09:03:38 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [200000], rate=12000000.00/min [210000], rate=12600000.00/min [220000], rate=13200000.00/min [230000], rate=13800000.00/min [240000], rate=14400000.00/min [250000], rate=15000000.00/min [260000], rate=15600000.00/min [270000], rate=16200000.00/min [280000], rate=16800000.00/min [290000], rate=17400000.00/min [300000], rate=18000000.00/min [310000], rate=18600000.00/min [320000], rate=19200000.00/min [330000], rate=19800000.00/min [340000], rate=20400000.00/min [350000], rate=21000000.00/min [360000], rate=21600000.00/min [370000], rate=22200000.00/min [380000], rate=22800000.00/min [390000], rate=23400000.00/min [400000], rate=24000000.00/min [410000], rate=24600000.00/min [420000], rate=25200000.00/min [430000], rate=25800000.00/min [440000], rate=26400000.00/min [450000], rate=27000000.00/min [460000], rate=27600000.00/min [470000], rate=28200000.00/min [480000], rate=28800000.00/min [490000], rate=29400000.00/min [500000], rate=15000000.00/min [510000], rate=15300000.00/min [520000], rate=15600000.00/min [530000], rate=15900000.00/min [540000], rate=16200000.00/min [550000], rate=16500000.00/min [560000], rate=16800000.00/min [570000], rate=17100000.00/min [580000], rate=17400000.00/min [590000], rate=17700000.00/min [600000], rate=18000000.00/min [610000], rate=18300000.00/min [620000], rate=18600000.00/min [630000], rate=18900000.00/min [640000], rate=19200000.00/min [650000], rate=19500000.00/min [660000], rate=19800000.00/min [670000], rate=20100000.00/min [680000], rate=20400000.00/min [690000], rate=20700000.00/min [700000], rate=21000000.00/min [710000], rate=21300000.00/min [720000], rate=21600000.00/min [730000], rate=21900000.00/min [740000], rate=22200000.00/min [750000], rate=22500000.00/min [760000], rate=22800000.00/min [770000], rate=23100000.00/min [780000], rate=23400000.00/min [790000], rate=15800000.00/min [800000], rate=16000000.00/min [810000], rate=16200000.00/min [820000], rate=16400000.00/min [830000], rate=16600000.00/min [840000], rate=16800000.00/min [850000], rate=17000000.00/min [860000], rate=17200000.00/min [870000], rate=17400000.00/min [880000], rate=17600000.00/min [890000], rate=17800000.00/min [900000], rate=18000000.00/min [910000], rate=18200000.00/min [920000], rate=18400000.00/min [930000], rate=18600000.00/min [940000], rate=18800000.00/min [950000], rate=19000000.00/min [960000], rate=19200000.00/min [970000], rate=19400000.00/min [980000], rate=19600000.00/min [990000], rate=19800000.00/min [1000000], rate=20000000.00/min [1010000], rate=20200000.00/min [1020000], rate=20400000.00/min [1030000], rate=20600000.00/min [1040000], rate=20800000.00/min [1050000], rate=21000000.00/min [1060000], rate=21200000.00/min [1070000], rate=16050000.00/min [1080000], rate=16200000.00/min [1090000], rate=16350000.00/min [1100000], rate=16500000.00/min [1110000], rate=16650000.00/min [1120000], rate=16800000.00/min [1130000], rate=16950000.00/min [1140000], rate=17100000.00/min [1150000], rate=17250000.00/min [1160000], rate=17400000.00/min [1170000], rate=17550000.00/min [1180000], rate=17700000.00/min [1190000], rate=17850000.00/min [1200000], rate=18000000.00/min [1210000], rate=18150000.00/min [1220000], rate=18300000.00/min [1230000], rate=18450000.00/min [1240000], rate=18600000.00/min [1250000], rate=18750000.00/min [1260000], rate=18900000.00/min [1270000], rate=19050000.00/min [1280000], rate=19200000.00/min [1290000], rate=19350000.00/min [1300000], rate=19500000.00/min [1310000], rate=19650000.00/min [1320000], rate=19800000.00/min [1330000], rate=19950000.00/min [1340000], rate=20100000.00/min [1350000], rate=20250000.00/min [1360000], rate=16320000.00/min [1370000], rate=16440000.00/min [1380000], rate=16560000.00/min [1390000], rate=16680000.00/min [1400000], rate=16800000.00/min [1410000], rate=16920000.00/min [1420000], rate=17040000.00/min [1430000], rate=17160000.00/min [1440000], rate=17280000.00/min [1450000], rate=17400000.00/min [1460000], rate=17520000.00/min [1470000], rate=17640000.00/min [1480000], rate=17760000.00/min [1490000], rate=17880000.00/min [1500000], rate=18000000.00/min [1510000], rate=18120000.00/min [1520000], rate=18240000.00/min [1530000], rate=18360000.00/min [1540000], rate=18480000.00/min [1550000], rate=18600000.00/min [1560000], rate=18720000.00/min [1570000], rate=18840000.00/min [1580000], rate=18960000.00/min [1590000], rate=19080000.00/min [1600000], rate=19200000.00/min [1610000], rate=16100000.00/min [1620000], rate=16200000.00/min [1630000], rate=16300000.00/min [1640000], rate=16400000.00/min [1650000], rate=16500000.00/min [1660000], rate=16600000.00/min [1670000], rate=16700000.00/min [1680000], rate=16800000.00/min [1690000], rate=16900000.00/min [1700000], rate=17000000.00/min [1710000], rate=17100000.00/min [1720000], rate=17200000.00/min [1730000], rate=17300000.00/min [1740000], rate=17400000.00/min [1750000], rate=17500000.00/min [1760000], rate=17600000.00/min [1770000], rate=15171428.57/min [1780000], rate=15257142.86/min [1790000], rate=15342857.14/min [1800000], rate=15428571.43/min [1810000], rate=15514285.71/min [1820000], rate=15600000.00/min [1830000], rate=15685714.29/min [1840000], rate=15771428.57/min [1850000], rate=15857142.86/min [1860000], rate=15942857.14/min [1870000], rate=16028571.43/min [1880000], rate=16114285.71/min [1890000], rate=16200000.00/min [1900000], rate=16285714.29/min [1910000], rate=16371428.57/min [1920000], rate=16457142.86/min [1930000], rate=16542857.14/min [1940000], rate=16628571.43/min [1950000], rate=16714285.71/min [1960000], rate=14700000.00/min [1970000], rate=14775000.00/min [1980000], rate=14850000.00/min [1990000], rate=14925000.00/min [2000000], rate=15000000.00/min [2010000], rate=15075000.00/min [2020000], rate=15150000.00/min [2030000], rate=15225000.00/min [2040000], rate=15300000.00/min [2050000], rate=15375000.00/min [2060000], rate=15450000.00/min [2070000], rate=15525000.00/min [2080000], rate=15600000.00/min [2090000], rate=15675000.00/min [2100000], rate=15750000.00/min [2110000], rate=15825000.00/min [2120000], rate=14133333.33/min [2130000], rate=14200000.00/min [2140000], rate=14266666.67/min [2150000], rate=14333333.33/min [2160000], rate=14400000.00/min [2170000], rate=14466666.67/min [2180000], rate=14533333.33/min [2190000], rate=14600000.00/min [2200000], rate=14666666.67/min [2210000], rate=14733333.33/min [2220000], rate=14800000.00/min [2230000], rate=14866666.67/min [2240000], rate=14933333.33/min [2250000], rate=15000000.00/min [2260000], rate=15066666.67/min [2270000], rate=15133333.33/min [2280000], rate=15200000.00/min [2290000], rate=15266666.67/min [2300000], rate=15333333.33/min [2310000], rate=15400000.00/min [2320000], rate=15466666.67/min [2330000], rate=15533333.33/min [2340000], rate=15600000.00/min [2350000], rate=15666666.67/min [2360000], rate=15733333.33/min [2370000], rate=15800000.00/min [2380000], rate=14280000.00/min [2390000], rate=14340000.00/min [2400000], rate=14400000.00/min [2410000], rate=14460000.00/min [2420000], rate=14520000.00/min [2430000], rate=14580000.00/min [2440000], rate=14640000.00/min [2450000], rate=14700000.00/min [2460000], rate=14760000.00/min [2470000], rate=14820000.00/min [2480000], rate=14880000.00/min [2490000], rate=14940000.00/min [2500000], rate=15000000.00/min [2510000], rate=15060000.00/min [2520000], rate=15120000.00/min [2530000], rate=15180000.00/min [2540000], rate=15240000.00/min [2550000], rate=15300000.00/min [2560000], rate=15360000.00/min [2570000], rate=15420000.00/min [2580000], rate=15480000.00/min [2590000], rate=15540000.00/min [2600000], rate=15600000.00/min [2610000], rate=15660000.00/min [2620000], rate=15720000.00/min [2630000], rate=15780000.00/min [2640000], rate=14400000.00/min [2650000], rate=14454545.45/min [2660000], rate=14509090.91/min [2670000], rate=14563636.36/min [2680000], rate=14618181.82/min [2690000], rate=14672727.27/min [2700000], rate=14727272.73/min [2710000], rate=14781818.18/min [2720000], rate=14836363.64/min [2730000], rate=14890909.09/min [2740000], rate=14945454.55/min [2750000], rate=15000000.00/min [2760000], rate=15054545.45/min [2770000], rate=15109090.91/min [2780000], rate=15163636.36/min [2790000], rate=15218181.82/min [2800000], rate=15272727.27/min [2810000], rate=15327272.73/min [2820000], rate=15381818.18/min [2830000], rate=15436363.64/min [2840000], rate=15490909.09/min [2850000], rate=15545454.55/min [2860000], rate=15600000.00/min [2870000], rate=14350000.00/min [2880000], rate=14400000.00/min [2890000], rate=14450000.00/min [2900000], rate=14500000.00/min [2910000], rate=14550000.00/min [2920000], rate=14600000.00/min [2930000], rate=14650000.00/min [2940000], rate=14700000.00/min [2950000], rate=14750000.00/min [2960000], rate=14800000.00/min [2970000], rate=14850000.00/min [2980000], rate=14900000.00/min [2990000], rate=14950000.00/min [3000000], rate=15000000.00/min [3010000], rate=15050000.00/min [3020000], rate=15100000.00/min [3030000], rate=15150000.00/min [3040000], rate=14030769.23/min [3050000], rate=14076923.08/min [3060000], rate=14123076.92/min [3070000], rate=14169230.77/min [3080000], rate=14215384.62/min [3090000], rate=14261538.46/min [3100000], rate=14307692.31/min [3110000], rate=14353846.15/min [3120000], rate=14400000.00/min [3130000], rate=14446153.85/min [3140000], rate=14492307.69/min [3150000], rate=14538461.54/min [3160000], rate=14584615.38/min [3170000], rate=14630769.23/min [3180000], rate=14676923.08/min [3190000], rate=14723076.92/min [3200000], rate=14769230.77/min [3210000], rate=13757142.86/min [3220000], rate=13800000.00/min [3230000], rate=13842857.14/min [3240000], rate=13885714.29/min [3250000], rate=13928571.43/min [3260000], rate=13971428.57/min [3270000], rate=14014285.71/min [3280000], rate=14057142.86/min [3290000], rate=14100000.00/min [3300000], rate=14142857.14/min [3310000], rate=14185714.29/min [3320000], rate=14228571.43/min [3330000], rate=14271428.57/min [3340000], rate=14314285.71/min [3350000], rate=14357142.86/min [3360000], rate=14400000.00/min [3370000], rate=14442857.14/min [3380000], rate=14485714.29/min [3390000], rate=13560000.00/min [3400000], rate=13600000.00/min [3410000], rate=13640000.00/min [3420000], rate=13680000.00/min [3430000], rate=13720000.00/min [3440000], rate=13760000.00/min [3450000], rate=13800000.00/min [3460000], rate=13840000.00/min [3470000], rate=13880000.00/min [3480000], rate=13920000.00/min [3490000], rate=13960000.00/min [3500000], rate=14000000.00/min [3510000], rate=14040000.00/min [3520000], rate=14080000.00/min [3530000], rate=14120000.00/min [3540000], rate=13275000.00/min [3550000], rate=13312500.00/min [3560000], rate=13350000.00/min [3570000], rate=13387500.00/min [3580000], rate=13425000.00/min [3590000], rate=13462500.00/min [3600000], rate=13500000.00/min [3610000], rate=13537500.00/min [3620000], rate=13575000.00/min [3630000], rate=13612500.00/min [3640000], rate=13650000.00/min [3650000], rate=13687500.00/min [3660000], rate=13725000.00/min [3670000], rate=12952941.18/min [3680000], rate=12988235.29/min [3690000], rate=13023529.41/min [3700000], rate=13058823.53/min [3710000], rate=13094117.65/min [3720000], rate=13129411.76/min [3730000], rate=13164705.88/min [3740000], rate=13200000.00/min [3750000], rate=13235294.12/min [3760000], rate=13270588.24/min [3770000], rate=13305882.35/min [3780000], rate=13341176.47/min [3790000], rate=13376470.59/min [3800000], rate=13411764.71/min [3810000], rate=13447058.82/min [3820000], rate=13482352.94/min [3830000], rate=13517647.06/min [3840000], rate=13552941.18/min [3850000], rate=13588235.29/min [3860000], rate=13623529.41/min [3870000], rate=13658823.53/min [3880000], rate=13694117.65/min [3890000], rate=13729411.76/min [3900000], rate=13764705.88/min [3910000], rate=13800000.00/min [3920000], rate=13835294.12/min [3930000], rate=13100000.00/min [3940000], rate=13133333.33/min [3950000], rate=13166666.67/min [3960000], rate=13200000.00/min [3970000], rate=13233333.33/min [3980000], rate=13266666.67/min [3990000], rate=13300000.00/min [4000000], rate=13333333.33/min [4010000], rate=13366666.67/min [4020000], rate=13400000.00/min [4030000], rate=13433333.33/min [4040000], rate=13466666.67/min [4050000], rate=13500000.00/min [4060000], rate=13533333.33/min [4070000], rate=13566666.67/min [4080000], rate=13600000.00/min [4090000], rate=13633333.33/min [4100000], rate=13666666.67/min [4110000], rate=13700000.00/min [4120000], rate=13733333.33/min [4130000], rate=13766666.67/min [4140000], rate=13800000.00/min [4150000], rate=13833333.33/min [4160000], rate=13866666.67/min [4170000], rate=13900000.00/min [4180000], rate=13933333.33/min [4190000], rate=13966666.67/min [4200000], rate=14000000.00/min [4210000], rate=13294736.84/min [4220000], rate=13326315.79/min [4230000], rate=13357894.74/min [4240000], rate=13389473.68/min [4250000], rate=13421052.63/min [4260000], rate=13452631.58/min [4270000], rate=13484210.53/min [4280000], rate=13515789.47/min [4290000], rate=13547368.42/min [4300000], rate=13578947.37/min [4310000], rate=13610526.32/min [4320000], rate=13642105.26/min [4330000], rate=13673684.21/min [4340000], rate=13705263.16/min [4350000], rate=13736842.11/min [4360000], rate=13768421.05/min [4370000], rate=13800000.00/min [4380000], rate=13140000.00/min [4390000], rate=13170000.00/min [4400000], rate=13200000.00/min [4410000], rate=13230000.00/min [4420000], rate=13260000.00/min [4430000], rate=13290000.00/min [4440000], rate=13320000.00/min [4450000], rate=13350000.00/min [4460000], rate=13380000.00/min [4470000], rate=13410000.00/min [4480000], rate=13440000.00/min [4490000], rate=13470000.00/min [4500000], rate=13500000.00/min [4510000], rate=13530000.00/min [4520000], rate=13560000.00/min [4530000], rate=13590000.00/min [4540000], rate=13620000.00/min [4550000], rate=13650000.00/min [4560000], rate=13680000.00/min [4570000], rate=13710000.00/min [4580000], rate=13740000.00/min [4590000], rate=13770000.00/min [4600000], rate=13800000.00/min [4610000], rate=13830000.00/min [4620000], rate=13860000.00/min [4630000], rate=13890000.00/min [4640000], rate=13920000.00/min [4650000], rate=13950000.00/min [4660000], rate=13980000.00/min [4670000], rate=13342857.14/min [4680000], rate=13371428.57/min [4690000], rate=13400000.00/min [4700000], rate=13428571.43/min [4710000], rate=13457142.86/min [4720000], rate=13485714.29/min [4730000], rate=13514285.71/min [4740000], rate=13542857.14/min [4750000], rate=13571428.57/min [4760000], rate=13600000.00/min [4770000], rate=13628571.43/min [4780000], rate=13657142.86/min [4790000], rate=13685714.29/min [4800000], rate=13714285.71/min [4810000], rate=13742857.14/min [4820000], rate=13771428.57/min [4830000], rate=13800000.00/min [4840000], rate=13828571.43/min [4850000], rate=13857142.86/min [4860000], rate=13885714.29/min [4870000], rate=13914285.71/min [4880000], rate=13942857.14/min [4890000], rate=13971428.57/min [4900000], rate=14000000.00/min [4910000], rate=14028571.43/min [4920000], rate=14057142.86/min [4930000], rate=14085714.29/min [4940000], rate=14114285.71/min [4950000], rate=13500000.00/min [4960000], rate=13527272.73/min [4970000], rate=13554545.45/min [4980000], rate=13581818.18/min [4990000], rate=13609090.91/min [5000000], rate=13636363.64/min [5010000], rate=13663636.36/min [5020000], rate=13690909.09/min [5030000], rate=13718181.82/min [5040000], rate=13745454.55/min [5050000], rate=13772727.27/min [5060000], rate=13800000.00/min [5070000], rate=13827272.73/min [5080000], rate=13854545.45/min [5090000], rate=13881818.18/min [5100000], rate=13909090.91/min [5110000], rate=13936363.64/min [5120000], rate=13963636.36/min [5130000], rate=13990909.09/min [5140000], rate=14018181.82/min [5150000], rate=14045454.55/min [5160000], rate=14072727.27/min [5170000], rate=13486956.52/min [5180000], rate=13513043.48/min [5190000], rate=13539130.43/min [5200000], rate=13565217.39/min [5210000], rate=13591304.35/min [5220000], rate=13617391.30/min [5230000], rate=13643478.26/min [5240000], rate=13669565.22/min [5250000], rate=13695652.17/min [5260000], rate=13721739.13/min [5270000], rate=13747826.09/min [5280000], rate=13200000.00/min [5290000], rate=13225000.00/min [5300000], rate=13250000.00/min [5310000], rate=13275000.00/min [5320000], rate=13300000.00/min [5330000], rate=13325000.00/min [5340000], rate=13350000.00/min [5350000], rate=13375000.00/min [5360000], rate=13400000.00/min [5370000], rate=13425000.00/min [5380000], rate=12912000.00/min [5390000], rate=12936000.00/min [5400000], rate=12960000.00/min [5410000], rate=12984000.00/min [5420000], rate=13008000.00/min [5430000], rate=13032000.00/min [5440000], rate=13056000.00/min [5450000], rate=13080000.00/min [5460000], rate=13104000.00/min [5470000], rate=13128000.00/min [5480000], rate=13152000.00/min [5490000], rate=13176000.00/min [5500000], rate=13200000.00/min [5510000], rate=13224000.00/min [5520000], rate=13248000.00/min [5530000], rate=13272000.00/min [5540000], rate=13296000.00/min [5550000], rate=12807692.31/min [5560000], rate=12830769.23/min [5570000], rate=12853846.15/min [5580000], rate=12876923.08/min [5590000], rate=12900000.00/min [5600000], rate=12923076.92/min [5610000], rate=12946153.85/min [5620000], rate=12969230.77/min [5630000], rate=12992307.69/min [5640000], rate=13015384.62/min [5650000], rate=13038461.54/min [5660000], rate=13061538.46/min [5670000], rate=13084615.38/min [5680000], rate=13107692.31/min [5690000], rate=13130769.23/min [5700000], rate=13153846.15/min [5710000], rate=13176923.08/min [5720000], rate=13200000.00/min [5730000], rate=13223076.92/min [5740000], rate=13246153.85/min [5750000], rate=13269230.77/min [5760000], rate=13292307.69/min [5770000], rate=13315384.62/min [5780000], rate=13338461.54/min [5790000], rate=13361538.46/min [5800000], rate=13384615.38/min [5810000], rate=13407692.31/min [5820000], rate=12933333.33/min [5830000], rate=12955555.56/min [5840000], rate=12977777.78/min [5850000], rate=13000000.00/min [5860000], rate=13022222.22/min [5870000], rate=13044444.44/min [5880000], rate=13066666.67/min [5890000], rate=13088888.89/min [5900000], rate=13111111.11/min [5910000], rate=13133333.33/min [5920000], rate=13155555.56/min [5930000], rate=13177777.78/min [5940000], rate=13200000.00/min [5950000], rate=13222222.22/min [5960000], rate=13244444.44/min [5970000], rate=13266666.67/min [5980000], rate=13288888.89/min [5990000], rate=13311111.11/min [6000000], rate=13333333.33/min [6010000], rate=13355555.56/min [6020000], rate=13377777.78/min [6030000], rate=13400000.00/min [6040000], rate=13422222.22/min [6050000], rate=13444444.44/min [6060000], rate=13466666.67/min [6070000], rate=13488888.89/min [6080000], rate=13511111.11/min [6090000], rate=13533333.33/min [6100000], rate=13555555.56/min [6110000], rate=13092857.14/min [6120000], rate=13114285.71/min [6130000], rate=13135714.29/min [6140000], rate=13157142.86/min [6150000], rate=13178571.43/min [6160000], rate=13200000.00/min [6170000], rate=13221428.57/min [6180000], rate=13242857.14/min [6190000], rate=13264285.71/min [6200000], rate=13285714.29/min [6210000], rate=13307142.86/min [6220000], rate=13328571.43/min [6230000], rate=13350000.00/min [6240000], rate=13371428.57/min [6250000], rate=13392857.14/min [6260000], rate=13414285.71/min [6270000], rate=13435714.29/min [6280000], rate=13457142.86/min [6290000], rate=13478571.43/min [6300000], rate=13500000.00/min [6310000], rate=13521428.57/min [6320000], rate=13542857.14/min [6330000], rate=13564285.71/min [6340000], rate=13585714.29/min [6350000], rate=13607142.86/min [6360000], rate=13628571.43/min [6370000], rate=13650000.00/min [6380000], rate=13671428.57/min [6390000], rate=13220689.66/min [6400000], rate=13241379.31/min [6410000], rate=13262068.97/min [6420000], rate=13282758.62/min [6430000], rate=13303448.28/min [6440000], rate=13324137.93/min [6450000], rate=13344827.59/min [6460000], rate=13365517.24/min [6470000], rate=13386206.90/min [6480000], rate=13406896.55/min [6490000], rate=13427586.21/min [6500000], rate=13448275.86/min [6510000], rate=13468965.52/min [6520000], rate=13489655.17/min [6530000], rate=13510344.83/min [6540000], rate=13531034.48/min [6550000], rate=13551724.14/min [6560000], rate=13572413.79/min [6570000], rate=13593103.45/min [6580000], rate=13613793.10/min [6590000], rate=13634482.76/min [6600000], rate=13655172.41/min [6610000], rate=13675862.07/min [6620000], rate=13696551.72/min [6630000], rate=13717241.38/min [6640000], rate=13737931.03/min [6650000], rate=13758620.69/min [6660000], rate=13779310.34/min [6670000], rate=13800000.00/min [6680000], rate=13360000.00/min [6690000], rate=13380000.00/min [6700000], rate=13400000.00/min [6710000], rate=13420000.00/min [6720000], rate=13440000.00/min [6730000], rate=13460000.00/min [6740000], rate=13480000.00/min [6750000], rate=13500000.00/min [6760000], rate=13520000.00/min [6770000], rate=13540000.00/min [6780000], rate=13560000.00/min [6790000], rate=13580000.00/min [6800000], rate=13600000.00/min [6810000], rate=13620000.00/min [6820000], rate=13640000.00/min [6830000], rate=13660000.00/min [6840000], rate=13680000.00/min [6850000], rate=13700000.00/min [6860000], rate=13720000.00/min [6870000], rate=13740000.00/min [6880000], rate=13760000.00/min [6890000], rate=13780000.00/min [6900000], rate=13800000.00/min [6910000], rate=13820000.00/min [6920000], rate=13840000.00/min [6930000], rate=13860000.00/min [6940000], rate=13880000.00/min [6950000], rate=13900000.00/min [6960000], rate=13470967.74/min [6970000], rate=13490322.58/min [6980000], rate=13509677.42/min [6990000], rate=13529032.26/min [7000000], rate=13548387.10/min [7010000], rate=13567741.94/min [7020000], rate=13587096.77/min [7030000], rate=13606451.61/min [7040000], rate=13625806.45/min [7050000], rate=13645161.29/min [7060000], rate=13664516.13/min [7070000], rate=13683870.97/min [7080000], rate=13703225.81/min [7090000], rate=13722580.65/min [7100000], rate=13741935.48/min [7110000], rate=13761290.32/min [7120000], rate=13780645.16/min [7130000], rate=13800000.00/min [7140000], rate=13819354.84/min [7150000], rate=13838709.68/min [7160000], rate=13858064.52/min [7170000], rate=13877419.35/min [7180000], rate=13896774.19/min [7190000], rate=13916129.03/min [7200000], rate=13935483.87/min [7210000], rate=13954838.71/min [7220000], rate=13974193.55/min [7230000], rate=13993548.39/min [7240000], rate=14012903.23/min [7250000], rate=13593750.00/min [7260000], rate=13612500.00/min [7270000], rate=13631250.00/min [7280000], rate=13650000.00/min [7290000], rate=13668750.00/min [7300000], rate=13687500.00/min [7310000], rate=13706250.00/min [7320000], rate=13725000.00/min [7330000], rate=13743750.00/min [7340000], rate=13762500.00/min [7350000], rate=13781250.00/min [7360000], rate=13800000.00/min [7370000], rate=13818750.00/min [7380000], rate=13837500.00/min [7390000], rate=13856250.00/min [7400000], rate=13875000.00/min [7410000], rate=13893750.00/min [7420000], rate=13912500.00/min [7430000], rate=13931250.00/min [7440000], rate=13950000.00/min [7450000], rate=13968750.00/min [7460000], rate=13987500.00/min [7470000], rate=14006250.00/min [7480000], rate=14025000.00/min [7490000], rate=14043750.00/min [7500000], rate=14062500.00/min [7510000], rate=14081250.00/min [7520000], rate=14100000.00/min [7530000], rate=14118750.00/min [7540000], rate=13709090.91/min [7550000], rate=13727272.73/min [7560000], rate=13745454.55/min [7570000], rate=13763636.36/min [7580000], rate=13781818.18/min [7590000], rate=13800000.00/min [7600000], rate=13818181.82/min [7610000], rate=13836363.64/min [7620000], rate=13854545.45/min [7630000], rate=13872727.27/min [7640000], rate=13890909.09/min [7650000], rate=13909090.91/min [7660000], rate=13927272.73/min [7670000], rate=13945454.55/min [7680000], rate=13963636.36/min [7690000], rate=13981818.18/min [7700000], rate=14000000.00/min [7710000], rate=14018181.82/min [7720000], rate=14036363.64/min [7730000], rate=14054545.45/min [7740000], rate=14072727.27/min [7750000], rate=14090909.09/min [7760000], rate=14109090.91/min [7770000], rate=14127272.73/min [7780000], rate=14145454.55/min [7790000], rate=14163636.36/min [7800000], rate=14181818.18/min [7810000], rate=14200000.00/min [7820000], rate=13800000.00/min [7830000], rate=13817647.06/min [7840000], rate=13835294.12/min [7850000], rate=13852941.18/min [7860000], rate=13870588.24/min [7870000], rate=13888235.29/min [7880000], rate=13905882.35/min [7890000], rate=13923529.41/min [7900000], rate=13941176.47/min [7910000], rate=13958823.53/min [7920000], rate=13976470.59/min [7930000], rate=13994117.65/min [7940000], rate=14011764.71/min [7950000], rate=14029411.76/min [7960000], rate=14047058.82/min [7970000], rate=14064705.88/min [7980000], rate=14082352.94/min [7990000], rate=14100000.00/min [8000000], rate=14117647.06/min [8010000], rate=14135294.12/min [8020000], rate=14152941.18/min [8030000], rate=14170588.24/min [8040000], rate=14188235.29/min [8050000], rate=13800000.00/min [8060000], rate=13817142.86/min [8070000], rate=13834285.71/min [8080000], rate=13851428.57/min [8090000], rate=13868571.43/min [8100000], rate=13885714.29/min [8110000], rate=13902857.14/min [8120000], rate=13920000.00/min [8130000], rate=13937142.86/min [8140000], rate=13954285.71/min [8150000], rate=13971428.57/min [8160000], rate=13988571.43/min [8170000], rate=14005714.29/min [8180000], rate=14022857.14/min [8190000], rate=14040000.00/min [8200000], rate=14057142.86/min [8210000], rate=14074285.71/min [8220000], rate=14091428.57/min [8230000], rate=14108571.43/min [8240000], rate=14125714.29/min [8250000], rate=14142857.14/min [8260000], rate=14160000.00/min [8270000], rate=14177142.86/min [8280000], rate=14194285.71/min [8290000], rate=14211428.57/min [8300000], rate=14228571.43/min [8310000], rate=14245714.29/min [8320000], rate=14262857.14/min [8330000], rate=14280000.00/min [8340000], rate=13900000.00/min [8350000], rate=13916666.67/min [8360000], rate=13933333.33/min [8370000], rate=13950000.00/min [8380000], rate=13966666.67/min [8390000], rate=13983333.33/min [8400000], rate=14000000.00/min [8410000], rate=14016666.67/min [8420000], rate=14033333.33/min [8430000], rate=14050000.00/min [8440000], rate=14066666.67/min [8450000], rate=14083333.33/min [8460000], rate=14100000.00/min [8470000], rate=14116666.67/min [8480000], rate=14133333.33/min [8490000], rate=14150000.00/min [8500000], rate=14166666.67/min [8510000], rate=14183333.33/min [8520000], rate=14200000.00/min [8530000], rate=14216666.67/min [8540000], rate=14233333.33/min [8550000], rate=14250000.00/min [8560000], rate=14266666.67/min [8570000], rate=14283333.33/min [8580000], rate=14300000.00/min [8590000], rate=14316666.67/min [8600000], rate=14333333.33/min [8610000], rate=14350000.00/min [8620000], rate=13978378.38/min [8630000], rate=13994594.59/min [8640000], rate=14010810.81/min [8650000], rate=14027027.03/min [8660000], rate=14043243.24/min [8670000], rate=14059459.46/min [8680000], rate=14075675.68/min [8690000], rate=14091891.89/min [8700000], rate=14108108.11/min [8710000], rate=14124324.32/min [8720000], rate=14140540.54/min [8730000], rate=14156756.76/min [8740000], rate=14172972.97/min [8750000], rate=14189189.19/min [8760000], rate=14205405.41/min [8770000], rate=14221621.62/min [8780000], rate=14237837.84/min [8790000], rate=14254054.05/min [8800000], rate=14270270.27/min [8810000], rate=14286486.49/min [8820000], rate=14302702.70/min [8830000], rate=14318918.92/min [8840000], rate=14335135.14/min [8850000], rate=14351351.35/min [8860000], rate=14367567.57/min [8870000], rate=14383783.78/min [8880000], rate=14400000.00/min [8890000], rate=14416216.22/min [8900000], rate=14052631.58/min [8910000], rate=14068421.05/min [8920000], rate=14084210.53/min [8930000], rate=14100000.00/min [8940000], rate=14115789.47/min [8950000], rate=14131578.95/min [8960000], rate=14147368.42/min [8970000], rate=14163157.89/min [8980000], rate=14178947.37/min [8990000], rate=14194736.84/min [9000000], rate=14210526.32/min [9010000], rate=14226315.79/min [9020000], rate=14242105.26/min [9030000], rate=14257894.74/min [9040000], rate=14273684.21/min [9050000], rate=14289473.68/min [9060000], rate=14305263.16/min [9070000], rate=14321052.63/min [9080000], rate=14336842.11/min [9090000], rate=14352631.58/min [9100000], rate=14368421.05/min [9110000], rate=14384210.53/min [9120000], rate=14400000.00/min [9130000], rate=14415789.47/min [9140000], rate=14431578.95/min [9150000], rate=14447368.42/min [9160000], rate=14463157.89/min [9170000], rate=14478947.37/min [9180000], rate=14494736.84/min [9190000], rate=14138461.54/min [9200000], rate=14153846.15/min [9210000], rate=14169230.77/min [9220000], rate=14184615.38/min [9230000], rate=14200000.00/min [9240000], rate=14215384.62/min [9250000], rate=14230769.23/min [9260000], rate=14246153.85/min [9270000], rate=14261538.46/min [9280000], rate=14276923.08/min [9290000], rate=14292307.69/min [9300000], rate=14307692.31/min [9310000], rate=14323076.92/min [9320000], rate=14338461.54/min [9330000], rate=14353846.15/min [9340000], rate=14369230.77/min [9350000], rate=14384615.38/min [9360000], rate=14400000.00/min [9370000], rate=14415384.62/min [9380000], rate=14430769.23/min [9390000], rate=14446153.85/min [9400000], rate=14461538.46/min [9410000], rate=14476923.08/min [9420000], rate=14492307.69/min [9430000], rate=14507692.31/min 09:04:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18. -FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns: identified 6167 cancer introns 09:04:29 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim 09:04:29 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/prelim_introns.ok 09:04:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns 09:04:30 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns 09:04:30 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/introns_filtered.ok 09:04:30 : INFO : -found 2885 cancer introns 09:04:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --cancer_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed 09:04:30 : INFO : Creating the BED File. 09:04:37 : INFO : Saving Bed File as FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed 09:04:37 : INFO : Execution Time = 0.13 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --cancer_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed 09:04:37 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/intron_igv_bed.ok 09:04:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix FFPE_V4_0001_RNA_0001_B23LG7FLT4_2 [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai 09:23:43 : INFO : Execution Time = 19.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix FFPE_V4_0001_RNA_0001_B23LG7FLT4_2 09:23:43 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok 09:23:43 : INFO : Running: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam 09:23:44 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam 09:23:44 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok 09:23:44 : INFO : Running: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.bam [bam_sort_core] merging from 86 files and 1 in-memory blocks... 09:43:47 : INFO : Execution Time = 20.04 minutes. CMD: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.bam 09:43:47 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/sort_gene_reads.ok 09:43:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam 09:49:24 : INFO : Execution Time = 5.62 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam 09:49:24 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp.ok 09:49:24 : INFO : Running: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:50:14 : INFO : Execution Time = 0.83 minutes. CMD: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp 09:50:14 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:50:14 : INFO : Running: samtools index FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 09:50:19 : INFO : Execution Time = 0.09 minutes. CMD: samtools index FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 09:50:19 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.indexed.ok 09:50:19 : INFO : Running: samtools index FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 09:50:20 : INFO : Execution Time = 0.00 minutes. CMD: samtools index FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 09:50:20 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam.indexed.ok 09:50:20 : INFO : Running: create_report FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.ctat-splicing.igv.html --track-config FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: FFPE_V4_0001_RNA_0001_B23LG7FLT4_2' [W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi 09:53:18 : INFO : Execution Time = 2.97 minutes. CMD: create_report FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.ctat-splicing.igv.html --track-config FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: FFPE_V4_0001_RNA_0001_B23LG7FLT4_2' 09:53:18 : INFO : Running: touch /tmp/nxf.U3cGnhaMse/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/igv_create_html.ok 09:53:18 : INFO : done.