Done. -parsing GTF file: /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.JjpTaMw6Cs/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.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' * Running CMD: mv Aligned.sortedByCoord.out.bam 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam 11:46:58 : INFO : Done. -parsing GTF file: /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf -parsing /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_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] 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[4820000] [4830000] [4840000] [4850000] [4860000] [4870000] [4880000] [4890000] [4900000] [4910000] [4920000] [4930000] [4940000] [4950000] [4960000] [4970000] [4980000] [4990000] [5000000] [5010000] [5020000] [5030000] [5040000] [5050000] [5060000] [5070000] [5080000] [5090000] -done parsing /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 6685, 'small anchor length' => 57, 'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 24, 'exons hit < 2' => 14, 'num genes matched < 2' => 27, 'seq-similar region overlap' => 3, 'low complexity anchor region' => 13, 'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 19, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 236, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2940, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 1676, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 796, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 72, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 381, 'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 12, ' ** passed ** ' => 10787, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 2091, 'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 174, 'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 28, 'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 1, 'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 912, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 768, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 750, 'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5, 'per_id < 96' => 39969, 'excessive soft clipping' => 61537, 'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 136, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2048 }; -writing fusion junction support info. -outputting the spanning read info: /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_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] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: ABCC4--RNY4P27 [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: ABCC4--MEMO1P5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -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] 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[2247000] [2248000] [2249000] [2250000] [2251000] [2252000] [2253000] [2254000] [2255000] [2256000] [2257000] [2258000] [2259000] [2260000] [2261000] [2262000] [2263000] [2264000] [2265000] [2266000] [2267000] [2268000] [2269000] [2270000] [2271000] [2272000] [2273000] [2274000] [2275000] [2276000] [2277000] [2278000] [2279000] [2280000] [2281000] [2282000] [2283000] [2284000] [2285000] [2286000] [2287000] [2288000] [2289000] [2290000] [2291000] [2292000] [2293000] [2294000] [2295000] [2296000] [2297000] [2298000] [2299000] [2300000] [2301000] [2302000] [2303000] [2304000] [2305000] [2306000] [2307000] [2308000] [2309000] [2310000] [2311000] [2312000] [2313000] [2314000] [2315000] [2316000] [2317000] [2318000] [2319000] [2320000] [2321000] [2322000] [2323000] [2324000] [2325000] [2326000] [2327000] [2328000] [2329000] [2330000] [2331000] [2332000] [2333000] [2334000] [2335000] [2336000] [2337000] [2338000] [2339000] [2340000] [2341000] [2342000] [2343000] [2344000] [2345000] [2346000] [2347000] [2348000] [2349000] [2350000] [2351000] [2352000] [2353000] [2354000] [2355000] [2356000] -fusion SPANNING read extraction for scaff: AC025884.2--IGH-@-ext [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] -fusion SPANNING read extraction for scaff: AC091132.4--AC091132.1 [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] [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] -fusion SPANNING read extraction for scaff: CCDC198--NPIPB12 [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] -fusion SPANNING read extraction for scaff: GLI3--AF246928.1 [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] -fusion SPANNING read extraction for scaff: GLI3--AJ009632.2 [1000] -fusion SPANNING read extraction for scaff: GTF2A1L--STON1-GTF2A1L [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: GUSBP13--NAIP [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] -fusion SPANNING read extraction for scaff: KIF5B--RET [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [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] -fusion SPANNING read extraction for scaff: MCM3AP--MTRNR2L12 [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: NOLC1--GBF1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -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--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -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] -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] [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] -fusion SPANNING read extraction for scaff: PTPN2--NPIPB12 [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: RITA1--GLT8D2 [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: RPSAP52--HMGA2 [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] -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] [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: TAF4--AC114498.1 [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] -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] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -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] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 38354, 'seq similar region alignment' => 15577 }; EM: Starting log likelihood: -7385.503179 EM: Round [1] log likelihood: -7380.744081 EM: Round [2] log likelihood: -7380.636381 EM: Round [3] log likelihood: -7380.615102 EM: Round [4] log likelihood: -7380.607357 EM: Round [5] log likelihood: -7380.602942 EM: Round [6] log likelihood: -7380.599381 EM: Round [7] log likelihood: -7380.596053 EM: Round [8] log likelihood: -7380.592806 EM: Round [9] log likelihood: -7380.589598 EM: Round [10] log likelihood: -7380.586422 EM: Round [11] log likelihood: -7380.583273 EM: Round [12] log likelihood: -7380.580151 EM: Round [13] log likelihood: -7380.577056 EM: Round [14] log likelihood: -7380.573987 EM: Round [15] log likelihood: -7380.570945 EM: Round [16] log likelihood: -7380.567928 EM: Round [17] log likelihood: -7380.564936 EM: Round [18] log likelihood: -7380.561970 EM: Round [19] log likelihood: -7380.559029 EM: Round [20] log likelihood: -7380.556112 EM: Round [21] log likelihood: -7380.553221 EM: Round [22] log likelihood: -7380.550353 EM: Round [23] log likelihood: -7380.547509 EM: Round [24] log likelihood: -7380.544690 EM: Round [25] log likelihood: -7380.541894 EM: Round [26] log likelihood: -7380.539121 EM: Round [27] log likelihood: -7380.536371 EM: Round [28] log likelihood: -7380.533645 EM: Round [29] log likelihood: -7380.530941 EM: Round [30] log likelihood: -7380.528259 EM: Round [31] log likelihood: -7380.525600 EM: Round [32] log likelihood: -7380.522962 EM: Round [33] log likelihood: -7380.520347 EM: Round [34] log likelihood: -7380.517753 EM: Round [35] log likelihood: -7380.515181 EM: Round [36] log likelihood: -7380.512629 EM: Round [37] log likelihood: -7380.510099 EM: Round [38] log likelihood: -7380.507590 EM: Round [39] log likelihood: -7380.505101 EM: Round [40] log likelihood: -7380.502632 EM: Round [41] log likelihood: -7380.500184 EM: Round [42] log likelihood: -7380.497756 EM: Round [43] log likelihood: -7380.495348 EM: Round [44] log likelihood: -7380.492959 EM: Round [45] log likelihood: -7380.490590 EM: Round [46] log likelihood: -7380.488240 EM: Round [47] log likelihood: -7380.485910 EM: Round [48] log likelihood: -7380.483598 EM: Round [49] log likelihood: -7380.481305 EM: Round [50] log likelihood: -7380.479030 EM: Round [51] log likelihood: -7380.476774 EM: Round [52] log likelihood: -7380.474537 EM: Round [53] log likelihood: -7380.472317 EM: Round [54] log likelihood: -7380.470115 EM: Round [55] log likelihood: -7380.467931 EM: Round [56] log likelihood: -7380.465765 EM: Round [57] log likelihood: -7380.463616 EM: Round [58] log likelihood: -7380.461484 EM: Round [59] log likelihood: -7380.459370 EM: Round [60] log likelihood: -7380.457272 EM: Round [61] log likelihood: -7380.455191 EM: Round [62] log likelihood: -7380.453127 EM: Round [63] log likelihood: -7380.451079 EM: Round [64] log likelihood: -7380.449048 EM: Round [65] log likelihood: -7380.447033 EM: Round [66] log likelihood: -7380.445034 EM: Round [67] log likelihood: -7380.443051 EM: Round [68] log likelihood: -7380.441084 EM: Round [69] log likelihood: -7380.439132 EM: Round [70] log likelihood: -7380.437196 EM: Round [71] log likelihood: -7380.435275 EM: Round [72] log likelihood: -7380.433370 EM: Round [73] log likelihood: -7380.431479 EM: Round [74] log likelihood: -7380.429604 EM: Round [75] log likelihood: -7380.427743 EM: Round [76] log likelihood: -7380.425897 EM: Round [77] log likelihood: -7380.424066 EM: Round [78] log likelihood: -7380.422249 EM: Round [79] log likelihood: -7380.420446 EM: Round [80] log likelihood: -7380.418658 EM: Round [81] log likelihood: -7380.416883 EM: Round [82] log likelihood: -7380.415123 EM: Round [83] log likelihood: -7380.413376 EM: Round [84] log likelihood: -7380.411643 EM: Round [85] log likelihood: -7380.409924 EM: Round [86] log likelihood: -7380.408218 EM: Round [87] log likelihood: -7380.406525 EM: Round [88] log likelihood: -7380.404846 EM: Round [89] log likelihood: -7380.403180 EM: Round [90] log likelihood: -7380.401527 EM: Round [91] log likelihood: -7380.399886 EM: Round [92] log likelihood: -7380.398259 EM: Round [93] log likelihood: -7380.396644 EM: Round [94] log likelihood: -7380.395042 EM: Round [95] log likelihood: -7380.393452 EM: Round [96] log likelihood: -7380.391874 EM: Round [97] log likelihood: -7380.390309 EM: Round [98] log likelihood: -7380.388756 EM: Round [99] log likelihood: -7380.387215 EM: Round [100] log likelihood: -7380.385686 EM: Round [101] log likelihood: -7380.384168 EM: Round [102] log likelihood: -7380.382663 EM: Round [103] log likelihood: -7380.381169 EM: Round [104] log likelihood: -7380.379686 EM: Round [105] log likelihood: -7380.378215 EM: Round [106] log likelihood: -7380.376756 EM: Round [107] log likelihood: -7380.375307 EM: Round [108] log likelihood: -7380.373870 EM: Round [109] log likelihood: -7380.372444 EM: Round [110] log likelihood: -7380.371029 EM: Round [111] log likelihood: -7380.369624 EM: Round [112] log likelihood: -7380.368231 EM: Round [113] log likelihood: -7380.366848 EM: Round [114] log likelihood: -7380.365476 EM: Round [115] log likelihood: -7380.364114 EM: Round [116] log likelihood: -7380.362763 EM: Round [117] log likelihood: -7380.361422 EM: Round [118] log likelihood: -7380.360091 EM: Round [119] log likelihood: -7380.358770 EM: Round [120] log likelihood: -7380.357460 EM: Round [121] log likelihood: -7380.356159 EM: Round [122] log likelihood: -7380.354869 EM: Round [123] log likelihood: -7380.353588 EM: Round [124] log likelihood: -7380.352317 EM: Round [125] log likelihood: -7380.351056 EM: Round [126] log likelihood: -7380.349804 EM: Round [127] log likelihood: -7380.348562 EM: Round [128] log likelihood: -7380.347329 EM: Round [129] log likelihood: -7380.346106 EM: Round [130] log likelihood: -7380.344892 EM: Round [131] log likelihood: -7380.343687 EM: Round [132] log likelihood: -7380.342491 EM: Round [133] log likelihood: -7380.341304 EM: Round [134] log likelihood: -7380.340126 EM: Round [135] log likelihood: -7380.338958 EM: Round [136] log likelihood: -7380.337798 EM: Round [137] log likelihood: -7380.336646 EM: Round [138] log likelihood: -7380.335504 EM: Round [139] log likelihood: -7380.334370 EM: Round [140] log likelihood: -7380.333245 EM: Round [141] log likelihood: -7380.332128 EM: Round [142] log likelihood: -7380.331019 EM: Round [143] log likelihood: -7380.329919 EM: Round [144] log likelihood: -7380.328828 EM: Round [145] log likelihood: -7380.327744 EM: Round [146] log likelihood: -7380.326668 EM: Round [147] log likelihood: -7380.325601 EM: Round [148] log likelihood: -7380.324542 EM: Round [149] log likelihood: -7380.323490 EM: Round [150] log likelihood: -7380.322447 EM: Round [151] log likelihood: -7380.321411 EM: Round [152] log likelihood: -7380.320383 EM: Round [153] log likelihood: -7380.319363 EM: Round [154] log likelihood: -7380.318351 EM: Round [155] log likelihood: -7380.317346 EM: Round [156] log likelihood: -7380.316348 EM: Round [157] log likelihood: -7380.315358 EM: Round [158] log likelihood: -7380.314376 EM: Round [159] log likelihood: -7380.313400 EM: Round [160] log likelihood: -7380.312432 EM: Round [161] log likelihood: -7380.311472 EM: Round [162] log likelihood: -7380.310518 EM: Round [163] log likelihood: -7380.309572 EM: Round [164] log likelihood: -7380.308632 EM: Round [165] log likelihood: -7380.307700 EM: Round [166] log likelihood: -7380.306774 EM: Round [167] log likelihood: -7380.305856 EM: Round [168] log likelihood: -7380.304944 EM: Round [169] log likelihood: -7380.304039 EM: Round [170] log likelihood: -7380.303141 EM: Round [171] log likelihood: -7380.302249 EM: Round [172] log likelihood: -7380.301364 EM: Round [173] log likelihood: -7380.300486 EM: Round [174] log likelihood: -7380.299614 EM: Round [175] log likelihood: -7380.298749 EM: Round [176] log likelihood: -7380.297890 EM: Round [177] log likelihood: -7380.297037 EM: Round [178] log likelihood: -7380.296191 EM: Round [179] log likelihood: -7380.295351 EM: Round [180] log likelihood: -7380.294517 EM: Round [181] log likelihood: -7380.293690 EM: Round [182] log likelihood: -7380.292868 EM: Round [183] log likelihood: -7380.292053 EM: Round [184] log likelihood: -7380.291243 EM: Round [185] log likelihood: -7380.290440 EM: Round [186] log likelihood: -7380.289642 EM: Round [187] log likelihood: -7380.288851 EM: Round [188] log likelihood: -7380.288065 EM: Round [189] log likelihood: -7380.287285 EM: Round [190] log likelihood: -7380.286511 EM: Round [191] log likelihood: -7380.285742 EM: Round [192] log likelihood: -7380.284979 EM: Round [193] log likelihood: -7380.284222 EM: Round [194] log likelihood: -7380.283471 EM: Round [195] log likelihood: -7380.282724 EM: Round [196] log likelihood: -7380.281984 EM: Round [197] log likelihood: -7380.281249 EM: Round [198] log likelihood: -7380.280519 EM: Round [199] log likelihood: -7380.279794 EM: Round [200] log likelihood: -7380.279075 EM: Round [201] log likelihood: -7380.278362 EM: Round [202] log likelihood: -7380.277653 EM: Round [203] log likelihood: -7380.276950 EM: Round [204] log likelihood: -7380.276251 EM: Round [205] log likelihood: -7380.275558 EM: Round [206] log likelihood: -7380.274870 EM: Round [207] log likelihood: -7380.274187 EM: Round [208] log likelihood: -7380.273509 EM: Round [209] log likelihood: -7380.272836 EM: Round [210] log likelihood: -7380.272168 EM: Round [211] log likelihood: -7380.271505 EM: Round [212] log likelihood: -7380.270847 EM: Round [213] log likelihood: -7380.270193 EM: Round [214] log likelihood: -7380.269544 EM: Round [215] log likelihood: -7380.268900 EM: Round [216] log likelihood: -7380.268261 EM: Round [217] log likelihood: -7380.267626 EM: Round [218] log likelihood: -7380.266996 EM: Round [219] log likelihood: -7380.266371 EM: Round [220] log likelihood: -7380.265750 EM: Round [221] log likelihood: -7380.265134 EM: Round [222] log likelihood: -7380.264522 EM: Round [223] log likelihood: -7380.263915 EM: Round [224] log likelihood: -7380.263312 EM: Round [225] log likelihood: -7380.262713 EM: Round [226] log likelihood: -7380.262119 EM: Round [227] log likelihood: -7380.261529 EM: Round [228] log likelihood: -7380.260944 EM: Round [229] log likelihood: -7380.260363 EM: Round [230] log likelihood: -7380.259785 EM: Round [231] log likelihood: -7380.259213 EM: Round [232] log likelihood: -7380.258644 EM: Round [233] log likelihood: -7380.258079 EM: Round [234] log likelihood: -7380.257519 EM: Round [235] log likelihood: -7380.256963 EM: Round [236] log likelihood: -7380.256410 EM: Round [237] log likelihood: -7380.255862 EM: Round [238] log likelihood: -7380.255318 EM: Round [239] log likelihood: -7380.254777 EM: Round [240] log likelihood: -7380.254241 EM: Round [241] log likelihood: -7380.253708 EM: Round [242] log likelihood: -7380.253179 EM: Round [243] log likelihood: -7380.252655 EM: Round [244] log likelihood: -7380.252133 EM: Round [245] log likelihood: -7380.251616 EM: Round [246] log likelihood: -7380.251103 EM: Round [247] log likelihood: -7380.250593 EM: Round [248] log likelihood: -7380.250087 EM: Round [249] log likelihood: -7380.249584 EM: Round [250] log likelihood: -7380.249085 EM: Round [251] log likelihood: -7380.248590 EM: Round [252] log likelihood: -7380.248098 EM: Round [253] log likelihood: -7380.247610 EM: Round [254] log likelihood: -7380.247126 EM: Round [255] log likelihood: -7380.246645 EM: Round [256] log likelihood: -7380.246167 EM: Round [257] log likelihood: -7380.245693 EM: Round [258] log likelihood: -7380.245222 EM: Round [259] log likelihood: -7380.244755 EM: Round [260] log likelihood: -7380.244291 EM: Round [261] log likelihood: -7380.243830 EM: Round [262] log likelihood: -7380.243373 EM: Round [263] log likelihood: -7380.242919 EM: Round [264] log likelihood: -7380.242469 EM: Round [265] log likelihood: -7380.242021 EM: Round [266] log likelihood: -7380.241577 EM: Round [267] log likelihood: -7380.241136 EM: Round [268] log likelihood: -7380.240698 EM: Round [269] log likelihood: -7380.240263 EM: Round [270] log likelihood: -7380.239832 EM: Round [271] log likelihood: -7380.239403 EM: Round [272] log likelihood: -7380.238978 EM: Round [273] log likelihood: -7380.238556 EM: Round [274] log likelihood: -7380.238137 EM: Round [275] log likelihood: -7380.237720 EM: Round [276] log likelihood: -7380.237307 EM: Round [277] log likelihood: -7380.236897 EM: Round [278] log likelihood: -7380.236489 EM: Round [279] log likelihood: -7380.236085 EM: Round [280] log likelihood: -7380.235684 EM: Round [281] log likelihood: -7380.235285 EM: Round [282] log likelihood: -7380.234889 EM: Round [283] log likelihood: -7380.234496 EM: Round [284] log likelihood: -7380.234106 EM: Round [285] log likelihood: -7380.233719 EM: Round [286] log likelihood: -7380.233335 EM: Round [287] log likelihood: -7380.232953 EM: Round [288] log likelihood: -7380.232574 EM: Round [289] log likelihood: -7380.232198 EM: Round [290] log likelihood: -7380.231824 EM: Round [291] log likelihood: -7380.231453 EM: Round [292] log likelihood: -7380.231085 EM: Round [293] log likelihood: -7380.230720 EM: Round [294] log likelihood: -7380.230357 EM: Round [295] log likelihood: -7380.229996 EM: Round [296] log likelihood: -7380.229638 EM: Round [297] log likelihood: -7380.229283 EM: Round [298] log likelihood: -7380.228931 EM: Round [299] log likelihood: -7380.228581 EM: Round [300] log likelihood: -7380.228233 EM: Round [301] log likelihood: -7380.227888 EM: Round [302] log likelihood: -7380.227545 EM: Round [303] log likelihood: -7380.227205 EM: Round [304] log likelihood: -7380.226867 EM: Round [305] log likelihood: -7380.226532 EM: Round [306] log likelihood: -7380.226199 EM: Round [307] log likelihood: -7380.225868 EM: Round [308] log likelihood: -7380.225540 EM: Round [309] log likelihood: -7380.225214 EM: Round [310] log likelihood: -7380.224891 EM: Round [311] log likelihood: -7380.224570 EM: Round [312] log likelihood: -7380.224251 EM: Round [313] log likelihood: -7380.223934 EM: Round [314] log likelihood: -7380.223620 EM: Round [315] log likelihood: -7380.223307 EM: Round [316] log likelihood: -7380.222998 EM: Round [317] log likelihood: -7380.222690 EM: Round [318] log likelihood: -7380.222384 EM: Round [319] log likelihood: -7380.222081 EM: Round [320] log likelihood: -7380.221780 EM: Round [321] log likelihood: -7380.221481 EM: Round [322] log likelihood: -7380.221184 EM: Round [323] log likelihood: -7380.220889 EM: Round [324] log likelihood: -7380.220597 EM: Round [325] log likelihood: -7380.220306 EM: Round [326] log likelihood: -7380.220018 EM: Round [327] log likelihood: -7380.219731 EM: Round [328] log likelihood: -7380.219447 EM: Round [329] log likelihood: -7380.219165 EM: Round [330] log likelihood: -7380.218884 EM: Round [331] log likelihood: -7380.218606 EM: Round [332] log likelihood: -7380.218330 EM: Round [333] log likelihood: -7380.218055 EM: Round [334] log likelihood: -7380.217783 EM: Round [335] log likelihood: -7380.217512 EM: Round [336] log likelihood: -7380.217244 EM: Round [337] log likelihood: -7380.216977 EM: Round [338] log likelihood: -7380.216712 EM: Round [339] log likelihood: -7380.216450 EM: Round [340] log likelihood: -7380.216189 EM: Round [341] log likelihood: -7380.215930 EM: Round [342] log likelihood: -7380.215672 EM: Round [343] log likelihood: -7380.215417 EM: Round [344] log likelihood: -7380.215163 EM: Round [345] log likelihood: -7380.214911 EM: Round [346] log likelihood: -7380.214661 EM: Round [347] log likelihood: -7380.214413 EM: Round [348] log likelihood: -7380.214167 EM: Round [349] log likelihood: -7380.213922 EM: Round [350] log likelihood: -7380.213679 EM: Round [351] log likelihood: -7380.213438 EM: Round [352] log likelihood: -7380.213198 EM: Round [353] log likelihood: -7380.212960 EM: Round [354] log likelihood: -7380.212724 EM: Round [355] log likelihood: -7380.212490 EM: Round [356] log likelihood: -7380.212257 EM: Round [357] log likelihood: -7380.212026 EM: Round [358] log likelihood: -7380.211796 EM: Round [359] log likelihood: -7380.211568 EM: Round [360] log likelihood: -7380.211342 EM: Round [361] log likelihood: -7380.211117 EM: Round [362] log likelihood: -7380.210894 EM: Round [363] log likelihood: -7380.210673 EM: Round [364] log likelihood: -7380.210453 EM: Round [365] log likelihood: -7380.210235 EM: Round [366] log likelihood: -7380.210018 EM: Round [367] log likelihood: -7380.209802 EM: Round [368] log likelihood: -7380.209589 EM: Round [369] log likelihood: -7380.209377 EM: Round [370] log likelihood: -7380.209166 EM: Round [371] log likelihood: -7380.208957 EM: Round [372] log likelihood: -7380.208749 EM: Round [373] log likelihood: -7380.208543 EM: Round [374] log likelihood: -7380.208338 EM: Round [375] log likelihood: -7380.208135 EM: Round [376] log likelihood: -7380.207933 EM: Round [377] log likelihood: -7380.207732 EM: Round [378] log likelihood: -7380.207533 EM: Round [379] log likelihood: -7380.207336 EM: Round [380] log likelihood: -7380.207139 EM: Round [381] log likelihood: -7380.206945 EM: Round [382] log likelihood: -7380.206751 EM: Round [383] log likelihood: -7380.206559 EM: Round [384] log likelihood: -7380.206368 EM: Round [385] log likelihood: -7380.206179 EM: Round [386] log likelihood: -7380.205991 EM: Round [387] log likelihood: -7380.205804 EM: Round [388] log likelihood: -7380.205619 EM: Round [389] log likelihood: -7380.205435 EM: Round [390] log likelihood: -7380.205252 EM: Round [391] log likelihood: -7380.205071 EM: Round [392] log likelihood: -7380.204890 EM: Round [393] log likelihood: -7380.204711 EM: Round [394] log likelihood: -7380.204534 EM: Round [395] log likelihood: -7380.204357 EM: Round [396] log likelihood: -7380.204182 EM: Round [397] log likelihood: -7380.204008 EM: Round [398] log likelihood: -7380.203836 EM: Round [399] log likelihood: -7380.203664 EM: Round [400] log likelihood: -7380.203494 EM: Round [401] log likelihood: -7380.203325 EM: Round [402] log likelihood: -7380.203157 EM: Round [403] log likelihood: -7380.202991 EM: Round [404] log likelihood: -7380.202825 EM: Round [405] log likelihood: -7380.202661 EM: Round [406] log likelihood: -7380.202498 EM: Round [407] log likelihood: -7380.202336 EM: Round [408] log likelihood: -7380.202175 EM: Round [409] log likelihood: -7380.202015 EM: Round [410] log likelihood: -7380.201857 EM: Round [411] log likelihood: -7380.201699 EM: Round [412] log likelihood: -7380.201543 EM: Round [413] log likelihood: -7380.201388 EM: Round [414] log likelihood: -7380.201234 EM: Round [415] log likelihood: -7380.201081 EM: Round [416] log likelihood: -7380.200929 EM: Round [417] log likelihood: -7380.200778 EM: Round [418] log likelihood: -7380.200628 EM: Round [419] log likelihood: -7380.200479 EM: Round [420] log likelihood: -7380.200331 EM: Round [421] log likelihood: -7380.200185 EM: Round [422] log likelihood: -7380.200039 EM: Round [423] log likelihood: -7380.199895 EM: Round [424] log likelihood: -7380.199751 EM: Round [425] log likelihood: -7380.199608 EM: Round [426] log likelihood: -7380.199467 EM: Round [427] log likelihood: -7380.199326 EM: Round [428] log likelihood: -7380.199187 EM: Round [429] log likelihood: -7380.199048 EM: Round [430] log likelihood: -7380.198911 EM: Round [431] log likelihood: -7380.198774 EM: Round [432] log likelihood: -7380.198638 EM: Round [433] log likelihood: -7380.198504 EM: Round [434] log likelihood: -7380.198370 EM: Round [435] log likelihood: -7380.198237 EM: Round [436] log likelihood: -7380.198105 EM: Round [437] log likelihood: -7380.197974 EM: Round [438] log likelihood: -7380.197844 EM: Round [439] log likelihood: -7380.197715 EM: Round [440] log likelihood: -7380.197587 EM: Round [441] log likelihood: -7380.197460 EM: Round [442] log likelihood: -7380.197333 EM: Round [443] log likelihood: -7380.197208 EM: Round [444] log likelihood: -7380.197083 EM: Round [445] log likelihood: -7380.196959 EM: Round [446] log likelihood: -7380.196837 EM: Round [447] log likelihood: -7380.196715 EM: Round [448] log likelihood: -7380.196594 EM: Round [449] log likelihood: -7380.196473 EM: Round [450] log likelihood: -7380.196354 EM: Round [451] log likelihood: -7380.196235 EM: Round [452] log likelihood: -7380.196117 EM: Round [453] log likelihood: -7380.196001 EM: Round [454] log likelihood: -7380.195884 EM: Round [455] log likelihood: -7380.195769 EM: Round [456] log likelihood: -7380.195655 EM: Round [457] log likelihood: -7380.195541 EM: Round [458] log likelihood: -7380.195428 EM: Round [459] log likelihood: -7380.195316 EM: Round [460] log likelihood: -7380.195205 EM: Round [461] log likelihood: -7380.195094 EM: Round [462] log likelihood: -7380.194985 EM: Round [463] log likelihood: -7380.194876 EM: Round [464] log likelihood: -7380.194768 EM: Round [465] log likelihood: -7380.194660 EM: Round [466] log likelihood: -7380.194554 EM: Round [467] log likelihood: -7380.194448 EM: Round [468] log likelihood: -7380.194343 EM: Round [469] log likelihood: -7380.194238 EM: Round [470] log likelihood: -7380.194134 EM: Round [471] log likelihood: -7380.194031 EM: Round [472] log likelihood: -7380.193929 EM: Round [473] log likelihood: -7380.193828 EM: Round [474] log likelihood: -7380.193727 EM: Round [475] log likelihood: -7380.193627 EM: Round [476] log likelihood: -7380.193528 EM: Stopping iterations at round 476 due to insufficient improvement in likelihood. [bam_sort_core] merging from 0 files and 8 in-memory blocks... -extracting read coordinates from /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_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.JjpTaMw6Cs/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter -done, see /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass EM: Starting log likelihood: -6939.091937 EM: Round [1] log likelihood: -6937.222830 EM: Round [2] log likelihood: -6937.204570 EM: Round [3] log likelihood: -6937.204430 EM: Round [4] log likelihood: -6937.204429 EM: Stopping iterations at round 4 due to insufficient improvement in likelihood. -total frags in /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295586759 Warning - not locating file: /tmp/nxf.JjpTaMw6Cs/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000198237.8] 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] WARNING, no entry stored in dbm for [ENSG00000286030.2] 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 [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] 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 [ENSG00000235146.2] WARNING, no entry stored in dbm for [ENSG00000267198.1] WARNING, no entry stored in dbm for [ENSG00000131484.4] WARNING, no entry stored in dbm for [ENSG00000241749.4] WARNING, no entry stored in dbm for [ENSG00000241749.4] WARNING, no entry stored in dbm for [ENSG00000068781.21] ls: cannot access 'IGV_inputs': No such file or directory