Done.
-parsing GTF file: /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.L2BqxZvgea/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.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00457_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00457_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:07:30 : INFO : Done.
-parsing GTF file: /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
[10000]
[20000]
[30000]
[40000]
[50000]
[60000]
[70000]
[80000]
[90000]
[100000]
[110000]
[120000]
[130000]
[140000]
[150000]
[160000]
[170000]
[180000]
[190000]
[200000]
[210000]
[220000]
[230000]
[240000]
[250000]
[260000]
[270000]
[280000]
[290000]
[300000]
[310000]
[320000]
[330000]
[340000]
[350000]
[360000]
[370000]
[380000]
[390000]
[400000]
[410000]
[420000]
[430000]
[440000]
[450000]
[460000]
[470000]
[480000]
[490000]
[500000]
[510000]
[520000]
[530000]
[540000]
[550000]
[560000]
[570000]
[580000]
[590000]
[600000]
[610000]
[620000]
[630000]
[640000]
[650000]
[660000]
[670000]
[680000]
[690000]
[700000]
[710000]
[720000] -done parsing /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 12,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 34,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'small anchor length' => 130,
'num genes matched < 2' => 9,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 9,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 148,
'excessive soft clipping' => 6298,
'seq-similar region overlap' => 77,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'per_id < 96' => 5453,
' ** passed ** ' => 21366,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 9,
'exons hit < 2' => 2
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000] -fusion SPANNING read extraction for scaff: CSNK1D--AC131274.3
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000] -fusion SPANNING read extraction for scaff: CSNK1D--AC069061.1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000] -fusion SPANNING read extraction for scaff: JPT1--C17orf58
[1000]
[2000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000]
[60000]
[61000]
[62000]
[63000]
[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000]
[74000]
[75000]
[76000]
[77000]
[78000]
[79000]
[80000]
[81000]
[82000]
[83000]
[84000]
[85000]
[86000]
[87000]
[88000]
[89000]
[90000]
[91000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000]
[60000]
[61000]
[62000]
[63000]
[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000] -fusion SPANNING read extraction for scaff: PRSS27--TPSB2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000]
[46000]
[47000]
[48000]
[49000]
[50000]
[51000]
[52000]
[53000]
[54000]
[55000]
[56000]
[57000]
[58000]
[59000]
[60000]
[61000]
[62000]
[63000]
[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000]
[74000]
[75000]
[76000]
[77000]
[78000]
[79000]
[80000]
[81000]
[82000]
[83000]
[84000]
[85000]
[86000]
[87000]
[88000]
[89000]
[90000]
[91000]
[92000]
[93000]
[94000]
[95000]
[96000]
[97000]
[98000]
[99000]
[100000]
[101000]
[102000]
[103000]
[104000]
[105000]
[106000]
[107000]
[108000]
[109000]
[110000]
[111000]
[112000]
[113000]
[114000]
[115000]
[116000]
[117000]
[118000]
[119000]
[120000]
[121000]
[122000] -fusion SPANNING read extraction for scaff: PSMD12--BPTF
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000] -fusion SPANNING read extraction for scaff: SLC39A11--LINC00511
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000] -fusion SPANNING read extraction for scaff: SOCS7--DBF4B
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000] -fusion SPANNING read extraction for scaff: SOCS7--ADAM11
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000]
[44000]
[45000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 22779,
'lacks exon overlap' => 2632
};
EM: Starting log likelihood: -1951.837462
EM: Round [1] log likelihood: -1951.557139
EM: Round [2] log likelihood: -1951.380350
EM: Round [3] log likelihood: -1951.225798
EM: Round [4] log likelihood: -1951.090103
EM: Round [5] log likelihood: -1950.970545
EM: Round [6] log likelihood: -1950.864889
EM: Round [7] log likelihood: -1950.771276
EM: Round [8] log likelihood: -1950.688147
EM: Round [9] log likelihood: -1950.614181
EM: Round [10] log likelihood: -1950.548257
EM: Round [11] log likelihood: -1950.489409
EM: Round [12] log likelihood: -1950.436810
EM: Round [13] log likelihood: -1950.389740
EM: Round [14] log likelihood: -1950.347574
EM: Round [15] log likelihood: -1950.309765
EM: Round [16] log likelihood: -1950.275837
EM: Round [17] log likelihood: -1950.245367
EM: Round [18] log likelihood: -1950.217986
EM: Round [19] log likelihood: -1950.193367
EM: Round [20] log likelihood: -1950.171218
EM: Round [21] log likelihood: -1950.151283
EM: Round [22] log likelihood: -1950.133333
EM: Round [23] log likelihood: -1950.117165
EM: Round [24] log likelihood: -1950.102595
EM: Round [25] log likelihood: -1950.089464
EM: Round [26] log likelihood: -1950.077624
EM: Round [27] log likelihood: -1950.066947
EM: Round [28] log likelihood: -1950.057316
EM: Round [29] log likelihood: -1950.048627
EM: Round [30] log likelihood: -1950.040787
EM: Round [31] log likelihood: -1950.033711
EM: Round [32] log likelihood: -1950.027324
EM: Round [33] log likelihood: -1950.021558
EM: Round [34] log likelihood: -1950.016352
EM: Round [35] log likelihood: -1950.011652
EM: Round [36] log likelihood: -1950.007407
EM: Round [37] log likelihood: -1950.003573
EM: Round [38] log likelihood: -1950.000111
EM: Round [39] log likelihood: -1949.996984
EM: Round [40] log likelihood: -1949.994159
EM: Round [41] log likelihood: -1949.991607
EM: Round [42] log likelihood: -1949.989301
EM: Round [43] log likelihood: -1949.987218
EM: Round [44] log likelihood: -1949.985336
EM: Round [45] log likelihood: -1949.983636
EM: Round [46] log likelihood: -1949.982100
EM: Round [47] log likelihood: -1949.980711
EM: Round [48] log likelihood: -1949.979457
EM: Round [49] log likelihood: -1949.978324
EM: Round [50] log likelihood: -1949.977299
EM: Round [51] log likelihood: -1949.976374
EM: Round [52] log likelihood: -1949.975537
EM: Round [53] log likelihood: -1949.974781
EM: Round [54] log likelihood: -1949.974098
EM: Round [55] log likelihood: -1949.973481
EM: Round [56] log likelihood: -1949.972923
EM: Round [57] log likelihood: -1949.972419
EM: Round [58] log likelihood: -1949.971963
EM: Round [59] log likelihood: -1949.971551
EM: Round [60] log likelihood: -1949.971179
EM: Round [61] log likelihood: -1949.970842
EM: Round [62] log likelihood: -1949.970538
EM: Round [63] log likelihood: -1949.970264
EM: Round [64] log likelihood: -1949.970015
EM: Round [65] log likelihood: -1949.969791
EM: Round [66] log likelihood: -1949.969588
EM: Round [67] log likelihood: -1949.969405
EM: Round [68] log likelihood: -1949.969239
EM: Round [69] log likelihood: -1949.969089
EM: Round [70] log likelihood: -1949.968954
EM: Round [71] log likelihood: -1949.968831
EM: Round [72] log likelihood: -1949.968721
EM: Round [73] log likelihood: -1949.968621
EM: Stopping iterations at round 73 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_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.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_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.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1793.315190
EM: Round [1] log likelihood: -1793.243426
EM: Round [2] log likelihood: -1793.243377
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1_1.fastp.fastq.gz: 295627857
Warning - not locating file: /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_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 [ENSG00000227036.8]
WARNING, no entry stored in dbm for [ENSG00000227036.8]
ls: cannot access 'IGV_inputs': No such file or directory