09:11:58 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [20000], rate=1200000.00/min [30000], rate=1800000.00/min [40000], rate=2400000.00/min [50000], rate=3000000.00/min [60000], rate=3600000.00/min [70000], rate=4200000.00/min [80000], rate=4800000.00/min [90000], rate=5400000.00/min [100000], rate=6000000.00/min [110000], rate=6600000.00/min [120000], rate=7200000.00/min [130000], rate=7800000.00/min [140000], rate=8400000.00/min [150000], rate=9000000.00/min [160000], rate=9600000.00/min [170000], rate=10200000.00/min [180000], rate=10800000.00/min [190000], rate=11400000.00/min [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=8700000.00/min [300000], rate=9000000.00/min [310000], rate=9300000.00/min [320000], rate=9600000.00/min [330000], rate=9900000.00/min [340000], rate=10200000.00/min [350000], rate=10500000.00/min [360000], rate=10800000.00/min [370000], rate=11100000.00/min [380000], rate=11400000.00/min [390000], rate=11700000.00/min [400000], rate=12000000.00/min [410000], rate=12300000.00/min [420000], rate=12600000.00/min [430000], rate=12900000.00/min [440000], rate=13200000.00/min [450000], rate=13500000.00/min [460000], rate=13800000.00/min [470000], rate=14100000.00/min [480000], rate=14400000.00/min [490000], rate=14700000.00/min [500000], rate=15000000.00/min [510000], rate=15300000.00/min [520000], rate=15600000.00/min [530000], rate=15900000.00/min [540000], rate=10800000.00/min [550000], rate=11000000.00/min [560000], rate=11200000.00/min [570000], rate=11400000.00/min [580000], rate=11600000.00/min [590000], rate=11800000.00/min [600000], rate=12000000.00/min [610000], rate=12200000.00/min [620000], rate=12400000.00/min [630000], rate=12600000.00/min [640000], rate=12800000.00/min [650000], rate=13000000.00/min [660000], rate=13200000.00/min [670000], rate=13400000.00/min [680000], rate=13600000.00/min [690000], rate=13800000.00/min [700000], rate=14000000.00/min [710000], rate=14200000.00/min [720000], rate=14400000.00/min [730000], rate=14600000.00/min [740000], rate=14800000.00/min [750000], rate=15000000.00/min [760000], rate=11400000.00/min [770000], rate=11550000.00/min [780000], rate=11700000.00/min [790000], rate=11850000.00/min [800000], rate=12000000.00/min [810000], rate=12150000.00/min [820000], rate=12300000.00/min [830000], rate=12450000.00/min [840000], rate=12600000.00/min [850000], rate=12750000.00/min [860000], rate=12900000.00/min [870000], rate=13050000.00/min [880000], rate=13200000.00/min [890000], rate=13350000.00/min [900000], rate=13500000.00/min [910000], rate=13650000.00/min [920000], rate=13800000.00/min [930000], rate=13950000.00/min [940000], rate=14100000.00/min [950000], rate=14250000.00/min [960000], rate=11520000.00/min [970000], rate=11640000.00/min [980000], rate=11760000.00/min [990000], rate=11880000.00/min [1000000], rate=12000000.00/min [1010000], rate=12120000.00/min [1020000], rate=12240000.00/min [1030000], rate=12360000.00/min [1040000], rate=12480000.00/min [1050000], rate=12600000.00/min [1060000], rate=12720000.00/min [1070000], rate=12840000.00/min [1080000], rate=12960000.00/min [1090000], rate=13080000.00/min [1100000], rate=13200000.00/min [1110000], rate=13320000.00/min [1120000], rate=13440000.00/min [1130000], rate=13560000.00/min [1140000], rate=13680000.00/min [1150000], rate=13800000.00/min [1160000], rate=13920000.00/min [1170000], rate=14040000.00/min [1180000], rate=14160000.00/min [1190000], rate=11900000.00/min [1200000], rate=12000000.00/min [1210000], rate=12100000.00/min [1220000], rate=12200000.00/min [1230000], rate=12300000.00/min [1240000], rate=12400000.00/min [1250000], rate=12500000.00/min [1260000], rate=12600000.00/min [1270000], rate=12700000.00/min [1280000], rate=12800000.00/min [1290000], rate=12900000.00/min [1300000], rate=13000000.00/min [1310000], rate=13100000.00/min [1320000], rate=13200000.00/min [1330000], rate=13300000.00/min [1340000], rate=13400000.00/min [1350000], rate=13500000.00/min [1360000], rate=13600000.00/min [1370000], rate=13700000.00/min [1380000], rate=13800000.00/min [1390000], rate=13900000.00/min [1400000], rate=14000000.00/min [1410000], rate=12085714.29/min [1420000], rate=12171428.57/min [1430000], rate=12257142.86/min [1440000], rate=12342857.14/min [1450000], rate=12428571.43/min [1460000], rate=12514285.71/min [1470000], rate=12600000.00/min [1480000], rate=12685714.29/min [1490000], rate=12771428.57/min [1500000], rate=12857142.86/min [1510000], rate=12942857.14/min [1520000], rate=13028571.43/min [1530000], rate=13114285.71/min [1540000], rate=13200000.00/min [1550000], rate=13285714.29/min [1560000], rate=13371428.57/min [1570000], rate=13457142.86/min [1580000], rate=13542857.14/min [1590000], rate=13628571.43/min [1600000], rate=13714285.71/min [1610000], rate=13800000.00/min [1620000], rate=13885714.29/min [1630000], rate=13971428.57/min [1640000], rate=14057142.86/min [1650000], rate=12375000.00/min [1660000], rate=12450000.00/min [1670000], rate=12525000.00/min [1680000], rate=12600000.00/min [1690000], rate=12675000.00/min [1700000], rate=12750000.00/min [1710000], rate=12825000.00/min [1720000], rate=12900000.00/min [1730000], rate=12975000.00/min [1740000], rate=13050000.00/min [1750000], rate=13125000.00/min [1760000], rate=13200000.00/min [1770000], rate=13275000.00/min [1780000], rate=13350000.00/min [1790000], rate=13425000.00/min [1800000], rate=13500000.00/min [1810000], rate=13575000.00/min [1820000], rate=13650000.00/min [1830000], rate=13725000.00/min [1840000], rate=13800000.00/min [1850000], rate=13875000.00/min [1860000], rate=13950000.00/min [1870000], rate=14025000.00/min [1880000], rate=14100000.00/min [1890000], rate=12600000.00/min [1900000], rate=12666666.67/min [1910000], rate=12733333.33/min [1920000], rate=12800000.00/min [1930000], rate=12866666.67/min [1940000], rate=12933333.33/min [1950000], rate=13000000.00/min [1960000], rate=13066666.67/min [1970000], rate=13133333.33/min [1980000], rate=13200000.00/min [1990000], rate=13266666.67/min [2000000], rate=13333333.33/min [2010000], rate=13400000.00/min [2020000], rate=13466666.67/min [2030000], rate=13533333.33/min [2040000], rate=13600000.00/min [2050000], rate=13666666.67/min [2060000], rate=13733333.33/min [2070000], rate=13800000.00/min [2080000], rate=13866666.67/min [2090000], rate=13933333.33/min [2100000], rate=12600000.00/min [2110000], rate=12660000.00/min [2120000], rate=12720000.00/min [2130000], rate=12780000.00/min [2140000], rate=12840000.00/min [2150000], rate=12900000.00/min [2160000], rate=12960000.00/min [2170000], rate=13020000.00/min [2180000], rate=13080000.00/min [2190000], rate=13140000.00/min [2200000], rate=13200000.00/min [2210000], rate=13260000.00/min [2220000], rate=13320000.00/min [2230000], rate=13380000.00/min [2240000], rate=13440000.00/min [2250000], rate=13500000.00/min [2260000], rate=13560000.00/min [2270000], rate=13620000.00/min [2280000], rate=13680000.00/min [2290000], rate=13740000.00/min [2300000], rate=13800000.00/min [2310000], rate=13860000.00/min [2320000], rate=12654545.45/min [2330000], rate=12709090.91/min [2340000], rate=12763636.36/min [2350000], rate=12818181.82/min [2360000], rate=12872727.27/min [2370000], rate=12927272.73/min [2380000], rate=12981818.18/min [2390000], rate=13036363.64/min [2400000], rate=13090909.09/min [2410000], rate=13145454.55/min [2420000], rate=13200000.00/min [2430000], rate=13254545.45/min [2440000], rate=13309090.91/min [2450000], rate=13363636.36/min [2460000], rate=13418181.82/min [2470000], rate=13472727.27/min [2480000], rate=13527272.73/min [2490000], rate=13581818.18/min [2500000], rate=13636363.64/min [2510000], rate=13690909.09/min [2520000], rate=13745454.55/min [2530000], rate=12650000.00/min [2540000], rate=12700000.00/min [2550000], rate=12750000.00/min [2560000], rate=12800000.00/min [2570000], rate=12850000.00/min [2580000], rate=12900000.00/min [2590000], rate=12950000.00/min [2600000], rate=13000000.00/min [2610000], rate=13050000.00/min [2620000], rate=13100000.00/min [2630000], rate=13150000.00/min [2640000], rate=13200000.00/min [2650000], rate=13250000.00/min [2660000], rate=13300000.00/min [2670000], rate=13350000.00/min [2680000], rate=13400000.00/min [2690000], rate=13450000.00/min [2700000], rate=13500000.00/min [2710000], rate=13550000.00/min [2720000], rate=13600000.00/min [2730000], rate=13650000.00/min [2740000], rate=13700000.00/min [2750000], rate=13750000.00/min [2760000], rate=12738461.54/min [2770000], rate=12784615.38/min [2780000], rate=12830769.23/min [2790000], rate=12876923.08/min [2800000], rate=12923076.92/min [2810000], rate=12969230.77/min [2820000], rate=13015384.62/min [2830000], rate=13061538.46/min [2840000], rate=13107692.31/min [2850000], rate=13153846.15/min [2860000], rate=13200000.00/min [2870000], rate=13246153.85/min [2880000], rate=13292307.69/min [2890000], rate=13338461.54/min [2900000], rate=13384615.38/min [2910000], rate=13430769.23/min [2920000], rate=13476923.08/min [2930000], rate=13523076.92/min [2940000], rate=13569230.77/min [2950000], rate=13615384.62/min [2960000], rate=13661538.46/min [2970000], rate=13707692.31/min [2980000], rate=12771428.57/min [2990000], rate=12814285.71/min [3000000], rate=12857142.86/min [3010000], rate=12900000.00/min [3020000], rate=12942857.14/min [3030000], rate=12985714.29/min [3040000], rate=13028571.43/min [3050000], rate=13071428.57/min [3060000], rate=13114285.71/min [3070000], rate=13157142.86/min [3080000], rate=13200000.00/min [3090000], rate=13242857.14/min [3100000], rate=13285714.29/min [3110000], rate=13328571.43/min [3120000], rate=13371428.57/min [3130000], rate=13414285.71/min [3140000], rate=13457142.86/min [3150000], rate=13500000.00/min [3160000], rate=13542857.14/min [3170000], rate=13585714.29/min [3180000], rate=13628571.43/min [3190000], rate=12760000.00/min [3200000], rate=12800000.00/min [3210000], rate=12840000.00/min [3220000], rate=12880000.00/min [3230000], rate=12920000.00/min [3240000], rate=12960000.00/min [3250000], rate=13000000.00/min [3260000], rate=13040000.00/min [3270000], rate=13080000.00/min [3280000], rate=13120000.00/min [3290000], rate=13160000.00/min [3300000], rate=13200000.00/min [3310000], rate=13240000.00/min [3320000], rate=13280000.00/min [3330000], rate=13320000.00/min [3340000], rate=13360000.00/min [3350000], rate=13400000.00/min [3360000], rate=13440000.00/min [3370000], rate=13480000.00/min [3380000], rate=13520000.00/min [3390000], rate=13560000.00/min [3400000], rate=12750000.00/min [3410000], rate=12787500.00/min [3420000], rate=12825000.00/min [3430000], rate=12862500.00/min [3440000], rate=12900000.00/min [3450000], rate=12937500.00/min [3460000], rate=12975000.00/min [3470000], rate=13012500.00/min [3480000], rate=13050000.00/min [3490000], rate=13087500.00/min [3500000], rate=13125000.00/min [3510000], rate=13162500.00/min [3520000], rate=13200000.00/min [3530000], rate=13237500.00/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=12670588.24/min [3600000], rate=12705882.35/min [3610000], rate=12741176.47/min [3620000], rate=12776470.59/min [3630000], rate=12811764.71/min [3640000], rate=12847058.82/min [3650000], rate=12882352.94/min [3660000], rate=12917647.06/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=12733333.33/min [3830000], rate=12766666.67/min [3840000], rate=12800000.00/min [3850000], rate=12833333.33/min [3860000], rate=12866666.67/min [3870000], rate=12900000.00/min [3880000], rate=12933333.33/min [3890000], rate=12966666.67/min [3900000], rate=13000000.00/min [3910000], rate=13033333.33/min [3920000], rate=13066666.67/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=12789473.68/min [4060000], rate=12821052.63/min [4070000], rate=12852631.58/min [4080000], rate=12884210.53/min [4090000], rate=12915789.47/min [4100000], rate=12947368.42/min [4110000], rate=12978947.37/min [4120000], rate=13010526.32/min [4130000], rate=13042105.26/min [4140000], rate=13073684.21/min [4150000], rate=13105263.16/min [4160000], rate=13136842.11/min [4170000], rate=13168421.05/min [4180000], rate=13200000.00/min [4190000], rate=13231578.95/min [4200000], rate=13263157.89/min [4210000], rate=13294736.84/min [4220000], rate=13326315.79/min [4230000], rate=13357894.74/min [4240000], rate=12720000.00/min [4250000], rate=12750000.00/min [4260000], rate=12780000.00/min [4270000], rate=12810000.00/min [4280000], rate=12840000.00/min [4290000], rate=12870000.00/min [4300000], rate=12900000.00/min [4310000], rate=12930000.00/min [4320000], rate=12960000.00/min [4330000], rate=12990000.00/min [4340000], rate=13020000.00/min [4350000], rate=13050000.00/min [4360000], rate=13080000.00/min [4370000], rate=13110000.00/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=12771428.57/min [4480000], rate=12800000.00/min [4490000], rate=12828571.43/min [4500000], rate=12857142.86/min [4510000], rate=12885714.29/min [4520000], rate=12914285.71/min [4530000], rate=12942857.14/min [4540000], rate=12971428.57/min [4550000], rate=13000000.00/min [4560000], rate=13028571.43/min [4570000], rate=13057142.86/min [4580000], rate=13085714.29/min [4590000], rate=13114285.71/min [4600000], rate=13142857.14/min [4610000], rate=13171428.57/min [4620000], rate=13200000.00/min [4630000], rate=13228571.43/min [4640000], rate=13257142.86/min [4650000], rate=13285714.29/min [4660000], rate=13314285.71/min [4670000], rate=13342857.14/min [4680000], rate=13371428.57/min [4690000], rate=12790909.09/min [4700000], rate=12818181.82/min [4710000], rate=12845454.55/min [4720000], rate=12872727.27/min [4730000], rate=12900000.00/min [4740000], rate=12927272.73/min [4750000], rate=12954545.45/min [4760000], rate=12981818.18/min [4770000], rate=13009090.91/min [4780000], rate=13036363.64/min [4790000], rate=13063636.36/min [4800000], rate=13090909.09/min [4810000], rate=13118181.82/min [4820000], rate=13145454.55/min [4830000], rate=13172727.27/min [4840000], rate=13200000.00/min [4850000], rate=13227272.73/min [4860000], rate=13254545.45/min [4870000], rate=13281818.18/min [4880000], rate=13309090.91/min [4890000], rate=13336363.64/min [4900000], rate=13363636.36/min [4910000], rate=12808695.65/min [4920000], rate=12834782.61/min [4930000], rate=12860869.57/min [4940000], rate=12886956.52/min [4950000], rate=12913043.48/min [4960000], rate=12939130.43/min [4970000], rate=12965217.39/min [4980000], rate=12991304.35/min [4990000], rate=13017391.30/min [5000000], rate=13043478.26/min [5010000], rate=13069565.22/min [5020000], rate=13095652.17/min [5030000], rate=13121739.13/min [5040000], rate=13147826.09/min [5050000], rate=13173913.04/min [5060000], rate=13200000.00/min [5070000], rate=13226086.96/min [5080000], rate=13252173.91/min [5090000], rate=13278260.87/min [5100000], rate=13304347.83/min [5110000], rate=13330434.78/min [5120000], rate=13356521.74/min [5130000], rate=13382608.70/min [5140000], rate=13408695.65/min [5150000], rate=13434782.61/min [5160000], rate=13460869.57/min [5170000], rate=13486956.52/min [5180000], rate=13513043.48/min [5190000], rate=13539130.43/min [5200000], rate=13565217.39/min [5210000], rate=13025000.00/min [5220000], rate=13050000.00/min [5230000], rate=13075000.00/min [5240000], rate=13100000.00/min [5250000], rate=13125000.00/min [5260000], rate=13150000.00/min [5270000], rate=13175000.00/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=13450000.00/min [5390000], rate=13475000.00/min [5400000], rate=13500000.00/min [5410000], rate=13525000.00/min [5420000], rate=13550000.00/min [5430000], rate=13575000.00/min [5440000], rate=13600000.00/min [5450000], rate=13625000.00/min [5460000], rate=13650000.00/min [5470000], rate=13675000.00/min [5480000], rate=13700000.00/min [5490000], rate=13725000.00/min [5500000], rate=13750000.00/min [5510000], rate=13775000.00/min [5520000], rate=13248000.00/min [5530000], rate=13272000.00/min [5540000], rate=13296000.00/min [5550000], rate=13320000.00/min [5560000], rate=13344000.00/min [5570000], rate=13368000.00/min [5580000], rate=13392000.00/min [5590000], rate=13416000.00/min [5600000], rate=13440000.00/min [5610000], rate=13464000.00/min [5620000], rate=13488000.00/min [5630000], rate=13512000.00/min [5640000], rate=13536000.00/min [5650000], rate=13560000.00/min [5660000], rate=13584000.00/min [5670000], rate=13608000.00/min [5680000], rate=13632000.00/min [5690000], rate=13656000.00/min [5700000], rate=13680000.00/min [5710000], rate=13704000.00/min [5720000], rate=13728000.00/min [5730000], rate=13752000.00/min [5740000], rate=13776000.00/min [5750000], rate=13800000.00/min [5760000], rate=13824000.00/min [5770000], rate=13848000.00/min [5780000], rate=13872000.00/min [5790000], rate=13896000.00/min [5800000], rate=13384615.38/min [5810000], rate=13407692.31/min [5820000], rate=13430769.23/min [5830000], rate=13453846.15/min [5840000], rate=13476923.08/min [5850000], rate=13500000.00/min [5860000], rate=13523076.92/min [5870000], rate=13546153.85/min [5880000], rate=13569230.77/min [5890000], rate=13592307.69/min [5900000], rate=13615384.62/min [5910000], rate=13638461.54/min [5920000], rate=13661538.46/min [5930000], rate=13684615.38/min [5940000], rate=13707692.31/min [5950000], rate=13730769.23/min [5960000], rate=13753846.15/min [5970000], rate=13776923.08/min [5980000], rate=13800000.00/min [5990000], rate=13823076.92/min [6000000], rate=13846153.85/min [6010000], rate=13869230.77/min [6020000], rate=13892307.69/min [6030000], rate=13915384.62/min [6040000], rate=13938461.54/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=13577777.78/min [6120000], rate=13600000.00/min [6130000], rate=13622222.22/min [6140000], rate=13644444.44/min [6150000], rate=13666666.67/min [6160000], rate=13688888.89/min [6170000], rate=13711111.11/min [6180000], rate=13733333.33/min [6190000], rate=13755555.56/min [6200000], rate=13777777.78/min [6210000], rate=13800000.00/min [6220000], rate=13822222.22/min [6230000], rate=13844444.44/min [6240000], rate=13866666.67/min [6250000], rate=13888888.89/min [6260000], rate=13911111.11/min [6270000], rate=13933333.33/min [6280000], rate=13955555.56/min [6290000], rate=13977777.78/min [6300000], rate=14000000.00/min [6310000], rate=14022222.22/min [6320000], rate=14044444.44/min [6330000], rate=14066666.67/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=13692857.14/min [6400000], rate=13714285.71/min [6410000], rate=13735714.29/min [6420000], rate=13757142.86/min [6430000], rate=13778571.43/min [6440000], rate=13800000.00/min [6450000], rate=13821428.57/min [6460000], rate=13842857.14/min [6470000], rate=13864285.71/min [6480000], rate=13885714.29/min [6490000], rate=13907142.86/min [6500000], rate=13928571.43/min [6510000], rate=13950000.00/min [6520000], rate=13971428.57/min [6530000], rate=13992857.14/min [6540000], rate=14014285.71/min [6550000], rate=14035714.29/min [6560000], rate=14057142.86/min [6570000], rate=14078571.43/min [6580000], rate=14100000.00/min [6590000], rate=14121428.57/min [6600000], rate=14142857.14/min [6610000], rate=14164285.71/min [6620000], rate=14185714.29/min [6630000], rate=14207142.86/min [6640000], rate=13737931.03/min [6650000], rate=13758620.69/min [6660000], rate=13779310.34/min [6670000], rate=13800000.00/min [6680000], rate=13820689.66/min [6690000], rate=13841379.31/min [6700000], rate=13862068.97/min [6710000], rate=13882758.62/min [6720000], rate=13903448.28/min [6730000], rate=13924137.93/min [6740000], rate=13944827.59/min [6750000], rate=13965517.24/min [6760000], rate=13986206.90/min [6770000], rate=14006896.55/min [6780000], rate=14027586.21/min [6790000], rate=14048275.86/min [6800000], rate=14068965.52/min [6810000], rate=14089655.17/min [6820000], rate=14110344.83/min [6830000], rate=14131034.48/min [6840000], rate=14151724.14/min [6850000], rate=14172413.79/min [6860000], rate=14193103.45/min [6870000], rate=14213793.10/min [6880000], rate=14234482.76/min [6890000], rate=14255172.41/min [6900000], rate=14275862.07/min [6910000], rate=14296551.72/min [6920000], rate=14317241.38/min [6930000], rate=13860000.00/min [6940000], rate=13880000.00/min [6950000], rate=13900000.00/min [6960000], rate=13920000.00/min [6970000], rate=13940000.00/min [6980000], rate=13960000.00/min [6990000], rate=13980000.00/min [7000000], rate=14000000.00/min [7010000], rate=14020000.00/min [7020000], rate=14040000.00/min [7030000], rate=14060000.00/min [7040000], rate=14080000.00/min [7050000], rate=14100000.00/min [7060000], rate=14120000.00/min [7070000], rate=14140000.00/min [7080000], rate=14160000.00/min [7090000], rate=14180000.00/min [7100000], rate=14200000.00/min [7110000], rate=14220000.00/min [7120000], rate=14240000.00/min [7130000], rate=14260000.00/min [7140000], rate=14280000.00/min [7150000], rate=14300000.00/min [7160000], rate=14320000.00/min [7170000], rate=14340000.00/min [7180000], rate=14360000.00/min [7190000], rate=14380000.00/min [7200000], rate=14400000.00/min [7210000], rate=14420000.00/min [7220000], rate=13974193.55/min [7230000], rate=13993548.39/min [7240000], rate=14012903.23/min [7250000], rate=14032258.06/min [7260000], rate=14051612.90/min [7270000], rate=14070967.74/min [7280000], rate=14090322.58/min [7290000], rate=14109677.42/min [7300000], rate=14129032.26/min [7310000], rate=14148387.10/min [7320000], rate=14167741.94/min [7330000], rate=14187096.77/min [7340000], rate=14206451.61/min [7350000], rate=14225806.45/min [7360000], rate=14245161.29/min [7370000], rate=14264516.13/min [7380000], rate=14283870.97/min [7390000], rate=14303225.81/min [7400000], rate=14322580.65/min [7410000], rate=14341935.48/min [7420000], rate=14361290.32/min [7430000], rate=14380645.16/min [7440000], rate=14400000.00/min [7450000], rate=14419354.84/min [7460000], rate=14438709.68/min [7470000], rate=14458064.52/min [7480000], rate=14477419.35/min [7490000], rate=14496774.19/min [7500000], rate=14516129.03/min [7510000], rate=14535483.87/min [7520000], rate=14100000.00/min [7530000], rate=14118750.00/min [7540000], rate=14137500.00/min [7550000], rate=14156250.00/min [7560000], rate=14175000.00/min [7570000], rate=14193750.00/min [7580000], rate=14212500.00/min [7590000], rate=14231250.00/min [7600000], rate=14250000.00/min [7610000], rate=14268750.00/min [7620000], rate=14287500.00/min [7630000], rate=14306250.00/min [7640000], rate=14325000.00/min [7650000], rate=14343750.00/min [7660000], rate=14362500.00/min [7670000], rate=14381250.00/min [7680000], rate=14400000.00/min [7690000], rate=14418750.00/min [7700000], rate=14437500.00/min [7710000], rate=14456250.00/min [7720000], rate=14475000.00/min [7730000], rate=14493750.00/min [7740000], rate=14512500.00/min [7750000], rate=14531250.00/min [7760000], rate=14550000.00/min [7770000], rate=14568750.00/min [7780000], rate=14587500.00/min [7790000], rate=14606250.00/min [7800000], rate=14181818.18/min [7810000], rate=14200000.00/min [7820000], rate=14218181.82/min [7830000], rate=14236363.64/min [7840000], rate=14254545.45/min [7850000], rate=14272727.27/min [7860000], rate=14290909.09/min [7870000], rate=14309090.91/min [7880000], rate=14327272.73/min [7890000], rate=14345454.55/min [7900000], rate=14363636.36/min [7910000], rate=14381818.18/min [7920000], rate=14400000.00/min [7930000], rate=14418181.82/min [7940000], rate=14436363.64/min [7950000], rate=14454545.45/min [7960000], rate=14472727.27/min [7970000], rate=14490909.09/min [7980000], rate=14509090.91/min [7990000], rate=14527272.73/min [8000000], rate=14545454.55/min [8010000], rate=14563636.36/min [8020000], rate=14581818.18/min [8030000], rate=14600000.00/min [8040000], rate=14618181.82/min [8050000], rate=14636363.64/min [8060000], rate=14654545.45/min [8070000], rate=14672727.27/min [8080000], rate=14690909.09/min [8090000], rate=14276470.59/min [8100000], rate=14294117.65/min [8110000], rate=14311764.71/min [8120000], rate=14329411.76/min [8130000], rate=14347058.82/min [8140000], rate=14364705.88/min [8150000], rate=14382352.94/min [8160000], rate=14400000.00/min [8170000], rate=14417647.06/min [8180000], rate=14435294.12/min [8190000], rate=14452941.18/min [8200000], rate=14470588.24/min [8210000], rate=14488235.29/min [8220000], rate=14505882.35/min [8230000], rate=14523529.41/min [8240000], rate=14541176.47/min [8250000], rate=14558823.53/min [8260000], rate=14576470.59/min [8270000], rate=14594117.65/min [8280000], rate=14611764.71/min [8290000], rate=14629411.76/min [8300000], rate=14647058.82/min [8310000], rate=14664705.88/min [8320000], rate=14682352.94/min [8330000], rate=14700000.00/min [8340000], rate=14717647.06/min [8350000], rate=14735294.12/min [8360000], rate=14331428.57/min [8370000], rate=14348571.43/min [8380000], rate=14365714.29/min [8390000], rate=14382857.14/min [8400000], rate=14400000.00/min [8410000], rate=14417142.86/min [8420000], rate=14434285.71/min [8430000], rate=14451428.57/min [8440000], rate=14468571.43/min [8450000], rate=14485714.29/min [8460000], rate=14502857.14/min [8470000], rate=14520000.00/min [8480000], rate=14537142.86/min [8490000], rate=14554285.71/min [8500000], rate=14571428.57/min [8510000], rate=14588571.43/min [8520000], rate=14605714.29/min [8530000], rate=14622857.14/min [8540000], rate=14640000.00/min [8550000], rate=14657142.86/min [8560000], rate=14674285.71/min [8570000], rate=14691428.57/min [8580000], rate=14708571.43/min [8590000], rate=14725714.29/min [8600000], rate=14742857.14/min [8610000], rate=14760000.00/min [8620000], rate=14777142.86/min [8630000], rate=14794285.71/min [8640000], rate=14811428.57/min [8650000], rate=14828571.43/min [8660000], rate=14845714.29/min 09:12:40 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-92d360-R1_A23YTGFLT4_1.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. -aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns: identified 4776 cancer introns 09:12:41 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns.prelim 09:12:41 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 09:12:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns 09:12:41 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns 09:12:41 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 09:12:41 : INFO : -found 1742 cancer introns 09:12:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:12:42 : INFO : Creating the BED File. 09:12:46 : INFO : Saving Bed File as aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:12:46 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:12:46 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 09:12:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-92d360-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 09:27:29 : INFO : Execution Time = 14.72 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-92d360-R1_A23YTGFLT4_1 09:27:29 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 09:27:29 : INFO : Running: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:27:30 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:27:30 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 09:27:30 : INFO : Running: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 68 files and 1 in-memory blocks... 09:43:53 : INFO : Execution Time = 16.39 minutes. CMD: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.bam 09:43:53 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok 09:43:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.bam 09:48:37 : INFO : Execution Time = 4.73 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.bam 09:48:37 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:48:37 : INFO : Running: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:49:29 : INFO : Execution Time = 0.87 minutes. CMD: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp 09:49:29 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:49:29 : INFO : Running: samtools index aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 09:49:34 : INFO : Execution Time = 0.09 minutes. CMD: samtools index aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 09:49:34 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:49:34 : INFO : Running: samtools index aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 09:49:34 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 09:49:34 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:49:34 : INFO : Running: create_report aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-92d360-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-92d360-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-92d360-R1_A23YTGFLT4_1' 09:55:05 : INFO : Execution Time = 5.51 minutes. CMD: create_report aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-92d360-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-92d360-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-92d360-R1_A23YTGFLT4_1' 09:55:05 : INFO : Running: touch /tmp/nxf.V12sRjL5qI/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok 09:55:05 : INFO : done.