Done.
-parsing GTF file: /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.i1B8rRXG8j/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.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:17:09 : INFO : Done.
-parsing GTF file: /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_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]
[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]
[1180000]
[1190000]
[1200000]
[1210000]
[1220000]
[1230000]
[1240000]
[1250000]
[1260000]
[1270000]
[1280000]
[1290000]
[1300000]
[1310000]
[1320000]
[1330000]
[1340000]
[1350000]
[1360000]
[1370000]
[1380000]
[1390000]
[1400000]
[1410000]
[1420000]
[1430000]
[1440000]
[1450000]
[1460000]
[1470000]
[1480000]
[1490000]
[1500000]
[1510000]
[1520000]
[1530000]
[1540000]
[1550000]
[1560000]
[1570000]
[1580000]
[1590000]
[1600000]
[1610000]
[1620000]
[1630000]
[1640000]
[1650000]
[1660000]
[1670000]
[1680000]
[1690000]
[1700000]
[1710000] -done parsing /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 231,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'low complexity anchor region' => 1,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
'num genes matched < 2' => 44,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 14,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 38,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 15,
' ** passed ** ' => 9658,
'small anchor length' => 119,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 251,
'excessive soft clipping' => 9567,
'per_id < 96' => 7261
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000] -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] -fusion SPANNING read extraction for scaff: ARHGAP1--AC068051.1
[1000]
[2000] -fusion SPANNING read extraction for scaff: CASC15--GRIA4
[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: MDH1--PAUPAR
[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] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
[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] -fusion SPANNING read extraction for scaff: PCDHA10--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] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000]
[15000]
[16000]
[17000]
[18000]
[19000]
[20000]
[21000] -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]
[21000]
[22000]
[23000]
[24000]
[25000]
[26000]
[27000]
[28000] -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] -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]
[24000]
[25000]
[26000]
[27000]
[28000]
[29000]
[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
[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: PCDHA6--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] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
[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] -fusion SPANNING read extraction for scaff: TNFAIP8L3--CYP19A1
[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]
[204000]
[205000]
[206000]
[207000]
[208000]
[209000]
[210000]
[211000]
[212000]
[213000]
[214000]
[215000]
[216000]
[217000]
[218000]
[219000]
[220000]
[221000]
[222000]
[223000]
[224000]
[225000]
[226000]
[227000]
[228000]
[229000]
[230000]
[231000]
[232000]
[233000]
[234000]
[235000]
[236000]
[237000]
[238000]
[239000]
[240000]
[241000]
[242000]
[243000]
[244000]
[245000]
[246000]
[247000]
[248000]
[249000]
[250000]
[251000]
[252000]
[253000]
[254000]
[255000]
[256000]
[257000]
[258000]
[259000]
[260000]
[261000]
[262000]
[263000]
[264000]
[265000]
[266000]
[267000]
[268000]
[269000]
[270000]
[271000]
[272000]
[273000]
[274000]
[275000]
[276000]
[277000]
[278000]
[279000]
[280000]
[281000]
[282000]
[283000]
[284000]
[285000]
[286000]
[287000]
[288000]
[289000]
[290000]
[291000]
[292000]
[293000]
[294000]
[295000]
[296000]
[297000]
[298000]
[299000]
[300000]
[301000]
[302000]
[303000]
[304000]
[305000]
[306000]
[307000]
[308000]
[309000]
[310000]
[311000]
[312000]
[313000]
[314000]
[315000]
[316000]
[317000]
[318000]
[319000]
[320000]
[321000]
[322000]
[323000]
[324000]
[325000]
[326000]
[327000]
[328000]
[329000]
[330000]
[331000]
[332000]
[333000]
[334000]
[335000]
[336000]
[337000]
[338000]
[339000]
[340000]
[341000]
[342000]
[343000]
[344000]
[345000]
[346000]
[347000]
[348000]
[349000]
[350000]
[351000]
[352000]
[353000]
[354000]
[355000]
[356000]
[357000]
[358000]
[359000]
[360000]
[361000]
[362000]
[363000]
[364000]
[365000]
[366000]
[367000]
[368000]
[369000]
[370000]
[371000]
[372000]
[373000]
[374000]
[375000]
[376000]
[377000]
[378000]
[379000]
[380000]
[381000]
[382000]
[383000]
[384000]
[385000]
[386000]
[387000]
[388000]
[389000]
[390000]
[391000]
[392000]
[393000]
[394000]
[395000]
[396000]
[397000]
[398000]
[399000]
[400000]
[401000]
[402000]
[403000]
[404000]
[405000]
[406000]
[407000]
[408000]
[409000]
[410000]
[411000]
[412000]
[413000]
[414000]
[415000]
[416000]
[417000]
[418000]
[419000]
[420000]
[421000]
[422000]
[423000]
[424000]
[425000]
[426000]
[427000]
[428000]
[429000]
[430000]
[431000]
[432000]
[433000]
[434000]
[435000]
[436000]
[437000]
[438000]
[439000]
[440000]
[441000]
[442000]
[443000]
[444000]
[445000]
[446000]
[447000]
[448000]
[449000]
[450000]
[451000]
[452000]
[453000]
[454000]
[455000]
[456000]
[457000]
[458000]
[459000]
[460000]
[461000]
[462000]
[463000]
[464000]
[465000]
[466000]
[467000]
[468000]
[469000]
[470000]
[471000]
[472000]
[473000]
[474000]
[475000]
[476000]
[477000]
[478000]
[479000]
[480000]
[481000]
[482000]
[483000]
[484000]
[485000]
[486000]
[487000]
[488000]
[489000]
[490000]
[491000]
[492000]
[493000]
[494000]
[495000]
[496000]
[497000]
[498000]
[499000]
[500000]
[501000]
[502000]
[503000]
[504000]
[505000]
[506000]
[507000]
[508000]
[509000]
[510000]
[511000]
[512000]
[513000]
[514000]
[515000]
[516000]
[517000]
[518000]
[519000]
[520000]
[521000]
[522000]
[523000]
[524000]
[525000]
[526000]
[527000]
[528000]
[529000]
[530000]
[531000]
[532000]
[533000]
[534000]
[535000]
[536000]
[537000]
[538000]
[539000]
[540000]
[541000]
[542000]
[543000]
[544000]
[545000]
[546000]
[547000]
[548000]
[549000]
[550000]
[551000]
[552000]
[553000]
[554000]
[555000]
[556000]
[557000]
[558000]
[559000]
[560000]
[561000]
[562000]
[563000]
[564000]
[565000]
[566000]
[567000]
[568000]
[569000]
[570000]
[571000]
[572000]
[573000]
[574000]
[575000]
[576000]
[577000]
[578000]
[579000]
[580000]
[581000]
[582000]
[583000]
[584000]
[585000]
[586000]
[587000]
[588000]
[589000]
[590000]
[591000]
[592000]
[593000]
[594000]
[595000]
[596000]
[597000]
[598000]
[599000]
[600000]
[601000]
[602000]
[603000]
[604000]
[605000]
[606000]
[607000]
[608000]
[609000]
[610000]
[611000]
[612000]
[613000]
[614000]
[615000]
[616000]
[617000]
[618000]
[619000]
[620000]
[621000]
[622000]
[623000]
[624000]
[625000]
[626000]
[627000]
[628000]
[629000]
[630000]
[631000]
[632000]
[633000]
[634000]
[635000]
[636000]
[637000]
[638000]
[639000]
[640000]
[641000]
[642000]
[643000]
[644000]
[645000]
[646000]
[647000]
[648000]
[649000]
[650000]
[651000]
[652000]
[653000]
[654000]
[655000]
[656000]
[657000]
[658000]
[659000]
[660000]
[661000]
[662000]
[663000]
[664000]
[665000]
[666000]
[667000]
[668000]
[669000]
[670000]
[671000]
[672000]
[673000]
[674000]
[675000]
[676000]
[677000]
[678000]
[679000]
[680000]
[681000]
[682000]
[683000]
[684000]
[685000]
[686000]
[687000]
[688000]
[689000]
[690000]
[691000]
[692000]
[693000]
[694000]
[695000]
[696000]
[697000]
[698000]
[699000]
[700000]
[701000]
[702000]
[703000]
[704000]
[705000]
[706000]
[707000]
[708000]
[709000]
[710000]
[711000]
[712000]
[713000]
[714000]
[715000]
[716000]
[717000]
[718000]
[719000]
[720000]
[721000]
[722000]
[723000]
[724000]
[725000]
[726000]
[727000]
[728000]
[729000]
[730000]
[731000]
[732000]
[733000]
[734000]
[735000]
[736000]
[737000]
[738000]
[739000]
[740000]
[741000]
[742000]
[743000]
[744000]
[745000]
[746000]
[747000]
[748000]
[749000]
[750000]
[751000]
[752000]
[753000]
[754000]
[755000]
[756000]
[757000]
[758000]
[759000]
[760000]
[761000]
[762000]
[763000]
[764000]
[765000]
[766000]
[767000]
[768000]
[769000]
[770000]
[771000]
[772000]
[773000]
[774000]
[775000]
[776000]
[777000]
[778000]
[779000]
[780000]
[781000]
[782000]
[783000]
[784000]
[785000]
[786000]
[787000]
[788000]
[789000]
[790000]
[791000]
[792000]
[793000]
[794000]
[795000]
[796000]
[797000]
[798000]
[799000]
[800000]
[801000]
[802000]
[803000]
[804000]
[805000]
[806000]
[807000]
[808000]
[809000]
[810000]
[811000]
[812000]
[813000]
[814000]
[815000]
[816000]
[817000]
[818000]
[819000]
[820000]
[821000]
[822000]
[823000]
[824000]
[825000]
[826000]
[827000]
[828000]
[829000]
[830000]
[831000]
[832000]
[833000]
[834000]
[835000]
[836000]
[837000]
[838000]
[839000]
[840000]
[841000]
[842000]
[843000]
[844000]
[845000]
[846000]
[847000]
[848000]
[849000]
[850000]
[851000]
[852000]
[853000]
[854000]
[855000]
[856000]
[857000]
[858000]
[859000]
[860000]
[861000]
[862000]
[863000]
[864000]
[865000]
[866000]
[867000]
[868000]
[869000]
[870000]
[871000]
[872000]
[873000]
[874000]
[875000]
[876000]
[877000]
[878000]
[879000]
[880000]
[881000]
[882000]
[883000]
[884000]
[885000]
[886000]
[887000]
[888000]
[889000]
[890000]
[891000]
[892000]
[893000]
[894000]
[895000]
[896000]
[897000]
[898000]
[899000]
[900000]
[901000]
[902000]
[903000]
[904000]
[905000]
[906000]
[907000]
[908000]
[909000]
[910000]
[911000]
[912000]
[913000]
[914000]
[915000]
[916000]
[917000]
[918000]
[919000]
[920000]
[921000]
[922000]
[923000]
[924000]
[925000]
[926000]
[927000]
[928000]
[929000]
[930000]
[931000]
[932000]
[933000]
[934000]
[935000]
[936000]
[937000]
[938000]
[939000]
[940000]
[941000]
[942000]
[943000]
[944000]
[945000]
[946000]
[947000]
[948000]
[949000]
[950000]
[951000]
[952000]
[953000]
[954000]
[955000]
[956000]
[957000]
[958000]
[959000]
[960000]
[961000]
[962000]
[963000]
[964000]
[965000]
[966000]
[967000]
[968000]
[969000]
[970000]
[971000]
[972000]
[973000]
[974000]
[975000]
[976000]
[977000]
[978000]
[979000]
[980000]
[981000]
[982000]
[983000]
[984000]
[985000]
[986000]
[987000]
[988000]
[989000]
[990000]
[991000]
[992000]
[993000]
[994000]
[995000]
[996000]
[997000]
[998000]
[999000]
[1000000]
[1001000]
[1002000]
[1003000]
[1004000]
[1005000]
[1006000]
[1007000]
[1008000]
[1009000]
[1010000]
[1011000]
[1012000]
[1013000]
[1014000]
[1015000]
[1016000]
[1017000]
[1018000]
[1019000]
[1020000]
[1021000]
[1022000]
[1023000]
[1024000]
[1025000]
[1026000]
[1027000]
[1028000]
[1029000]
[1030000]
[1031000]
[1032000]
[1033000]
[1034000]
[1035000]
[1036000]
[1037000]
[1038000]
[1039000]
[1040000]
[1041000]
[1042000]
[1043000]
[1044000]
[1045000]
[1046000]
[1047000]
[1048000]
[1049000]
[1050000]
[1051000]
[1052000]
[1053000]
[1054000]
[1055000]
[1056000]
[1057000]
[1058000]
[1059000]
[1060000]
[1061000]
[1062000]
[1063000]
[1064000]
[1065000]
[1066000]
[1067000]
[1068000]
[1069000]
[1070000]
[1071000]
[1072000]
[1073000]
[1074000]
[1075000]
[1076000]
[1077000]
[1078000]
[1079000]
[1080000]
[1081000]
[1082000]
[1083000]
[1084000]
[1085000]
[1086000]
[1087000]
[1088000]
[1089000]
[1090000]
[1091000]
[1092000]
[1093000]
[1094000]
[1095000]
[1096000]
[1097000]
[1098000]
[1099000]
[1100000]
[1101000]
[1102000]
[1103000]
[1104000]
[1105000]
[1106000]
[1107000]
[1108000]
[1109000]
[1110000]
[1111000]
[1112000]
[1113000]
[1114000]
[1115000]
[1116000]
[1117000]
[1118000]
[1119000]
[1120000]
[1121000]
[1122000]
[1123000]
[1124000]
[1125000]
[1126000]
[1127000]
[1128000]
[1129000]
[1130000]
[1131000]
[1132000]
[1133000]
[1134000]
[1135000]
[1136000]
[1137000]
[1138000]
[1139000]
[1140000]
[1141000]
[1142000]
[1143000]
[1144000] -fusion SPANNING read extraction for scaff: TNS1--ALK
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
[12000]
[13000]
[14000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 55828,
'lacks exon overlap' => 4308
};
EM: Starting log likelihood: -5303.008241
EM: Round [1] log likelihood: -5299.278672
EM: Round [2] log likelihood: -5299.228764
EM: Round [3] log likelihood: -5299.199553
EM: Round [4] log likelihood: -5299.171896
EM: Round [5] log likelihood: -5299.144917
EM: Round [6] log likelihood: -5299.118555
EM: Round [7] log likelihood: -5299.092790
EM: Round [8] log likelihood: -5299.067604
EM: Round [9] log likelihood: -5299.042980
EM: Round [10] log likelihood: -5299.018901
EM: Round [11] log likelihood: -5298.995351
EM: Round [12] log likelihood: -5298.972314
EM: Round [13] log likelihood: -5298.949777
EM: Round [14] log likelihood: -5298.927724
EM: Round [15] log likelihood: -5298.906142
EM: Round [16] log likelihood: -5298.885018
EM: Round [17] log likelihood: -5298.864339
EM: Round [18] log likelihood: -5298.844094
EM: Round [19] log likelihood: -5298.824271
EM: Round [20] log likelihood: -5298.804857
EM: Round [21] log likelihood: -5298.785843
EM: Round [22] log likelihood: -5298.767218
EM: Round [23] log likelihood: -5298.748972
EM: Round [24] log likelihood: -5298.731095
EM: Round [25] log likelihood: -5298.713578
EM: Round [26] log likelihood: -5298.696411
EM: Round [27] log likelihood: -5298.679586
EM: Round [28] log likelihood: -5298.663094
EM: Round [29] log likelihood: -5298.646926
EM: Round [30] log likelihood: -5298.631076
EM: Round [31] log likelihood: -5298.615535
EM: Round [32] log likelihood: -5298.600296
EM: Round [33] log likelihood: -5298.585351
EM: Round [34] log likelihood: -5298.570694
EM: Round [35] log likelihood: -5298.556317
EM: Round [36] log likelihood: -5298.542215
EM: Round [37] log likelihood: -5298.528380
EM: Round [38] log likelihood: -5298.514806
EM: Round [39] log likelihood: -5298.501489
EM: Round [40] log likelihood: -5298.488420
EM: Round [41] log likelihood: -5298.475596
EM: Round [42] log likelihood: -5298.463010
EM: Round [43] log likelihood: -5298.450657
EM: Round [44] log likelihood: -5298.438532
EM: Round [45] log likelihood: -5298.426630
EM: Round [46] log likelihood: -5298.414945
EM: Round [47] log likelihood: -5298.403474
EM: Round [48] log likelihood: -5298.392211
EM: Round [49] log likelihood: -5298.381153
EM: Round [50] log likelihood: -5298.370293
EM: Round [51] log likelihood: -5298.359629
EM: Round [52] log likelihood: -5298.349157
EM: Round [53] log likelihood: -5298.338871
EM: Round [54] log likelihood: -5298.328768
EM: Round [55] log likelihood: -5298.318845
EM: Round [56] log likelihood: -5298.309097
EM: Round [57] log likelihood: -5298.299521
EM: Round [58] log likelihood: -5298.290113
EM: Round [59] log likelihood: -5298.280870
EM: Round [60] log likelihood: -5298.271789
EM: Round [61] log likelihood: -5298.262866
EM: Round [62] log likelihood: -5298.254097
EM: Round [63] log likelihood: -5298.245481
EM: Round [64] log likelihood: -5298.237013
EM: Round [65] log likelihood: -5298.228691
EM: Round [66] log likelihood: -5298.220512
EM: Round [67] log likelihood: -5298.212473
EM: Round [68] log likelihood: -5298.204571
EM: Round [69] log likelihood: -5298.196804
EM: Round [70] log likelihood: -5298.189169
EM: Round [71] log likelihood: -5298.181663
EM: Round [72] log likelihood: -5298.174284
EM: Round [73] log likelihood: -5298.167029
EM: Round [74] log likelihood: -5298.159896
EM: Round [75] log likelihood: -5298.152883
EM: Round [76] log likelihood: -5298.145987
EM: Round [77] log likelihood: -5298.139206
EM: Round [78] log likelihood: -5298.132538
EM: Round [79] log likelihood: -5298.125981
EM: Round [80] log likelihood: -5298.119532
EM: Round [81] log likelihood: -5298.113190
EM: Round [82] log likelihood: -5298.106952
EM: Round [83] log likelihood: -5298.100818
EM: Round [84] log likelihood: -5298.094783
EM: Round [85] log likelihood: -5298.088848
EM: Round [86] log likelihood: -5298.083010
EM: Round [87] log likelihood: -5298.077267
EM: Round [88] log likelihood: -5298.071617
EM: Round [89] log likelihood: -5298.066059
EM: Round [90] log likelihood: -5298.060592
EM: Round [91] log likelihood: -5298.055212
EM: Round [92] log likelihood: -5298.049920
EM: Round [93] log likelihood: -5298.044712
EM: Round [94] log likelihood: -5298.039589
EM: Round [95] log likelihood: -5298.034547
EM: Round [96] log likelihood: -5298.029587
EM: Round [97] log likelihood: -5298.024705
EM: Round [98] log likelihood: -5298.019901
EM: Round [99] log likelihood: -5298.015174
EM: Round [100] log likelihood: -5298.010522
EM: Round [101] log likelihood: -5298.005944
EM: Round [102] log likelihood: -5298.001438
EM: Round [103] log likelihood: -5297.997003
EM: Round [104] log likelihood: -5297.992639
EM: Round [105] log likelihood: -5297.988343
EM: Round [106] log likelihood: -5297.984114
EM: Round [107] log likelihood: -5297.979952
EM: Round [108] log likelihood: -5297.975855
EM: Round [109] log likelihood: -5297.971822
EM: Round [110] log likelihood: -5297.967852
EM: Round [111] log likelihood: -5297.963944
EM: Round [112] log likelihood: -5297.960096
EM: Round [113] log likelihood: -5297.956308
EM: Round [114] log likelihood: -5297.952579
EM: Round [115] log likelihood: -5297.948908
EM: Round [116] log likelihood: -5297.945293
EM: Round [117] log likelihood: -5297.941734
EM: Round [118] log likelihood: -5297.938230
EM: Round [119] log likelihood: -5297.934780
EM: Round [120] log likelihood: -5297.931382
EM: Round [121] log likelihood: -5297.928037
EM: Round [122] log likelihood: -5297.924743
EM: Round [123] log likelihood: -5297.921499
EM: Round [124] log likelihood: -5297.918305
EM: Round [125] log likelihood: -5297.915159
EM: Round [126] log likelihood: -5297.912061
EM: Round [127] log likelihood: -5297.909010
EM: Round [128] log likelihood: -5297.906005
EM: Round [129] log likelihood: -5297.903046
EM: Round [130] log likelihood: -5297.900132
EM: Round [131] log likelihood: -5297.897261
EM: Round [132] log likelihood: -5297.894434
EM: Round [133] log likelihood: -5297.891649
EM: Round [134] log likelihood: -5297.888906
EM: Round [135] log likelihood: -5297.886205
EM: Round [136] log likelihood: -5297.883543
EM: Round [137] log likelihood: -5297.880922
EM: Round [138] log likelihood: -5297.878340
EM: Round [139] log likelihood: -5297.875796
EM: Round [140] log likelihood: -5297.873290
EM: Round [141] log likelihood: -5297.870821
EM: Round [142] log likelihood: -5297.868389
EM: Round [143] log likelihood: -5297.865994
EM: Round [144] log likelihood: -5297.863633
EM: Round [145] log likelihood: -5297.861308
EM: Round [146] log likelihood: -5297.859017
EM: Round [147] log likelihood: -5297.856760
EM: Round [148] log likelihood: -5297.854536
EM: Round [149] log likelihood: -5297.852344
EM: Round [150] log likelihood: -5297.850185
EM: Round [151] log likelihood: -5297.848058
EM: Round [152] log likelihood: -5297.845962
EM: Round [153] log likelihood: -5297.843896
EM: Round [154] log likelihood: -5297.841861
EM: Round [155] log likelihood: -5297.839855
EM: Round [156] log likelihood: -5297.837879
EM: Round [157] log likelihood: -5297.835932
EM: Round [158] log likelihood: -5297.834012
EM: Round [159] log likelihood: -5297.832121
EM: Round [160] log likelihood: -5297.830257
EM: Round [161] log likelihood: -5297.828420
EM: Round [162] log likelihood: -5297.826610
EM: Round [163] log likelihood: -5297.824826
EM: Round [164] log likelihood: -5297.823068
EM: Round [165] log likelihood: -5297.821335
EM: Round [166] log likelihood: -5297.819627
EM: Round [167] log likelihood: -5297.817944
EM: Round [168] log likelihood: -5297.816285
EM: Round [169] log likelihood: -5297.814649
EM: Round [170] log likelihood: -5297.813037
EM: Round [171] log likelihood: -5297.811449
EM: Round [172] log likelihood: -5297.809882
EM: Round [173] log likelihood: -5297.808339
EM: Round [174] log likelihood: -5297.806817
EM: Round [175] log likelihood: -5297.805317
EM: Round [176] log likelihood: -5297.803839
EM: Round [177] log likelihood: -5297.802381
EM: Round [178] log likelihood: -5297.800944
EM: Round [179] log likelihood: -5297.799528
EM: Round [180] log likelihood: -5297.798132
EM: Round [181] log likelihood: -5297.796755
EM: Round [182] log likelihood: -5297.795398
EM: Round [183] log likelihood: -5297.794060
EM: Round [184] log likelihood: -5297.792741
EM: Round [185] log likelihood: -5297.791441
EM: Round [186] log likelihood: -5297.790159
EM: Round [187] log likelihood: -5297.788895
EM: Round [188] log likelihood: -5297.787648
EM: Round [189] log likelihood: -5297.786420
EM: Round [190] log likelihood: -5297.785208
EM: Round [191] log likelihood: -5297.784014
EM: Round [192] log likelihood: -5297.782836
EM: Round [193] log likelihood: -5297.781674
EM: Round [194] log likelihood: -5297.780529
EM: Round [195] log likelihood: -5297.779400
EM: Round [196] log likelihood: -5297.778287
EM: Round [197] log likelihood: -5297.777189
EM: Round [198] log likelihood: -5297.776106
EM: Round [199] log likelihood: -5297.775039
EM: Round [200] log likelihood: -5297.773986
EM: Round [201] log likelihood: -5297.772948
EM: Round [202] log likelihood: -5297.771924
EM: Round [203] log likelihood: -5297.770915
EM: Round [204] log likelihood: -5297.769919
EM: Round [205] log likelihood: -5297.768937
EM: Round [206] log likelihood: -5297.767969
EM: Round [207] log likelihood: -5297.767014
EM: Round [208] log likelihood: -5297.766072
EM: Round [209] log likelihood: -5297.765143
EM: Round [210] log likelihood: -5297.764227
EM: Round [211] log likelihood: -5297.763324
EM: Round [212] log likelihood: -5297.762433
EM: Round [213] log likelihood: -5297.761554
EM: Round [214] log likelihood: -5297.760687
EM: Round [215] log likelihood: -5297.759832
EM: Round [216] log likelihood: -5297.758989
EM: Round [217] log likelihood: -5297.758157
EM: Round [218] log likelihood: -5297.757337
EM: Round [219] log likelihood: -5297.756528
EM: Round [220] log likelihood: -5297.755730
EM: Round [221] log likelihood: -5297.754942
EM: Round [222] log likelihood: -5297.754166
EM: Round [223] log likelihood: -5297.753400
EM: Round [224] log likelihood: -5297.752644
EM: Round [225] log likelihood: -5297.751899
EM: Round [226] log likelihood: -5297.751163
EM: Round [227] log likelihood: -5297.750438
EM: Round [228] log likelihood: -5297.749723
EM: Round [229] log likelihood: -5297.749017
EM: Round [230] log likelihood: -5297.748320
EM: Round [231] log likelihood: -5297.747634
EM: Round [232] log likelihood: -5297.746956
EM: Round [233] log likelihood: -5297.746287
EM: Round [234] log likelihood: -5297.745628
EM: Round [235] log likelihood: -5297.744977
EM: Round [236] log likelihood: -5297.744335
EM: Round [237] log likelihood: -5297.743702
EM: Round [238] log likelihood: -5297.743077
EM: Round [239] log likelihood: -5297.742461
EM: Round [240] log likelihood: -5297.741853
EM: Round [241] log likelihood: -5297.741253
EM: Round [242] log likelihood: -5297.740661
EM: Round [243] log likelihood: -5297.740076
EM: Round [244] log likelihood: -5297.739500
EM: Round [245] log likelihood: -5297.738932
EM: Round [246] log likelihood: -5297.738370
EM: Round [247] log likelihood: -5297.737817
EM: Round [248] log likelihood: -5297.737271
EM: Round [249] log likelihood: -5297.736732
EM: Round [250] log likelihood: -5297.736200
EM: Round [251] log likelihood: -5297.735675
EM: Round [252] log likelihood: -5297.735157
EM: Round [253] log likelihood: -5297.734647
EM: Round [254] log likelihood: -5297.734142
EM: Round [255] log likelihood: -5297.733645
EM: Round [256] log likelihood: -5297.733154
EM: Round [257] log likelihood: -5297.732670
EM: Round [258] log likelihood: -5297.732192
EM: Round [259] log likelihood: -5297.731720
EM: Round [260] log likelihood: -5297.731254
EM: Round [261] log likelihood: -5297.730795
EM: Round [262] log likelihood: -5297.730342
EM: Round [263] log likelihood: -5297.729894
EM: Round [264] log likelihood: -5297.729453
EM: Round [265] log likelihood: -5297.729017
EM: Round [266] log likelihood: -5297.728587
EM: Round [267] log likelihood: -5297.728163
EM: Round [268] log likelihood: -5297.727744
EM: Round [269] log likelihood: -5297.727331
EM: Round [270] log likelihood: -5297.726923
EM: Round [271] log likelihood: -5297.726520
EM: Round [272] log likelihood: -5297.726123
EM: Round [273] log likelihood: -5297.725731
EM: Round [274] log likelihood: -5297.725344
EM: Round [275] log likelihood: -5297.724962
EM: Round [276] log likelihood: -5297.724585
EM: Round [277] log likelihood: -5297.724213
EM: Round [278] log likelihood: -5297.723846
EM: Round [279] log likelihood: -5297.723483
EM: Round [280] log likelihood: -5297.723126
EM: Round [281] log likelihood: -5297.722773
EM: Round [282] log likelihood: -5297.722424
EM: Round [283] log likelihood: -5297.722080
EM: Round [284] log likelihood: -5297.721741
EM: Round [285] log likelihood: -5297.721406
EM: Round [286] log likelihood: -5297.721075
EM: Round [287] log likelihood: -5297.720748
EM: Round [288] log likelihood: -5297.720426
EM: Round [289] log likelihood: -5297.720108
EM: Round [290] log likelihood: -5297.719794
EM: Round [291] log likelihood: -5297.719484
EM: Round [292] log likelihood: -5297.719178
EM: Round [293] log likelihood: -5297.718876
EM: Round [294] log likelihood: -5297.718578
EM: Round [295] log likelihood: -5297.718283
EM: Round [296] log likelihood: -5297.717993
EM: Round [297] log likelihood: -5297.717706
EM: Round [298] log likelihood: -5297.717423
EM: Round [299] log likelihood: -5297.717144
EM: Round [300] log likelihood: -5297.716868
EM: Round [301] log likelihood: -5297.716595
EM: Round [302] log likelihood: -5297.716326
EM: Round [303] log likelihood: -5297.716061
EM: Round [304] log likelihood: -5297.715799
EM: Round [305] log likelihood: -5297.715540
EM: Round [306] log likelihood: -5297.715285
EM: Round [307] log likelihood: -5297.715033
EM: Round [308] log likelihood: -5297.714784
EM: Round [309] log likelihood: -5297.714538
EM: Round [310] log likelihood: -5297.714296
EM: Round [311] log likelihood: -5297.714056
EM: Round [312] log likelihood: -5297.713820
EM: Round [313] log likelihood: -5297.713586
EM: Round [314] log likelihood: -5297.713356
EM: Round [315] log likelihood: -5297.713128
EM: Round [316] log likelihood: -5297.712904
EM: Round [317] log likelihood: -5297.712682
EM: Round [318] log likelihood: -5297.712463
EM: Round [319] log likelihood: -5297.712247
EM: Round [320] log likelihood: -5297.712033
EM: Round [321] log likelihood: -5297.711822
EM: Round [322] log likelihood: -5297.711614
EM: Round [323] log likelihood: -5297.711409
EM: Round [324] log likelihood: -5297.711206
EM: Round [325] log likelihood: -5297.711006
EM: Round [326] log likelihood: -5297.710808
EM: Round [327] log likelihood: -5297.710613
EM: Round [328] log likelihood: -5297.710420
EM: Round [329] log likelihood: -5297.710230
EM: Round [330] log likelihood: -5297.710042
EM: Round [331] log likelihood: -5297.709856
EM: Round [332] log likelihood: -5297.709673
EM: Round [333] log likelihood: -5297.709492
EM: Round [334] log likelihood: -5297.709313
EM: Round [335] log likelihood: -5297.709137
EM: Round [336] log likelihood: -5297.708963
EM: Round [337] log likelihood: -5297.708791
EM: Round [338] log likelihood: -5297.708621
EM: Round [339] log likelihood: -5297.708453
EM: Round [340] log likelihood: -5297.708287
EM: Round [341] log likelihood: -5297.708124
EM: Round [342] log likelihood: -5297.707962
EM: Round [343] log likelihood: -5297.707803
EM: Round [344] log likelihood: -5297.707645
EM: Round [345] log likelihood: -5297.707490
EM: Round [346] log likelihood: -5297.707336
EM: Round [347] log likelihood: -5297.707185
EM: Round [348] log likelihood: -5297.707035
EM: Round [349] log likelihood: -5297.706887
EM: Round [350] log likelihood: -5297.706741
EM: Round [351] log likelihood: -5297.706597
EM: Round [352] log likelihood: -5297.706455
EM: Round [353] log likelihood: -5297.706314
EM: Round [354] log likelihood: -5297.706175
EM: Round [355] log likelihood: -5297.706038
EM: Round [356] log likelihood: -5297.705902
EM: Round [357] log likelihood: -5297.705769
EM: Round [358] log likelihood: -5297.705637
EM: Round [359] log likelihood: -5297.705506
EM: Round [360] log likelihood: -5297.705377
EM: Round [361] log likelihood: -5297.705250
EM: Round [362] log likelihood: -5297.705124
EM: Round [363] log likelihood: -5297.705000
EM: Round [364] log likelihood: -5297.704878
EM: Round [365] log likelihood: -5297.704757
EM: Round [366] log likelihood: -5297.704637
EM: Round [367] log likelihood: -5297.704519
EM: Round [368] log likelihood: -5297.704403
EM: Round [369] log likelihood: -5297.704288
EM: Round [370] log likelihood: -5297.704174
EM: Round [371] log likelihood: -5297.704062
EM: Round [372] log likelihood: -5297.703951
EM: Round [373] log likelihood: -5297.703841
EM: Round [374] log likelihood: -5297.703733
EM: Round [375] log likelihood: -5297.703626
EM: Round [376] log likelihood: -5297.703520
EM: Round [377] log likelihood: -5297.703416
EM: Round [378] log likelihood: -5297.703313
EM: Round [379] log likelihood: -5297.703212
EM: Round [380] log likelihood: -5297.703111
EM: Round [381] log likelihood: -5297.703012
EM: Stopping iterations at round 381 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_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.i1B8rRXG8j/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3717.800335
EM: Round [1] log likelihood: -3716.061491
EM: Round [2] log likelihood: -3716.061419
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 295822882
Warning - not locating file: /tmp/nxf.i1B8rRXG8j/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000197585.10]
WARNING, no entry stored in dbm for [ENSG00000197585.10]
WARNING, no entry stored in dbm for [ENSG00000197585.10]
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 [ENSG00000272168.8]
WARNING, no entry stored in dbm for [ENSG00000272168.8]
WARNING, no entry stored in dbm for [ENSG00000272168.8]
ls: cannot access 'IGV_inputs': No such file or directory