Done.
-parsing GTF file: /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.bZuhpufnsu/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.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-da06ce-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-da06ce-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:52:43 : INFO : Done.
-parsing GTF file: /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[390000]   -done parsing /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 3821,
          'seq-similar region overlap' => 117,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 111,
          ' ** passed ** ' => 1666,
          'low complexity anchor region' => 4,
          'per_id < 96' => 1826,
          'num genes matched < 2' => 1,
          'small anchor length' => 54,
          'exons hit < 2' => 1
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[7000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[204000]   -fusion SPANNING read extraction for scaff: CCAR2--AC055854.1

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[26000]   -fusion SPANNING read extraction for scaff: PAPOLA--RBMXP1

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[26000]   -fusion SPANNING read extraction for scaff: PAPOLA--FO393412.1

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[16000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[22000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

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[13000]   -fusion SPANNING read extraction for scaff: STON1--GTF2A1L

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[20000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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

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[18000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 3756,
          'seq similar region alignment' => 13295
        };
EM: Starting log likelihood: -1869.509848
EM: Round [1] log likelihood: -1869.402485
EM: Round [2] log likelihood: -1869.358123
EM: Round [3] log likelihood: -1869.316906
EM: Round [4] log likelihood: -1869.278339
EM: Round [5] log likelihood: -1869.242166
EM: Round [6] log likelihood: -1869.208168
EM: Round [7] log likelihood: -1869.176154
EM: Round [8] log likelihood: -1869.145956
EM: Round [9] log likelihood: -1869.117427
EM: Round [10] log likelihood: -1869.090434
EM: Round [11] log likelihood: -1869.064861
EM: Round [12] log likelihood: -1869.040603
EM: Round [13] log likelihood: -1869.017566
EM: Round [14] log likelihood: -1868.995665
EM: Round [15] log likelihood: -1868.974824
EM: Round [16] log likelihood: -1868.954971
EM: Round [17] log likelihood: -1868.936045
EM: Round [18] log likelihood: -1868.917986
EM: Round [19] log likelihood: -1868.900741
EM: Round [20] log likelihood: -1868.884262
EM: Round [21] log likelihood: -1868.868503
EM: Round [22] log likelihood: -1868.853424
EM: Round [23] log likelihood: -1868.838985
EM: Round [24] log likelihood: -1868.825151
EM: Round [25] log likelihood: -1868.811890
EM: Round [26] log likelihood: -1868.799170
EM: Round [27] log likelihood: -1868.786964
EM: Round [28] log likelihood: -1868.775244
EM: Round [29] log likelihood: -1868.763985
EM: Round [30] log likelihood: -1868.753165
EM: Round [31] log likelihood: -1868.742762
EM: Round [32] log likelihood: -1868.732756
EM: Round [33] log likelihood: -1868.723126
EM: Round [34] log likelihood: -1868.713856
EM: Round [35] log likelihood: -1868.704929
EM: Round [36] log likelihood: -1868.696328
EM: Round [37] log likelihood: -1868.688039
EM: Round [38] log likelihood: -1868.680047
EM: Round [39] log likelihood: -1868.672340
EM: Round [40] log likelihood: -1868.664904
EM: Round [41] log likelihood: -1868.657727
EM: Round [42] log likelihood: -1868.650799
EM: Round [43] log likelihood: -1868.644109
EM: Round [44] log likelihood: -1868.637646
EM: Round [45] log likelihood: -1868.631401
EM: Round [46] log likelihood: -1868.625365
EM: Round [47] log likelihood: -1868.619530
EM: Round [48] log likelihood: -1868.613886
EM: Round [49] log likelihood: -1868.608427
EM: Round [50] log likelihood: -1868.603144
EM: Round [51] log likelihood: -1868.598031
EM: Round [52] log likelihood: -1868.593081
EM: Round [53] log likelihood: -1868.588287
EM: Round [54] log likelihood: -1868.583644
EM: Round [55] log likelihood: -1868.579145
EM: Round [56] log likelihood: -1868.574786
EM: Round [57] log likelihood: -1868.570560
EM: Round [58] log likelihood: -1868.566463
EM: Round [59] log likelihood: -1868.562490
EM: Round [60] log likelihood: -1868.558637
EM: Round [61] log likelihood: -1868.554898
EM: Round [62] log likelihood: -1868.551269
EM: Round [63] log likelihood: -1868.547747
EM: Round [64] log likelihood: -1868.544328
EM: Round [65] log likelihood: -1868.541008
EM: Round [66] log likelihood: -1868.537784
EM: Round [67] log likelihood: -1868.534651
EM: Round [68] log likelihood: -1868.531608
EM: Round [69] log likelihood: -1868.528650
EM: Round [70] log likelihood: -1868.525775
EM: Round [71] log likelihood: -1868.522979
EM: Round [72] log likelihood: -1868.520261
EM: Round [73] log likelihood: -1868.517618
EM: Round [74] log likelihood: -1868.515046
EM: Round [75] log likelihood: -1868.512545
EM: Round [76] log likelihood: -1868.510110
EM: Round [77] log likelihood: -1868.507740
EM: Round [78] log likelihood: -1868.505434
EM: Round [79] log likelihood: -1868.503188
EM: Round [80] log likelihood: -1868.501001
EM: Round [81] log likelihood: -1868.498871
EM: Round [82] log likelihood: -1868.496796
EM: Round [83] log likelihood: -1868.494774
EM: Round [84] log likelihood: -1868.492804
EM: Round [85] log likelihood: -1868.490885
EM: Round [86] log likelihood: -1868.489013
EM: Round [87] log likelihood: -1868.487189
EM: Round [88] log likelihood: -1868.485410
EM: Round [89] log likelihood: -1868.483675
EM: Round [90] log likelihood: -1868.481983
EM: Round [91] log likelihood: -1868.480333
EM: Round [92] log likelihood: -1868.478722
EM: Round [93] log likelihood: -1868.477151
EM: Round [94] log likelihood: -1868.475618
EM: Round [95] log likelihood: -1868.474121
EM: Round [96] log likelihood: -1868.472660
EM: Round [97] log likelihood: -1868.471234
EM: Round [98] log likelihood: -1868.469841
EM: Round [99] log likelihood: -1868.468481
EM: Round [100] log likelihood: -1868.467153
EM: Round [101] log likelihood: -1868.465855
EM: Round [102] log likelihood: -1868.464587
EM: Round [103] log likelihood: -1868.463349
EM: Round [104] log likelihood: -1868.462139
EM: Round [105] log likelihood: -1868.460956
EM: Round [106] log likelihood: -1868.459800
EM: Round [107] log likelihood: -1868.458670
EM: Round [108] log likelihood: -1868.457565
EM: Round [109] log likelihood: -1868.456485
EM: Round [110] log likelihood: -1868.455429
EM: Round [111] log likelihood: -1868.454396
EM: Round [112] log likelihood: -1868.453386
EM: Round [113] log likelihood: -1868.452398
EM: Round [114] log likelihood: -1868.451432
EM: Round [115] log likelihood: -1868.450486
EM: Round [116] log likelihood: -1868.449561
EM: Round [117] log likelihood: -1868.448656
EM: Round [118] log likelihood: -1868.447770
EM: Round [119] log likelihood: -1868.446903
EM: Round [120] log likelihood: -1868.446055
EM: Round [121] log likelihood: -1868.445224
EM: Round [122] log likelihood: -1868.444411
EM: Round [123] log likelihood: -1868.443615
EM: Round [124] log likelihood: -1868.442835
EM: Round [125] log likelihood: -1868.442072
EM: Round [126] log likelihood: -1868.441325
EM: Round [127] log likelihood: -1868.440593
EM: Round [128] log likelihood: -1868.439876
EM: Round [129] log likelihood: -1868.439174
EM: Round [130] log likelihood: -1868.438486
EM: Round [131] log likelihood: -1868.437812
EM: Round [132] log likelihood: -1868.437152
EM: Round [133] log likelihood: -1868.436505
EM: Round [134] log likelihood: -1868.435871
EM: Round [135] log likelihood: -1868.435250
EM: Round [136] log likelihood: -1868.434641
EM: Round [137] log likelihood: -1868.434045
EM: Round [138] log likelihood: -1868.433460
EM: Round [139] log likelihood: -1868.432887
EM: Round [140] log likelihood: -1868.432326
EM: Round [141] log likelihood: -1868.431775
EM: Round [142] log likelihood: -1868.431235
EM: Round [143] log likelihood: -1868.430706
EM: Round [144] log likelihood: -1868.430187
EM: Round [145] log likelihood: -1868.429678
EM: Round [146] log likelihood: -1868.429180
EM: Round [147] log likelihood: -1868.428691
EM: Round [148] log likelihood: -1868.428211
EM: Round [149] log likelihood: -1868.427740
EM: Round [150] log likelihood: -1868.427279
EM: Round [151] log likelihood: -1868.426827
EM: Round [152] log likelihood: -1868.426383
EM: Round [153] log likelihood: -1868.425948
EM: Round [154] log likelihood: -1868.425521
EM: Round [155] log likelihood: -1868.425102
EM: Round [156] log likelihood: -1868.424691
EM: Round [157] log likelihood: -1868.424288
EM: Round [158] log likelihood: -1868.423892
EM: Round [159] log likelihood: -1868.423504
EM: Round [160] log likelihood: -1868.423123
EM: Round [161] log likelihood: -1868.422750
EM: Round [162] log likelihood: -1868.422383
EM: Round [163] log likelihood: -1868.422023
EM: Round [164] log likelihood: -1868.421670
EM: Round [165] log likelihood: -1868.421324
EM: Round [166] log likelihood: -1868.420984
EM: Round [167] log likelihood: -1868.420651
EM: Round [168] log likelihood: -1868.420323
EM: Round [169] log likelihood: -1868.420002
EM: Round [170] log likelihood: -1868.419686
EM: Round [171] log likelihood: -1868.419377
EM: Round [172] log likelihood: -1868.419073
EM: Round [173] log likelihood: -1868.418775
EM: Round [174] log likelihood: -1868.418482
EM: Round [175] log likelihood: -1868.418194
EM: Round [176] log likelihood: -1868.417912
EM: Round [177] log likelihood: -1868.417635
EM: Round [178] log likelihood: -1868.417363
EM: Round [179] log likelihood: -1868.417096
EM: Round [180] log likelihood: -1868.416834
EM: Round [181] log likelihood: -1868.416577
EM: Round [182] log likelihood: -1868.416324
EM: Round [183] log likelihood: -1868.416076
EM: Round [184] log likelihood: -1868.415833
EM: Round [185] log likelihood: -1868.415594
EM: Round [186] log likelihood: -1868.415359
EM: Round [187] log likelihood: -1868.415128
EM: Round [188] log likelihood: -1868.414902
EM: Round [189] log likelihood: -1868.414680
EM: Round [190] log likelihood: -1868.414461
EM: Round [191] log likelihood: -1868.414247
EM: Round [192] log likelihood: -1868.414036
EM: Round [193] log likelihood: -1868.413830
EM: Round [194] log likelihood: -1868.413627
EM: Round [195] log likelihood: -1868.413427
EM: Round [196] log likelihood: -1868.413231
EM: Round [197] log likelihood: -1868.413039
EM: Round [198] log likelihood: -1868.412850
EM: Round [199] log likelihood: -1868.412665
EM: Round [200] log likelihood: -1868.412483
EM: Round [201] log likelihood: -1868.412304
EM: Round [202] log likelihood: -1868.412128
EM: Round [203] log likelihood: -1868.411955
EM: Round [204] log likelihood: -1868.411786
EM: Round [205] log likelihood: -1868.411619
EM: Round [206] log likelihood: -1868.411456
EM: Round [207] log likelihood: -1868.411295
EM: Round [208] log likelihood: -1868.411137
EM: Round [209] log likelihood: -1868.410982
EM: Round [210] log likelihood: -1868.410830
EM: Round [211] log likelihood: -1868.410681
EM: Round [212] log likelihood: -1868.410534
EM: Round [213] log likelihood: -1868.410389
EM: Round [214] log likelihood: -1868.410248
EM: Round [215] log likelihood: -1868.410108
EM: Round [216] log likelihood: -1868.409972
EM: Round [217] log likelihood: -1868.409837
EM: Round [218] log likelihood: -1868.409705
EM: Round [219] log likelihood: -1868.409576
EM: Round [220] log likelihood: -1868.409448
EM: Round [221] log likelihood: -1868.409323
EM: Round [222] log likelihood: -1868.409200
EM: Round [223] log likelihood: -1868.409079
EM: Round [224] log likelihood: -1868.408961
EM: Round [225] log likelihood: -1868.408844
EM: Round [226] log likelihood: -1868.408730
EM: Round [227] log likelihood: -1868.408617
EM: Round [228] log likelihood: -1868.408507
EM: Round [229] log likelihood: -1868.408398
EM: Round [230] log likelihood: -1868.408291
EM: Round [231] log likelihood: -1868.408187
EM: Round [232] log likelihood: -1868.408084
EM: Round [233] log likelihood: -1868.407982
EM: Round [234] log likelihood: -1868.407883
EM: Stopping iterations at round 234 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-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.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-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.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-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.bZuhpufnsu/fi_workdir/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1825.647436
EM: Round [1] log likelihood: -1825.587519
EM: Round [2] log likelihood: -1825.587314
EM: Round [3] log likelihood: -1825.587314
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296209672
Warning - not locating file: /tmp/nxf.bZuhpufnsu/aih-tih-sc-da06ce-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000253125.1]
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 [ENSG00000280136.2]
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 [ENSG00000282057.1]
ls: cannot access 'IGV_inputs': No such file or directory