09:04:21 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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=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=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=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=15600000.00/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=21400000.00/min
[1080000], rate=21600000.00/min
[1090000], rate=21800000.00/min
[1100000], rate=22000000.00/min
[1110000], rate=22200000.00/min
[1120000], rate=22400000.00/min
[1130000], rate=22600000.00/min
[1140000], rate=22800000.00/min
[1150000], rate=23000000.00/min
[1160000], rate=23200000.00/min
[1170000], rate=23400000.00/min
[1180000], rate=23600000.00/min
[1190000], rate=23800000.00/min
[1200000], rate=24000000.00/min
[1210000], rate=24200000.00/min
[1220000], rate=24400000.00/min
[1230000], rate=24600000.00/min
[1240000], rate=24800000.00/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=20400000.00/min
[1370000], rate=20550000.00/min
[1380000], rate=20700000.00/min
[1390000], rate=20850000.00/min
[1400000], rate=21000000.00/min
[1410000], rate=21150000.00/min
[1420000], rate=21300000.00/min
[1430000], rate=21450000.00/min
[1440000], rate=21600000.00/min
[1450000], rate=21750000.00/min
[1460000], rate=21900000.00/min
[1470000], rate=22050000.00/min
[1480000], rate=22200000.00/min
[1490000], rate=22350000.00/min
[1500000], rate=22500000.00/min
[1510000], rate=22650000.00/min
[1520000], rate=22800000.00/min
[1530000], rate=22950000.00/min
[1540000], rate=23100000.00/min
[1550000], rate=23250000.00/min
[1560000], rate=23400000.00/min
[1570000], rate=23550000.00/min
[1580000], rate=23700000.00/min
[1590000], rate=23850000.00/min
[1600000], rate=24000000.00/min
[1610000], rate=24150000.00/min
[1620000], rate=24300000.00/min
[1630000], rate=24450000.00/min
[1640000], rate=24600000.00/min
[1650000], rate=24750000.00/min
[1660000], rate=24900000.00/min
[1670000], rate=25050000.00/min
[1680000], rate=25200000.00/min
[1690000], rate=25350000.00/min
[1700000], rate=20400000.00/min
[1710000], rate=20520000.00/min
[1720000], rate=20640000.00/min
[1730000], rate=20760000.00/min
[1740000], rate=20880000.00/min
[1750000], rate=21000000.00/min
[1760000], rate=21120000.00/min
[1770000], rate=21240000.00/min
[1780000], rate=21360000.00/min
[1790000], rate=21480000.00/min
[1800000], rate=21600000.00/min
[1810000], rate=21720000.00/min
[1820000], rate=21840000.00/min
[1830000], rate=21960000.00/min
[1840000], rate=22080000.00/min
[1850000], rate=22200000.00/min
[1860000], rate=22320000.00/min
[1870000], rate=22440000.00/min
[1880000], rate=22560000.00/min
[1890000], rate=22680000.00/min
[1900000], rate=22800000.00/min
[1910000], rate=22920000.00/min
[1920000], rate=23040000.00/min
[1930000], rate=23160000.00/min
[1940000], rate=23280000.00/min
[1950000], rate=23400000.00/min
[1960000], rate=23520000.00/min
[1970000], rate=23640000.00/min
[1980000], rate=23760000.00/min
[1990000], rate=23880000.00/min
[2000000], rate=24000000.00/min
[2010000], rate=24120000.00/min
[2020000], rate=24240000.00/min
[2030000], rate=24360000.00/min
[2040000], rate=24480000.00/min
[2050000], rate=24600000.00/min
[2060000], rate=24720000.00/min
[2070000], rate=24840000.00/min
[2080000], rate=24960000.00/min
[2090000], rate=25080000.00/min
[2100000], rate=25200000.00/min
[2110000], rate=25320000.00/min
[2120000], rate=25440000.00/min
[2130000], rate=25560000.00/min
[2140000], rate=25680000.00/min
[2150000], rate=25800000.00/min
[2160000], rate=21600000.00/min
[2170000], rate=21700000.00/min
[2180000], rate=21800000.00/min
[2190000], rate=21900000.00/min
[2200000], rate=22000000.00/min
[2210000], rate=22100000.00/min
[2220000], rate=22200000.00/min
[2230000], rate=22300000.00/min
[2240000], rate=22400000.00/min
[2250000], rate=22500000.00/min
[2260000], rate=22600000.00/min
[2270000], rate=22700000.00/min
[2280000], rate=22800000.00/min
[2290000], rate=22900000.00/min
[2300000], rate=23000000.00/min
[2310000], rate=23100000.00/min
[2320000], rate=23200000.00/min
[2330000], rate=23300000.00/min
[2340000], rate=23400000.00/min
[2350000], rate=23500000.00/min
[2360000], rate=23600000.00/min
[2370000], rate=23700000.00/min
[2380000], rate=23800000.00/min
[2390000], rate=23900000.00/min
[2400000], rate=24000000.00/min
[2410000], rate=24100000.00/min
[2420000], rate=24200000.00/min
[2430000], rate=24300000.00/min
[2440000], rate=24400000.00/min
[2450000], rate=24500000.00/min
[2460000], rate=24600000.00/min
[2470000], rate=24700000.00/min
[2480000], rate=24800000.00/min
[2490000], rate=24900000.00/min
[2500000], rate=25000000.00/min
[2510000], rate=25100000.00/min
[2520000], rate=25200000.00/min
[2530000], rate=25300000.00/min
[2540000], rate=25400000.00/min
[2550000], rate=25500000.00/min
[2560000], rate=25600000.00/min
[2570000], rate=25700000.00/min
[2580000], rate=25800000.00/min
[2590000], rate=25900000.00/min
[2600000], rate=26000000.00/min
[2610000], rate=26100000.00/min
[2620000], rate=26200000.00/min
[2630000], rate=26300000.00/min
[2640000], rate=26400000.00/min
[2650000], rate=22714285.71/min
[2660000], rate=22800000.00/min
[2670000], rate=22885714.29/min
[2680000], rate=22971428.57/min
[2690000], rate=23057142.86/min
[2700000], rate=23142857.14/min
[2710000], rate=23228571.43/min
[2720000], rate=23314285.71/min
[2730000], rate=23400000.00/min
[2740000], rate=23485714.29/min
[2750000], rate=23571428.57/min
[2760000], rate=23657142.86/min
[2770000], rate=23742857.14/min
[2780000], rate=23828571.43/min
[2790000], rate=23914285.71/min
[2800000], rate=24000000.00/min
[2810000], rate=24085714.29/min
[2820000], rate=24171428.57/min
[2830000], rate=24257142.86/min
[2840000], rate=24342857.14/min
[2850000], rate=24428571.43/min
[2860000], rate=24514285.71/min
[2870000], rate=24600000.00/min
[2880000], rate=24685714.29/min
[2890000], rate=24771428.57/min
[2900000], rate=24857142.86/min
[2910000], rate=24942857.14/min
[2920000], rate=25028571.43/min
[2930000], rate=25114285.71/min
[2940000], rate=25200000.00/min
[2950000], rate=25285714.29/min
[2960000], rate=25371428.57/min
[2970000], rate=25457142.86/min
[2980000], rate=25542857.14/min
[2990000], rate=25628571.43/min
[3000000], rate=25714285.71/min
[3010000], rate=25800000.00/min
[3020000], rate=25885714.29/min
[3030000], rate=25971428.57/min
[3040000], rate=26057142.86/min
[3050000], rate=26142857.14/min
[3060000], rate=26228571.43/min
[3070000], rate=26314285.71/min
[3080000], rate=26400000.00/min
[3090000], rate=26485714.29/min
[3100000], rate=26571428.57/min
[3110000], rate=23325000.00/min
[3120000], rate=23400000.00/min
[3130000], rate=23475000.00/min
[3140000], rate=23550000.00/min
[3150000], rate=23625000.00/min
[3160000], rate=23700000.00/min
[3170000], rate=23775000.00/min
[3180000], rate=23850000.00/min
[3190000], rate=23925000.00/min
[3200000], rate=24000000.00/min
[3210000], rate=24075000.00/min
[3220000], rate=24150000.00/min
[3230000], rate=24225000.00/min
[3240000], rate=24300000.00/min
[3250000], rate=24375000.00/min
[3260000], rate=24450000.00/min
[3270000], rate=24525000.00/min
[3280000], rate=24600000.00/min
[3290000], rate=24675000.00/min
[3300000], rate=24750000.00/min
[3310000], rate=24825000.00/min
[3320000], rate=24900000.00/min
[3330000], rate=24975000.00/min
[3340000], rate=25050000.00/min
[3350000], rate=25125000.00/min
[3360000], rate=25200000.00/min
[3370000], rate=25275000.00/min
[3380000], rate=25350000.00/min
[3390000], rate=25425000.00/min
[3400000], rate=25500000.00/min
[3410000], rate=25575000.00/min
[3420000], rate=25650000.00/min
[3430000], rate=25725000.00/min
[3440000], rate=25800000.00/min
[3450000], rate=25875000.00/min
[3460000], rate=25950000.00/min
[3470000], rate=26025000.00/min
[3480000], rate=26100000.00/min
[3490000], rate=26175000.00/min
[3500000], rate=26250000.00/min
[3510000], rate=26325000.00/min
[3520000], rate=26400000.00/min
[3530000], rate=26475000.00/min
[3540000], rate=26550000.00/min
[3550000], rate=23666666.67/min
[3560000], rate=23733333.33/min
[3570000], rate=23800000.00/min
[3580000], rate=23866666.67/min
[3590000], rate=23933333.33/min
[3600000], rate=24000000.00/min
[3610000], rate=24066666.67/min
[3620000], rate=24133333.33/min
[3630000], rate=24200000.00/min
[3640000], rate=24266666.67/min
[3650000], rate=24333333.33/min
[3660000], rate=24400000.00/min
[3670000], rate=24466666.67/min
[3680000], rate=24533333.33/min
[3690000], rate=24600000.00/min
[3700000], rate=24666666.67/min
[3710000], rate=24733333.33/min
[3720000], rate=24800000.00/min
[3730000], rate=24866666.67/min
[3740000], rate=24933333.33/min
[3750000], rate=25000000.00/min
[3760000], rate=25066666.67/min
[3770000], rate=25133333.33/min
[3780000], rate=25200000.00/min
[3790000], rate=25266666.67/min
[3800000], rate=25333333.33/min
[3810000], rate=25400000.00/min
[3820000], rate=25466666.67/min
[3830000], rate=25533333.33/min
[3840000], rate=25600000.00/min
[3850000], rate=25666666.67/min
[3860000], rate=25733333.33/min
[3870000], rate=25800000.00/min
[3880000], rate=25866666.67/min
[3890000], rate=25933333.33/min
[3900000], rate=26000000.00/min
[3910000], rate=26066666.67/min
[3920000], rate=26133333.33/min
[3930000], rate=26200000.00/min
[3940000], rate=26266666.67/min
[3950000], rate=26333333.33/min
[3960000], rate=26400000.00/min
[3970000], rate=26466666.67/min
[3980000], rate=26533333.33/min
[3990000], rate=26600000.00/min
[4000000], rate=24000000.00/min
[4010000], rate=24060000.00/min
[4020000], rate=24120000.00/min
[4030000], rate=24180000.00/min
[4040000], rate=24240000.00/min
[4050000], rate=24300000.00/min
[4060000], rate=24360000.00/min
[4070000], rate=24420000.00/min
[4080000], rate=24480000.00/min
[4090000], rate=24540000.00/min
[4100000], rate=24600000.00/min
[4110000], rate=24660000.00/min
[4120000], rate=24720000.00/min
[4130000], rate=24780000.00/min
[4140000], rate=24840000.00/min
[4150000], rate=24900000.00/min
[4160000], rate=24960000.00/min
[4170000], rate=25020000.00/min
[4180000], rate=25080000.00/min
[4190000], rate=25140000.00/min
[4200000], rate=25200000.00/min
[4210000], rate=25260000.00/min
[4220000], rate=25320000.00/min
[4230000], rate=25380000.00/min
[4240000], rate=25440000.00/min
[4250000], rate=25500000.00/min
[4260000], rate=25560000.00/min
[4270000], rate=25620000.00/min
[4280000], rate=25680000.00/min
[4290000], rate=25740000.00/min
[4300000], rate=25800000.00/min
[4310000], rate=25860000.00/min
[4320000], rate=25920000.00/min
[4330000], rate=25980000.00/min
[4340000], rate=26040000.00/min
[4350000], rate=26100000.00/min
[4360000], rate=26160000.00/min
[4370000], rate=26220000.00/min
[4380000], rate=26280000.00/min
[4390000], rate=26340000.00/min
[4400000], rate=26400000.00/min
[4410000], rate=26460000.00/min
[4420000], rate=26520000.00/min
[4430000], rate=26580000.00/min
[4440000], rate=26640000.00/min
[4450000], rate=26700000.00/min
[4460000], rate=26760000.00/min
[4470000], rate=26820000.00/min
[4480000], rate=26880000.00/min
[4490000], rate=24490909.09/min
[4500000], rate=24545454.55/min
[4510000], rate=24600000.00/min
[4520000], rate=24654545.45/min
[4530000], rate=24709090.91/min
[4540000], rate=24763636.36/min
[4550000], rate=24818181.82/min
[4560000], rate=24872727.27/min
[4570000], rate=24927272.73/min
[4580000], rate=24981818.18/min
[4590000], rate=25036363.64/min
[4600000], rate=25090909.09/min
[4610000], rate=25145454.55/min
[4620000], rate=25200000.00/min
[4630000], rate=25254545.45/min
[4640000], rate=25309090.91/min
[4650000], rate=25363636.36/min
[4660000], rate=25418181.82/min
[4670000], rate=25472727.27/min
[4680000], rate=25527272.73/min
[4690000], rate=25581818.18/min
[4700000], rate=25636363.64/min
[4710000], rate=25690909.09/min
[4720000], rate=25745454.55/min
[4730000], rate=25800000.00/min
[4740000], rate=25854545.45/min
[4750000], rate=25909090.91/min
[4760000], rate=25963636.36/min
[4770000], rate=26018181.82/min
[4780000], rate=26072727.27/min
[4790000], rate=26127272.73/min
[4800000], rate=26181818.18/min
[4810000], rate=26236363.64/min
[4820000], rate=26290909.09/min
[4830000], rate=26345454.55/min
[4840000], rate=26400000.00/min
[4850000], rate=24250000.00/min
[4860000], rate=24300000.00/min
[4870000], rate=24350000.00/min
[4880000], rate=24400000.00/min
[4890000], rate=24450000.00/min
[4900000], rate=24500000.00/min
[4910000], rate=24550000.00/min
[4920000], rate=24600000.00/min
[4930000], rate=24650000.00/min
[4940000], rate=24700000.00/min
[4950000], rate=24750000.00/min
[4960000], rate=24800000.00/min
[4970000], rate=24850000.00/min
[4980000], rate=24900000.00/min
[4990000], rate=24950000.00/min
[5000000], rate=25000000.00/min
[5010000], rate=25050000.00/min
[5020000], rate=25100000.00/min
[5030000], rate=25150000.00/min
[5040000], rate=25200000.00/min
[5050000], rate=25250000.00/min
[5060000], rate=25300000.00/min
[5070000], rate=25350000.00/min
[5080000], rate=25400000.00/min
[5090000], rate=25450000.00/min
[5100000], rate=25500000.00/min
[5110000], rate=25550000.00/min
[5120000], rate=25600000.00/min
[5130000], rate=25650000.00/min
[5140000], rate=25700000.00/min
[5150000], rate=25750000.00/min
[5160000], rate=25800000.00/min
[5170000], rate=25850000.00/min
[5180000], rate=25900000.00/min
[5190000], rate=25950000.00/min
[5200000], rate=26000000.00/min
[5210000], rate=26050000.00/min
[5220000], rate=26100000.00/min
[5230000], rate=26150000.00/min
[5240000], rate=26200000.00/min
[5250000], rate=26250000.00/min
[5260000], rate=26300000.00/min
[5270000], rate=26350000.00/min
[5280000], rate=26400000.00/min
[5290000], rate=24415384.62/min
[5300000], rate=24461538.46/min
[5310000], rate=24507692.31/min
[5320000], rate=24553846.15/min
[5330000], rate=24600000.00/min
[5340000], rate=24646153.85/min
[5350000], rate=24692307.69/min
[5360000], rate=24738461.54/min
[5370000], rate=24784615.38/min
[5380000], rate=24830769.23/min
[5390000], rate=24876923.08/min
[5400000], rate=24923076.92/min
[5410000], rate=24969230.77/min
[5420000], rate=25015384.62/min
[5430000], rate=25061538.46/min
[5440000], rate=25107692.31/min
[5450000], rate=25153846.15/min
[5460000], rate=25200000.00/min
[5470000], rate=25246153.85/min
[5480000], rate=25292307.69/min
[5490000], rate=25338461.54/min
[5500000], rate=25384615.38/min
[5510000], rate=25430769.23/min
[5520000], rate=25476923.08/min
[5530000], rate=25523076.92/min
[5540000], rate=25569230.77/min
[5550000], rate=25615384.62/min
[5560000], rate=25661538.46/min
[5570000], rate=25707692.31/min
[5580000], rate=25753846.15/min
[5590000], rate=25800000.00/min
[5600000], rate=25846153.85/min
[5610000], rate=25892307.69/min
[5620000], rate=25938461.54/min
[5630000], rate=25984615.38/min
[5640000], rate=26030769.23/min
[5650000], rate=26076923.08/min
[5660000], rate=26123076.92/min
[5670000], rate=26169230.77/min
[5680000], rate=26215384.62/min
[5690000], rate=26261538.46/min
[5700000], rate=26307692.31/min
[5710000], rate=26353846.15/min
[5720000], rate=26400000.00/min
[5730000], rate=26446153.85/min
[5740000], rate=26492307.69/min
[5750000], rate=26538461.54/min
[5760000], rate=26584615.38/min
[5770000], rate=26630769.23/min
[5780000], rate=26676923.08/min
[5790000], rate=26723076.92/min
[5800000], rate=26769230.77/min
[5810000], rate=26815384.62/min
[5820000], rate=24942857.14/min
[5830000], rate=24985714.29/min
[5840000], rate=25028571.43/min
[5850000], rate=25071428.57/min
[5860000], rate=25114285.71/min
[5870000], rate=25157142.86/min
[5880000], rate=25200000.00/min
[5890000], rate=25242857.14/min
[5900000], rate=25285714.29/min
[5910000], rate=25328571.43/min
[5920000], rate=25371428.57/min
[5930000], rate=25414285.71/min
[5940000], rate=25457142.86/min
[5950000], rate=25500000.00/min
[5960000], rate=25542857.14/min
[5970000], rate=25585714.29/min
[5980000], rate=25628571.43/min
[5990000], rate=25671428.57/min
[6000000], rate=25714285.71/min
[6010000], rate=25757142.86/min
[6020000], rate=25800000.00/min
[6030000], rate=25842857.14/min
[6040000], rate=25885714.29/min
[6050000], rate=25928571.43/min
[6060000], rate=25971428.57/min
[6070000], rate=26014285.71/min
[6080000], rate=26057142.86/min
[6090000], rate=26100000.00/min
[6100000], rate=26142857.14/min
[6110000], rate=26185714.29/min
[6120000], rate=26228571.43/min
[6130000], rate=26271428.57/min
[6140000], rate=26314285.71/min
[6150000], rate=26357142.86/min
[6160000], rate=26400000.00/min
[6170000], rate=26442857.14/min
[6180000], rate=26485714.29/min
[6190000], rate=26528571.43/min
[6200000], rate=26571428.57/min
[6210000], rate=26614285.71/min
[6220000], rate=26657142.86/min
[6230000], rate=26700000.00/min
[6240000], rate=26742857.14/min
[6250000], rate=26785714.29/min
[6260000], rate=25040000.00/min
[6270000], rate=25080000.00/min
[6280000], rate=25120000.00/min
[6290000], rate=25160000.00/min
[6300000], rate=25200000.00/min
[6310000], rate=25240000.00/min
[6320000], rate=25280000.00/min
[6330000], rate=25320000.00/min
[6340000], rate=25360000.00/min
[6350000], rate=25400000.00/min
[6360000], rate=25440000.00/min
[6370000], rate=25480000.00/min
[6380000], rate=25520000.00/min
[6390000], rate=25560000.00/min
[6400000], rate=25600000.00/min
[6410000], rate=25640000.00/min
[6420000], rate=25680000.00/min
[6430000], rate=25720000.00/min
[6440000], rate=25760000.00/min
[6450000], rate=25800000.00/min
[6460000], rate=25840000.00/min
[6470000], rate=25880000.00/min
[6480000], rate=25920000.00/min
[6490000], rate=25960000.00/min
[6500000], rate=26000000.00/min
[6510000], rate=26040000.00/min
[6520000], rate=26080000.00/min
[6530000], rate=26120000.00/min
[6540000], rate=26160000.00/min
[6550000], rate=26200000.00/min
[6560000], rate=26240000.00/min
[6570000], rate=26280000.00/min
[6580000], rate=26320000.00/min
[6590000], rate=26360000.00/min
[6600000], rate=26400000.00/min
[6610000], rate=26440000.00/min
[6620000], rate=26480000.00/min
[6630000], rate=26520000.00/min
[6640000], rate=26560000.00/min
[6650000], rate=26600000.00/min
[6660000], rate=26640000.00/min
[6670000], rate=26680000.00/min
[6680000], rate=26720000.00/min
[6690000], rate=26760000.00/min
[6700000], rate=26800000.00/min
[6710000], rate=26840000.00/min
[6720000], rate=26880000.00/min
[6730000], rate=26920000.00/min
[6740000], rate=26960000.00/min
[6750000], rate=25312500.00/min
[6760000], rate=25350000.00/min
[6770000], rate=25387500.00/min
[6780000], rate=25425000.00/min
[6790000], rate=25462500.00/min
[6800000], rate=25500000.00/min
[6810000], rate=25537500.00/min
[6820000], rate=25575000.00/min
[6830000], rate=25612500.00/min
[6840000], rate=25650000.00/min
[6850000], rate=25687500.00/min
[6860000], rate=25725000.00/min
[6870000], rate=25762500.00/min
[6880000], rate=25800000.00/min
[6890000], rate=25837500.00/min
[6900000], rate=25875000.00/min
[6910000], rate=25912500.00/min
[6920000], rate=25950000.00/min
[6930000], rate=25987500.00/min
[6940000], rate=26025000.00/min
[6950000], rate=26062500.00/min
[6960000], rate=26100000.00/min
[6970000], rate=26137500.00/min
[6980000], rate=26175000.00/min
[6990000], rate=26212500.00/min
[7000000], rate=26250000.00/min
[7010000], rate=26287500.00/min
[7020000], rate=26325000.00/min
[7030000], rate=26362500.00/min
[7040000], rate=26400000.00/min
[7050000], rate=26437500.00/min
[7060000], rate=26475000.00/min
[7070000], rate=26512500.00/min
[7080000], rate=26550000.00/min
[7090000], rate=26587500.00/min
[7100000], rate=26625000.00/min
[7110000], rate=26662500.00/min
[7120000], rate=26700000.00/min
[7130000], rate=26737500.00/min
[7140000], rate=26775000.00/min
[7150000], rate=26812500.00/min
[7160000], rate=26850000.00/min
[7170000], rate=26887500.00/min
[7180000], rate=26925000.00/min
[7190000], rate=26962500.00/min
[7200000], rate=27000000.00/min
[7210000], rate=27037500.00/min
[7220000], rate=27075000.00/min
[7230000], rate=27112500.00/min
[7240000], rate=27150000.00/min
[7250000], rate=25588235.29/min
[7260000], rate=25623529.41/min
[7270000], rate=25658823.53/min
[7280000], rate=25694117.65/min
[7290000], rate=25729411.76/min
[7300000], rate=25764705.88/min
[7310000], rate=25800000.00/min
[7320000], rate=25835294.12/min
[7330000], rate=25870588.24/min
[7340000], rate=25905882.35/min
[7350000], rate=25941176.47/min
[7360000], rate=25976470.59/min
[7370000], rate=26011764.71/min
[7380000], rate=26047058.82/min
[7390000], rate=26082352.94/min
[7400000], rate=26117647.06/min
[7410000], rate=26152941.18/min
[7420000], rate=26188235.29/min
[7430000], rate=26223529.41/min
[7440000], rate=26258823.53/min
[7450000], rate=26294117.65/min
[7460000], rate=26329411.76/min
[7470000], rate=26364705.88/min
[7480000], rate=26400000.00/min
[7490000], rate=26435294.12/min
[7500000], rate=26470588.24/min
[7510000], rate=26505882.35/min
[7520000], rate=26541176.47/min
[7530000], rate=26576470.59/min
[7540000], rate=26611764.71/min
[7550000], rate=26647058.82/min
[7560000], rate=26682352.94/min
[7570000], rate=26717647.06/min
[7580000], rate=26752941.18/min
[7590000], rate=26788235.29/min
[7600000], rate=26823529.41/min
[7610000], rate=26858823.53/min
[7620000], rate=26894117.65/min
[7630000], rate=26929411.76/min
[7640000], rate=26964705.88/min
[7650000], rate=27000000.00/min
[7660000], rate=25533333.33/min
[7670000], rate=25566666.67/min
[7680000], rate=25600000.00/min
[7690000], rate=25633333.33/min
[7700000], rate=25666666.67/min
[7710000], rate=25700000.00/min
[7720000], rate=25733333.33/min
[7730000], rate=25766666.67/min
[7740000], rate=25800000.00/min
[7750000], rate=25833333.33/min
[7760000], rate=25866666.67/min
[7770000], rate=25900000.00/min
[7780000], rate=25933333.33/min
[7790000], rate=25966666.67/min
[7800000], rate=26000000.00/min
[7810000], rate=26033333.33/min
[7820000], rate=26066666.67/min
[7830000], rate=26100000.00/min
[7840000], rate=26133333.33/min
[7850000], rate=26166666.67/min
[7860000], rate=26200000.00/min
[7870000], rate=26233333.33/min
[7880000], rate=26266666.67/min
[7890000], rate=26300000.00/min
[7900000], rate=26333333.33/min
[7910000], rate=26366666.67/min
[7920000], rate=26400000.00/min
[7930000], rate=26433333.33/min
[7940000], rate=26466666.67/min
[7950000], rate=26500000.00/min
[7960000], rate=26533333.33/min
[7970000], rate=26566666.67/min
[7980000], rate=26600000.00/min
[7990000], rate=26633333.33/min
[8000000], rate=26666666.67/min
[8010000], rate=26700000.00/min
[8020000], rate=26733333.33/min
[8030000], rate=26766666.67/min
[8040000], rate=26800000.00/min
[8050000], rate=26833333.33/min
[8060000], rate=26866666.67/min
[8070000], rate=26900000.00/min
[8080000], rate=26933333.33/min
[8090000], rate=26966666.67/min
[8100000], rate=27000000.00/min
[8110000], rate=25610526.32/min
[8120000], rate=25642105.26/min
[8130000], rate=25673684.21/min
[8140000], rate=25705263.16/min
[8150000], rate=25736842.11/min
[8160000], rate=25768421.05/min
[8170000], rate=25800000.00/min
[8180000], rate=25831578.95/min
[8190000], rate=25863157.89/min
[8200000], rate=25894736.84/min
[8210000], rate=25926315.79/min
[8220000], rate=25957894.74/min
[8230000], rate=25989473.68/min
[8240000], rate=26021052.63/min
[8250000], rate=26052631.58/min
[8260000], rate=26084210.53/min
[8270000], rate=26115789.47/min
[8280000], rate=26147368.42/min
[8290000], rate=26178947.37/min
[8300000], rate=26210526.32/min
[8310000], rate=26242105.26/min
[8320000], rate=26273684.21/min
[8330000], rate=26305263.16/min
[8340000], rate=26336842.11/min
[8350000], rate=26368421.05/min
[8360000], rate=26400000.00/min
[8370000], rate=26431578.95/min
[8380000], rate=26463157.89/min
[8390000], rate=26494736.84/min
[8400000], rate=26526315.79/min
[8410000], rate=26557894.74/min
[8420000], rate=26589473.68/min
[8430000], rate=26621052.63/min
[8440000], rate=26652631.58/min
[8450000], rate=26684210.53/min
[8460000], rate=26715789.47/min
[8470000], rate=26747368.42/min
[8480000], rate=26778947.37/min
[8490000], rate=26810526.32/min
[8500000], rate=26842105.26/min
[8510000], rate=26873684.21/min
[8520000], rate=26905263.16/min
[8530000], rate=26936842.11/min
[8540000], rate=26968421.05/min
[8550000], rate=27000000.00/min
[8560000], rate=27031578.95/min
[8570000], rate=27063157.89/min
[8580000], rate=27094736.84/min
[8590000], rate=25770000.00/min
[8600000], rate=25800000.00/min
[8610000], rate=25830000.00/min
[8620000], rate=25860000.00/min
[8630000], rate=25890000.00/min
[8640000], rate=25920000.00/min
[8650000], rate=25950000.00/min
[8660000], rate=25980000.00/min
[8670000], rate=26010000.00/min
[8680000], rate=26040000.00/min
[8690000], rate=26070000.00/min
[8700000], rate=26100000.00/min
[8710000], rate=26130000.00/min
[8720000], rate=26160000.00/min
[8730000], rate=26190000.00/min
[8740000], rate=26220000.00/min
[8750000], rate=26250000.00/min
[8760000], rate=26280000.00/min
[8770000], rate=26310000.00/min 09:04:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1.introns: identified 7604 cancer introns
09:04:47 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer.introns.prelim
09:04:47 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok
09:04:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer.introns
09:04:47 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer.introns
09:04:47 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok
09:04:47 : INFO : -found 3210 cancer introns
09:04:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns.for_IGV.bed
09:04:48 : INFO : Creating the BED File.
09:04:51 : INFO : Saving Bed File as aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns.for_IGV.bed
09:04:51 : INFO : Execution Time = 0.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns.for_IGV.bed
09:04:51 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok
09:04:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-28eb14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-28eb14-R1_A23YTGFLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
09:19:26 : INFO : Execution Time = 14.58 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-28eb14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-28eb14-R1_A23YTGFLT4_1
09:19:26 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok
09:19:26 : INFO : Running: samtools sort -o aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer_intron_reads.bam
09:19:26 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer_intron_reads.bam
09:19:26 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok
09:19:26 : INFO : Running: samtools sort -o aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.bam
[bam_sort_core] merging from 118 files and 1 in-memory blocks...
09:36:58 : INFO : Execution Time = 17.53 minutes. CMD: samtools sort -o aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.bam
09:36:58 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok
09:36:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.bam
09:42:35 : INFO : Execution Time = 5.62 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.bam
09:42:35 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
09:42:35 : INFO : Running: samtools sort -o aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 4 files and 1 in-memory blocks...
09:43:17 : INFO : Execution Time = 0.69 minutes. CMD: samtools sort -o aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp
09:43:17 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:43:17 : INFO : Running: samtools index aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam
09:43:21 : INFO : Execution Time = 0.08 minutes. CMD: samtools index aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam
09:43:21 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
09:43:21 : INFO : Running: samtools index aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam
09:43:22 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam
09:43:22 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
09:43:22 : INFO : Running: create_report aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-28eb14-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-28eb14-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-28eb14-R1_A23YTGFLT4_1'
09:47:13 : INFO : Execution Time = 3.86 minutes. CMD: create_report aih-tih-sc-28eb14-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-28eb14-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-28eb14-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-28eb14-R1_A23YTGFLT4_1'
09:47:13 : INFO : Running: touch /tmp/nxf.TMaUWkgns6/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok
09:47:13 : INFO : done.