Done.
-parsing GTF file: /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.p4ZFwUXnBn/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.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00711_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00711_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:21:49 : INFO : Done.
-parsing GTF file: /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_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]
[730000]
[740000]
[750000]
[760000]
[770000]
[780000]
[790000]
[800000]
[810000]
[820000]
[830000]
[840000]
[850000]
[860000]
[870000]
[880000]
[890000]
[900000]
[910000]
[920000]
[930000]
[940000]
[950000]
[960000]
[970000]
[980000]
[990000]
[1000000]
[1010000] -done parsing /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 395,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 57,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 176,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 88,
'exons hit < 2' => 7,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 28,
'num genes matched < 2' => 636,
'excessive soft clipping' => 4800,
'per_id < 96' => 2549,
' ** passed ** ' => 4040,
'small anchor length' => 24,
'low complexity anchor region' => 1,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L
[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]
[123000]
[124000]
[125000]
[126000]
[127000]
[128000]
[129000]
[130000]
[131000]
[132000]
[133000]
[134000]
[135000]
[136000]
[137000]
[138000]
[139000]
[140000]
[141000]
[142000]
[143000]
[144000]
[145000]
[146000]
[147000]
[148000]
[149000]
[150000]
[151000]
[152000]
[153000]
[154000]
[155000]
[156000]
[157000]
[158000]
[159000]
[160000]
[161000]
[162000]
[163000] -fusion SPANNING read extraction for scaff: ARHGAP12--SVIL
[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] -fusion SPANNING read extraction for scaff: ARHGAP12--AL353093.1
[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]
[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]
[123000]
[124000]
[125000]
[126000]
[127000]
[128000]
[129000]
[130000]
[131000]
[132000]
[133000]
[134000]
[135000]
[136000]
[137000]
[138000] -fusion SPANNING read extraction for scaff: ARHGEF35--GFM1
[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] -fusion SPANNING read extraction for scaff: ATG12--PGGT1B
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000] -fusion SPANNING read extraction for scaff: BMS1P7--AGAP14P
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000] -fusion SPANNING read extraction for scaff: COX6CP1--COX6C
[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] -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B
[1000]
[2000]
[3000] -fusion SPANNING read extraction for scaff: LRRC25--AP002414.4
[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]
[123000]
[124000]
[125000]
[126000]
[127000]
[128000]
[129000]
[130000]
[131000]
[132000]
[133000]
[134000]
[135000]
[136000]
[137000] -fusion SPANNING read extraction for scaff: NF1--GABBR2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000] -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146
[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: SIRT2--NFKBIB
[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] -fusion SPANNING read extraction for scaff: SSBP4--AP002414.4
[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] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
[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] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
[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] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
[1000]
[2000]
[3000]
[4000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[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] -fusion SPANNING read extraction for scaff: UBXN6--AC011498.1
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 13756
};
EM: Starting log likelihood: -6350.899182
EM: Round [1] log likelihood: -6348.871683
EM: Round [2] log likelihood: -6348.839084
EM: Round [3] log likelihood: -6348.830780
EM: Round [4] log likelihood: -6348.823669
EM: Round [5] log likelihood: -6348.816813
EM: Round [6] log likelihood: -6348.810121
EM: Round [7] log likelihood: -6348.803579
EM: Round [8] log likelihood: -6348.797179
EM: Round [9] log likelihood: -6348.790917
EM: Round [10] log likelihood: -6348.784790
EM: Round [11] log likelihood: -6348.778793
EM: Round [12] log likelihood: -6348.772923
EM: Round [13] log likelihood: -6348.767178
EM: Round [14] log likelihood: -6348.761553
EM: Round [15] log likelihood: -6348.756045
EM: Round [16] log likelihood: -6348.750651
EM: Round [17] log likelihood: -6348.745368
EM: Round [18] log likelihood: -6348.740194
EM: Round [19] log likelihood: -6348.735126
EM: Round [20] log likelihood: -6348.730160
EM: Round [21] log likelihood: -6348.725295
EM: Round [22] log likelihood: -6348.720528
EM: Round [23] log likelihood: -6348.715856
EM: Round [24] log likelihood: -6348.711277
EM: Round [25] log likelihood: -6348.706790
EM: Round [26] log likelihood: -6348.702390
EM: Round [27] log likelihood: -6348.698078
EM: Round [28] log likelihood: -6348.693849
EM: Round [29] log likelihood: -6348.689703
EM: Round [30] log likelihood: -6348.685638
EM: Round [31] log likelihood: -6348.681651
EM: Round [32] log likelihood: -6348.677741
EM: Round [33] log likelihood: -6348.673907
EM: Round [34] log likelihood: -6348.670145
EM: Round [35] log likelihood: -6348.666455
EM: Round [36] log likelihood: -6348.662835
EM: Round [37] log likelihood: -6348.659284
EM: Round [38] log likelihood: -6348.655799
EM: Round [39] log likelihood: -6348.652380
EM: Round [40] log likelihood: -6348.649025
EM: Round [41] log likelihood: -6348.645732
EM: Round [42] log likelihood: -6348.642501
EM: Round [43] log likelihood: -6348.639330
EM: Round [44] log likelihood: -6348.636217
EM: Round [45] log likelihood: -6348.633161
EM: Round [46] log likelihood: -6348.630162
EM: Round [47] log likelihood: -6348.627217
EM: Round [48] log likelihood: -6348.624326
EM: Round [49] log likelihood: -6348.621488
EM: Round [50] log likelihood: -6348.618702
EM: Round [51] log likelihood: -6348.615965
EM: Round [52] log likelihood: -6348.613279
EM: Round [53] log likelihood: -6348.610640
EM: Round [54] log likelihood: -6348.608049
EM: Round [55] log likelihood: -6348.605504
EM: Round [56] log likelihood: -6348.603005
EM: Round [57] log likelihood: -6348.600550
EM: Round [58] log likelihood: -6348.598139
EM: Round [59] log likelihood: -6348.595771
EM: Round [60] log likelihood: -6348.593445
EM: Round [61] log likelihood: -6348.591159
EM: Round [62] log likelihood: -6348.588914
EM: Round [63] log likelihood: -6348.586709
EM: Round [64] log likelihood: -6348.584542
EM: Round [65] log likelihood: -6348.582413
EM: Round [66] log likelihood: -6348.580321
EM: Round [67] log likelihood: -6348.578266
EM: Round [68] log likelihood: -6348.576246
EM: Round [69] log likelihood: -6348.574261
EM: Round [70] log likelihood: -6348.572311
EM: Round [71] log likelihood: -6348.570395
EM: Round [72] log likelihood: -6348.568511
EM: Round [73] log likelihood: -6348.566660
EM: Round [74] log likelihood: -6348.564841
EM: Round [75] log likelihood: -6348.563053
EM: Round [76] log likelihood: -6348.561296
EM: Round [77] log likelihood: -6348.559568
EM: Round [78] log likelihood: -6348.557870
EM: Round [79] log likelihood: -6348.556202
EM: Round [80] log likelihood: -6348.554561
EM: Round [81] log likelihood: -6348.552948
EM: Round [82] log likelihood: -6348.551363
EM: Round [83] log likelihood: -6348.549805
EM: Round [84] log likelihood: -6348.548273
EM: Round [85] log likelihood: -6348.546766
EM: Round [86] log likelihood: -6348.545286
EM: Round [87] log likelihood: -6348.543830
EM: Round [88] log likelihood: -6348.542398
EM: Round [89] log likelihood: -6348.540991
EM: Round [90] log likelihood: -6348.539607
EM: Round [91] log likelihood: -6348.538246
EM: Round [92] log likelihood: -6348.536908
EM: Round [93] log likelihood: -6348.535593
EM: Round [94] log likelihood: -6348.534299
EM: Round [95] log likelihood: -6348.533027
EM: Round [96] log likelihood: -6348.531776
EM: Round [97] log likelihood: -6348.530545
EM: Round [98] log likelihood: -6348.529336
EM: Round [99] log likelihood: -6348.528146
EM: Round [100] log likelihood: -6348.526976
EM: Round [101] log likelihood: -6348.525825
EM: Round [102] log likelihood: -6348.524693
EM: Round [103] log likelihood: -6348.523580
EM: Round [104] log likelihood: -6348.522485
EM: Round [105] log likelihood: -6348.521408
EM: Round [106] log likelihood: -6348.520349
EM: Round [107] log likelihood: -6348.519308
EM: Round [108] log likelihood: -6348.518283
EM: Round [109] log likelihood: -6348.517275
EM: Round [110] log likelihood: -6348.516284
EM: Round [111] log likelihood: -6348.515309
EM: Round [112] log likelihood: -6348.514350
EM: Round [113] log likelihood: -6348.513406
EM: Round [114] log likelihood: -6348.512478
EM: Round [115] log likelihood: -6348.511565
EM: Round [116] log likelihood: -6348.510667
EM: Round [117] log likelihood: -6348.509783
EM: Round [118] log likelihood: -6348.508914
EM: Round [119] log likelihood: -6348.508059
EM: Round [120] log likelihood: -6348.507218
EM: Round [121] log likelihood: -6348.506390
EM: Round [122] log likelihood: -6348.505576
EM: Round [123] log likelihood: -6348.504775
EM: Round [124] log likelihood: -6348.503987
EM: Round [125] log likelihood: -6348.503212
EM: Round [126] log likelihood: -6348.502449
EM: Round [127] log likelihood: -6348.501698
EM: Round [128] log likelihood: -6348.500960
EM: Round [129] log likelihood: -6348.500233
EM: Round [130] log likelihood: -6348.499519
EM: Round [131] log likelihood: -6348.498815
EM: Round [132] log likelihood: -6348.498123
EM: Round [133] log likelihood: -6348.497442
EM: Round [134] log likelihood: -6348.496772
EM: Round [135] log likelihood: -6348.496113
EM: Round [136] log likelihood: -6348.495464
EM: Round [137] log likelihood: -6348.494826
EM: Round [138] log likelihood: -6348.494198
EM: Round [139] log likelihood: -6348.493580
EM: Round [140] log likelihood: -6348.492972
EM: Round [141] log likelihood: -6348.492374
EM: Round [142] log likelihood: -6348.491785
EM: Round [143] log likelihood: -6348.491205
EM: Round [144] log likelihood: -6348.490635
EM: Round [145] log likelihood: -6348.490074
EM: Round [146] log likelihood: -6348.489522
EM: Round [147] log likelihood: -6348.488978
EM: Round [148] log likelihood: -6348.488443
EM: Round [149] log likelihood: -6348.487917
EM: Round [150] log likelihood: -6348.487399
EM: Round [151] log likelihood: -6348.486890
EM: Round [152] log likelihood: -6348.486388
EM: Round [153] log likelihood: -6348.485895
EM: Round [154] log likelihood: -6348.485409
EM: Round [155] log likelihood: -6348.484931
EM: Round [156] log likelihood: -6348.484460
EM: Round [157] log likelihood: -6348.483997
EM: Round [158] log likelihood: -6348.483542
EM: Round [159] log likelihood: -6348.483093
EM: Round [160] log likelihood: -6348.482652
EM: Round [161] log likelihood: -6348.482217
EM: Round [162] log likelihood: -6348.481790
EM: Round [163] log likelihood: -6348.481369
EM: Round [164] log likelihood: -6348.480955
EM: Round [165] log likelihood: -6348.480547
EM: Round [166] log likelihood: -6348.480146
EM: Round [167] log likelihood: -6348.479751
EM: Round [168] log likelihood: -6348.479363
EM: Round [169] log likelihood: -6348.478980
EM: Round [170] log likelihood: -6348.478604
EM: Round [171] log likelihood: -6348.478233
EM: Round [172] log likelihood: -6348.477869
EM: Round [173] log likelihood: -6348.477510
EM: Round [174] log likelihood: -6348.477156
EM: Round [175] log likelihood: -6348.476809
EM: Round [176] log likelihood: -6348.476466
EM: Round [177] log likelihood: -6348.476129
EM: Round [178] log likelihood: -6348.475798
EM: Round [179] log likelihood: -6348.475471
EM: Round [180] log likelihood: -6348.475150
EM: Round [181] log likelihood: -6348.474834
EM: Round [182] log likelihood: -6348.474523
EM: Round [183] log likelihood: -6348.474216
EM: Round [184] log likelihood: -6348.473915
EM: Round [185] log likelihood: -6348.473618
EM: Round [186] log likelihood: -6348.473326
EM: Round [187] log likelihood: -6348.473038
EM: Round [188] log likelihood: -6348.472755
EM: Round [189] log likelihood: -6348.472476
EM: Round [190] log likelihood: -6348.472202
EM: Round [191] log likelihood: -6348.471932
EM: Round [192] log likelihood: -6348.471666
EM: Round [193] log likelihood: -6348.471405
EM: Round [194] log likelihood: -6348.471147
EM: Round [195] log likelihood: -6348.470893
EM: Round [196] log likelihood: -6348.470644
EM: Round [197] log likelihood: -6348.470398
EM: Round [198] log likelihood: -6348.470156
EM: Round [199] log likelihood: -6348.469918
EM: Round [200] log likelihood: -6348.469684
EM: Round [201] log likelihood: -6348.469453
EM: Round [202] log likelihood: -6348.469226
EM: Round [203] log likelihood: -6348.469003
EM: Round [204] log likelihood: -6348.468783
EM: Round [205] log likelihood: -6348.468566
EM: Round [206] log likelihood: -6348.468353
EM: Round [207] log likelihood: -6348.468143
EM: Round [208] log likelihood: -6348.467937
EM: Round [209] log likelihood: -6348.467733
EM: Round [210] log likelihood: -6348.467533
EM: Round [211] log likelihood: -6348.467336
EM: Round [212] log likelihood: -6348.467142
EM: Round [213] log likelihood: -6348.466951
EM: Round [214] log likelihood: -6348.466763
EM: Round [215] log likelihood: -6348.466578
EM: Round [216] log likelihood: -6348.466395
EM: Round [217] log likelihood: -6348.466216
EM: Round [218] log likelihood: -6348.466039
EM: Round [219] log likelihood: -6348.465865
EM: Round [220] log likelihood: -6348.465694
EM: Round [221] log likelihood: -6348.465526
EM: Round [222] log likelihood: -6348.465360
EM: Round [223] log likelihood: -6348.465197
EM: Round [224] log likelihood: -6348.465036
EM: Round [225] log likelihood: -6348.464878
EM: Round [226] log likelihood: -6348.464722
EM: Round [227] log likelihood: -6348.464568
EM: Round [228] log likelihood: -6348.464417
EM: Round [229] log likelihood: -6348.464269
EM: Round [230] log likelihood: -6348.464122
EM: Round [231] log likelihood: -6348.463978
EM: Round [232] log likelihood: -6348.463837
EM: Round [233] log likelihood: -6348.463697
EM: Round [234] log likelihood: -6348.463559
EM: Round [235] log likelihood: -6348.463424
EM: Round [236] log likelihood: -6348.463291
EM: Round [237] log likelihood: -6348.463160
EM: Round [238] log likelihood: -6348.463031
EM: Round [239] log likelihood: -6348.462904
EM: Round [240] log likelihood: -6348.462778
EM: Round [241] log likelihood: -6348.462655
EM: Round [242] log likelihood: -6348.462534
EM: Round [243] log likelihood: -6348.462414
EM: Round [244] log likelihood: -6348.462297
EM: Round [245] log likelihood: -6348.462181
EM: Round [246] log likelihood: -6348.462067
EM: Round [247] log likelihood: -6348.461955
EM: Round [248] log likelihood: -6348.461844
EM: Round [249] log likelihood: -6348.461736
EM: Round [250] log likelihood: -6348.461629
EM: Round [251] log likelihood: -6348.461523
EM: Round [252] log likelihood: -6348.461420
EM: Round [253] log likelihood: -6348.461317
EM: Round [254] log likelihood: -6348.461217
EM: Round [255] log likelihood: -6348.461118
EM: Stopping iterations at round 255 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_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.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_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.p4ZFwUXnBn/fi_workdir/tih_rna_sample_00711_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -5449.205586
EM: Round [1] log likelihood: -5448.161578
EM: Round [2] log likelihood: -5448.156341
EM: Round [3] log likelihood: -5448.156261
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1_1.fastp.fastq.gz: 295812390
Warning - not locating file: /tmp/nxf.p4ZFwUXnBn/tih_rna_sample_00711_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
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 [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000267011.5]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
ls: cannot access 'IGV_inputs': No such file or directory