Done.
-parsing GTF file: /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.Cs2qPAqHAB/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.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.Cs2qPAqHAB/fi_workdir/tih_rna_sample_00574_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.Cs2qPAqHAB/fi_workdir/tih_rna_sample_00574_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00574_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00574_B23MVV7LT4_1.star.sortedByCoord.out.bam
12:04:35 : INFO : Done.
-parsing GTF file: /tmp/nxf.Cs2qPAqHAB/fi_workdir/tih_rna_sample_00574_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.Cs2qPAqHAB/fi_workdir/tih_rna_sample_00574_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[4330000] -done parsing /tmp/nxf.Cs2qPAqHAB/fi_workdir/tih_rna_sample_00574_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 8,
'per_id < 96' => 18320,
'num genes matched < 2' => 118,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 300,
'seq-similar region overlap' => 41,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 930,
' ** passed ** ' => 11836,
'small anchor length' => 95,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 95,
'excessive soft clipping' => 27188,
'low complexity anchor region' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 78,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 9,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 66
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.Cs2qPAqHAB/fi_workdir/tih_rna_sample_00574_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[20000] -fusion SPANNING read extraction for scaff: AC091132.4--AC091132.1
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[63000] -fusion SPANNING read extraction for scaff: AGO3--AGO1
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[61000] -fusion SPANNING read extraction for scaff: ATP10A--ANKS1B
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[104000] -fusion SPANNING read extraction for scaff: CRK--NTRK3
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[34000] -fusion SPANNING read extraction for scaff: DDHD2--ADAM2
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[71000] -fusion SPANNING read extraction for scaff: DDT--CCDC117
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[49000] -fusion SPANNING read extraction for scaff: DDTL--CCDC117
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[322000] -fusion SPANNING read extraction for scaff: ESR1--UBR5-AS1
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[323000] -fusion SPANNING read extraction for scaff: ESR1--RRM2B
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[158000] -fusion SPANNING read extraction for scaff: FRY--UACA
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[63000] -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1
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[112000] -fusion SPANNING read extraction for scaff: GLI3--AC034187.1
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[322000] -fusion SPANNING read extraction for scaff: GNA13--BPTF
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[204000] -fusion SPANNING read extraction for scaff: GREB1--E2F6
[1000]
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[3000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[123000] -fusion SPANNING read extraction for scaff: LMBR1--ESYT2
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[71000] -fusion SPANNING read extraction for scaff: LMBR1--DYNC2I1
[1000]
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[324000] -fusion SPANNING read extraction for scaff: MARK2--CD44
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[77000] -fusion SPANNING read extraction for scaff: MFSD6--TLK1
[1000]
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[3000] -fusion SPANNING read extraction for scaff: MIR4713HG--GLDN
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[175000] -fusion SPANNING read extraction for scaff: NACA--PRIM1
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[65000] -fusion SPANNING read extraction for scaff: NFE2L2--PDE11A
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[62000] -fusion SPANNING read extraction for scaff: NFE2L2--CYCTP
[1000]
[2000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2
[1000]
[2000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1
[1000]
[2000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13
[1000]
[2000]
[3000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
[1000]
[2000]
[3000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
[1000]
[2000]
[3000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
[1000]
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[3000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
[1000]
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[3000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
[1000]
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[3000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
[1000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
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[13000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
[1000]
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[6000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
[1000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
[1000]
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[6000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
[1000]
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
[1000]
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[43000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
[1000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
[1000]
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[13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
[1000]
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
[1000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
[1000]
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[51000] -fusion SPANNING read extraction for scaff: TAF4--CDH4
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[49000] -fusion SPANNING read extraction for scaff: TAX1BP1--AC007130.1
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[71000] -fusion SPANNING read extraction for scaff: TBK1--SRGAP1
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[41000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[36000] -fusion SPANNING read extraction for scaff: ZDHHC17--PLD1
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[35000] -fusion SPANNING read extraction for scaff: ZNF236--ALG1L2
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 75839,
'seq similar region alignment' => 39386
};
EM: Starting log likelihood: -12338.875937
EM: Round [1] log likelihood: -12327.031553
EM: Round [2] log likelihood: -12326.478694
EM: Round [3] log likelihood: -12325.996443
EM: Round [4] log likelihood: -12325.568560
EM: Round [5] log likelihood: -12325.187313
EM: Round [6] log likelihood: -12324.846401
EM: Round [7] log likelihood: -12324.540617
EM: Round [8] log likelihood: -12324.265607
EM: Round [9] log likelihood: -12324.017693
EM: Round [10] log likelihood: -12323.793746
EM: Round [11] log likelihood: -12323.591078
EM: Round [12] log likelihood: -12323.407367
EM: Round [13] log likelihood: -12323.240599
EM: Round [14] log likelihood: -12323.089011
EM: Round [15] log likelihood: -12322.951057
EM: Round [16] log likelihood: -12322.825378
EM: Round [17] log likelihood: -12322.710768
EM: Round [18] log likelihood: -12322.606160
EM: Round [19] log likelihood: -12322.510602
EM: Round [20] log likelihood: -12322.423246
EM: Round [21] log likelihood: -12322.343334
EM: Round [22] log likelihood: -12322.270184
EM: Round [23] log likelihood: -12322.203185
EM: Round [24] log likelihood: -12322.141786
EM: Round [25] log likelihood: -12322.085491
EM: Round [26] log likelihood: -12322.033852
EM: Round [27] log likelihood: -12321.986463
EM: Round [28] log likelihood: -12321.942956
EM: Round [29] log likelihood: -12321.902999
EM: Round [30] log likelihood: -12321.866288
EM: Round [31] log likelihood: -12321.832549
EM: Round [32] log likelihood: -12321.801531
EM: Round [33] log likelihood: -12321.773007
EM: Round [34] log likelihood: -12321.746770
EM: Round [35] log likelihood: -12321.722628
EM: Round [36] log likelihood: -12321.700411
EM: Round [37] log likelihood: -12321.679959
EM: Round [38] log likelihood: -12321.661128
EM: Round [39] log likelihood: -12321.643787
EM: Round [40] log likelihood: -12321.627814
EM: Round [41] log likelihood: -12321.613098
EM: Round [42] log likelihood: -12321.599539
EM: Round [43] log likelihood: -12321.587043
EM: Round [44] log likelihood: -12321.575526
EM: Round [45] log likelihood: -12321.564908
EM: Round [46] log likelihood: -12321.555119
EM: Round [47] log likelihood: -12321.546092
EM: Round [48] log likelihood: -12321.537768
EM: Round [49] log likelihood: -12321.530090
EM: Round [50] log likelihood: -12321.523007
EM: Round [51] log likelihood: -12321.516473
EM: Round [52] log likelihood: -12321.510444
EM: Round [53] log likelihood: -12321.504881
EM: Round [54] log likelihood: -12321.499747
EM: Round [55] log likelihood: -12321.495009
EM: Round [56] log likelihood: -12321.490636
EM: Round [57] log likelihood: -12321.486599
EM: Round [58] log likelihood: -12321.482873
EM: Round [59] log likelihood: -12321.479432
EM: Round [60] log likelihood: -12321.476256
EM: Round [61] log likelihood: -12321.473322
EM: Round [62] log likelihood: -12321.470614
EM: Round [63] log likelihood: -12321.468112
EM: Round [64] log likelihood: -12321.465802
EM: Round [65] log likelihood: -12321.463668
EM: Round [66] log likelihood: -12321.461697
EM: Round [67] log likelihood: -12321.459877
EM: Round [68] log likelihood: -12321.458195
EM: Round [69] log likelihood: -12321.456641
EM: Round [70] log likelihood: -12321.455206
EM: Round [71] log likelihood: -12321.453880
EM: Round [72] log likelihood: -12321.452654
EM: Round [73] log likelihood: -12321.451522
EM: Round [74] log likelihood: -12321.450476
EM: Round [75] log likelihood: -12321.449509
EM: Round [76] log likelihood: -12321.448615
EM: Round [77] log likelihood: -12321.447790
EM: Round [78] log likelihood: -12321.447026
EM: Round [79] log likelihood: -12321.446321
EM: Round [80] log likelihood: -12321.445669
EM: Round [81] log likelihood: -12321.445066
EM: Round [82] log likelihood: -12321.444509
EM: Round [83] log likelihood: -12321.443994
EM: Round [84] log likelihood: -12321.443518
EM: Round [85] log likelihood: -12321.443078
EM: Round [86] log likelihood: -12321.442671
EM: Round [87] log likelihood: -12321.442295
EM: Round [88] log likelihood: -12321.441947
EM: Round [89] log likelihood: -12321.441626
EM: Round [90] log likelihood: -12321.441329
EM: Round [91] log likelihood: -12321.441054
EM: Round [92] log likelihood: -12321.440800
EM: Round [93] log likelihood: -12321.440565
EM: Round [94] log likelihood: -12321.440347
EM: Round [95] log likelihood: -12321.440146
EM: Round [96] log likelihood: -12321.439960
EM: Round [97] log likelihood: -12321.439789
EM: Round [98] log likelihood: -12321.439630
EM: Round [99] log likelihood: -12321.439483
EM: Round [100] log likelihood: -12321.439347
EM: Round [101] log likelihood: -12321.439221
EM: Round [102] log likelihood: -12321.439105
EM: Round [103] log likelihood: -12321.438997
EM: Round [104] log likelihood: -12321.438898
EM: Stopping iterations at round 104 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Cs2qPAqHAB/fi_workdir/tih_rna_sample_00574_B23MVV7LT4_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.Cs2qPAqHAB/fi_workdir/tih_rna_sample_00574_B23MVV7LT4_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.Cs2qPAqHAB/fi_workdir/tih_rna_sample_00574_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -11511.258544
EM: Round [1] log likelihood: -11506.028161
EM: Round [2] log likelihood: -11506.024951
EM: Round [3] log likelihood: -11506.024938
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1_1.fastp.fastq.gz: 296395707
Warning - not locating file: /tmp/nxf.Cs2qPAqHAB/tih_rna_sample_00574_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000246263.3]
WARNING, no entry stored in dbm for [ENSG00000246263.3]
WARNING, no entry stored in dbm for [ENSG00000246263.3]
WARNING, no entry stored in dbm for [ENSG00000246263.3]
WARNING, no entry stored in dbm for [ENSG00000246263.3]
WARNING, no entry stored in dbm for [ENSG00000246263.3]
WARNING, no entry stored in dbm for [ENSG00000246263.3]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000199839.1]
WARNING, no entry stored in dbm for [ENSG00000259240.1]
WARNING, no entry stored in dbm for [ENSG00000259240.1]
WARNING, no entry stored in dbm for [ENSG00000259240.1]
WARNING, no entry stored in dbm for [ENSG00000259240.1]
WARNING, no entry stored in dbm for [ENSG00000259240.1]
WARNING, no entry stored in dbm for [ENSG00000286478.1]
WARNING, no entry stored in dbm for [ENSG00000224884.1]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000131484.4]
WARNING, no entry stored in dbm for [ENSG00000249909.1]
ls: cannot access 'IGV_inputs': No such file or directory