Done.
-parsing GTF file: /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.lxEUMOIMc1/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.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00096_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00096_B23WHTKLT4_2.star.sortedByCoord.out.bam
11:07:37 : INFO : Done.
-parsing GTF file: /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

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[2510000]   -done parsing /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num genes matched < 2' => 83,
          'excessive soft clipping' => 14433,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 68,
          'seq-similar region overlap' => 156,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 349,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
          ' ** passed ** ' => 6568,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 17,
          'small anchor length' => 27,
          'exons hit < 2' => 1,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 3,
          'low complexity anchor region' => 35,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
          'per_id < 96' => 9328,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.
-fusion SPANNING read extraction for scaff: AC016629.1--RPL23AP53

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[8000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

[1000]   -fusion SPANNING read extraction for scaff: AC239859.5--AC013734.1

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[241000]   -fusion SPANNING read extraction for scaff: ARHGEF17--CCS

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[54000]   -fusion SPANNING read extraction for scaff: CCS--ACTN3

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[55000]   -fusion SPANNING read extraction for scaff: CHERP--OR2Z1

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[115000]   -fusion SPANNING read extraction for scaff: CTTN--SPCS2

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[77000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

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[98000]   -fusion SPANNING read extraction for scaff: GRPEL2--HSPA9

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[253000]   
[254000]   -fusion SPANNING read extraction for scaff: KDM2A--AP000446.1

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[249000]   
[250000]   -fusion SPANNING read extraction for scaff: KDM4B--NFIC

[1000]   
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[167000]   
[168000]   -fusion SPANNING read extraction for scaff: NCOA6--AHCY

[1000]   
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[8000]   
[9000]   
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[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[1000]   
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[6000]   
[7000]   
[8000]   
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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

[1000]   
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[294000]   
[295000]   -fusion SPANNING read extraction for scaff: SEMA4B--EVL

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[80000]   
[81000]   -fusion SPANNING read extraction for scaff: SHANK2--DLG2

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[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   -fusion SPANNING read extraction for scaff: SSRP1--BDNF

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[6000]   
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[8000]   
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[83000]   
[84000]   
[85000]   -fusion SPANNING read extraction for scaff: ST3GAL1--NDRG1

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[128000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
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[46000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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

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[33000]   -fusion SPANNING read extraction for scaff: TMEM138--AP001107.6

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[54000]   -fusion SPANNING read extraction for scaff: TSG101--CLPB

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

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[344000]   -fusion SPANNING read extraction for scaff: UVRAG--KDM2A
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 10668,
          'lacks exon overlap' => 55735
        };
EM: Starting log likelihood: -9115.685203
EM: Round [1] log likelihood: -9106.411869
EM: Round [2] log likelihood: -9106.052890
EM: Round [3] log likelihood: -9105.762603
EM: Round [4] log likelihood: -9105.519288
EM: Round [5] log likelihood: -9105.314240
EM: Round [6] log likelihood: -9105.140687
EM: Round [7] log likelihood: -9104.993260
EM: Round [8] log likelihood: -9104.867651
EM: Round [9] log likelihood: -9104.760363
EM: Round [10] log likelihood: -9104.668530
EM: Round [11] log likelihood: -9104.589786
EM: Round [12] log likelihood: -9104.522162
EM: Round [13] log likelihood: -9104.464013
EM: Round [14] log likelihood: -9104.413957
EM: Round [15] log likelihood: -9104.370827
EM: Round [16] log likelihood: -9104.333635
EM: Round [17] log likelihood: -9104.301541
EM: Round [18] log likelihood: -9104.273831
EM: Round [19] log likelihood: -9104.249892
EM: Round [20] log likelihood: -9104.229203
EM: Round [21] log likelihood: -9104.211315
EM: Round [22] log likelihood: -9104.195845
EM: Round [23] log likelihood: -9104.182462
EM: Round [24] log likelihood: -9104.170881
EM: Round [25] log likelihood: -9104.160858
EM: Round [26] log likelihood: -9104.152182
EM: Round [27] log likelihood: -9104.144670
EM: Round [28] log likelihood: -9104.138165
EM: Round [29] log likelihood: -9104.132532
EM: Round [30] log likelihood: -9104.127653
EM: Round [31] log likelihood: -9104.123427
EM: Round [32] log likelihood: -9104.119766
EM: Round [33] log likelihood: -9104.116595
EM: Round [34] log likelihood: -9104.113847
EM: Round [35] log likelihood: -9104.111467
EM: Round [36] log likelihood: -9104.109405
EM: Round [37] log likelihood: -9104.107618
EM: Round [38] log likelihood: -9104.106069
EM: Round [39] log likelihood: -9104.104728
EM: Round [40] log likelihood: -9104.103565
EM: Round [41] log likelihood: -9104.102558
EM: Round [42] log likelihood: -9104.101685
EM: Round [43] log likelihood: -9104.100928
EM: Round [44] log likelihood: -9104.100273
EM: Round [45] log likelihood: -9104.099704
EM: Round [46] log likelihood: -9104.099212
EM: Round [47] log likelihood: -9104.098785
EM: Round [48] log likelihood: -9104.098416
EM: Round [49] log likelihood: -9104.098095
EM: Round [50] log likelihood: -9104.097817
EM: Round [51] log likelihood: -9104.097577
EM: Round [52] log likelihood: -9104.097368
EM: Round [53] log likelihood: -9104.097187
EM: Round [54] log likelihood: -9104.097031
EM: Round [55] log likelihood: -9104.096895
EM: Round [56] log likelihood: -9104.096777
EM: Round [57] log likelihood: -9104.096675
EM: Round [58] log likelihood: -9104.096587
EM: Stopping iterations at round 58 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_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.lxEUMOIMc1/fi_workdir/tih_rna_sample_00096_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -8940.540134
EM: Round [1] log likelihood: -8934.700336
EM: Round [2] log likelihood: -8934.692570
EM: Round [3] log likelihood: -8934.692547
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2_1.fastp.fastq.gz: 295827505
Warning - not locating file: /tmp/nxf.lxEUMOIMc1/tih_rna_sample_00096_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000277702.1]
WARNING, no entry stored in dbm for [ENSG00000277146.1]
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 [ENSG00000255234.6]
WARNING, no entry stored in dbm for [ENSG00000255234.6]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000254756.1]
WARNING, no entry stored in dbm for [ENSG00000254756.1]
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 [ENSG00000269032.1]
WARNING, no entry stored in dbm for [ENSG00000223508.5]
WARNING, no entry stored in dbm for [ENSG00000269032.1]
WARNING, no entry stored in dbm for [ENSG00000223508.5]
ls: cannot access 'IGV_inputs': No such file or directory