Done.
-parsing GTF file: /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.ZgoIkpRV0X/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.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
10:15:04 : INFO : Done.
-parsing GTF file: /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
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[1890000] -done parsing /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'num genes matched < 2' => 3,
'excessive soft clipping' => 14533,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 28,
' ** passed ** ' => 11220,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'per_id < 96' => 10891,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 176,
'seq-similar region overlap' => 381,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 17,
'small anchor length' => 19,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[119000] -fusion SPANNING read extraction for scaff: ATP13A4--OPA1
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[107000] -fusion SPANNING read extraction for scaff: CREBBP--LINC02861
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[16000] -fusion SPANNING read extraction for scaff: LGALS8--EDARADD
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[361000] -fusion SPANNING read extraction for scaff: MYH9--TXN2
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[58000] -fusion SPANNING read extraction for scaff: PCCA--CLYBL
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[33000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[30000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[33000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[28000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[25000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[28000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
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[24000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
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[44000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
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[33000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
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[30000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
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[24000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
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[95000] -fusion SPANNING read extraction for scaff: PNPLA7--ZMYND19
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[156000] -fusion SPANNING read extraction for scaff: PNPLA7--ARRDC1
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[34000] -fusion SPANNING read extraction for scaff: RNF111--MINDY2
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[26000] -fusion SPANNING read extraction for scaff: RNF169--POLD3
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[69000] -fusion SPANNING read extraction for scaff: TBC1D22A--GRAMD4
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[33000] -fusion SPANNING read extraction for scaff: WAPL--AL731569.1
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[33000] -fusion SPANNING read extraction for scaff: WAPL--RPL7AP8
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 6879,
'seq similar region alignment' => 65001
};
EM: Starting log likelihood: -3005.335728
EM: Round [1] log likelihood: -3000.279441
EM: Round [2] log likelihood: -2998.132781
EM: Round [3] log likelihood: -2997.010723
EM: Round [4] log likelihood: -2996.296180
EM: Round [5] log likelihood: -2995.762482
EM: Round [6] log likelihood: -2995.321486
EM: Round [7] log likelihood: -2994.937051
EM: Round [8] log likelihood: -2994.593123
EM: Round [9] log likelihood: -2994.281623
EM: Round [10] log likelihood: -2993.997761
EM: Round [11] log likelihood: -2993.738214
EM: Round [12] log likelihood: -2993.500392
EM: Round [13] log likelihood: -2993.282132
EM: Round [14] log likelihood: -2993.081564
EM: Round [15] log likelihood: -2992.897037
EM: Round [16] log likelihood: -2992.727086
EM: Round [17] log likelihood: -2992.570396
EM: Round [18] log likelihood: -2992.425789
EM: Round [19] log likelihood: -2992.292201
EM: Round [20] log likelihood: -2992.168675
EM: Round [21] log likelihood: -2992.054344
EM: Round [22] log likelihood: -2991.948423
EM: Round [23] log likelihood: -2991.850200
EM: Round [24] log likelihood: -2991.759029
EM: Round [25] log likelihood: -2991.674322
EM: Round [26] log likelihood: -2991.595545
EM: Round [27] log likelihood: -2991.522210
EM: Round [28] log likelihood: -2991.453872
EM: Round [29] log likelihood: -2991.390126
EM: Round [30] log likelihood: -2991.330602
EM: Round [31] log likelihood: -2991.274960
EM: Round [32] log likelihood: -2991.222891
EM: Round [33] log likelihood: -2991.174112
EM: Round [34] log likelihood: -2991.128363
EM: Round [35] log likelihood: -2991.085405
EM: Round [36] log likelihood: -2991.045022
EM: Round [37] log likelihood: -2991.007013
EM: Round [38] log likelihood: -2990.971194
EM: Round [39] log likelihood: -2990.937397
EM: Round [40] log likelihood: -2990.905468
EM: Round [41] log likelihood: -2990.875265
EM: Round [42] log likelihood: -2990.846657
EM: Round [43] log likelihood: -2990.819523
EM: Round [44] log likelihood: -2990.793755
EM: Round [45] log likelihood: -2990.769250
EM: Round [46] log likelihood: -2990.745916
EM: Round [47] log likelihood: -2990.723665
EM: Round [48] log likelihood: -2990.702420
EM: Round [49] log likelihood: -2990.682108
EM: Round [50] log likelihood: -2990.662661
EM: Round [51] log likelihood: -2990.644018
EM: Round [52] log likelihood: -2990.626121
EM: Round [53] log likelihood: -2990.608920
EM: Round [54] log likelihood: -2990.592364
EM: Round [55] log likelihood: -2990.576410
EM: Round [56] log likelihood: -2990.561016
EM: Round [57] log likelihood: -2990.546145
EM: Round [58] log likelihood: -2990.531761
EM: Round [59] log likelihood: -2990.517832
EM: Round [60] log likelihood: -2990.504329
EM: Round [61] log likelihood: -2990.491224
EM: Round [62] log likelihood: -2990.478491
EM: Round [63] log likelihood: -2990.466107
EM: Round [64] log likelihood: -2990.454049
EM: Round [65] log likelihood: -2990.442299
EM: Round [66] log likelihood: -2990.430837
EM: Round [67] log likelihood: -2990.419646
EM: Round [68] log likelihood: -2990.408711
EM: Round [69] log likelihood: -2990.398016
EM: Round [70] log likelihood: -2990.387547
EM: Round [71] log likelihood: -2990.377293
EM: Round [72] log likelihood: -2990.367241
EM: Round [73] log likelihood: -2990.357380
EM: Round [74] log likelihood: -2990.347701
EM: Round [75] log likelihood: -2990.338194
EM: Round [76] log likelihood: -2990.328851
EM: Round [77] log likelihood: -2990.319662
EM: Round [78] log likelihood: -2990.310621
EM: Round [79] log likelihood: -2990.301721
EM: Round [80] log likelihood: -2990.292956
EM: Round [81] log likelihood: -2990.284318
EM: Round [82] log likelihood: -2990.275803
EM: Round [83] log likelihood: -2990.267405
EM: Round [84] log likelihood: -2990.259120
EM: Round [85] log likelihood: -2990.250942
EM: Round [86] log likelihood: -2990.242868
EM: Round [87] log likelihood: -2990.234894
EM: Round [88] log likelihood: -2990.227016
EM: Round [89] log likelihood: -2990.219230
EM: Round [90] log likelihood: -2990.211533
EM: Round [91] log likelihood: -2990.203922
EM: Round [92] log likelihood: -2990.196394
EM: Round [93] log likelihood: -2990.188947
EM: Round [94] log likelihood: -2990.181578
EM: Round [95] log likelihood: -2990.174284
EM: Round [96] log likelihood: -2990.167064
EM: Round [97] log likelihood: -2990.159915
EM: Round [98] log likelihood: -2990.152835
EM: Round [99] log likelihood: -2990.145823
EM: Round [100] log likelihood: -2990.138876
EM: Round [101] log likelihood: -2990.131994
EM: Round [102] log likelihood: -2990.125173
EM: Round [103] log likelihood: -2990.118414
EM: Round [104] log likelihood: -2990.111714
EM: Round [105] log likelihood: -2990.105072
EM: Round [106] log likelihood: -2990.098487
EM: Round [107] log likelihood: -2990.091958
EM: Round [108] log likelihood: -2990.085483
EM: Round [109] log likelihood: -2990.079062
EM: Round [110] log likelihood: -2990.072692
EM: Round [111] log likelihood: -2990.066375
EM: Round [112] log likelihood: -2990.060107
EM: Round [113] log likelihood: -2990.053889
EM: Round [114] log likelihood: -2990.047720
EM: Round [115] log likelihood: -2990.041598
EM: Round [116] log likelihood: -2990.035523
EM: Round [117] log likelihood: -2990.029495
EM: Round [118] log likelihood: -2990.023512
EM: Round [119] log likelihood: -2990.017573
EM: Round [120] log likelihood: -2990.011679
EM: Round [121] log likelihood: -2990.005828
EM: Round [122] log likelihood: -2990.000019
EM: Round [123] log likelihood: -2989.994253
EM: Round [124] log likelihood: -2989.988528
EM: Round [125] log likelihood: -2989.982843
EM: Round [126] log likelihood: -2989.977200
EM: Round [127] log likelihood: -2989.971596
EM: Round [128] log likelihood: -2989.966031
EM: Round [129] log likelihood: -2989.960505
EM: Round [130] log likelihood: -2989.955017
EM: Round [131] log likelihood: -2989.949567
EM: Round [132] log likelihood: -2989.944154
EM: Round [133] log likelihood: -2989.938778
EM: Round [134] log likelihood: -2989.933439
EM: Round [135] log likelihood: -2989.928135
EM: Round [136] log likelihood: -2989.922867
EM: Round [137] log likelihood: -2989.917634
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[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_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.ZgoIkpRV0X/fi_workdir/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2634.415508
EM: Round [1] log likelihood: -2634.415508
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 189923055
Warning - not locating file: /tmp/nxf.ZgoIkpRV0X/aih-tih-sc-0419d4-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000262185.3]
WARNING, no entry stored in dbm for [ENSG00000262185.3]
WARNING, no entry stored in dbm for [ENSG00000261145.1]
WARNING, no entry stored in dbm for [ENSG00000259768.6]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
ls: cannot access 'IGV_inputs': No such file or directory