Done.
-parsing GTF file: /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
11:28:17 : INFO : Done.
-parsing GTF file: /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[1410000] -done parsing /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 11,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 174,
'exons hit < 2' => 5,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
'small anchor length' => 2,
'excessive soft clipping' => 9651,
'per_id < 96' => 5169,
'low complexity anchor region' => 1,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 16,
'seq-similar region overlap' => 387,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
' ** passed ** ' => 7264,
'num genes matched < 2' => 12
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[27000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
[1000]
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
[1000]
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[30000]
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[33000]
[34000]
[35000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
[1000]
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[20000]
[21000]
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[23000]
[24000]
[25000]
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[27000]
[28000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
[1000]
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[5000]
[6000]
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[11000] -fusion SPANNING read extraction for scaff: PHEX--AC004470.2
[1000]
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[6000]
[7000]
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[13000] -fusion SPANNING read extraction for scaff: PXMP4--ZNF341
[1000]
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[27000] -fusion SPANNING read extraction for scaff: RASSF8--CMAS
[1000]
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[47000] -fusion SPANNING read extraction for scaff: RNF217--PARD3B
[1000]
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[57000] -fusion SPANNING read extraction for scaff: SENP6--EYS
[1000]
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[7000] -fusion SPANNING read extraction for scaff: SKP1P2--SOX5
[1000]
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[6000] -fusion SPANNING read extraction for scaff: SLC2A13--IL1RAPL1
[1000]
[2000]
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[10000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
[1000]
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[23000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
[1000]
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[24000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
[1000]
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[4000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[1000]
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[40000] -fusion SPANNING read extraction for scaff: TRHDE--CYP27B1
[1000]
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[6000]
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[18000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 66817,
'lacks exon overlap' => 16884
};
EM: Starting log likelihood: -4385.554985
EM: Round [1] log likelihood: -4382.836654
EM: Round [2] log likelihood: -4382.122546
EM: Round [3] log likelihood: -4381.504305
EM: Round [4] log likelihood: -4380.962129
EM: Round [5] log likelihood: -4380.485415
EM: Round [6] log likelihood: -4380.065278
EM: Round [7] log likelihood: -4379.694209
EM: Round [8] log likelihood: -4379.365830
EM: Round [9] log likelihood: -4379.074697
EM: Round [10] log likelihood: -4378.816142
EM: Round [11] log likelihood: -4378.586153
EM: Round [12] log likelihood: -4378.381263
EM: Round [13] log likelihood: -4378.198473
EM: Round [14] log likelihood: -4378.035179
EM: Round [15] log likelihood: -4377.889113
EM: Round [16] log likelihood: -4377.758299
EM: Round [17] log likelihood: -4377.641007
EM: Round [18] log likelihood: -4377.535722
EM: Round [19] log likelihood: -4377.441114
EM: Round [20] log likelihood: -4377.356014
EM: Round [21] log likelihood: -4377.279391
EM: Round [22] log likelihood: -4377.210336
EM: Round [23] log likelihood: -4377.148046
EM: Round [24] log likelihood: -4377.091809
EM: Round [25] log likelihood: -4377.040997
EM: Round [26] log likelihood: -4376.995049
EM: Round [27] log likelihood: -4376.953468
EM: Round [28] log likelihood: -4376.915812
EM: Round [29] log likelihood: -4376.881687
EM: Round [30] log likelihood: -4376.850742
EM: Round [31] log likelihood: -4376.822662
EM: Round [32] log likelihood: -4376.797166
EM: Round [33] log likelihood: -4376.774004
EM: Round [34] log likelihood: -4376.752951
EM: Round [35] log likelihood: -4376.733803
EM: Round [36] log likelihood: -4376.716381
EM: Round [37] log likelihood: -4376.700521
EM: Round [38] log likelihood: -4376.686076
EM: Round [39] log likelihood: -4376.672914
EM: Round [40] log likelihood: -4376.660917
EM: Round [41] log likelihood: -4376.649978
EM: Round [42] log likelihood: -4376.639998
EM: Round [43] log likelihood: -4376.630892
EM: Round [44] log likelihood: -4376.622579
EM: Round [45] log likelihood: -4376.614988
EM: Round [46] log likelihood: -4376.608055
EM: Round [47] log likelihood: -4376.601720
EM: Round [48] log likelihood: -4376.595931
EM: Round [49] log likelihood: -4376.590638
EM: Round [50] log likelihood: -4376.585799
EM: Round [51] log likelihood: -4376.581373
EM: Round [52] log likelihood: -4376.577325
EM: Round [53] log likelihood: -4376.573620
EM: Round [54] log likelihood: -4376.570230
EM: Round [55] log likelihood: -4376.567127
EM: Round [56] log likelihood: -4376.564287
EM: Round [57] log likelihood: -4376.561686
EM: Round [58] log likelihood: -4376.559304
EM: Round [59] log likelihood: -4376.557123
EM: Round [60] log likelihood: -4376.555124
EM: Round [61] log likelihood: -4376.553294
EM: Round [62] log likelihood: -4376.551616
EM: Round [63] log likelihood: -4376.550079
EM: Round [64] log likelihood: -4376.548671
EM: Round [65] log likelihood: -4376.547380
EM: Round [66] log likelihood: -4376.546196
EM: Round [67] log likelihood: -4376.545111
EM: Round [68] log likelihood: -4376.544117
EM: Round [69] log likelihood: -4376.543205
EM: Round [70] log likelihood: -4376.542369
EM: Round [71] log likelihood: -4376.541602
EM: Round [72] log likelihood: -4376.540899
EM: Round [73] log likelihood: -4376.540254
EM: Round [74] log likelihood: -4376.539662
EM: Round [75] log likelihood: -4376.539119
EM: Round [76] log likelihood: -4376.538622
EM: Round [77] log likelihood: -4376.538165
EM: Round [78] log likelihood: -4376.537746
EM: Round [79] log likelihood: -4376.537362
EM: Round [80] log likelihood: -4376.537009
EM: Round [81] log likelihood: -4376.536686
EM: Round [82] log likelihood: -4376.536389
EM: Round [83] log likelihood: -4376.536117
EM: Round [84] log likelihood: -4376.535867
EM: Round [85] log likelihood: -4376.535637
EM: Round [86] log likelihood: -4376.535427
EM: Round [87] log likelihood: -4376.535234
EM: Round [88] log likelihood: -4376.535057
EM: Round [89] log likelihood: -4376.534894
EM: Round [90] log likelihood: -4376.534745
EM: Round [91] log likelihood: -4376.534608
EM: Round [92] log likelihood: -4376.534482
EM: Round [93] log likelihood: -4376.534367
EM: Round [94] log likelihood: -4376.534261
EM: Round [95] log likelihood: -4376.534163
EM: Stopping iterations at round 95 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3842.033512
EM: Round [1] log likelihood: -3841.500271
EM: Round [2] log likelihood: -3841.498032
EM: Round [3] log likelihood: -3841.498010
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295130272
Warning - not locating file: /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000288546.1]
WARNING, no entry stored in dbm for [ENSG00000288546.1]
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 [ENSG00000228933.8]
WARNING, no entry stored in dbm for [ENSG00000228933.8]
WARNING, no entry stored in dbm for [ENSG00000228933.8]
WARNING, no entry stored in dbm for [ENSG00000228933.8]
ls: cannot access 'IGV_inputs': No such file or directory