Done.
-parsing GTF file: /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.8Y0BsPg7Kt/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.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00150_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00150_B23WHTKLT4_1.star.sortedByCoord.out.bam
10:58:37 : INFO : Done.
-parsing GTF file: /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[130000]   -done parsing /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num genes matched < 2' => 6,
          'per_id < 96' => 550,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4,
          'excessive soft clipping' => 1539,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 440,
          'seq-similar region overlap' => 190,
          ' ** passed ** ' => 1614,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 14
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[16000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

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[18000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

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[17000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

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[17000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[12000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 372,
          'seq similar region alignment' => 10164
        };
EM: Starting log likelihood: -967.193665
EM: Round [1] log likelihood: -966.888224
EM: Round [2] log likelihood: -966.818459
EM: Round [3] log likelihood: -966.754080
EM: Round [4] log likelihood: -966.694521
EM: Round [5] log likelihood: -966.639336
EM: Round [6] log likelihood: -966.588133
EM: Round [7] log likelihood: -966.540563
EM: Round [8] log likelihood: -966.496319
EM: Round [9] log likelihood: -966.455124
EM: Round [10] log likelihood: -966.416729
EM: Round [11] log likelihood: -966.380914
EM: Round [12] log likelihood: -966.347476
EM: Round [13] log likelihood: -966.316235
EM: Round [14] log likelihood: -966.287025
EM: Round [15] log likelihood: -966.259696
EM: Round [16] log likelihood: -966.234113
EM: Round [17] log likelihood: -966.210149
EM: Round [18] log likelihood: -966.187691
EM: Round [19] log likelihood: -966.166634
EM: Round [20] log likelihood: -966.146882
EM: Round [21] log likelihood: -966.128346
EM: Round [22] log likelihood: -966.110944
EM: Round [23] log likelihood: -966.094601
EM: Round [24] log likelihood: -966.079247
EM: Round [25] log likelihood: -966.064818
EM: Round [26] log likelihood: -966.051254
EM: Round [27] log likelihood: -966.038500
EM: Round [28] log likelihood: -966.026503
EM: Round [29] log likelihood: -966.015218
EM: Round [30] log likelihood: -966.004598
EM: Round [31] log likelihood: -965.994602
EM: Round [32] log likelihood: -965.985192
EM: Round [33] log likelihood: -965.976332
EM: Round [34] log likelihood: -965.967988
EM: Round [35] log likelihood: -965.960129
EM: Round [36] log likelihood: -965.952726
EM: Round [37] log likelihood: -965.945750
EM: Round [38] log likelihood: -965.939177
EM: Round [39] log likelihood: -965.932982
EM: Round [40] log likelihood: -965.927143
EM: Round [41] log likelihood: -965.921639
EM: Round [42] log likelihood: -965.916450
EM: Round [43] log likelihood: -965.911558
EM: Round [44] log likelihood: -965.906944
EM: Round [45] log likelihood: -965.902594
EM: Round [46] log likelihood: -965.898491
EM: Round [47] log likelihood: -965.894621
EM: Round [48] log likelihood: -965.890970
EM: Round [49] log likelihood: -965.887527
EM: Round [50] log likelihood: -965.884278
EM: Round [51] log likelihood: -965.881213
EM: Round [52] log likelihood: -965.878321
EM: Round [53] log likelihood: -965.875593
EM: Round [54] log likelihood: -965.873018
EM: Round [55] log likelihood: -965.870588
EM: Round [56] log likelihood: -965.868295
EM: Round [57] log likelihood: -965.866131
EM: Round [58] log likelihood: -965.864089
EM: Round [59] log likelihood: -965.862162
EM: Round [60] log likelihood: -965.860343
EM: Round [61] log likelihood: -965.858625
EM: Round [62] log likelihood: -965.857004
EM: Round [63] log likelihood: -965.855474
EM: Round [64] log likelihood: -965.854030
EM: Round [65] log likelihood: -965.852667
EM: Round [66] log likelihood: -965.851380
EM: Round [67] log likelihood: -965.850164
EM: Round [68] log likelihood: -965.849017
EM: Round [69] log likelihood: -965.847934
EM: Round [70] log likelihood: -965.846912
EM: Round [71] log likelihood: -965.845946
EM: Round [72] log likelihood: -965.845035
EM: Round [73] log likelihood: -965.844174
EM: Round [74] log likelihood: -965.843362
EM: Round [75] log likelihood: -965.842595
EM: Round [76] log likelihood: -965.841870
EM: Round [77] log likelihood: -965.841186
EM: Round [78] log likelihood: -965.840541
EM: Round [79] log likelihood: -965.839931
EM: Round [80] log likelihood: -965.839355
EM: Round [81] log likelihood: -965.838811
EM: Round [82] log likelihood: -965.838298
EM: Round [83] log likelihood: -965.837813
EM: Round [84] log likelihood: -965.837355
EM: Round [85] log likelihood: -965.836923
EM: Round [86] log likelihood: -965.836514
EM: Round [87] log likelihood: -965.836129
EM: Round [88] log likelihood: -965.835765
EM: Round [89] log likelihood: -965.835421
EM: Round [90] log likelihood: -965.835096
EM: Round [91] log likelihood: -965.834790
EM: Round [92] log likelihood: -965.834500
EM: Round [93] log likelihood: -965.834227
EM: Round [94] log likelihood: -965.833969
EM: Round [95] log likelihood: -965.833725
EM: Round [96] log likelihood: -965.833495
EM: Round [97] log likelihood: -965.833277
EM: Round [98] log likelihood: -965.833072
EM: Round [99] log likelihood: -965.832878
EM: Round [100] log likelihood: -965.832695
EM: Round [101] log likelihood: -965.832522
EM: Round [102] log likelihood: -965.832358
EM: Round [103] log likelihood: -965.832204
EM: Round [104] log likelihood: -965.832058
EM: Round [105] log likelihood: -965.831921
EM: Round [106] log likelihood: -965.831791
EM: Round [107] log likelihood: -965.831668
EM: Round [108] log likelihood: -965.831552
EM: Round [109] log likelihood: -965.831443
EM: Round [110] log likelihood: -965.831339
EM: Round [111] log likelihood: -965.831242
EM: Stopping iterations at round 111 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_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.8Y0BsPg7Kt/fi_workdir/tih_rna_sample_00150_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -681.783093
EM: Round [1] log likelihood: -681.782283
EM: Round [2] log likelihood: -681.782282
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1_1.fastp.fastq.gz: 247680642
Warning - not locating file: /tmp/nxf.8Y0BsPg7Kt/tih_rna_sample_00150_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000272578.5]
WARNING, no entry stored in dbm for [ENSG00000272578.5]
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