Done.
-parsing GTF file: /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.VcqDx5JPL2/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.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.VcqDx5JPL2/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.VcqDx5JPL2/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-3270ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-3270ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:04:56 : INFO : Done.
-parsing GTF file: /tmp/nxf.VcqDx5JPL2/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.VcqDx5JPL2/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[1920000] -done parsing /tmp/nxf.VcqDx5JPL2/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 10774,
' ** passed ** ' => 3728,
'seq-similar region overlap' => 27,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
'num genes matched < 2' => 20,
'small anchor length' => 86,
'exons hit < 2' => 4,
'excessive soft clipping' => 12812,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 7,
'num_hits: 8 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 270,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'low complexity anchor region' => 1,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 52,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 33
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.VcqDx5JPL2/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[65000] -fusion SPANNING read extraction for scaff: ABLIM1--WAPL
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[38000] -fusion SPANNING read extraction for scaff: GSR--AC068672.1
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[38000] -fusion SPANNING read extraction for scaff: GSR--AC090816.1
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[57000] -fusion SPANNING read extraction for scaff: GSR--NRG1
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[38000] -fusion SPANNING read extraction for scaff: GSR--NRG1-IT3
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[21000] -fusion SPANNING read extraction for scaff: LRP12--ZFPM2
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[21000] -fusion SPANNING read extraction for scaff: MACROD2--NRG1
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[64000] -fusion SPANNING read extraction for scaff: MLKL--CHSY1
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[40000] -fusion SPANNING read extraction for scaff: SEC24B--CDKL2
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[450000] -fusion SPANNING read extraction for scaff: TAF15--AP2B1
[1000]
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[29000] -fusion SPANNING read extraction for scaff: TLK2--AL669831.1
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[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[1000]
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[14000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[34000] -fusion SPANNING read extraction for scaff: UHRF1BP1--EYS
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[530000] -fusion SPANNING read extraction for scaff: ZNF318--DST
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[88000] -fusion SPANNING read extraction for scaff: ZSWIM6--CFTR
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 19197,
'lacks exon overlap' => 9433
};
EM: Starting log likelihood: -3029.974092
EM: Round [1] log likelihood: -3029.869827
EM: Round [2] log likelihood: -3029.854839
EM: Round [3] log likelihood: -3029.840963
EM: Round [4] log likelihood: -3029.827723
EM: Round [5] log likelihood: -3029.815076
EM: Round [6] log likelihood: -3029.802987
EM: Round [7] log likelihood: -3029.791425
EM: Round [8] log likelihood: -3029.780363
EM: Round [9] log likelihood: -3029.769772
EM: Round [10] log likelihood: -3029.759629
EM: Round [11] log likelihood: -3029.749910
EM: Round [12] log likelihood: -3029.740593
EM: Round [13] log likelihood: -3029.731659
EM: Round [14] log likelihood: -3029.723089
EM: Round [15] log likelihood: -3029.714864
EM: Round [16] log likelihood: -3029.706969
EM: Round [17] log likelihood: -3029.699387
EM: Round [18] log likelihood: -3029.692104
EM: Round [19] log likelihood: -3029.685106
EM: Round [20] log likelihood: -3029.678380
EM: Round [21] log likelihood: -3029.671914
EM: Round [22] log likelihood: -3029.665696
EM: Round [23] log likelihood: -3029.659715
EM: Round [24] log likelihood: -3029.653961
EM: Round [25] log likelihood: -3029.648424
EM: Round [26] log likelihood: -3029.643095
EM: Round [27] log likelihood: -3029.637964
EM: Round [28] log likelihood: -3029.633024
EM: Round [29] log likelihood: -3029.628267
EM: Round [30] log likelihood: -3029.623684
EM: Round [31] log likelihood: -3029.619269
EM: Round [32] log likelihood: -3029.615015
EM: Round [33] log likelihood: -3029.610915
EM: Round [34] log likelihood: -3029.606964
EM: Round [35] log likelihood: -3029.603154
EM: Round [36] log likelihood: -3029.599482
EM: Round [37] log likelihood: -3029.595941
EM: Round [38] log likelihood: -3029.592525
EM: Round [39] log likelihood: -3029.589231
EM: Round [40] log likelihood: -3029.586054
EM: Round [41] log likelihood: -3029.582989
EM: Round [42] log likelihood: -3029.580031
EM: Round [43] log likelihood: -3029.577177
EM: Round [44] log likelihood: -3029.574423
EM: Round [45] log likelihood: -3029.571765
EM: Round [46] log likelihood: -3029.569200
EM: Round [47] log likelihood: -3029.566723
EM: Round [48] log likelihood: -3029.564333
EM: Round [49] log likelihood: -3029.562024
EM: Round [50] log likelihood: -3029.559796
EM: Round [51] log likelihood: -3029.557643
EM: Round [52] log likelihood: -3029.555565
EM: Round [53] log likelihood: -3029.553558
EM: Round [54] log likelihood: -3029.551619
EM: Round [55] log likelihood: -3029.549747
EM: Round [56] log likelihood: -3029.547938
EM: Round [57] log likelihood: -3029.546191
EM: Round [58] log likelihood: -3029.544503
EM: Round [59] log likelihood: -3029.542872
EM: Round [60] log likelihood: -3029.541296
EM: Round [61] log likelihood: -3029.539774
EM: Round [62] log likelihood: -3029.538303
EM: Round [63] log likelihood: -3029.536881
EM: Round [64] log likelihood: -3029.535507
EM: Round [65] log likelihood: -3029.534179
EM: Round [66] log likelihood: -3029.532896
EM: Round [67] log likelihood: -3029.531656
EM: Round [68] log likelihood: -3029.530457
EM: Round [69] log likelihood: -3029.529298
EM: Round [70] log likelihood: -3029.528178
EM: Round [71] log likelihood: -3029.527095
EM: Round [72] log likelihood: -3029.526048
EM: Round [73] log likelihood: -3029.525036
EM: Round [74] log likelihood: -3029.524058
EM: Round [75] log likelihood: -3029.523112
EM: Round [76] log likelihood: -3029.522198
EM: Round [77] log likelihood: -3029.521313
EM: Round [78] log likelihood: -3029.520458
EM: Round [79] log likelihood: -3029.519632
EM: Round [80] log likelihood: -3029.518832
EM: Round [81] log likelihood: -3029.518059
EM: Round [82] log likelihood: -3029.517312
EM: Round [83] log likelihood: -3029.516589
EM: Round [84] log likelihood: -3029.515890
EM: Round [85] log likelihood: -3029.515214
EM: Round [86] log likelihood: -3029.514560
EM: Round [87] log likelihood: -3029.513928
EM: Round [88] log likelihood: -3029.513317
EM: Round [89] log likelihood: -3029.512725
EM: Round [90] log likelihood: -3029.512153
EM: Round [91] log likelihood: -3029.511600
EM: Round [92] log likelihood: -3029.511065
EM: Round [93] log likelihood: -3029.510547
EM: Round [94] log likelihood: -3029.510047
EM: Round [95] log likelihood: -3029.509563
EM: Round [96] log likelihood: -3029.509094
EM: Round [97] log likelihood: -3029.508641
EM: Round [98] log likelihood: -3029.508203
EM: Round [99] log likelihood: -3029.507779
EM: Round [100] log likelihood: -3029.507369
EM: Round [101] log likelihood: -3029.506972
EM: Round [102] log likelihood: -3029.506588
EM: Round [103] log likelihood: -3029.506217
EM: Round [104] log likelihood: -3029.505858
EM: Round [105] log likelihood: -3029.505511
EM: Round [106] log likelihood: -3029.505175
EM: Round [107] log likelihood: -3029.504849
EM: Round [108] log likelihood: -3029.504535
EM: Round [109] log likelihood: -3029.504231
EM: Round [110] log likelihood: -3029.503936
EM: Round [111] log likelihood: -3029.503651
EM: Round [112] log likelihood: -3029.503376
EM: Round [113] log likelihood: -3029.503109
EM: Round [114] log likelihood: -3029.502851
EM: Round [115] log likelihood: -3029.502602
EM: Round [116] log likelihood: -3029.502360
EM: Round [117] log likelihood: -3029.502127
EM: Round [118] log likelihood: -3029.501901
EM: Round [119] log likelihood: -3029.501682
EM: Round [120] log likelihood: -3029.501470
EM: Round [121] log likelihood: -3029.501266
EM: Round [122] log likelihood: -3029.501068
EM: Round [123] log likelihood: -3029.500876
EM: Round [124] log likelihood: -3029.500691
EM: Round [125] log likelihood: -3029.500511
EM: Round [126] log likelihood: -3029.500338
EM: Round [127] log likelihood: -3029.500170
EM: Round [128] log likelihood: -3029.500007
EM: Round [129] log likelihood: -3029.499850
EM: Round [130] log likelihood: -3029.499698
EM: Round [131] log likelihood: -3029.499550
EM: Round [132] log likelihood: -3029.499408
EM: Round [133] log likelihood: -3029.499270
EM: Round [134] log likelihood: -3029.499137
EM: Round [135] log likelihood: -3029.499008
EM: Round [136] log likelihood: -3029.498883
EM: Round [137] log likelihood: -3029.498762
EM: Round [138] log likelihood: -3029.498645
EM: Round [139] log likelihood: -3029.498532
EM: Round [140] log likelihood: -3029.498423
EM: Round [141] log likelihood: -3029.498317
EM: Round [142] log likelihood: -3029.498214
EM: Round [143] log likelihood: -3029.498115
EM: Stopping iterations at round 143 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-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.VcqDx5JPL2/fi_workdir/aih-tih-sc-3270ab-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.VcqDx5JPL2/fi_workdir/aih-tih-sc-3270ab-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.VcqDx5JPL2/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2665.860183
EM: Round [1] log likelihood: -2665.771162
EM: Round [2] log likelihood: -2665.770708
EM: Round [3] log likelihood: -2665.770700
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296063924
Warning - not locating file: /tmp/nxf.VcqDx5JPL2/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000228327.3]
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