Done.
-parsing GTF file: /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.VleedfCDzv/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.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:27:18 : INFO : Done.
-parsing GTF file: /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[760000]   -done parsing /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 32,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 24,
          ' ** passed ** ' => 3968,
          'small anchor length' => 14,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'low complexity anchor region' => 5,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 45,
          'num genes matched < 2' => 76,
          'excessive soft clipping' => 5967,
          'per_id < 96' => 2875
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[5000]   -fusion SPANNING read extraction for scaff: AC006197.2--NKAIN2

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[341000]   
[342000]   -fusion SPANNING read extraction for scaff: AC136431.1--PKD1P5

[1000]   
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[20000]   
[21000]   
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[24000]   
[25000]   -fusion SPANNING read extraction for scaff: ENOPH1--AC002451.1

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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: ENOPH1--DYNC1I1

[1000]   
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[5000]   -fusion SPANNING read extraction for scaff: GUCY1B2--NKAIN2

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[5000]   -fusion SPANNING read extraction for scaff: LINC00381--NKAIN2

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[7000]   
[8000]   
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[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

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[15000]   -fusion SPANNING read extraction for scaff: PTPN20--BMS1P7

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

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[10000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[16000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[111000]   -fusion SPANNING read extraction for scaff: WAC--AC023141.7

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[110000]   
[111000]   -fusion SPANNING read extraction for scaff: WAC--AC128676.1

[1000]   
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[7000]   
[8000]   -fusion SPANNING read extraction for scaff: ZNF66--ZNF626
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 30566
        };
EM: Starting log likelihood: -3160.781060
EM: Round [1] log likelihood: -3147.275592
EM: Round [2] log likelihood: -3141.923629
EM: Round [3] log likelihood: -3139.613174
EM: Round [4] log likelihood: -3138.384885
EM: Round [5] log likelihood: -3137.537748
EM: Round [6] log likelihood: -3136.849239
EM: Round [7] log likelihood: -3136.252073
EM: Round [8] log likelihood: -3135.723109
EM: Round [9] log likelihood: -3135.251283
EM: Round [10] log likelihood: -3134.829226
EM: Round [11] log likelihood: -3134.451113
EM: Round [12] log likelihood: -3134.112029
EM: Round [13] log likelihood: -3133.807735
EM: Round [14] log likelihood: -3133.534536
EM: Round [15] log likelihood: -3133.289186
EM: Round [16] log likelihood: -3133.068825
EM: Round [17] log likelihood: -3132.870919
EM: Round [18] log likelihood: -3132.693215
EM: Round [19] log likelihood: -3132.533703
EM: Round [20] log likelihood: -3132.390583
EM: Round [21] log likelihood: -3132.262244
EM: Round [22] log likelihood: -3132.147233
EM: Round [23] log likelihood: -3132.044243
EM: Round [24] log likelihood: -3131.952093
EM: Round [25] log likelihood: -3131.869718
EM: Round [26] log likelihood: -3131.796151
EM: Round [27] log likelihood: -3131.730518
EM: Round [28] log likelihood: -3131.672027
EM: Round [29] log likelihood: -3131.619959
EM: Round [30] log likelihood: -3131.573663
EM: Round [31] log likelihood: -3131.532548
EM: Round [32] log likelihood: -3131.496080
EM: Round [33] log likelihood: -3131.463772
EM: Round [34] log likelihood: -3131.435186
EM: Round [35] log likelihood: -3131.409925
EM: Round [36] log likelihood: -3131.387631
EM: Round [37] log likelihood: -3131.367980
EM: Round [38] log likelihood: -3131.350679
EM: Round [39] log likelihood: -3131.335467
EM: Round [40] log likelihood: -3131.322107
EM: Round [41] log likelihood: -3131.310388
EM: Round [42] log likelihood: -3131.300121
EM: Round [43] log likelihood: -3131.291135
EM: Round [44] log likelihood: -3131.283280
EM: Round [45] log likelihood: -3131.276420
EM: Round [46] log likelihood: -3131.270436
EM: Round [47] log likelihood: -3131.265221
EM: Round [48] log likelihood: -3131.260680
EM: Round [49] log likelihood: -3131.256730
EM: Round [50] log likelihood: -3131.253297
EM: Round [51] log likelihood: -3131.250317
EM: Round [52] log likelihood: -3131.247730
EM: Round [53] log likelihood: -3131.245488
EM: Round [54] log likelihood: -3131.243545
EM: Round [55] log likelihood: -3131.241863
EM: Round [56] log likelihood: -3131.240408
EM: Round [57] log likelihood: -3131.239150
EM: Round [58] log likelihood: -3131.238063
EM: Round [59] log likelihood: -3131.237123
EM: Round [60] log likelihood: -3131.236313
EM: Round [61] log likelihood: -3131.235613
EM: Round [62] log likelihood: -3131.235010
EM: Round [63] log likelihood: -3131.234490
EM: Round [64] log likelihood: -3131.234042
EM: Round [65] log likelihood: -3131.233656
EM: Round [66] log likelihood: -3131.233323
EM: Round [67] log likelihood: -3131.233037
EM: Round [68] log likelihood: -3131.232791
EM: Round [69] log likelihood: -3131.232579
EM: Round [70] log likelihood: -3131.232397
EM: Round [71] log likelihood: -3131.232240
EM: Round [72] log likelihood: -3131.232106
EM: Round [73] log likelihood: -3131.231990
EM: Round [74] log likelihood: -3131.231891
EM: Stopping iterations at round 74 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3015.222079
EM: Round [1] log likelihood: -3001.716611
EM: Round [2] log likelihood: -2996.364649
EM: Round [3] log likelihood: -2994.054193
EM: Round [4] log likelihood: -2992.825904
EM: Round [5] log likelihood: -2991.978768
EM: Round [6] log likelihood: -2991.290258
EM: Round [7] log likelihood: -2990.693092
EM: Round [8] log likelihood: -2990.164128
EM: Round [9] log likelihood: -2989.692302
EM: Round [10] log likelihood: -2989.270245
EM: Round [11] log likelihood: -2988.892132
EM: Round [12] log likelihood: -2988.553048
EM: Round [13] log likelihood: -2988.248755
EM: Round [14] log likelihood: -2987.975555
EM: Round [15] log likelihood: -2987.730205
EM: Round [16] log likelihood: -2987.509844
EM: Round [17] log likelihood: -2987.311938
EM: Round [18] log likelihood: -2987.134234
EM: Round [19] log likelihood: -2986.974722
EM: Round [20] log likelihood: -2986.831603
EM: Round [21] log likelihood: -2986.703263
EM: Round [22] log likelihood: -2986.588252
EM: Round [23] log likelihood: -2986.485262
EM: Round [24] log likelihood: -2986.393112
EM: Round [25] log likelihood: -2986.310737
EM: Round [26] log likelihood: -2986.237170
EM: Round [27] log likelihood: -2986.171537
EM: Round [28] log likelihood: -2986.113046
EM: Round [29] log likelihood: -2986.060978
EM: Round [30] log likelihood: -2986.014682
EM: Round [31] log likelihood: -2985.973567
EM: Round [32] log likelihood: -2985.937099
EM: Round [33] log likelihood: -2985.904791
EM: Round [34] log likelihood: -2985.876205
EM: Round [35] log likelihood: -2985.850945
EM: Round [36] log likelihood: -2985.828650
EM: Round [37] log likelihood: -2985.808999
EM: Round [38] log likelihood: -2985.791698
EM: Round [39] log likelihood: -2985.776486
EM: Round [40] log likelihood: -2985.763126
EM: Round [41] log likelihood: -2985.751408
EM: Round [42] log likelihood: -2985.741140
EM: Round [43] log likelihood: -2985.732154
EM: Round [44] log likelihood: -2985.724299
EM: Round [45] log likelihood: -2985.717439
EM: Round [46] log likelihood: -2985.711455
EM: Round [47] log likelihood: -2985.706240
EM: Round [48] log likelihood: -2985.701699
EM: Round [49] log likelihood: -2985.697749
EM: Round [50] log likelihood: -2985.694317
EM: Round [51] log likelihood: -2985.691336
EM: Round [52] log likelihood: -2985.688749
EM: Round [53] log likelihood: -2985.686507
EM: Round [54] log likelihood: -2985.684564
EM: Round [55] log likelihood: -2985.682882
EM: Round [56] log likelihood: -2985.681427
EM: Round [57] log likelihood: -2985.680169
EM: Round [58] log likelihood: -2985.679082
EM: Round [59] log likelihood: -2985.678142
EM: Round [60] log likelihood: -2985.677332
EM: Round [61] log likelihood: -2985.676632
EM: Round [62] log likelihood: -2985.676029
EM: Round [63] log likelihood: -2985.675509
EM: Round [64] log likelihood: -2985.675061
EM: Round [65] log likelihood: -2985.674675
EM: Round [66] log likelihood: -2985.674342
EM: Round [67] log likelihood: -2985.674056
EM: Round [68] log likelihood: -2985.673810
EM: Round [69] log likelihood: -2985.673598
EM: Round [70] log likelihood: -2985.673416
EM: Round [71] log likelihood: -2985.673259
EM: Round [72] log likelihood: -2985.673125
EM: Round [73] log likelihood: -2985.673009
EM: Round [74] log likelihood: -2985.672910
EM: Stopping iterations at round 74 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 295708708
Warning - not locating file: /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000226240.2]
WARNING, no entry stored in dbm for [ENSG00000286591.1]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000260126.2]
WARNING, no entry stored in dbm for [ENSG00000254681.6]
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]
ls: cannot access 'IGV_inputs': No such file or directory