Done.
-parsing GTF file: /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.tExeCh6s5b/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.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_rd-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_rd-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
10:29:13 : INFO : Done.
-parsing GTF file: /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[3130000] -done parsing /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 8538,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4774,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
'exons hit < 2' => 9,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 13,
' ** passed ** ' => 86732,
'low complexity anchor region' => 164,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 48,
'excessive soft clipping' => 14574,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 14,
'small anchor length' => 1032,
'num genes matched < 2' => 675,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 439,
'seq-similar region overlap' => 1950
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[3000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[50000] -fusion SPANNING read extraction for scaff: AL591378.1--DMD
-fusion SPANNING read extraction for scaff: CCDC169--SOHLH2
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[1111000]
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[1118000]
[1119000] -fusion SPANNING read extraction for scaff: NAB2--STAT6
[1000]
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[21000]
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[30000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC1
[1000]
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[6000]
[7000]
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[31000]
[32000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC2
[1000]
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[6000]
[7000]
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[9000]
[10000]
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[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHA13
[1000]
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[6000]
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[29000]
[30000]
[31000]
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[33000]
[34000]
[35000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8
[1000]
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[6000]
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[30000]
[31000]
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[34000]
[35000]
[36000]
[37000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9
[1000]
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[4000]
[5000]
[6000]
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[9000]
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[20000]
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[28000]
[29000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6
[1000]
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[5000]
[6000]
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[20000]
[21000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10
[1000]
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[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7
[1000]
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[6000]
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[33000]
[34000]
[35000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11
[1000]
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[9000]
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[11000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12
[1000]
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[76000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3
[1000]
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[8000]
[9000]
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[11000]
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4
[1000]
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5
[1000]
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
[1000]
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[8000]
[9000]
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
[1000]
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[22000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
[1000]
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
[1000]
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
[1000]
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[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
[1000]
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[3000]
[4000]
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[6000]
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[8000]
[9000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
[1000]
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[69000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[20000]
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
[1000]
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[33000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
[1000]
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[1109000] -fusion SPANNING read extraction for scaff: STAT6--NAB2
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[55000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
[1000]
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[3000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[1000]
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[33000] -fusion SPANNING read extraction for scaff: TMEM14B--FER1L5
[1000]
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[14000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
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[49000] -fusion SPANNING read extraction for scaff: XACT--LRRTM4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 40031,
'lacks exon overlap' => 83379
};
EM: Starting log likelihood: -28022.081655
EM: Round [1] log likelihood: -27862.529170
EM: Round [2] log likelihood: -27842.984221
EM: Round [3] log likelihood: -27829.961751
EM: Round [4] log likelihood: -27820.699505
EM: Round [5] log likelihood: -27814.022304
EM: Round [6] log likelihood: -27809.140933
EM: Round [7] log likelihood: -27805.515813
EM: Round [8] log likelihood: -27802.774392
EM: Round [9] log likelihood: -27800.657620
EM: Round [10] log likelihood: -27798.984458
EM: Round [11] log likelihood: -27797.627941
EM: Round [12] log likelihood: -27796.498800
EM: Round [13] log likelihood: -27795.534148
EM: Round [14] log likelihood: -27794.689605
EM: Round [15] log likelihood: -27793.933803
EM: Round [16] log likelihood: -27793.244525
EM: Round [17] log likelihood: -27792.605998
EM: Round [18] log likelihood: -27792.006989
EM: Round [19] log likelihood: -27791.439463
EM: Round [20] log likelihood: -27790.897641
EM: Round [21] log likelihood: -27790.377340
EM: Round [22] log likelihood: -27789.875498
EM: Round [23] log likelihood: -27789.389852
EM: Round [24] log likelihood: -27788.918703
EM: Round [25] log likelihood: -27788.460752
EM: Round [26] log likelihood: -27788.014989
EM: Round [27] log likelihood: -27787.580607
EM: Round [28] log likelihood: -27787.156950
EM: Round [29] log likelihood: -27786.743467
EM: Round [30] log likelihood: -27786.339687
EM: Round [31] log likelihood: -27785.945199
EM: Round [32] log likelihood: -27785.559636
EM: Round [33] log likelihood: -27785.182666
EM: Round [34] log likelihood: -27784.813981
EM: Round [35] log likelihood: -27784.453300
EM: Round [36] log likelihood: -27784.100354
EM: Round [37] log likelihood: -27783.754892
EM: Round [38] log likelihood: -27783.416677
EM: Round [39] log likelihood: -27783.085480
EM: Round [40] log likelihood: -27782.761084
EM: Round [41] log likelihood: -27782.443282
EM: Round [42] log likelihood: -27782.131874
EM: Round [43] log likelihood: -27781.826668
EM: Round [44] log likelihood: -27781.527480
EM: Round [45] log likelihood: -27781.234131
EM: Round [46] log likelihood: -27780.946453
EM: Round [47] log likelihood: -27780.664279
EM: Round [48] log likelihood: -27780.387451
EM: Round [49] log likelihood: -27780.115816
EM: Round [50] log likelihood: -27779.849226
EM: Round [51] log likelihood: -27779.587540
EM: Round [52] log likelihood: -27779.330620
EM: Round [53] log likelihood: -27779.078334
EM: Round [54] log likelihood: -27778.830554
EM: Round [55] log likelihood: -27778.587157
EM: Round [56] log likelihood: -27778.348023
EM: Round [57] log likelihood: -27778.113039
EM: Round [58] log likelihood: -27777.882093
EM: Round [59] log likelihood: -27777.655079
EM: Round [60] log likelihood: -27777.431893
EM: Round [61] log likelihood: -27777.212435
EM: Round [62] log likelihood: -27776.996610
EM: Round [63] log likelihood: -27776.784324
EM: Round [64] log likelihood: -27776.575488
EM: Round [65] log likelihood: -27776.370015
EM: Round [66] log likelihood: -27776.167821
EM: Round [67] log likelihood: -27775.968825
EM: Round [68] log likelihood: -27775.772948
EM: Round [69] log likelihood: -27775.580116
EM: Round [70] log likelihood: -27775.390255
EM: Round [71] log likelihood: -27775.203294
EM: Round [72] log likelihood: -27775.019164
EM: Round [73] log likelihood: -27774.837801
EM: Round [74] log likelihood: -27774.659139
EM: Round [75] log likelihood: -27774.483117
EM: Round [76] log likelihood: -27774.309674
EM: Round [77] log likelihood: -27774.138753
EM: Round [78] log likelihood: -27773.970297
EM: Round [79] log likelihood: -27773.804252
EM: Round [80] log likelihood: -27773.640566
EM: Round [81] log likelihood: -27773.479186
EM: Round [82] log likelihood: -27773.320064
EM: Round [83] log likelihood: -27773.163151
EM: Round [84] log likelihood: -27773.008401
EM: Round [85] log likelihood: -27772.855768
EM: Round [86] log likelihood: -27772.705210
EM: Round [87] log likelihood: -27772.556682
EM: Round [88] log likelihood: -27772.410145
EM: Round [89] log likelihood: -27772.265558
EM: Round [90] log likelihood: -27772.122881
EM: Round [91] log likelihood: -27771.982078
EM: Round [92] log likelihood: -27771.843112
EM: Round [93] log likelihood: -27771.705946
EM: Round [94] log likelihood: -27771.570546
EM: Round [95] log likelihood: -27771.436879
EM: Round [96] log likelihood: -27771.304911
EM: Round [97] log likelihood: -27771.174611
EM: Round [98] log likelihood: -27771.045947
EM: Round [99] log likelihood: -27770.918890
EM: Round [100] log likelihood: -27770.793411
EM: Round [101] log likelihood: -27770.669479
EM: Round [102] log likelihood: -27770.547069
EM: Round [103] log likelihood: -27770.426151
EM: Round [104] log likelihood: -27770.306701
EM: Round [105] log likelihood: -27770.188692
EM: Round [106] log likelihood: -27770.072099
EM: Round [107] log likelihood: -27769.956897
EM: Round [108] log likelihood: -27769.843063
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[bam_sort_core] merging from 0 files and 8 in-memory blocks...
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_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.tExeCh6s5b/fi_workdir/659_rd-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -24629.476793
EM: Round [1] log likelihood: -24531.877036
EM: Round [2] log likelihood: -24530.785641
EM: Round [3] log likelihood: -24530.780129
EM: Round [4] log likelihood: -24530.780106
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 209192447
Warning - not locating file: /tmp/nxf.tExeCh6s5b/659_rd-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
ls: cannot access 'IGV_inputs': No such file or directory