Done.
-parsing GTF file: /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.rp7J7QBQpz/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.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.rp7J7QBQpz/fi_workdir/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.rp7J7QBQpz/fi_workdir/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
21:40:01 : INFO : Done.
-parsing GTF file: /tmp/nxf.rp7J7QBQpz/fi_workdir/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.rp7J7QBQpz/fi_workdir/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[2180000] -done parsing /tmp/nxf.rp7J7QBQpz/fi_workdir/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 275,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 15,
'num genes matched < 2' => 34,
'low complexity anchor region' => 5,
'small anchor length' => 2,
' ** passed ** ' => 3247,
'excessive soft clipping' => 19930,
'exons hit < 2' => 2,
'per_id < 96' => 14147,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 50,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 24,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 22,
'seq-similar region overlap' => 51
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.rp7J7QBQpz/fi_workdir/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[29000] -fusion SPANNING read extraction for scaff: AC024901.1--COL4A5
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[622000] -fusion SPANNING read extraction for scaff: AKAP12--ESR1
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[52000] -fusion SPANNING read extraction for scaff: BCL3--ETHE1
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[63000] -fusion SPANNING read extraction for scaff: ERBB4--AC093865.1
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[17000] -fusion SPANNING read extraction for scaff: FBN2--AL356022.1
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[17000] -fusion SPANNING read extraction for scaff: FBN2--LINC02302
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[124000] -fusion SPANNING read extraction for scaff: GTF2IRD1--GTF2I
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[33000] -fusion SPANNING read extraction for scaff: MAP2--POFUT1
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[21000] -fusion SPANNING read extraction for scaff: NF2--ZNF804B
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[18000] -fusion SPANNING read extraction for scaff: PAICS--RPS4XP18
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[18000] -fusion SPANNING read extraction for scaff: PAICS--RNU6-1032P
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[55000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[51000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[52000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[239000] -fusion SPANNING read extraction for scaff: PITPNA--PRPF8
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[96000] -fusion SPANNING read extraction for scaff: REST--TENM3
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[36000] -fusion SPANNING read extraction for scaff: SPIDR--EFCAB1
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[36000] -fusion SPANNING read extraction for scaff: SPIDR--AC100805.1
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[113000] -fusion SPANNING read extraction for scaff: SYMPK--PTH2
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[28000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 6397,
'seq similar region alignment' => 38049
};
EM: Starting log likelihood: -2975.630484
EM: Round [1] log likelihood: -2975.576586
EM: Round [2] log likelihood: -2975.524452
EM: Round [3] log likelihood: -2975.474007
EM: Round [4] log likelihood: -2975.425181
EM: Round [5] log likelihood: -2975.377905
EM: Round [6] log likelihood: -2975.332118
EM: Round [7] log likelihood: -2975.287759
EM: Round [8] log likelihood: -2975.244772
EM: Round [9] log likelihood: -2975.203103
EM: Round [10] log likelihood: -2975.162701
EM: Round [11] log likelihood: -2975.123518
EM: Round [12] log likelihood: -2975.085508
EM: Round [13] log likelihood: -2975.048627
EM: Round [14] log likelihood: -2975.012835
EM: Round [15] log likelihood: -2974.978091
EM: Round [16] log likelihood: -2974.944358
EM: Round [17] log likelihood: -2974.911599
EM: Round [18] log likelihood: -2974.879782
EM: Round [19] log likelihood: -2974.848872
EM: Round [20] log likelihood: -2974.818839
EM: Round [21] log likelihood: -2974.789652
EM: Round [22] log likelihood: -2974.761284
EM: Round [23] log likelihood: -2974.733707
EM: Round [24] log likelihood: -2974.706894
EM: Round [25] log likelihood: -2974.680820
EM: Round [26] log likelihood: -2974.655462
EM: Round [27] log likelihood: -2974.630796
EM: Round [28] log likelihood: -2974.606800
EM: Round [29] log likelihood: -2974.583453
EM: Round [30] log likelihood: -2974.560735
EM: Round [31] log likelihood: -2974.538625
EM: Round [32] log likelihood: -2974.517105
EM: Round [33] log likelihood: -2974.496156
EM: Round [34] log likelihood: -2974.475762
EM: Round [35] log likelihood: -2974.455905
EM: Round [36] log likelihood: -2974.436570
EM: Round [37] log likelihood: -2974.417740
EM: Round [38] log likelihood: -2974.399400
EM: Round [39] log likelihood: -2974.381536
EM: Round [40] log likelihood: -2974.364135
EM: Round [41] log likelihood: -2974.347181
EM: Round [42] log likelihood: -2974.330664
EM: Round [43] log likelihood: -2974.314569
EM: Round [44] log likelihood: -2974.298885
EM: Round [45] log likelihood: -2974.283600
EM: Round [46] log likelihood: -2974.268703
EM: Round [47] log likelihood: -2974.254183
EM: Round [48] log likelihood: -2974.240029
EM: Round [49] log likelihood: -2974.226231
EM: Round [50] log likelihood: -2974.212779
EM: Round [51] log likelihood: -2974.199663
EM: Round [52] log likelihood: -2974.186875
EM: Round [53] log likelihood: -2974.174405
EM: Round [54] log likelihood: -2974.162244
EM: Round [55] log likelihood: -2974.150385
EM: Round [56] log likelihood: -2974.138819
EM: Round [57] log likelihood: -2974.127538
EM: Round [58] log likelihood: -2974.116534
EM: Round [59] log likelihood: -2974.105800
EM: Round [60] log likelihood: -2974.095330
EM: Round [61] log likelihood: -2974.085115
EM: Round [62] log likelihood: -2974.075149
EM: Round [63] log likelihood: -2974.065426
EM: Round [64] log likelihood: -2974.055940
EM: Round [65] log likelihood: -2974.046683
EM: Round [66] log likelihood: -2974.037650
EM: Round [67] log likelihood: -2974.028836
EM: Round [68] log likelihood: -2974.020234
EM: Round [69] log likelihood: -2974.011840
EM: Round [70] log likelihood: -2974.003647
EM: Round [71] log likelihood: -2973.995651
EM: Round [72] log likelihood: -2973.987847
EM: Round [73] log likelihood: -2973.980229
EM: Round [74] log likelihood: -2973.972793
EM: Round [75] log likelihood: -2973.965535
EM: Round [76] log likelihood: -2973.958450
EM: Round [77] log likelihood: -2973.951533
EM: Round [78] log likelihood: -2973.944780
EM: Round [79] log likelihood: -2973.938188
EM: Round [80] log likelihood: -2973.931752
EM: Round [81] log likelihood: -2973.925468
EM: Round [82] log likelihood: -2973.919333
EM: Round [83] log likelihood: -2973.913342
EM: Round [84] log likelihood: -2973.907493
EM: Round [85] log likelihood: -2973.901782
EM: Round [86] log likelihood: -2973.896204
EM: Round [87] log likelihood: -2973.890758
EM: Round [88] log likelihood: -2973.885440
EM: Round [89] log likelihood: -2973.880247
EM: Round [90] log likelihood: -2973.875175
EM: Round [91] log likelihood: -2973.870222
EM: Round [92] log likelihood: -2973.865384
EM: Round [93] log likelihood: -2973.860660
EM: Round [94] log likelihood: -2973.856046
EM: Round [95] log likelihood: -2973.851539
EM: Round [96] log likelihood: -2973.847138
EM: Round [97] log likelihood: -2973.842838
EM: Round [98] log likelihood: -2973.838639
EM: Round [99] log likelihood: -2973.834538
EM: Round [100] log likelihood: -2973.830531
EM: Round [101] log likelihood: -2973.826618
EM: Round [102] log likelihood: -2973.822795
EM: Round [103] log likelihood: -2973.819061
EM: Round [104] log likelihood: -2973.815413
EM: Round [105] log likelihood: -2973.811849
EM: Round [106] log likelihood: -2973.808368
EM: Round [107] log likelihood: -2973.804967
EM: Round [108] log likelihood: -2973.801645
EM: Round [109] log likelihood: -2973.798399
EM: Round [110] log likelihood: -2973.795229
EM: Round [111] log likelihood: -2973.792131
EM: Round [112] log likelihood: -2973.789104
EM: Round [113] log likelihood: -2973.786147
EM: Round [114] log likelihood: -2973.783259
EM: Round [115] log likelihood: -2973.780436
EM: Round [116] log likelihood: -2973.777679
EM: Round [117] log likelihood: -2973.774984
EM: Round [118] log likelihood: -2973.772352
EM: Round [119] log likelihood: -2973.769779
EM: Round [120] log likelihood: -2973.767266
EM: Round [121] log likelihood: -2973.764811
EM: Round [122] log likelihood: -2973.762411
EM: Round [123] log likelihood: -2973.760067
EM: Round [124] log likelihood: -2973.757776
EM: Round [125] log likelihood: -2973.755537
EM: Round [126] log likelihood: -2973.753350
EM: Round [127] log likelihood: -2973.751212
EM: Round [128] log likelihood: -2973.749124
EM: Round [129] log likelihood: -2973.747083
EM: Round [130] log likelihood: -2973.745089
EM: Round [131] log likelihood: -2973.743140
EM: Round [132] log likelihood: -2973.741235
EM: Round [133] log likelihood: -2973.739374
EM: Round [134] log likelihood: -2973.737556
EM: Round [135] log likelihood: -2973.735779
EM: Round [136] log likelihood: -2973.734042
EM: Round [137] log likelihood: -2973.732345
EM: Round [138] log likelihood: -2973.730686
EM: Round [139] log likelihood: -2973.729065
EM: Round [140] log likelihood: -2973.727481
EM: Round [141] log likelihood: -2973.725933
EM: Round [142] log likelihood: -2973.724420
EM: Round [143] log likelihood: -2973.722942
EM: Round [144] log likelihood: -2973.721497
EM: Round [145] log likelihood: -2973.720084
EM: Round [146] log likelihood: -2973.718704
EM: Round [147] log likelihood: -2973.717356
EM: Round [148] log likelihood: -2973.716037
EM: Round [149] log likelihood: -2973.714749
EM: Round [150] log likelihood: -2973.713490
EM: Round [151] log likelihood: -2973.712260
EM: Round [152] log likelihood: -2973.711057
EM: Round [153] log likelihood: -2973.709881
EM: Round [154] log likelihood: -2973.708733
EM: Round [155] log likelihood: -2973.707610
EM: Round [156] log likelihood: -2973.706513
EM: Round [157] log likelihood: -2973.705440
EM: Round [158] log likelihood: -2973.704392
EM: Round [159] log likelihood: -2973.703367
EM: Round [160] log likelihood: -2973.702366
EM: Round [161] log likelihood: -2973.701387
EM: Round [162] log likelihood: -2973.700430
EM: Round [163] log likelihood: -2973.699496
EM: Round [164] log likelihood: -2973.698582
EM: Round [165] log likelihood: -2973.697689
EM: Round [166] log likelihood: -2973.696816
EM: Round [167] log likelihood: -2973.695962
EM: Round [168] log likelihood: -2973.695128
EM: Round [169] log likelihood: -2973.694313
EM: Round [170] log likelihood: -2973.693516
EM: Round [171] log likelihood: -2973.692737
EM: Round [172] log likelihood: -2973.691976
EM: Round [173] log likelihood: -2973.691232
EM: Round [174] log likelihood: -2973.690505
EM: Round [175] log likelihood: -2973.689794
EM: Round [176] log likelihood: -2973.689099
EM: Round [177] log likelihood: -2973.688420
EM: Round [178] log likelihood: -2973.687756
EM: Round [179] log likelihood: -2973.687108
EM: Round [180] log likelihood: -2973.686473
EM: Round [181] log likelihood: -2973.685854
EM: Round [182] log likelihood: -2973.685248
EM: Round [183] log likelihood: -2973.684655
EM: Round [184] log likelihood: -2973.684076
EM: Round [185] log likelihood: -2973.683511
EM: Round [186] log likelihood: -2973.682957
EM: Round [187] log likelihood: -2973.682417
EM: Round [188] log likelihood: -2973.681888
EM: Round [189] log likelihood: -2973.681372
EM: Round [190] log likelihood: -2973.680867
EM: Round [191] log likelihood: -2973.680373
EM: Round [192] log likelihood: -2973.679891
EM: Round [193] log likelihood: -2973.679419
EM: Round [194] log likelihood: -2973.678958
EM: Round [195] log likelihood: -2973.678507
EM: Round [196] log likelihood: -2973.678067
EM: Round [197] log likelihood: -2973.677636
EM: Round [198] log likelihood: -2973.677215
EM: Round [199] log likelihood: -2973.676804
EM: Round [200] log likelihood: -2973.676402
EM: Round [201] log likelihood: -2973.676009
EM: Round [202] log likelihood: -2973.675625
EM: Round [203] log likelihood: -2973.675249
EM: Round [204] log likelihood: -2973.674882
EM: Round [205] log likelihood: -2973.674523
EM: Round [206] log likelihood: -2973.674172
EM: Round [207] log likelihood: -2973.673829
EM: Round [208] log likelihood: -2973.673494
EM: Round [209] log likelihood: -2973.673166
EM: Round [210] log likelihood: -2973.672846
EM: Round [211] log likelihood: -2973.672533
EM: Round [212] log likelihood: -2973.672227
EM: Round [213] log likelihood: -2973.671928
EM: Round [214] log likelihood: -2973.671635
EM: Round [215] log likelihood: -2973.671349
EM: Round [216] log likelihood: -2973.671070
EM: Round [217] log likelihood: -2973.670797
EM: Round [218] log likelihood: -2973.670530
EM: Round [219] log likelihood: -2973.670268
EM: Round [220] log likelihood: -2973.670013
EM: Round [221] log likelihood: -2973.669764
EM: Round [222] log likelihood: -2973.669520
EM: Round [223] log likelihood: -2973.669282
EM: Round [224] log likelihood: -2973.669049
EM: Round [225] log likelihood: -2973.668821
EM: Round [226] log likelihood: -2973.668598
EM: Round [227] log likelihood: -2973.668381
EM: Round [228] log likelihood: -2973.668168
EM: Round [229] log likelihood: -2973.667960
EM: Round [230] log likelihood: -2973.667756
EM: Round [231] log likelihood: -2973.667558
EM: Round [232] log likelihood: -2973.667363
EM: Round [233] log likelihood: -2973.667174
EM: Round [234] log likelihood: -2973.666988
EM: Round [235] log likelihood: -2973.666806
EM: Round [236] log likelihood: -2973.666629
EM: Round [237] log likelihood: -2973.666456
EM: Round [238] log likelihood: -2973.666286
EM: Round [239] log likelihood: -2973.666120
EM: Round [240] log likelihood: -2973.665958
EM: Round [241] log likelihood: -2973.665800
EM: Round [242] log likelihood: -2973.665645
EM: Round [243] log likelihood: -2973.665494
EM: Round [244] log likelihood: -2973.665346
EM: Round [245] log likelihood: -2973.665201
EM: Round [246] log likelihood: -2973.665060
EM: Round [247] log likelihood: -2973.664922
EM: Round [248] log likelihood: -2973.664787
EM: Round [249] log likelihood: -2973.664654
EM: Round [250] log likelihood: -2973.664525
EM: Round [251] log likelihood: -2973.664399
EM: Round [252] log likelihood: -2973.664276
EM: Round [253] log likelihood: -2973.664155
EM: Round [254] log likelihood: -2973.664037
EM: Round [255] log likelihood: -2973.663922
EM: Round [256] log likelihood: -2973.663809
EM: Round [257] log likelihood: -2973.663699
EM: Round [258] log likelihood: -2973.663592
EM: Round [259] log likelihood: -2973.663486
EM: Round [260] log likelihood: -2973.663384
EM: Round [261] log likelihood: -2973.663283
EM: Round [262] log likelihood: -2973.663185
EM: Stopping iterations at round 262 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-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.rp7J7QBQpz/fi_workdir/aih-tih-sc-bbc28d-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.rp7J7QBQpz/fi_workdir/aih-tih-sc-bbc28d-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.rp7J7QBQpz/fi_workdir/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2783.221854
EM: Round [1] log likelihood: -2783.221854
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 207049612
Warning - not locating file: /tmp/nxf.rp7J7QBQpz/aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000255910.2]
WARNING, no entry stored in dbm for [ENSG00000255910.2]
ls: cannot access 'IGV_inputs': No such file or directory