num genes matched < 2' => 67,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 696,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 150,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 381,
          'per_id < 96' => 16116,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 88,
          'low complexity anchor region' => 9,
          ' ** passed ** ' => 15492,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 33,
          'excessive soft clipping' => 25547,
          'exons hit < 2' => 36,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 4,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
          'small anchor length' => 41
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.2j0AlTEFrB/fi_workdir/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[67000]   -fusion SPANNING read extraction for scaff: AC004980.3--UPK3BL1

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[226000]   -fusion SPANNING read extraction for scaff: AC060780.1--ANKS1A

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[23000]   -fusion SPANNING read extraction for scaff: ARG2--MPP5

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[167000]   
[168000]   -fusion SPANNING read extraction for scaff: BCKDHA--ANKRD27

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[167000]   -fusion SPANNING read extraction for scaff: CAMK1D--ZNF345

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[161000]   -fusion SPANNING read extraction for scaff: CYP20A1--NBEAL1

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[55000]   
[56000]   -fusion SPANNING read extraction for scaff: EML1--SLC20A2

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[134000]   -fusion SPANNING read extraction for scaff: ITCH--AL031668.2

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[135000]   -fusion SPANNING read extraction for scaff: ITCH--ASIP

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[40000]   -fusion SPANNING read extraction for scaff: LRRC1--RPL31P33

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[80000]   -fusion SPANNING read extraction for scaff: LUC7L3--SERHL

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[172000]   -fusion SPANNING read extraction for scaff: MAPRE1--ASXL1

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[80000]   -fusion SPANNING read extraction for scaff: METTL17--PRR14L

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[16000]   -fusion SPANNING read extraction for scaff: MRPL48--PLEKHB1

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[135000]   
[136000]   -fusion SPANNING read extraction for scaff: NCOR1--FTLP12

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[104000]   -fusion SPANNING read extraction for scaff: NFRKB--ZBTB44

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[95000]   
[96000]   -fusion SPANNING read extraction for scaff: NLRC5--NUP93

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[47000]   
[48000]   -fusion SPANNING read extraction for scaff: PARP8--RASGRF2

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[39000]   
[40000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[34000]   
[35000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[39000]   
[40000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[162000]   -fusion SPANNING read extraction for scaff: PNPO--KPNB1

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[88000]   
[89000]   -fusion SPANNING read extraction for scaff: PRDM15--YIF1B

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[204000]   
[205000]   -fusion SPANNING read extraction for scaff: RBM14--RBM4

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[394000]   -fusion SPANNING read extraction for scaff: RCAN3--GRHL3

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[143000]   -fusion SPANNING read extraction for scaff: RIT1--SMG5

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[40000]   -fusion SPANNING read extraction for scaff: SFI1--RNF185

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[172000]   -fusion SPANNING read extraction for scaff: SLC10A4--SORBS2

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: SNX29P1--AC009060.2

[1000]   
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[60000]   -fusion SPANNING read extraction for scaff: SNX31--P3H2

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[160000]   
[161000]   -fusion SPANNING read extraction for scaff: SORBS2--ZAR1

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[802000]   
[803000]   -fusion SPANNING read extraction for scaff: SPINT2--SIPA1L3

[1000]   
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[8000]   
[9000]   
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[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
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[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
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[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   -fusion SPANNING read extraction for scaff: TBC1D19--RBPJ

[1000]   
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[163000]   
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[168000]   
[169000]   -fusion SPANNING read extraction for scaff: TEPSIN--NPLOC4

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[8000]   
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[38000]   
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[41000]   
[42000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
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[9000]   
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[38000]   
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[42000]   
[43000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

[1000]   
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[4000]   
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[6000]   
[7000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   -fusion SPANNING read extraction for scaff: TPTE2P4--AC013734.1

[1000]   
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[4000]   
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[6000]   
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[8000]   
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[31000]   
[32000]   
[33000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[6000]   
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[8000]   
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[25000]   
[26000]   -fusion SPANNING read extraction for scaff: UBE2Q2P1--GOLGA6L10

[1000]   
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[6000]   
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[8000]   
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[71000]   
[72000]   -fusion SPANNING read extraction for scaff: VCL--USP54

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[171000]   
[172000]   -fusion SPANNING read extraction for scaff: XPO1--FAM161A
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 55476,
          'seq similar region alignment' => 20215
        };
EM: Starting log likelihood: -32229.672954
EM: Round [1] log likelihood: -32210.384554
EM: Round [2] log likelihood: -32210.309679
EM: Round [3] log likelihood: -32210.288914
EM: Round [4] log likelihood: -32210.269166
EM: Round [5] log likelihood: -32210.249711
EM: Round [6] log likelihood: -32210.230519
EM: Round [7] log likelihood: -32210.211585
EM: Round [8] log likelihood: -32210.192903
EM: Round [9] log likelihood: -32210.174470
EM: Round [10] log likelihood: -32210.156280
EM: Round [11] log likelihood: -32210.138329
EM: Round [12] log likelihood: -32210.120613
EM: Round [13] log likelihood: -32210.103128
EM: Round [14] log likelihood: -32210.085870
EM: Round [15] log likelihood: -32210.068834
EM: Round [16] log likelihood: -32210.052017
EM: Round [17] log likelihood: -32210.035416
EM: Round [18] log likelihood: -32210.019026
EM: Round [19] log likelihood: -32210.002844
EM: Round [20] log likelihood: -32209.986866
EM: Round [21] log likelihood: -32209.971090
EM: Round [22] log likelihood: -32209.955511
EM: Round [23] log likelihood: -32209.940126
EM: Round [24] log likelihood: -32209.924932
EM: Round [25] log likelihood: -32209.909926
EM: Round [26] log likelihood: -32209.895106
EM: Round [27] log likelihood: -32209.880467
EM: Round [28] log likelihood: -32209.866007
EM: Round [29] log likelihood: -32209.851724
EM: Round [30] log likelihood: -32209.837614
EM: Round [31] log likelihood: -32209.823674
EM: Round [32] log likelihood: -32209.809903
EM: Round [33] log likelihood: -32209.796297
EM: Round [34] log likelihood: -32209.782853
EM: Round [35] log likelihood: -32209.769570
EM: Round [36] log likelihood: -32209.756445
EM: Round [37] log likelihood: -32209.743475
EM: Round [38] log likelihood: -32209.730658
EM: Round [39] log likelihood: -32209.717992
EM: Round [40] log likelihood: -32209.705475
EM: Round [41] log likelihood: -32209.693103
EM: Round [42] log likelihood: -32209.680876
EM: Round [43] log likelihood: -32209.668791
EM: Round [44] log likelihood: -32209.656845
EM: Round [45] log likelihood: -32209.645037
EM: Round [46] log likelihood: -32209.633365
EM: Round [47] log likelihood: -32209.621827
EM: Round [48] log likelihood: -32209.610421
EM: Round [49] log likelihood: -32209.599145
EM: Round [50] log likelihood: -32209.587997
EM: Round [51] log likelihood: -32209.576975
EM: Round [52] log likelihood: -32209.566078
EM: Round [53] log likelihood: -32209.555303
EM: Round [54] log likelihood: -32209.544650
EM: Round [55] log likelihood: -32209.534116
EM: Round [56] log likelihood: -32209.523699
EM: Round [57] log likelihood: -32209.513399
EM: Round [58] log likelihood: -32209.503213
EM: Round [59] log likelihood: -32209.493140
EM: Round [60] log likelihood: -32209.483178
EM: Round [61] log likelihood: -32209.473326
EM: Round [62] log likelihood: -32209.463583
EM: Round [63] log likelihood: -32209.453946
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EM: Round [525] log likelihood: -32208.479819
EM: Round [526] log likelihood: -32208.479666
EM: Round [527] log likelihood: -32208.479514
EM: Round [528] log likelihood: -32208.479364
EM: Round [529] log likelihood: -32208.479215
EM: Round [530] log likelihood: -32208.479067
EM: Round [531] log likelihood: -32208.478920
EM: Round [532] log likelihood: -32208.478775
EM: Round [533] log likelihood: -32208.478631
EM: Round [534] log likelihood: -32208.478488
EM: Round [535] log likelihood: -32208.478346
EM: Round [536] log likelihood: -32208.478205
EM: Round [537] log likelihood: -32208.478065
EM: Round [538] log likelihood: -32208.477927
EM: Round [539] log likelihood: -32208.477790
EM: Round [540] log likelihood: -32208.477653
EM: Round [541] log likelihood: -32208.477518
EM: Round [542] log likelihood: -32208.477385
EM: Round [543] log likelihood: -32208.477252
EM: Round [544] log likelihood: -32208.477120
EM: Round [545] log likelihood: -32208.476989
EM: Round [546] log likelihood: -32208.476860
EM: Round [547] log likelihood: -32208.476731
EM: Round [548] log likelihood: -32208.476604
EM: Round [549] log likelihood: -32208.476478
EM: Round [550] log likelihood: -32208.476352
EM: Round [551] log likelihood: -32208.476228
EM: Round [552] log likelihood: -32208.476105
EM: Round [553] log likelihood: -32208.475982
EM: Round [554] log likelihood: -32208.475861
EM: Round [555] log likelihood: -32208.475741
EM: Round [556] log likelihood: -32208.475622
EM: Round [557] log likelihood: -32208.475503
EM: Round [558] log likelihood: -32208.475386
EM: Round [559] log likelihood: -32208.475270
EM: Round [560] log likelihood: -32208.475154
EM: Round [561] log likelihood: -32208.475040
EM: Round [562] log likelihood: -32208.474926
EM: Round [563] log likelihood: -32208.474814
EM: Round [564] log likelihood: -32208.474702
EM: Round [565] log likelihood: -32208.474591
EM: Round [566] log likelihood: -32208.474482
EM: Round [567] log likelihood: -32208.474373
EM: Round [568] log likelihood: -32208.474265
EM: Round [569] log likelihood: -32208.474158
EM: Round [570] log likelihood: -32208.474051
EM: Round [571] log likelihood: -32208.473946
EM: Round [572] log likelihood: -32208.473841
EM: Round [573] log likelihood: -32208.473738
EM: Round [574] log likelihood: -32208.473635
EM: Round [575] log likelihood: -32208.473533
EM: Round [576] log likelihood: -32208.473432
EM: Round [577] log likelihood: -32208.473332
EM: Round [578] log likelihood: -32208.473232
EM: Stopping iterations at round 578 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-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.2j0AlTEFrB/fi_workdir/aih-tih-sc-6c4b48-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.2j0AlTEFrB/fi_workdir/aih-tih-sc-6c4b48-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.2j0AlTEFrB/fi_workdir/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -31198.572816
EM: Round [1] log likelihood: -31184.481364
EM: Round [2] log likelihood: -31184.442639
EM: Round [3] log likelihood: -31184.442589
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296687971
Warning - not locating file: /tmp/nxf.2j0AlTEFrB/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000172250.16]
WARNING, no entry stored in dbm for [ENSG00000172250.16]
WARNING, no entry stored in dbm for [ENSG00000172250.16]
WARNING, no entry stored in dbm for [ENSG00000172250.16]
WARNING, no entry stored in dbm for [ENSG00000267002.4]
WARNING, no entry stored in dbm for [ENSG00000267002.4]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000189136.9]
WARNING, no entry stored in dbm for [ENSG00000189136.9]
WARNING, no entry stored in dbm for [ENSG00000218049.1]
WARNING, no entry stored in dbm for [ENSG00000218049.1]
WARNING, no entry stored in dbm for [ENSG00000218049.1]
WARNING, no entry stored in dbm for [ENSG00000218049.1]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
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 [ENSG00000215506.5]
WARNING, no entry stored in dbm for [ENSG00000277146.1]
WARNING, no entry stored in dbm for [ENSG00000215506.5]
WARNING, no entry stored in dbm for [ENSG00000277146.1]
WARNING, no entry stored in dbm for [ENSG00000158482.10]
WARNING, no entry stored in dbm for [ENSG00000261145.1]
ls: cannot access 'IGV_inputs': No such file or directory