Done.
-parsing GTF file: /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.u6OmFZLRev/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.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
08:39:46 : INFO : Done.
-parsing GTF file: /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[820000]   -done parsing /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 6018,
          'per_id < 96' => 4143,
          'low complexity anchor region' => 46,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 21,
          ' ** passed ** ' => 8740,
          'seq-similar region overlap' => 3
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

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[697000]   -fusion SPANNING read extraction for scaff: TMPRSS2--ERG
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 6355,
          'lacks exon overlap' => 4176
        };
EM: Starting log likelihood: -2410.042375
EM: Round [1] log likelihood: -2410.038336
EM: Round [2] log likelihood: -2410.034351
EM: Round [3] log likelihood: -2410.030420
EM: Round [4] log likelihood: -2410.026543
EM: Round [5] log likelihood: -2410.022719
EM: Round [6] log likelihood: -2410.018946
EM: Round [7] log likelihood: -2410.015224
EM: Round [8] log likelihood: -2410.011553
EM: Round [9] log likelihood: -2410.007931
EM: Round [10] log likelihood: -2410.004358
EM: Round [11] log likelihood: -2410.000833
EM: Round [12] log likelihood: -2409.997355
EM: Round [13] log likelihood: -2409.993924
EM: Round [14] log likelihood: -2409.990539
EM: Round [15] log likelihood: -2409.987200
EM: Round [16] log likelihood: -2409.983905
EM: Round [17] log likelihood: -2409.980654
EM: Round [18] log likelihood: -2409.977447
EM: Round [19] log likelihood: -2409.974282
EM: Round [20] log likelihood: -2409.971160
EM: Round [21] log likelihood: -2409.968079
EM: Round [22] log likelihood: -2409.965040
EM: Round [23] log likelihood: -2409.962040
EM: Round [24] log likelihood: -2409.959081
EM: Round [25] log likelihood: -2409.956160
EM: Round [26] log likelihood: -2409.953279
EM: Round [27] log likelihood: -2409.950435
EM: Round [28] log likelihood: -2409.947629
EM: Round [29] log likelihood: -2409.944861
EM: Round [30] log likelihood: -2409.942128
EM: Round [31] log likelihood: -2409.939432
EM: Round [32] log likelihood: -2409.936772
EM: Round [33] log likelihood: -2409.934146
EM: Round [34] log likelihood: -2409.931555
EM: Round [35] log likelihood: -2409.928998
EM: Round [36] log likelihood: -2409.926474
EM: Round [37] log likelihood: -2409.923984
EM: Round [38] log likelihood: -2409.921526
EM: Round [39] log likelihood: -2409.919101
EM: Round [40] log likelihood: -2409.916707
EM: Round [41] log likelihood: -2409.914344
EM: Round [42] log likelihood: -2409.912013
EM: Round [43] log likelihood: -2409.909711
EM: Round [44] log likelihood: -2409.907440
EM: Round [45] log likelihood: -2409.905199
EM: Round [46] log likelihood: -2409.902986
EM: Round [47] log likelihood: -2409.900803
EM: Round [48] log likelihood: -2409.898648
EM: Round [49] log likelihood: -2409.896521
EM: Round [50] log likelihood: -2409.894421
EM: Round [51] log likelihood: -2409.892349
EM: Round [52] log likelihood: -2409.890304
EM: Round [53] log likelihood: -2409.888285
EM: Round [54] log likelihood: -2409.886292
EM: Round [55] log likelihood: -2409.884325
EM: Round [56] log likelihood: -2409.882384
EM: Round [57] log likelihood: -2409.880468
EM: Round [58] log likelihood: -2409.878576
EM: Round [59] log likelihood: -2409.876709
EM: Round [60] log likelihood: -2409.874866
EM: Round [61] log likelihood: -2409.873047
EM: Round [62] log likelihood: -2409.871251
EM: Round [63] log likelihood: -2409.869478
EM: Round [64] log likelihood: -2409.867728
EM: Round [65] log likelihood: -2409.866001
EM: Round [66] log likelihood: -2409.864296
EM: Round [67] log likelihood: -2409.862612
EM: Round [68] log likelihood: -2409.860951
EM: Round [69] log likelihood: -2409.859311
EM: Round [70] log likelihood: -2409.857691
EM: Round [71] log likelihood: -2409.856093
EM: Round [72] log likelihood: -2409.854515
EM: Round [73] log likelihood: -2409.852957
EM: Round [74] log likelihood: -2409.851419
EM: Round [75] log likelihood: -2409.849901
EM: Round [76] log likelihood: -2409.848403
EM: Round [77] log likelihood: -2409.846923
EM: Round [78] log likelihood: -2409.845463
EM: Round [79] log likelihood: -2409.844021
EM: Round [80] log likelihood: -2409.842597
EM: Round [81] log likelihood: -2409.841192
EM: Round [82] log likelihood: -2409.839804
EM: Round [83] log likelihood: -2409.838434
EM: Round [84] log likelihood: -2409.837082
EM: Round [85] log likelihood: -2409.835747
EM: Round [86] log likelihood: -2409.834429
EM: Round [87] log likelihood: -2409.833127
EM: Round [88] log likelihood: -2409.831843
EM: Round [89] log likelihood: -2409.830574
EM: Round [90] log likelihood: -2409.829322
EM: Round [91] log likelihood: -2409.828086
EM: Round [92] log likelihood: -2409.826865
EM: Round [93] log likelihood: -2409.825660
EM: Round [94] log likelihood: -2409.824470
EM: Round [95] log likelihood: -2409.823295
EM: Round [96] log likelihood: -2409.822135
EM: Round [97] log likelihood: -2409.820990
EM: Round [98] log likelihood: -2409.819859
EM: Round [99] log likelihood: -2409.818743
EM: Round [100] log likelihood: -2409.817640
EM: Round [101] log likelihood: -2409.816552
EM: Round [102] log likelihood: -2409.815477
EM: Round [103] log likelihood: -2409.814417
EM: Round [104] log likelihood: -2409.813369
EM: Round [105] log likelihood: -2409.812335
EM: Round [106] log likelihood: -2409.811313
EM: Round [107] log likelihood: -2409.810305
EM: Round [108] log likelihood: -2409.809309
EM: Round [109] log likelihood: -2409.808326
EM: Round [110] log likelihood: -2409.807356
EM: Round [111] log likelihood: -2409.806397
EM: Round [112] log likelihood: -2409.805451
EM: Round [113] log likelihood: -2409.804517
EM: Round [114] log likelihood: -2409.803594
EM: Round [115] log likelihood: -2409.802683
EM: Round [116] log likelihood: -2409.801784
EM: Round [117] log likelihood: -2409.800895
EM: Round [118] log likelihood: -2409.800018
EM: Round [119] log likelihood: -2409.799152
EM: Round [120] log likelihood: -2409.798297
EM: Round [121] log likelihood: -2409.797453
EM: Round [122] log likelihood: -2409.796619
EM: Round [123] log likelihood: -2409.795796
EM: Round [124] log likelihood: -2409.794983
EM: Round [125] log likelihood: -2409.794180
EM: Round [126] log likelihood: -2409.793388
EM: Round [127] log likelihood: -2409.792605
EM: Round [128] log likelihood: -2409.791832
EM: Round [129] log likelihood: -2409.791069
EM: Round [130] log likelihood: -2409.790316
EM: Round [131] log likelihood: -2409.789571
EM: Round [132] log likelihood: -2409.788837
EM: Round [133] log likelihood: -2409.788111
EM: Round [134] log likelihood: -2409.787395
EM: Round [135] log likelihood: -2409.786687
EM: Round [136] log likelihood: -2409.785988
EM: Round [137] log likelihood: -2409.785299
EM: Round [138] log likelihood: -2409.784617
EM: Round [139] log likelihood: -2409.783945
EM: Round [140] log likelihood: -2409.783280
EM: Round [141] log likelihood: -2409.782624
EM: Round [142] log likelihood: -2409.781977
EM: Round [143] log likelihood: -2409.781337
EM: Round [144] log likelihood: -2409.780705
EM: Round [145] log likelihood: -2409.780081
EM: Round [146] log likelihood: -2409.779465
EM: Round [147] log likelihood: -2409.778857
EM: Round [148] log likelihood: -2409.778256
EM: Round [149] log likelihood: -2409.777663
EM: Round [150] log likelihood: -2409.777077
EM: Round [151] log likelihood: -2409.776499
EM: Round [152] log likelihood: -2409.775928
EM: Round [153] log likelihood: -2409.775364
EM: Round [154] log likelihood: -2409.774807
EM: Round [155] log likelihood: -2409.774256
EM: Round [156] log likelihood: -2409.773713
EM: Round [157] log likelihood: -2409.773177
EM: Round [158] log likelihood: -2409.772647
EM: Round [159] log likelihood: -2409.772124
EM: Round [160] log likelihood: -2409.771607
EM: Round [161] log likelihood: -2409.771097
EM: Round [162] log likelihood: -2409.770593
EM: Round [163] log likelihood: -2409.770095
EM: Round [164] log likelihood: -2409.769604
EM: Round [165] log likelihood: -2409.769119
EM: Round [166] log likelihood: -2409.768639
EM: Round [167] log likelihood: -2409.768166
EM: Round [168] log likelihood: -2409.767699
EM: Round [169] log likelihood: -2409.767237
EM: Round [170] log likelihood: -2409.766781
EM: Round [171] log likelihood: -2409.766331
EM: Round [172] log likelihood: -2409.765887
EM: Round [173] log likelihood: -2409.765448
EM: Round [174] log likelihood: -2409.765014
EM: Round [175] log likelihood: -2409.764586
EM: Round [176] log likelihood: -2409.764163
EM: Round [177] log likelihood: -2409.763746
EM: Round [178] log likelihood: -2409.763333
EM: Round [179] log likelihood: -2409.762926
EM: Round [180] log likelihood: -2409.762524
EM: Round [181] log likelihood: -2409.762127
EM: Round [182] log likelihood: -2409.761734
EM: Round [183] log likelihood: -2409.761347
EM: Round [184] log likelihood: -2409.760964
EM: Round [185] log likelihood: -2409.760587
EM: Round [186] log likelihood: -2409.760213
EM: Round [187] log likelihood: -2409.759845
EM: Round [188] log likelihood: -2409.759481
EM: Round [189] log likelihood: -2409.759122
EM: Round [190] log likelihood: -2409.758767
EM: Round [191] log likelihood: -2409.758416
EM: Round [192] log likelihood: -2409.758070
EM: Round [193] log likelihood: -2409.757728
EM: Round [194] log likelihood: -2409.757390
EM: Round [195] log likelihood: -2409.757057
EM: Round [196] log likelihood: -2409.756728
EM: Round [197] log likelihood: -2409.756402
EM: Round [198] log likelihood: -2409.756081
EM: Round [199] log likelihood: -2409.755764
EM: Round [200] log likelihood: -2409.755451
EM: Round [201] log likelihood: -2409.755141
EM: Round [202] log likelihood: -2409.754836
EM: Round [203] log likelihood: -2409.754534
EM: Round [204] log likelihood: -2409.754236
EM: Round [205] log likelihood: -2409.753942
EM: Round [206] log likelihood: -2409.753651
EM: Round [207] log likelihood: -2409.753364
EM: Round [208] log likelihood: -2409.753080
EM: Round [209] log likelihood: -2409.752800
EM: Round [210] log likelihood: -2409.752524
EM: Round [211] log likelihood: -2409.752250
EM: Round [212] log likelihood: -2409.751981
EM: Round [213] log likelihood: -2409.751714
EM: Round [214] log likelihood: -2409.751451
EM: Round [215] log likelihood: -2409.751191
EM: Round [216] log likelihood: -2409.750935
EM: Round [217] log likelihood: -2409.750681
EM: Round [218] log likelihood: -2409.750431
EM: Round [219] log likelihood: -2409.750184
EM: Round [220] log likelihood: -2409.749940
EM: Round [221] log likelihood: -2409.749698
EM: Round [222] log likelihood: -2409.749460
EM: Round [223] log likelihood: -2409.749225
EM: Round [224] log likelihood: -2409.748993
EM: Round [225] log likelihood: -2409.748763
EM: Round [226] log likelihood: -2409.748537
EM: Round [227] log likelihood: -2409.748313
EM: Round [228] log likelihood: -2409.748092
EM: Round [229] log likelihood: -2409.747874
EM: Round [230] log likelihood: -2409.747658
EM: Round [231] log likelihood: -2409.747445
EM: Round [232] log likelihood: -2409.747235
EM: Round [233] log likelihood: -2409.747027
EM: Round [234] log likelihood: -2409.746822
EM: Round [235] log likelihood: -2409.746619
EM: Round [236] log likelihood: -2409.746419
EM: Round [237] log likelihood: -2409.746222
EM: Round [238] log likelihood: -2409.746026
EM: Round [239] log likelihood: -2409.745834
EM: Round [240] log likelihood: -2409.745643
EM: Round [241] log likelihood: -2409.745455
EM: Round [242] log likelihood: -2409.745270
EM: Round [243] log likelihood: -2409.745086
EM: Round [244] log likelihood: -2409.744905
EM: Round [245] log likelihood: -2409.744726
EM: Round [246] log likelihood: -2409.744550
EM: Round [247] log likelihood: -2409.744375
EM: Round [248] log likelihood: -2409.744203
EM: Round [249] log likelihood: -2409.744032
EM: Round [250] log likelihood: -2409.743864
EM: Round [251] log likelihood: -2409.743698
EM: Round [252] log likelihood: -2409.743534
EM: Round [253] log likelihood: -2409.743372
EM: Round [254] log likelihood: -2409.743212
EM: Round [255] log likelihood: -2409.743054
EM: Round [256] log likelihood: -2409.742898
EM: Round [257] log likelihood: -2409.742744
EM: Round [258] log likelihood: -2409.742592
EM: Round [259] log likelihood: -2409.742442
EM: Round [260] log likelihood: -2409.742293
EM: Round [261] log likelihood: -2409.742147
EM: Round [262] log likelihood: -2409.742002
EM: Round [263] log likelihood: -2409.741859
EM: Round [264] log likelihood: -2409.741717
EM: Round [265] log likelihood: -2409.741578
EM: Round [266] log likelihood: -2409.741440
EM: Round [267] log likelihood: -2409.741304
EM: Round [268] log likelihood: -2409.741169
EM: Round [269] log likelihood: -2409.741037
EM: Round [270] log likelihood: -2409.740906
EM: Round [271] log likelihood: -2409.740776
EM: Round [272] log likelihood: -2409.740648
EM: Round [273] log likelihood: -2409.740522
EM: Round [274] log likelihood: -2409.740397
EM: Round [275] log likelihood: -2409.740274
EM: Round [276] log likelihood: -2409.740152
EM: Round [277] log likelihood: -2409.740032
EM: Round [278] log likelihood: -2409.739913
EM: Round [279] log likelihood: -2409.739796
EM: Round [280] log likelihood: -2409.739680
EM: Round [281] log likelihood: -2409.739566
EM: Round [282] log likelihood: -2409.739453
EM: Round [283] log likelihood: -2409.739341
EM: Round [284] log likelihood: -2409.739231
EM: Round [285] log likelihood: -2409.739122
EM: Round [286] log likelihood: -2409.739014
EM: Round [287] log likelihood: -2409.738908
EM: Round [288] log likelihood: -2409.738803
EM: Round [289] log likelihood: -2409.738700
EM: Round [290] log likelihood: -2409.738597
EM: Round [291] log likelihood: -2409.738496
EM: Round [292] log likelihood: -2409.738396
EM: Stopping iterations at round 292 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_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.u6OmFZLRev/fi_workdir/659_dm4-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1859.620900
EM: Round [1] log likelihood: -1859.620900
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 102160001
Warning - not locating file: /tmp/nxf.u6OmFZLRev/659_dm4-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
ls: cannot access 'IGV_inputs': No such file or directory