Done.
-parsing GTF file: /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.YGSl4tcF7M/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.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
10:25:23 : INFO : Done.
-parsing GTF file: /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_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]
[1020000]
[1030000]
[1040000]
[1050000]
[1060000]
[1070000]
[1080000]
[1090000]
[1100000]
[1110000]
[1120000]
[1130000]
[1140000]
[1150000]
[1160000]
[1170000] -done parsing /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 53,
'num genes matched < 2' => 12,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 20,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
'small anchor length' => 1,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 21,
'seq-similar region overlap' => 98,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 15,
'excessive soft clipping' => 7695,
'low complexity anchor region' => 2,
'per_id < 96' => 4603,
' ** passed ** ' => 3210
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000]
[2000]
[3000]
[4000]
[5000]
[6000] -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]
[60000]
[61000]
[62000]
[63000]
[64000]
[65000]
[66000]
[67000]
[68000]
[69000]
[70000]
[71000]
[72000]
[73000]
[74000]
[75000]
[76000]
[77000]
[78000]
[79000]
[80000]
[81000]
[82000]
[83000] -fusion SPANNING read extraction for scaff: CPSF7--PIEZO2
[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: CPSF7--AP005139.1
[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]
[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]
[164000]
[165000]
[166000]
[167000]
[168000] -fusion SPANNING read extraction for scaff: DDX5--SMURF2
[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] -fusion SPANNING read extraction for scaff: DHX38--WWOX
[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: ERC1--RASSF7
[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] -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1
[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] -fusion SPANNING read extraction for scaff: KIAA1958--NTRK2
[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] -fusion SPANNING read extraction for scaff: LMNTD2--ERC1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000] -fusion SPANNING read extraction for scaff: NAE1--CAPNS2
[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: PCDHA11--PCDHAC2
[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: PCDHA11--PCDHAC1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000]
[22000]
[23000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
[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] -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]
[28000]
[29000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
[1000]
[2000]
[3000]
[4000]
[5000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[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: 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]
[27000]
[28000]
[29000]
[30000] -fusion SPANNING read extraction for scaff: TXNL4B--CTCF
[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] -fusion SPANNING read extraction for scaff: TXNL4B--CARMIL2
[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] -fusion SPANNING read extraction for scaff: WWP2--MPHOSPH6
[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]
[164000]
[165000]
[166000]
[167000]
[168000]
[169000]
[170000]
[171000]
[172000]
[173000]
[174000]
[175000]
[176000]
[177000]
[178000]
[179000]
[180000]
[181000]
[182000]
[183000]
[184000]
[185000]
[186000]
[187000]
[188000]
[189000]
[190000]
[191000]
[192000]
[193000]
[194000]
[195000]
[196000]
[197000]
[198000]
[199000]
[200000]
[201000]
[202000]
[203000] -fusion SPANNING read extraction for scaff: ZFHX3--CNTNAP4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 47046,
'seq similar region alignment' => 19027
};
EM: Starting log likelihood: -3012.042627
EM: Round [1] log likelihood: -3011.682253
EM: Round [2] log likelihood: -3011.396539
EM: Round [3] log likelihood: -3011.133574
EM: Round [4] log likelihood: -3010.890806
EM: Round [5] log likelihood: -3010.666324
EM: Round [6] log likelihood: -3010.458448
EM: Round [7] log likelihood: -3010.265695
EM: Round [8] log likelihood: -3010.086749
EM: Round [9] log likelihood: -3009.920437
EM: Round [10] log likelihood: -3009.765713
EM: Round [11] log likelihood: -3009.621635
EM: Round [12] log likelihood: -3009.487357
EM: Round [13] log likelihood: -3009.362113
EM: Round [14] log likelihood: -3009.245211
EM: Round [15] log likelihood: -3009.136023
EM: Round [16] log likelihood: -3009.033976
EM: Round [17] log likelihood: -3008.938549
EM: Round [18] log likelihood: -3008.849264
EM: Round [19] log likelihood: -3008.765686
EM: Round [20] log likelihood: -3008.687413
EM: Round [21] log likelihood: -3008.614078
EM: Round [22] log likelihood: -3008.545341
EM: Round [23] log likelihood: -3008.480891
EM: Round [24] log likelihood: -3008.420439
EM: Round [25] log likelihood: -3008.363719
EM: Round [26] log likelihood: -3008.310485
EM: Round [27] log likelihood: -3008.260508
EM: Round [28] log likelihood: -3008.213576
EM: Round [29] log likelihood: -3008.169494
EM: Round [30] log likelihood: -3008.128079
EM: Round [31] log likelihood: -3008.089161
EM: Round [32] log likelihood: -3008.052582
EM: Round [33] log likelihood: -3008.018195
EM: Round [34] log likelihood: -3007.985863
EM: Round [35] log likelihood: -3007.955458
EM: Round [36] log likelihood: -3007.926861
EM: Round [37] log likelihood: -3007.899960
EM: Round [38] log likelihood: -3007.874652
EM: Round [39] log likelihood: -3007.850838
EM: Round [40] log likelihood: -3007.828429
EM: Round [41] log likelihood: -3007.807338
EM: Round [42] log likelihood: -3007.787487
EM: Round [43] log likelihood: -3007.768800
EM: Round [44] log likelihood: -3007.751207
EM: Round [45] log likelihood: -3007.734643
EM: Round [46] log likelihood: -3007.719047
EM: Round [47] log likelihood: -3007.704360
EM: Round [48] log likelihood: -3007.690529
EM: Round [49] log likelihood: -3007.677503
EM: Round [50] log likelihood: -3007.665234
EM: Round [51] log likelihood: -3007.653678
EM: Round [52] log likelihood: -3007.642792
EM: Round [53] log likelihood: -3007.632538
EM: Round [54] log likelihood: -3007.622877
EM: Round [55] log likelihood: -3007.613776
EM: Round [56] log likelihood: -3007.605201
EM: Round [57] log likelihood: -3007.597121
EM: Round [58] log likelihood: -3007.589509
EM: Round [59] log likelihood: -3007.582335
EM: Round [60] log likelihood: -3007.575576
EM: Round [61] log likelihood: -3007.569206
EM: Round [62] log likelihood: -3007.563203
EM: Round [63] log likelihood: -3007.557546
EM: Round [64] log likelihood: -3007.552215
EM: Round [65] log likelihood: -3007.547191
EM: Round [66] log likelihood: -3007.542455
EM: Round [67] log likelihood: -3007.537992
EM: Round [68] log likelihood: -3007.533786
EM: Round [69] log likelihood: -3007.529821
EM: Round [70] log likelihood: -3007.526084
EM: Round [71] log likelihood: -3007.522562
EM: Round [72] log likelihood: -3007.519241
EM: Round [73] log likelihood: -3007.516112
EM: Round [74] log likelihood: -3007.513162
EM: Round [75] log likelihood: -3007.510381
EM: Round [76] log likelihood: -3007.507760
EM: Round [77] log likelihood: -3007.505289
EM: Round [78] log likelihood: -3007.502959
EM: Round [79] log likelihood: -3007.500763
EM: Round [80] log likelihood: -3007.498693
EM: Round [81] log likelihood: -3007.496742
EM: Round [82] log likelihood: -3007.494902
EM: Round [83] log likelihood: -3007.493168
EM: Round [84] log likelihood: -3007.491533
EM: Round [85] log likelihood: -3007.489992
EM: Round [86] log likelihood: -3007.488539
EM: Round [87] log likelihood: -3007.487169
EM: Round [88] log likelihood: -3007.485878
EM: Round [89] log likelihood: -3007.484661
EM: Round [90] log likelihood: -3007.483513
EM: Round [91] log likelihood: -3007.482431
EM: Round [92] log likelihood: -3007.481410
EM: Round [93] log likelihood: -3007.480449
EM: Round [94] log likelihood: -3007.479542
EM: Round [95] log likelihood: -3007.478687
EM: Round [96] log likelihood: -3007.477881
EM: Round [97] log likelihood: -3007.477121
EM: Round [98] log likelihood: -3007.476405
EM: Round [99] log likelihood: -3007.475729
EM: Round [100] log likelihood: -3007.475093
EM: Round [101] log likelihood: -3007.474492
EM: Round [102] log likelihood: -3007.473926
EM: Round [103] log likelihood: -3007.473392
EM: Round [104] log likelihood: -3007.472889
EM: Round [105] log likelihood: -3007.472415
EM: Round [106] log likelihood: -3007.471968
EM: Round [107] log likelihood: -3007.471546
EM: Round [108] log likelihood: -3007.471148
EM: Round [109] log likelihood: -3007.470774
EM: Round [110] log likelihood: -3007.470420
EM: Round [111] log likelihood: -3007.470087
EM: Round [112] log likelihood: -3007.469773
EM: Round [113] log likelihood: -3007.469477
EM: Round [114] log likelihood: -3007.469197
EM: Round [115] log likelihood: -3007.468934
EM: Round [116] log likelihood: -3007.468686
EM: Round [117] log likelihood: -3007.468452
EM: Round [118] log likelihood: -3007.468231
EM: Round [119] log likelihood: -3007.468023
EM: Round [120] log likelihood: -3007.467827
EM: Round [121] log likelihood: -3007.467642
EM: Round [122] log likelihood: -3007.467467
EM: Round [123] log likelihood: -3007.467303
EM: Round [124] log likelihood: -3007.467148
EM: Round [125] log likelihood: -3007.467002
EM: Round [126] log likelihood: -3007.466864
EM: Round [127] log likelihood: -3007.466734
EM: Round [128] log likelihood: -3007.466611
EM: Round [129] log likelihood: -3007.466496
EM: Round [130] log likelihood: -3007.466387
EM: Round [131] log likelihood: -3007.466284
EM: Round [132] log likelihood: -3007.466188
EM: Stopping iterations at round 132 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_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.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_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.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2836.006779
EM: Round [1] log likelihood: -2836.006748
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 241112810
Warning - not locating file: /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [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 [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
ls: cannot access 'IGV_inputs': No such file or directory