Done.
-parsing GTF file: /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.Iz2yB19JfN/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.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00163_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00163_B23WHTKLT4_1.star.sortedByCoord.out.bam
09:44:46 : INFO : Done.
-parsing GTF file: /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[540000]   -done parsing /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 34,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 22,
          'num genes matched < 2' => 35,
          'seq-similar region overlap' => 99,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 39,
          'low complexity anchor region' => 6,
          'per_id < 96' => 3683,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 4,
          'excessive soft clipping' => 5438,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 56,
          ' ** passed ** ' => 3103
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[83000]   -fusion SPANNING read extraction for scaff: RUNX1--LINC01674

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[69000]   -fusion SPANNING read extraction for scaff: SCARF2--EHMT1

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[12000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[14000]   -fusion SPANNING read extraction for scaff: ZNF44--AC024563.1
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 9337,
          'lacks exon overlap' => 6171
        };
EM: Starting log likelihood: -4649.446790
EM: Round [1] log likelihood: -4647.168424
EM: Round [2] log likelihood: -4647.050761
EM: Round [3] log likelihood: -4646.943859
EM: Round [4] log likelihood: -4646.845782
EM: Round [5] log likelihood: -4646.755660
EM: Round [6] log likelihood: -4646.672728
EM: Round [7] log likelihood: -4646.596314
EM: Round [8] log likelihood: -4646.525824
EM: Round [9] log likelihood: -4646.460729
EM: Round [10] log likelihood: -4646.400558
EM: Round [11] log likelihood: -4646.344890
EM: Round [12] log likelihood: -4646.293346
EM: Round [13] log likelihood: -4646.245586
EM: Round [14] log likelihood: -4646.201302
EM: Round [15] log likelihood: -4646.160216
EM: Round [16] log likelihood: -4646.122074
EM: Round [17] log likelihood: -4646.086647
EM: Round [18] log likelihood: -4646.053727
EM: Round [19] log likelihood: -4646.023122
EM: Round [20] log likelihood: -4645.994657
EM: Round [21] log likelihood: -4645.968173
EM: Round [22] log likelihood: -4645.943523
EM: Round [23] log likelihood: -4645.920573
EM: Round [24] log likelihood: -4645.899199
EM: Round [25] log likelihood: -4645.879287
EM: Round [26] log likelihood: -4645.860733
EM: Round [27] log likelihood: -4645.843439
EM: Round [28] log likelihood: -4645.827317
EM: Round [29] log likelihood: -4645.812284
EM: Round [30] log likelihood: -4645.798263
EM: Round [31] log likelihood: -4645.785185
EM: Round [32] log likelihood: -4645.772983
EM: Round [33] log likelihood: -4645.761597
EM: Round [34] log likelihood: -4645.750972
EM: Round [35] log likelihood: -4645.741054
EM: Round [36] log likelihood: -4645.731797
EM: Round [37] log likelihood: -4645.723154
EM: Round [38] log likelihood: -4645.715084
EM: Round [39] log likelihood: -4645.707548
EM: Round [40] log likelihood: -4645.700510
EM: Round [41] log likelihood: -4645.693938
EM: Round [42] log likelihood: -4645.687799
EM: Round [43] log likelihood: -4645.682064
EM: Round [44] log likelihood: -4645.676707
EM: Round [45] log likelihood: -4645.671702
EM: Round [46] log likelihood: -4645.667026
EM: Round [47] log likelihood: -4645.662657
EM: Round [48] log likelihood: -4645.658574
EM: Round [49] log likelihood: -4645.654759
EM: Round [50] log likelihood: -4645.651194
EM: Round [51] log likelihood: -4645.647863
EM: Round [52] log likelihood: -4645.644749
EM: Round [53] log likelihood: -4645.641839
EM: Round [54] log likelihood: -4645.639119
EM: Round [55] log likelihood: -4645.636577
EM: Round [56] log likelihood: -4645.634201
EM: Round [57] log likelihood: -4645.631979
EM: Round [58] log likelihood: -4645.629903
EM: Round [59] log likelihood: -4645.627962
EM: Round [60] log likelihood: -4645.626148
EM: Round [61] log likelihood: -4645.624452
EM: Round [62] log likelihood: -4645.622866
EM: Round [63] log likelihood: -4645.621384
EM: Round [64] log likelihood: -4645.619998
EM: Round [65] log likelihood: -4645.618703
EM: Round [66] log likelihood: -4645.617491
EM: Round [67] log likelihood: -4645.616359
EM: Round [68] log likelihood: -4645.615300
EM: Round [69] log likelihood: -4645.614310
EM: Round [70] log likelihood: -4645.613385
EM: Round [71] log likelihood: -4645.612520
EM: Round [72] log likelihood: -4645.611710
EM: Round [73] log likelihood: -4645.610954
EM: Round [74] log likelihood: -4645.610247
EM: Round [75] log likelihood: -4645.609585
EM: Round [76] log likelihood: -4645.608967
EM: Round [77] log likelihood: -4645.608389
EM: Round [78] log likelihood: -4645.607848
EM: Round [79] log likelihood: -4645.607343
EM: Round [80] log likelihood: -4645.606870
EM: Round [81] log likelihood: -4645.606428
EM: Round [82] log likelihood: -4645.606015
EM: Round [83] log likelihood: -4645.605628
EM: Round [84] log likelihood: -4645.605267
EM: Round [85] log likelihood: -4645.604929
EM: Round [86] log likelihood: -4645.604613
EM: Round [87] log likelihood: -4645.604318
EM: Round [88] log likelihood: -4645.604042
EM: Round [89] log likelihood: -4645.603783
EM: Round [90] log likelihood: -4645.603542
EM: Round [91] log likelihood: -4645.603316
EM: Round [92] log likelihood: -4645.603105
EM: Round [93] log likelihood: -4645.602907
EM: Round [94] log likelihood: -4645.602723
EM: Round [95] log likelihood: -4645.602550
EM: Round [96] log likelihood: -4645.602388
EM: Round [97] log likelihood: -4645.602237
EM: Round [98] log likelihood: -4645.602096
EM: Round [99] log likelihood: -4645.601964
EM: Round [100] log likelihood: -4645.601841
EM: Round [101] log likelihood: -4645.601725
EM: Round [102] log likelihood: -4645.601617
EM: Round [103] log likelihood: -4645.601516
EM: Round [104] log likelihood: -4645.601422
EM: Stopping iterations at round 104 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_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.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_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.Iz2yB19JfN/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -4414.825998
EM: Round [1] log likelihood: -4414.547973
EM: Round [2] log likelihood: -4414.547836
EM: Round [3] log likelihood: -4414.547835
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1_1.fastp.fastq.gz: 186358289
Warning - not locating file: /tmp/nxf.Iz2yB19JfN/tih_rna_sample_00163_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
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 [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000268981.5]
WARNING, no entry stored in dbm for [ENSG00000268981.5]
ls: cannot access 'IGV_inputs': No such file or directory