Done.
-parsing GTF file: /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.DtEFR52ATH/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.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.DtEFR52ATH/fi_workdir/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.DtEFR52ATH/fi_workdir/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:58:43 : INFO : Done.
-parsing GTF file: /tmp/nxf.DtEFR52ATH/fi_workdir/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.DtEFR52ATH/fi_workdir/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

[10000]   
[20000]   
[30000]   
[40000]   
[50000]   
[60000]   
[70000]   
[80000]   
[90000]   
[100000]   
[110000]   
[120000]   
[130000]   
[140000]   
[150000]   
[160000]   
[170000]   
[180000]   
[190000]   
[200000]   
[210000]   
[220000]   
[230000]   
[240000]   
[250000]   
[260000]   
[270000]   
[280000]   
[290000]   
[300000]   
[310000]   
[320000]   
[330000]   
[340000]   
[350000]   
[360000]   
[370000]   
[380000]   
[390000]   
[400000]   -done parsing /tmp/nxf.DtEFR52ATH/fi_workdir/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 75,
          'per_id < 96' => 10868,
          'small anchor length' => 402,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'seq-similar region overlap' => 351,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 182,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 36,
          ' ** passed ** ' => 2017,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 8,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 30,
          'excessive soft clipping' => 8196
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.DtEFR52ATH/fi_workdir/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   -fusion SPANNING read extraction for scaff: CGNL1--NDUFB10P1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   
[119000]   
[120000]   
[121000]   
[122000]   
[123000]   
[124000]   
[125000]   
[126000]   
[127000]   
[128000]   
[129000]   
[130000]   
[131000]   
[132000]   
[133000]   
[134000]   
[135000]   
[136000]   
[137000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: TRAPPC9--KCNK9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 44202,
          'lacks exon overlap' => 183
        };
EM: Starting log likelihood: -947.804278
EM: Round [1] log likelihood: -947.090958
EM: Round [2] log likelihood: -946.466931
EM: Round [3] log likelihood: -945.918153
EM: Round [4] log likelihood: -945.433395
EM: Round [5] log likelihood: -945.003544
EM: Round [6] log likelihood: -944.621109
EM: Round [7] log likelihood: -944.279862
EM: Round [8] log likelihood: -943.974579
EM: Round [9] log likelihood: -943.700836
EM: Round [10] log likelihood: -943.454864
EM: Round [11] log likelihood: -943.233430
EM: Round [12] log likelihood: -943.033743
EM: Round [13] log likelihood: -942.853383
EM: Round [14] log likelihood: -942.690240
EM: Round [15] log likelihood: -942.542473
EM: Round [16] log likelihood: -942.408460
EM: Round [17] log likelihood: -942.286777
EM: Round [18] log likelihood: -942.176165
EM: Round [19] log likelihood: -942.075507
EM: Round [20] log likelihood: -941.983815
EM: Round [21] log likelihood: -941.900206
EM: Round [22] log likelihood: -941.823897
EM: Round [23] log likelihood: -941.754185
EM: Round [24] log likelihood: -941.690444
EM: Round [25] log likelihood: -941.632111
EM: Round [26] log likelihood: -941.578683
EM: Round [27] log likelihood: -941.529706
EM: Round [28] log likelihood: -941.484773
EM: Round [29] log likelihood: -941.443517
EM: Round [30] log likelihood: -941.405608
EM: Round [31] log likelihood: -941.370747
EM: Round [32] log likelihood: -941.338664
EM: Round [33] log likelihood: -941.309116
EM: Round [34] log likelihood: -941.281883
EM: Round [35] log likelihood: -941.256765
EM: Round [36] log likelihood: -941.233580
EM: Round [37] log likelihood: -941.212166
EM: Round [38] log likelihood: -941.192372
EM: Round [39] log likelihood: -941.174063
EM: Round [40] log likelihood: -941.157116
EM: Round [41] log likelihood: -941.141420
EM: Round [42] log likelihood: -941.126873
EM: Round [43] log likelihood: -941.113381
EM: Round [44] log likelihood: -941.100860
EM: Round [45] log likelihood: -941.089232
EM: Round [46] log likelihood: -941.078428
EM: Round [47] log likelihood: -941.068382
EM: Round [48] log likelihood: -941.059037
EM: Round [49] log likelihood: -941.050337
EM: Round [50] log likelihood: -941.042235
EM: Round [51] log likelihood: -941.034683
EM: Round [52] log likelihood: -941.027642
EM: Round [53] log likelihood: -941.021073
EM: Round [54] log likelihood: -941.014942
EM: Round [55] log likelihood: -941.009215
EM: Round [56] log likelihood: -941.003865
EM: Round [57] log likelihood: -940.998863
EM: Round [58] log likelihood: -940.994185
EM: Round [59] log likelihood: -940.989807
EM: Round [60] log likelihood: -940.985710
EM: Round [61] log likelihood: -940.981873
EM: Round [62] log likelihood: -940.978277
EM: Round [63] log likelihood: -940.974908
EM: Round [64] log likelihood: -940.971748
EM: Round [65] log likelihood: -940.968784
EM: Round [66] log likelihood: -940.966003
EM: Round [67] log likelihood: -940.963393
EM: Round [68] log likelihood: -940.960942
EM: Round [69] log likelihood: -940.958639
EM: Round [70] log likelihood: -940.956476
EM: Round [71] log likelihood: -940.954443
EM: Round [72] log likelihood: -940.952531
EM: Round [73] log likelihood: -940.950733
EM: Round [74] log likelihood: -940.949042
EM: Round [75] log likelihood: -940.947451
EM: Round [76] log likelihood: -940.945953
EM: Round [77] log likelihood: -940.944543
EM: Round [78] log likelihood: -940.943216
EM: Round [79] log likelihood: -940.941966
EM: Round [80] log likelihood: -940.940788
EM: Round [81] log likelihood: -940.939678
EM: Round [82] log likelihood: -940.938632
EM: Round [83] log likelihood: -940.937646
EM: Round [84] log likelihood: -940.936717
EM: Round [85] log likelihood: -940.935841
EM: Round [86] log likelihood: -940.935015
EM: Round [87] log likelihood: -940.934235
EM: Round [88] log likelihood: -940.933500
EM: Round [89] log likelihood: -940.932806
EM: Round [90] log likelihood: -940.932152
EM: Round [91] log likelihood: -940.931534
EM: Round [92] log likelihood: -940.930951
EM: Round [93] log likelihood: -940.930400
EM: Round [94] log likelihood: -940.929881
EM: Round [95] log likelihood: -940.929390
EM: Round [96] log likelihood: -940.928927
EM: Round [97] log likelihood: -940.928489
EM: Round [98] log likelihood: -940.928076
EM: Round [99] log likelihood: -940.927686
EM: Round [100] log likelihood: -940.927317
EM: Round [101] log likelihood: -940.926969
EM: Round [102] log likelihood: -940.926640
EM: Round [103] log likelihood: -940.926329
EM: Round [104] log likelihood: -940.926035
EM: Round [105] log likelihood: -940.925757
EM: Round [106] log likelihood: -940.925495
EM: Round [107] log likelihood: -940.925247
EM: Round [108] log likelihood: -940.925013
EM: Round [109] log likelihood: -940.924791
EM: Round [110] log likelihood: -940.924582
EM: Round [111] log likelihood: -940.924384
EM: Round [112] log likelihood: -940.924197
EM: Round [113] log likelihood: -940.924020
EM: Round [114] log likelihood: -940.923852
EM: Round [115] log likelihood: -940.923694
EM: Round [116] log likelihood: -940.923545
EM: Round [117] log likelihood: -940.923403
EM: Round [118] log likelihood: -940.923270
EM: Round [119] log likelihood: -940.923143
EM: Round [120] log likelihood: -940.923024
EM: Round [121] log likelihood: -940.922911
EM: Round [122] log likelihood: -940.922804
EM: Round [123] log likelihood: -940.922703
EM: Round [124] log likelihood: -940.922607
EM: Stopping iterations at round 124 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-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.DtEFR52ATH/fi_workdir/aih-tih-sc-eecf9f-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.DtEFR52ATH/fi_workdir/aih-tih-sc-eecf9f-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.DtEFR52ATH/fi_workdir/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -400.876300
EM: Round [1] log likelihood: -400.876300
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296219478
Warning - not locating file: /tmp/nxf.DtEFR52ATH/aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
ls: cannot access 'IGV_inputs': No such file or directory