Done.
-parsing GTF file: /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00596_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00596_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:50:04 : INFO : Done.
-parsing GTF file: /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[6910000] -done parsing /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1056,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 47,
' ** passed ** ' => 16682,
'num_hits: 10 != num_counted_on_fusion_contigs 7 ' => 7,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 242,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 21,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 232,
'per_id < 96' => 26122,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 45,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 464,
'exons hit < 2' => 9,
'num_hits: 9 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 10,
'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 8,
'small anchor length' => 83,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 30,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 2137,
'num_hits: 8 != num_counted_on_fusion_contigs 3 ' => 3,
'low complexity anchor region' => 29,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 129,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 44,
'excessive soft clipping' => 67034,
'num genes matched < 2' => 157,
'num_hits: 8 != num_counted_on_fusion_contigs 5 ' => 10,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 48,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[83000] -fusion SPANNING read extraction for scaff: ADAP1--C7orf50
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[6000] -fusion SPANNING read extraction for scaff: ADCY1--GCK
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[156000] -fusion SPANNING read extraction for scaff: ADGRF1--TNFRSF21
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[45000] -fusion SPANNING read extraction for scaff: AHCY--AL356299.1
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[395000] -fusion SPANNING read extraction for scaff: AKAP8L--BRD4
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[18000] -fusion SPANNING read extraction for scaff: ANKRD45--KLHL20
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[167000] -fusion SPANNING read extraction for scaff: ASPH--TACC2
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[145000] -fusion SPANNING read extraction for scaff: ATP7A--ATRX
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[45000] -fusion SPANNING read extraction for scaff: ATP7A--MAGT1
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[41000] -fusion SPANNING read extraction for scaff: ATXN10--TTC38
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[11000] -fusion SPANNING read extraction for scaff: AVL9--DPY19L1P2
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[111000] -fusion SPANNING read extraction for scaff: BPTF--LINC00674
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[307000] -fusion SPANNING read extraction for scaff: CCT2--FRS2
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[38000] -fusion SPANNING read extraction for scaff: CDC42--CELA3B
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[18000] -fusion SPANNING read extraction for scaff: CERS6--NOSTRIN
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[90000] -fusion SPANNING read extraction for scaff: CLIP2--LAT2
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[78000] -fusion SPANNING read extraction for scaff: CNOT2--TPH2
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[76000] -fusion SPANNING read extraction for scaff: COX19--C7orf50
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[67000] -fusion SPANNING read extraction for scaff: CPD--RIT1
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[30000] -fusion SPANNING read extraction for scaff: CPNE3--AC060765.2
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[16000] -fusion SPANNING read extraction for scaff: DCUN1D2--GRTP1
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[13000] -fusion SPANNING read extraction for scaff: DIAPH3--RIOK3P1
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[13000] -fusion SPANNING read extraction for scaff: DIAPH3--RNU6-38P
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[49000] -fusion SPANNING read extraction for scaff: FBXW7--SLC39A8
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[380000] -fusion SPANNING read extraction for scaff: FRS2--LYZ
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[387000] -fusion SPANNING read extraction for scaff: GRIP1--CPSF6
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[155000] -fusion SPANNING read extraction for scaff: GRIP1--NUP107
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[278000] -fusion SPANNING read extraction for scaff: GTF2IRD1--POM121
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[51000] -fusion SPANNING read extraction for scaff: HELB--GRIP1
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[47000] -fusion SPANNING read extraction for scaff: ITGB6--RBMS1
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[174000] -fusion SPANNING read extraction for scaff: JUP--P3H4
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[133000] -fusion SPANNING read extraction for scaff: KANSL1--ARL17B
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[9000] -fusion SPANNING read extraction for scaff: LINC02408--GRIP1
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[67000] -fusion SPANNING read extraction for scaff: MARK4--BRSK1
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[20000] -fusion SPANNING read extraction for scaff: MIA2--AL049828.1
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[154000] -fusion SPANNING read extraction for scaff: NBPF14--GNG12
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[305000] -fusion SPANNING read extraction for scaff: PAF1--PLEKHG2
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[22000] -fusion SPANNING read extraction for scaff: PLEKHA2--ADAM2
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[333000] -fusion SPANNING read extraction for scaff: PRPF8--YWHAE
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[118000] -fusion SPANNING read extraction for scaff: RBM4--PDPK1
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[63000] -fusion SPANNING read extraction for scaff: RBM4B--PDPK1
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[36000] -fusion SPANNING read extraction for scaff: RCOR1--TRAF3
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[20000] -fusion SPANNING read extraction for scaff: RPS6KB1--RNU6-450P
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[30000] -fusion SPANNING read extraction for scaff: RPS6KB1--TUBD1
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[11000] -fusion SPANNING read extraction for scaff: SH2D4A--AC100849.1
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[16000] -fusion SPANNING read extraction for scaff: SLC9A2--IL18RAP
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[10000] -fusion SPANNING read extraction for scaff: STON1--GTF2A1L
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[114000] -fusion SPANNING read extraction for scaff: THADA--AC012409.2
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[26000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[5000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[120000] -fusion SPANNING read extraction for scaff: TMED10--CENPT
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[67000] -fusion SPANNING read extraction for scaff: TMED10--THAP11
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[17000] -fusion SPANNING read extraction for scaff: TMEM163--CCNT2-AS1
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[66000] -fusion SPANNING read extraction for scaff: TRA2B--VPS8
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[40000] -fusion SPANNING read extraction for scaff: TRA2B--C3orf70
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[22000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[130000] -fusion SPANNING read extraction for scaff: UNC13D--FBF1
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[53000] -fusion SPANNING read extraction for scaff: ZNF552--RPS29P30
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[53000] -fusion SPANNING read extraction for scaff: ZNF552--LGALS16
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[75000] -fusion SPANNING read extraction for scaff: ZNF587--ZSCAN5C
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 5388,
'lacks exon overlap' => 72348
};
EM: Starting log likelihood: -27654.689121
EM: Round [1] log likelihood: -27613.951167
EM: Round [2] log likelihood: -27598.640474
EM: Round [3] log likelihood: -27586.664461
EM: Round [4] log likelihood: -27577.130748
EM: Round [5] log likelihood: -27569.451215
EM: Round [6] log likelihood: -27563.208906
EM: Round [7] log likelihood: -27558.098626
EM: Round [8] log likelihood: -27553.891292
EM: Round [9] log likelihood: -27550.411450
EM: Round [10] log likelihood: -27547.522502
EM: Round [11] log likelihood: -27545.116669
EM: Round [12] log likelihood: -27543.107971
EM: Round [13] log likelihood: -27541.427189
EM: Round [14] log likelihood: -27540.018177
EM: Round [15] log likelihood: -27538.835103
EM: Round [16] log likelihood: -27537.840354
EM: Round [17] log likelihood: -27537.002927
EM: Round [18] log likelihood: -27536.297174
EM: Round [19] log likelihood: -27535.701804
EM: Round [20] log likelihood: -27535.199100
EM: Round [21] log likelihood: -27534.774285
EM: Round [22] log likelihood: -27534.415009
EM: Round [23] log likelihood: -27534.110933
EM: Round [24] log likelihood: -27533.853389
EM: Round [25] log likelihood: -27533.635104
EM: Round [26] log likelihood: -27533.449964
EM: Round [27] log likelihood: -27533.292826
EM: Round [28] log likelihood: -27533.159363
EM: Round [29] log likelihood: -27533.045928
EM: Round [30] log likelihood: -27532.949445
EM: Round [31] log likelihood: -27532.867322
EM: Round [32] log likelihood: -27532.797369
EM: Round [33] log likelihood: -27532.737736
EM: Round [34] log likelihood: -27532.686860
EM: Round [35] log likelihood: -27532.643420
EM: Round [36] log likelihood: -27532.606298
EM: Round [37] log likelihood: -27532.574546
EM: Round [38] log likelihood: -27532.547365
EM: Round [39] log likelihood: -27532.524074
EM: Round [40] log likelihood: -27532.504097
EM: Round [41] log likelihood: -27532.486947
EM: Round [42] log likelihood: -27532.472208
EM: Round [43] log likelihood: -27532.459529
EM: Round [44] log likelihood: -27532.448609
EM: Round [45] log likelihood: -27532.439196
EM: Round [46] log likelihood: -27532.431071
EM: Round [47] log likelihood: -27532.424051
EM: Round [48] log likelihood: -27532.417979
EM: Round [49] log likelihood: -27532.412720
EM: Round [50] log likelihood: -27532.408160
EM: Round [51] log likelihood: -27532.404202
EM: Round [52] log likelihood: -27532.400763
EM: Round [53] log likelihood: -27532.397770
EM: Round [54] log likelihood: -27532.395162
EM: Round [55] log likelihood: -27532.392888
EM: Round [56] log likelihood: -27532.390902
EM: Round [57] log likelihood: -27532.389166
EM: Round [58] log likelihood: -27532.387646
EM: Round [59] log likelihood: -27532.386315
EM: Round [60] log likelihood: -27532.385146
EM: Round [61] log likelihood: -27532.384120
EM: Round [62] log likelihood: -27532.383218
EM: Round [63] log likelihood: -27532.382423
EM: Round [64] log likelihood: -27532.381723
EM: Round [65] log likelihood: -27532.381106
EM: Round [66] log likelihood: -27532.380560
EM: Round [67] log likelihood: -27532.380078
EM: Round [68] log likelihood: -27532.379652
EM: Round [69] log likelihood: -27532.379274
EM: Round [70] log likelihood: -27532.378939
EM: Round [71] log likelihood: -27532.378642
EM: Round [72] log likelihood: -27532.378378
EM: Round [73] log likelihood: -27532.378144
EM: Round [74] log likelihood: -27532.377935
EM: Round [75] log likelihood: -27532.377750
EM: Round [76] log likelihood: -27532.377585
EM: Round [77] log likelihood: -27532.377437
EM: Round [78] log likelihood: -27532.377306
EM: Round [79] log likelihood: -27532.377188
EM: Round [80] log likelihood: -27532.377084
EM: Round [81] log likelihood: -27532.376990
EM: Stopping iterations at round 81 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -27053.256799
EM: Round [1] log likelihood: -27050.230377
EM: Round [2] log likelihood: -27050.223842
EM: Round [3] log likelihood: -27050.223829
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz: 295821566
Warning - not locating file: /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000231952.3]
WARNING, no entry stored in dbm for [ENSG00000237854.3]
WARNING, no entry stored in dbm for [ENSG00000237854.3]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
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 [ENSG00000224043.8]
WARNING, no entry stored in dbm for [ENSG00000275443.2]
WARNING, no entry stored in dbm for [ENSG00000203585.4]
WARNING, no entry stored in dbm for [ENSG00000258526.7]
WARNING, no entry stored in dbm for [ENSG00000258526.7]
WARNING, no entry stored in dbm for [ENSG00000258526.7]
ls: cannot access 'IGV_inputs': No such file or directory