09:07:48 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=17400000.00/min [300000], rate=18000000.00/min [310000], rate=18600000.00/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=8800000.00/min [450000], rate=9000000.00/min [460000], rate=9200000.00/min [470000], rate=9400000.00/min [480000], rate=9600000.00/min [490000], rate=9800000.00/min [500000], rate=10000000.00/min [510000], rate=10200000.00/min [520000], rate=10400000.00/min [530000], rate=10600000.00/min [540000], rate=10800000.00/min [550000], rate=11000000.00/min [560000], rate=11200000.00/min [570000], rate=8550000.00/min [580000], rate=8700000.00/min [590000], rate=8850000.00/min [600000], rate=9000000.00/min [610000], rate=9150000.00/min [620000], rate=9300000.00/min [630000], rate=9450000.00/min [640000], rate=9600000.00/min [650000], rate=9750000.00/min [660000], rate=9900000.00/min [670000], rate=10050000.00/min [680000], rate=10200000.00/min [690000], rate=10350000.00/min [700000], rate=8400000.00/min [710000], rate=8520000.00/min [720000], rate=8640000.00/min [730000], rate=8760000.00/min [740000], rate=8880000.00/min [750000], rate=9000000.00/min [760000], rate=9120000.00/min [770000], rate=9240000.00/min [780000], rate=9360000.00/min [790000], rate=9480000.00/min [800000], rate=9600000.00/min [810000], rate=9720000.00/min [820000], rate=8200000.00/min [830000], rate=8300000.00/min [840000], rate=8400000.00/min [850000], rate=8500000.00/min [860000], rate=8600000.00/min [870000], rate=8700000.00/min [880000], rate=8800000.00/min [890000], rate=8900000.00/min [900000], rate=9000000.00/min [910000], rate=9100000.00/min [920000], rate=9200000.00/min [930000], rate=9300000.00/min [940000], rate=9400000.00/min [950000], rate=8142857.14/min [960000], rate=8228571.43/min [970000], rate=8314285.71/min [980000], rate=8400000.00/min [990000], rate=8485714.29/min [1000000], rate=8571428.57/min [1010000], rate=8657142.86/min [1020000], rate=8742857.14/min [1030000], rate=8828571.43/min [1040000], rate=8914285.71/min [1050000], rate=9000000.00/min [1060000], rate=9085714.29/min [1070000], rate=9171428.57/min [1080000], rate=8100000.00/min [1090000], rate=8175000.00/min [1100000], rate=8250000.00/min [1110000], rate=8325000.00/min [1120000], rate=8400000.00/min [1130000], rate=8475000.00/min [1140000], rate=8550000.00/min [1150000], rate=8625000.00/min [1160000], rate=8700000.00/min [1170000], rate=8775000.00/min [1180000], rate=8850000.00/min [1190000], rate=8925000.00/min [1200000], rate=9000000.00/min [1210000], rate=8066666.67/min [1220000], rate=8133333.33/min [1230000], rate=8200000.00/min [1240000], rate=8266666.67/min [1250000], rate=8333333.33/min [1260000], rate=8400000.00/min [1270000], rate=8466666.67/min [1280000], rate=8533333.33/min [1290000], rate=8600000.00/min [1300000], rate=8666666.67/min [1310000], rate=8733333.33/min [1320000], rate=8800000.00/min [1330000], rate=8866666.67/min [1340000], rate=8040000.00/min [1350000], rate=8100000.00/min [1360000], rate=8160000.00/min [1370000], rate=8220000.00/min [1380000], rate=8280000.00/min [1390000], rate=8340000.00/min [1400000], rate=8400000.00/min [1410000], rate=8460000.00/min [1420000], rate=8520000.00/min [1430000], rate=8580000.00/min [1440000], rate=8640000.00/min [1450000], rate=8700000.00/min [1460000], rate=8760000.00/min [1470000], rate=8820000.00/min [1480000], rate=8072727.27/min [1490000], rate=8127272.73/min [1500000], rate=8181818.18/min [1510000], rate=8236363.64/min [1520000], rate=8290909.09/min [1530000], rate=8345454.55/min [1540000], rate=8400000.00/min [1550000], rate=8454545.45/min [1560000], rate=8509090.91/min [1570000], rate=8563636.36/min [1580000], rate=8618181.82/min [1590000], rate=8672727.27/min [1600000], rate=8727272.73/min [1610000], rate=8781818.18/min [1620000], rate=8100000.00/min [1630000], rate=8150000.00/min [1640000], rate=8200000.00/min [1650000], rate=8250000.00/min [1660000], rate=8300000.00/min [1670000], rate=8350000.00/min [1680000], rate=8400000.00/min [1690000], rate=8450000.00/min [1700000], rate=8500000.00/min [1710000], rate=8550000.00/min [1720000], rate=8600000.00/min [1730000], rate=8650000.00/min [1740000], rate=8700000.00/min [1750000], rate=8076923.08/min [1760000], rate=8123076.92/min [1770000], rate=8169230.77/min [1780000], rate=8215384.62/min [1790000], rate=8261538.46/min [1800000], rate=8307692.31/min [1810000], rate=8353846.15/min [1820000], rate=8400000.00/min [1830000], rate=8446153.85/min [1840000], rate=8492307.69/min [1850000], rate=8538461.54/min [1860000], rate=8584615.38/min [1870000], rate=8630769.23/min [1880000], rate=8057142.86/min [1890000], rate=8100000.00/min [1900000], rate=8142857.14/min [1910000], rate=8185714.29/min [1920000], rate=8228571.43/min [1930000], rate=8271428.57/min [1940000], rate=8314285.71/min [1950000], rate=8357142.86/min [1960000], rate=8400000.00/min [1970000], rate=8442857.14/min [1980000], rate=8485714.29/min [1990000], rate=8528571.43/min [2000000], rate=8571428.57/min [2010000], rate=8614285.71/min [2020000], rate=8657142.86/min [2030000], rate=8700000.00/min [2040000], rate=8742857.14/min [2050000], rate=8785714.29/min [2060000], rate=8828571.43/min [2070000], rate=8871428.57/min [2080000], rate=8320000.00/min [2090000], rate=8360000.00/min [2100000], rate=8400000.00/min [2110000], rate=8440000.00/min [2120000], rate=8480000.00/min [2130000], rate=8520000.00/min [2140000], rate=8560000.00/min [2150000], rate=8600000.00/min [2160000], rate=8640000.00/min [2170000], rate=8680000.00/min [2180000], rate=8720000.00/min [2190000], rate=8760000.00/min [2200000], rate=8800000.00/min [2210000], rate=8840000.00/min [2220000], rate=8880000.00/min [2230000], rate=8920000.00/min [2240000], rate=8960000.00/min [2250000], rate=9000000.00/min [2260000], rate=9040000.00/min [2270000], rate=9080000.00/min [2280000], rate=9120000.00/min [2290000], rate=9160000.00/min [2300000], rate=9200000.00/min [2310000], rate=9240000.00/min [2320000], rate=8700000.00/min [2330000], rate=8737500.00/min [2340000], rate=8775000.00/min [2350000], rate=8812500.00/min [2360000], rate=8850000.00/min [2370000], rate=8887500.00/min [2380000], rate=8925000.00/min [2390000], rate=8962500.00/min [2400000], rate=9000000.00/min [2410000], rate=9037500.00/min [2420000], rate=9075000.00/min [2430000], rate=9112500.00/min [2440000], rate=9150000.00/min [2450000], rate=9187500.00/min [2460000], rate=9225000.00/min [2470000], rate=9262500.00/min [2480000], rate=8752941.18/min [2490000], rate=8788235.29/min [2500000], rate=8823529.41/min [2510000], rate=8858823.53/min [2520000], rate=8894117.65/min [2530000], rate=8929411.76/min [2540000], rate=8964705.88/min [2550000], rate=9000000.00/min [2560000], rate=9035294.12/min [2570000], rate=9070588.24/min [2580000], rate=9105882.35/min [2590000], rate=9141176.47/min [2600000], rate=9176470.59/min [2610000], rate=8700000.00/min [2620000], rate=8733333.33/min [2630000], rate=8766666.67/min [2640000], rate=8800000.00/min [2650000], rate=8833333.33/min [2660000], rate=8866666.67/min [2670000], rate=8900000.00/min [2680000], rate=8933333.33/min [2690000], rate=8966666.67/min [2700000], rate=9000000.00/min [2710000], rate=9033333.33/min [2720000], rate=9066666.67/min [2730000], rate=9100000.00/min [2740000], rate=8652631.58/min [2750000], rate=8684210.53/min [2760000], rate=8715789.47/min [2770000], rate=8747368.42/min [2780000], rate=8778947.37/min [2790000], rate=8810526.32/min [2800000], rate=8842105.26/min [2810000], rate=8873684.21/min [2820000], rate=8905263.16/min [2830000], rate=8936842.11/min [2840000], rate=8968421.05/min [2850000], rate=9000000.00/min [2860000], rate=9031578.95/min [2870000], rate=9063157.89/min [2880000], rate=9094736.84/min [2890000], rate=9126315.79/min [2900000], rate=9157894.74/min [2910000], rate=9189473.68/min [2920000], rate=9221052.63/min [2930000], rate=8790000.00/min [2940000], rate=8820000.00/min [2950000], rate=8850000.00/min [2960000], rate=8880000.00/min [2970000], rate=8910000.00/min [2980000], rate=8940000.00/min [2990000], rate=8970000.00/min [3000000], rate=9000000.00/min [3010000], rate=9030000.00/min [3020000], rate=9060000.00/min [3030000], rate=9090000.00/min [3040000], rate=9120000.00/min [3050000], rate=9150000.00/min [3060000], rate=9180000.00/min [3070000], rate=9210000.00/min [3080000], rate=9240000.00/min [3090000], rate=9270000.00/min [3100000], rate=9300000.00/min [3110000], rate=9330000.00/min [3120000], rate=9360000.00/min [3130000], rate=8942857.14/min [3140000], rate=8971428.57/min [3150000], rate=9000000.00/min [3160000], rate=9028571.43/min [3170000], rate=9057142.86/min [3180000], rate=9085714.29/min [3190000], rate=9114285.71/min [3200000], rate=9142857.14/min [3210000], rate=9171428.57/min [3220000], rate=9200000.00/min [3230000], rate=9228571.43/min [3240000], rate=9257142.86/min [3250000], rate=9285714.29/min [3260000], rate=9314285.71/min [3270000], rate=9342857.14/min [3280000], rate=9371428.57/min [3290000], rate=9400000.00/min [3300000], rate=9428571.43/min [3310000], rate=9457142.86/min [3320000], rate=9485714.29/min [3330000], rate=9514285.71/min [3340000], rate=9542857.14/min [3350000], rate=9136363.64/min [3360000], rate=9163636.36/min [3370000], rate=9190909.09/min [3380000], rate=9218181.82/min [3390000], rate=9245454.55/min [3400000], rate=9272727.27/min [3410000], rate=9300000.00/min [3420000], rate=9327272.73/min [3430000], rate=9354545.45/min [3440000], rate=9381818.18/min [3450000], rate=9409090.91/min [3460000], rate=9436363.64/min [3470000], rate=9463636.36/min [3480000], rate=9490909.09/min [3490000], rate=9518181.82/min [3500000], rate=9545454.55/min [3510000], rate=9572727.27/min [3520000], rate=9600000.00/min [3530000], rate=9627272.73/min [3540000], rate=9654545.45/min [3550000], rate=9681818.18/min [3560000], rate=9286956.52/min [3570000], rate=9313043.48/min [3580000], rate=9339130.43/min [3590000], rate=9365217.39/min [3600000], rate=9391304.35/min [3610000], rate=9417391.30/min [3620000], rate=9443478.26/min [3630000], rate=9469565.22/min [3640000], rate=9495652.17/min [3650000], rate=9521739.13/min [3660000], rate=9547826.09/min [3670000], rate=9573913.04/min [3680000], rate=9600000.00/min [3690000], rate=9626086.96/min [3700000], rate=9652173.91/min [3710000], rate=9678260.87/min [3720000], rate=9704347.83/min [3730000], rate=9730434.78/min [3740000], rate=9756521.74/min [3750000], rate=9782608.70/min [3760000], rate=9808695.65/min [3770000], rate=9834782.61/min [3780000], rate=9860869.57/min [3790000], rate=9886956.52/min [3800000], rate=9500000.00/min [3810000], rate=9525000.00/min [3820000], rate=9550000.00/min [3830000], rate=9575000.00/min [3840000], rate=9600000.00/min [3850000], rate=9625000.00/min [3860000], rate=9650000.00/min [3870000], rate=9675000.00/min [3880000], rate=9700000.00/min [3890000], rate=9725000.00/min [3900000], rate=9750000.00/min [3910000], rate=9775000.00/min [3920000], rate=9800000.00/min [3930000], rate=9825000.00/min [3940000], rate=9850000.00/min [3950000], rate=9875000.00/min [3960000], rate=9900000.00/min [3970000], rate=9925000.00/min [3980000], rate=9950000.00/min [3990000], rate=9975000.00/min [4000000], rate=10000000.00/min [4010000], rate=10025000.00/min [4020000], rate=10050000.00/min [4030000], rate=10075000.00/min [4040000], rate=9696000.00/min [4050000], rate=9720000.00/min [4060000], rate=9744000.00/min [4070000], rate=9768000.00/min [4080000], rate=9792000.00/min [4090000], rate=9816000.00/min [4100000], rate=9840000.00/min [4110000], rate=9864000.00/min [4120000], rate=9888000.00/min [4130000], rate=9912000.00/min [4140000], rate=9936000.00/min [4150000], rate=9960000.00/min [4160000], rate=9984000.00/min [4170000], rate=10008000.00/min [4180000], rate=10032000.00/min [4190000], rate=10056000.00/min [4200000], rate=10080000.00/min [4210000], rate=10104000.00/min [4220000], rate=10128000.00/min [4230000], rate=10152000.00/min [4240000], rate=10176000.00/min [4250000], rate=10200000.00/min [4260000], rate=10224000.00/min [4270000], rate=10248000.00/min [4280000], rate=10272000.00/min [4290000], rate=9900000.00/min [4300000], rate=9923076.92/min [4310000], rate=9946153.85/min [4320000], rate=9969230.77/min [4330000], rate=9992307.69/min [4340000], rate=10015384.62/min [4350000], rate=10038461.54/min [4360000], rate=10061538.46/min [4370000], rate=10084615.38/min [4380000], rate=10107692.31/min [4390000], rate=10130769.23/min [4400000], rate=10153846.15/min [4410000], rate=10176923.08/min [4420000], rate=10200000.00/min [4430000], rate=10223076.92/min [4440000], rate=10246153.85/min [4450000], rate=10269230.77/min [4460000], rate=10292307.69/min [4470000], rate=10315384.62/min [4480000], rate=10338461.54/min [4490000], rate=10361538.46/min [4500000], rate=10384615.38/min [4510000], rate=10407692.31/min [4520000], rate=10044444.44/min [4530000], rate=10066666.67/min [4540000], rate=10088888.89/min [4550000], rate=10111111.11/min [4560000], rate=10133333.33/min [4570000], rate=10155555.56/min [4580000], rate=10177777.78/min [4590000], rate=10200000.00/min [4600000], rate=10222222.22/min [4610000], rate=10244444.44/min [4620000], rate=10266666.67/min [4630000], rate=10288888.89/min [4640000], rate=10311111.11/min [4650000], rate=10333333.33/min [4660000], rate=10355555.56/min [4670000], rate=10377777.78/min [4680000], rate=10400000.00/min [4690000], rate=10050000.00/min [4700000], rate=10071428.57/min [4710000], rate=10092857.14/min [4720000], rate=10114285.71/min [4730000], rate=10135714.29/min [4740000], rate=10157142.86/min [4750000], rate=10178571.43/min [4760000], rate=10200000.00/min [4770000], rate=10221428.57/min [4780000], rate=10242857.14/min [4790000], rate=9910344.83/min [4800000], rate=9931034.48/min [4810000], rate=9951724.14/min [4820000], rate=9972413.79/min [4830000], rate=9993103.45/min [4840000], rate=10013793.10/min [4850000], rate=10034482.76/min [4860000], rate=10055172.41/min [4870000], rate=10075862.07/min [4880000], rate=10096551.72/min [4890000], rate=9780000.00/min [4900000], rate=9800000.00/min [4910000], rate=9820000.00/min [4920000], rate=9840000.00/min [4930000], rate=9860000.00/min [4940000], rate=9880000.00/min [4950000], rate=9900000.00/min [4960000], rate=9920000.00/min [4970000], rate=9940000.00/min [4980000], rate=9960000.00/min [4990000], rate=9980000.00/min [5000000], rate=9677419.35/min [5010000], rate=9696774.19/min [5020000], rate=9716129.03/min [5030000], rate=9735483.87/min [5040000], rate=9754838.71/min [5050000], rate=9774193.55/min [5060000], rate=9793548.39/min [5070000], rate=9812903.23/min [5080000], rate=9832258.06/min [5090000], rate=9851612.90/min [5100000], rate=9870967.74/min [5110000], rate=9581250.00/min [5120000], rate=9600000.00/min [5130000], rate=9618750.00/min [5140000], rate=9637500.00/min [5150000], rate=9656250.00/min [5160000], rate=9675000.00/min [5170000], rate=9693750.00/min [5180000], rate=9712500.00/min [5190000], rate=9731250.00/min [5200000], rate=9750000.00/min [5210000], rate=9768750.00/min [5220000], rate=9787500.00/min [5230000], rate=9806250.00/min [5240000], rate=9527272.73/min [5250000], rate=9545454.55/min [5260000], rate=9563636.36/min [5270000], rate=9581818.18/min [5280000], rate=9600000.00/min [5290000], rate=9618181.82/min [5300000], rate=9636363.64/min [5310000], rate=9654545.45/min [5320000], rate=9672727.27/min [5330000], rate=9690909.09/min [5340000], rate=9709090.91/min [5350000], rate=9727272.73/min [5360000], rate=9745454.55/min [5370000], rate=9476470.59/min [5380000], rate=9494117.65/min [5390000], rate=9511764.71/min [5400000], rate=9529411.76/min [5410000], rate=9547058.82/min [5420000], rate=9564705.88/min [5430000], rate=9582352.94/min [5440000], rate=9600000.00/min [5450000], rate=9617647.06/min [5460000], rate=9635294.12/min [5470000], rate=9652941.18/min [5480000], rate=9670588.24/min [5490000], rate=9688235.29/min [5500000], rate=9705882.35/min [5510000], rate=9723529.41/min [5520000], rate=9741176.47/min [5530000], rate=9758823.53/min [5540000], rate=9776470.59/min [5550000], rate=9514285.71/min [5560000], rate=9531428.57/min [5570000], rate=9548571.43/min [5580000], rate=9565714.29/min [5590000], rate=9582857.14/min [5600000], rate=9600000.00/min [5610000], rate=9617142.86/min [5620000], rate=9634285.71/min [5630000], rate=9651428.57/min [5640000], rate=9668571.43/min [5650000], rate=9685714.29/min [5660000], rate=9702857.14/min [5670000], rate=9720000.00/min [5680000], rate=9737142.86/min [5690000], rate=9754285.71/min [5700000], rate=9500000.00/min [5710000], rate=9516666.67/min [5720000], rate=9533333.33/min [5730000], rate=9550000.00/min [5740000], rate=9566666.67/min [5750000], rate=9583333.33/min [5760000], rate=9600000.00/min [5770000], rate=9616666.67/min [5780000], rate=9633333.33/min [5790000], rate=9650000.00/min [5800000], rate=9666666.67/min [5810000], rate=9683333.33/min [5820000], rate=9700000.00/min [5830000], rate=9716666.67/min [5840000], rate=9733333.33/min [5850000], rate=9486486.49/min [5860000], rate=9502702.70/min [5870000], rate=9518918.92/min [5880000], rate=9535135.14/min [5890000], rate=9551351.35/min [5900000], rate=9567567.57/min [5910000], rate=9583783.78/min [5920000], rate=9600000.00/min [5930000], rate=9616216.22/min [5940000], rate=9632432.43/min [5950000], rate=9648648.65/min [5960000], rate=9664864.86/min [5970000], rate=9681081.08/min [5980000], rate=9697297.30/min [5990000], rate=9713513.51/min [6000000], rate=9473684.21/min [6010000], rate=9489473.68/min [6020000], rate=9505263.16/min [6030000], rate=9521052.63/min [6040000], rate=9536842.11/min [6050000], rate=9552631.58/min [6060000], rate=9568421.05/min [6070000], rate=9584210.53/min [6080000], rate=9600000.00/min [6090000], rate=9615789.47/min [6100000], rate=9631578.95/min [6110000], rate=9647368.42/min [6120000], rate=9663157.89/min [6130000], rate=9678947.37/min [6140000], rate=9446153.85/min [6150000], rate=9461538.46/min [6160000], rate=9476923.08/min [6170000], rate=9492307.69/min [6180000], rate=9507692.31/min [6190000], rate=9523076.92/min [6200000], rate=9538461.54/min [6210000], rate=9553846.15/min [6220000], rate=9569230.77/min [6230000], rate=9584615.38/min [6240000], rate=9600000.00/min [6250000], rate=9615384.62/min [6260000], rate=9630769.23/min [6270000], rate=9405000.00/min [6280000], rate=9420000.00/min [6290000], rate=9435000.00/min [6300000], rate=9450000.00/min [6310000], rate=9465000.00/min [6320000], rate=9480000.00/min [6330000], rate=9495000.00/min [6340000], rate=9510000.00/min [6350000], rate=9525000.00/min [6360000], rate=9540000.00/min [6370000], rate=9555000.00/min [6380000], rate=9570000.00/min [6390000], rate=9585000.00/min [6400000], rate=9365853.66/min [6410000], rate=9380487.80/min [6420000], rate=9395121.95/min [6430000], rate=9409756.10/min [6440000], rate=9424390.24/min [6450000], rate=9439024.39/min [6460000], rate=9453658.54/min [6470000], rate=9468292.68/min [6480000], rate=9482926.83/min [6490000], rate=9497560.98/min [6500000], rate=9512195.12/min [6510000], rate=9526829.27/min [6520000], rate=9541463.41/min [6530000], rate=9556097.56/min [6540000], rate=9342857.14/min [6550000], rate=9357142.86/min [6560000], rate=9371428.57/min [6570000], rate=9385714.29/min [6580000], rate=9400000.00/min [6590000], rate=9414285.71/min [6600000], rate=9428571.43/min [6610000], rate=9442857.14/min [6620000], rate=9457142.86/min [6630000], rate=9471428.57/min [6640000], rate=9485714.29/min [6650000], rate=9500000.00/min [6660000], rate=9514285.71/min [6670000], rate=9528571.43/min [6680000], rate=9542857.14/min [6690000], rate=9334883.72/min [6700000], rate=9348837.21/min [6710000], rate=9362790.70/min [6720000], rate=9376744.19/min [6730000], rate=9390697.67/min [6740000], rate=9404651.16/min [6750000], rate=9418604.65/min [6760000], rate=9432558.14/min [6770000], rate=9446511.63/min [6780000], rate=9460465.12/min [6790000], rate=9474418.60/min [6800000], rate=9488372.09/min [6810000], rate=9502325.58/min [6820000], rate=9516279.07/min [6830000], rate=9313636.36/min [6840000], rate=9327272.73/min [6850000], rate=9340909.09/min [6860000], rate=9354545.45/min [6870000], rate=9368181.82/min [6880000], rate=9381818.18/min [6890000], rate=9395454.55/min [6900000], rate=9409090.91/min [6910000], rate=9422727.27/min [6920000], rate=9436363.64/min [6930000], rate=9450000.00/min [6940000], rate=9463636.36/min [6950000], rate=9477272.73/min [6960000], rate=9490909.09/min [6970000], rate=9504545.45/min [6980000], rate=9518181.82/min [6990000], rate=9531818.18/min [7000000], rate=9545454.55/min [7010000], rate=9559090.91/min [7020000], rate=9572727.27/min [7030000], rate=9586363.64/min [7040000], rate=9600000.00/min [7050000], rate=9613636.36/min [7060000], rate=9627272.73/min [7070000], rate=9426666.67/min [7080000], rate=9440000.00/min [7090000], rate=9453333.33/min [7100000], rate=9466666.67/min [7110000], rate=9480000.00/min [7120000], rate=9493333.33/min [7130000], rate=9506666.67/min [7140000], rate=9520000.00/min [7150000], rate=9533333.33/min [7160000], rate=9546666.67/min [7170000], rate=9560000.00/min [7180000], rate=9573333.33/min [7190000], rate=9586666.67/min [7200000], rate=9600000.00/min [7210000], rate=9613333.33/min [7220000], rate=9626666.67/min [7230000], rate=9640000.00/min [7240000], rate=9653333.33/min [7250000], rate=9666666.67/min [7260000], rate=9680000.00/min [7270000], rate=9482608.70/min [7280000], rate=9495652.17/min [7290000], rate=9508695.65/min [7300000], rate=9521739.13/min [7310000], rate=9534782.61/min [7320000], rate=9547826.09/min [7330000], rate=9560869.57/min [7340000], rate=9573913.04/min [7350000], rate=9586956.52/min [7360000], rate=9600000.00/min [7370000], rate=9613043.48/min [7380000], rate=9626086.96/min [7390000], rate=9639130.43/min [7400000], rate=9652173.91/min [7410000], rate=9665217.39/min [7420000], rate=9678260.87/min [7430000], rate=9691304.35/min [7440000], rate=9704347.83/min [7450000], rate=9717391.30/min [7460000], rate=9730434.78/min [7470000], rate=9743478.26/min [7480000], rate=9756521.74/min [7490000], rate=9769565.22/min [7500000], rate=9782608.70/min [7510000], rate=9587234.04/min [7520000], rate=9600000.00/min [7530000], rate=9612765.96/min [7540000], rate=9625531.91/min [7550000], rate=9638297.87/min [7560000], rate=9651063.83/min [7570000], rate=9663829.79/min [7580000], rate=9676595.74/min [7590000], rate=9689361.70/min [7600000], rate=9702127.66/min [7610000], rate=9714893.62/min [7620000], rate=9727659.57/min [7630000], rate=9740425.53/min [7640000], rate=9753191.49/min [7650000], rate=9765957.45/min [7660000], rate=9778723.40/min [7670000], rate=9791489.36/min [7680000], rate=9804255.32/min [7690000], rate=9817021.28/min [7700000], rate=9829787.23/min [7710000], rate=9842553.19/min [7720000], rate=9855319.15/min [7730000], rate=9868085.11/min [7740000], rate=9880851.06/min [7750000], rate=9687500.00/min [7760000], rate=9700000.00/min [7770000], rate=9712500.00/min [7780000], rate=9725000.00/min [7790000], rate=9737500.00/min [7800000], rate=9750000.00/min [7810000], rate=9762500.00/min [7820000], rate=9775000.00/min [7830000], rate=9787500.00/min [7840000], rate=9800000.00/min [7850000], rate=9812500.00/min [7860000], rate=9825000.00/min [7870000], rate=9837500.00/min [7880000], rate=9850000.00/min [7890000], rate=9862500.00/min [7900000], rate=9875000.00/min [7910000], rate=9887500.00/min [7920000], rate=9900000.00/min [7930000], rate=9912500.00/min [7940000], rate=9925000.00/min [7950000], rate=9937500.00/min [7960000], rate=9950000.00/min [7970000], rate=9962500.00/min [7980000], rate=9975000.00/min [7990000], rate=9987500.00/min [8000000], rate=9795918.37/min [8010000], rate=9808163.27/min [8020000], rate=9820408.16/min [8030000], rate=9832653.06/min [8040000], rate=9844897.96/min [8050000], rate=9857142.86/min [8060000], rate=9869387.76/min [8070000], rate=9881632.65/min [8080000], rate=9893877.55/min [8090000], rate=9906122.45/min [8100000], rate=9918367.35/min [8110000], rate=9930612.24/min [8120000], rate=9942857.14/min [8130000], rate=9955102.04/min [8140000], rate=9967346.94/min [8150000], rate=9979591.84/min [8160000], rate=9991836.73/min [8170000], rate=10004081.63/min [8180000], rate=10016326.53/min [8190000], rate=10028571.43/min [8200000], rate=10040816.33/min [8210000], rate=10053061.22/min [8220000], rate=10065306.12/min [8230000], rate=10077551.02/min [8240000], rate=9888000.00/min [8250000], rate=9900000.00/min [8260000], rate=9912000.00/min [8270000], rate=9924000.00/min [8280000], rate=9936000.00/min [8290000], rate=9948000.00/min [8300000], rate=9960000.00/min [8310000], rate=9972000.00/min [8320000], rate=9984000.00/min [8330000], rate=9996000.00/min [8340000], rate=10008000.00/min [8350000], rate=10020000.00/min [8360000], rate=10032000.00/min [8370000], rate=10044000.00/min [8380000], rate=10056000.00/min [8390000], rate=10068000.00/min [8400000], rate=10080000.00/min [8410000], rate=10092000.00/min [8420000], rate=10104000.00/min [8430000], rate=10116000.00/min [8440000], rate=10128000.00/min [8450000], rate=10140000.00/min [8460000], rate=10152000.00/min [8470000], rate=10164000.00/min [8480000], rate=10176000.00/min [8490000], rate=10188000.00/min [8500000], rate=10000000.00/min [8510000], rate=10011764.71/min [8520000], rate=10023529.41/min 09:08:52 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-6c4b48-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-6c4b48-R1_A23YTGFLT4_1.introns: identified 8169 cancer introns 09:08:53 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer.introns.prelim 09:08:53 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 09:08:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer.introns 09:08:54 : 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-6c4b48-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer.introns 09:08:54 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 09:08:54 : INFO : -found 3989 cancer introns 09:08:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:08:54 : INFO : Creating the BED File. 09:09:10 : INFO : Saving Bed File as aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:09:11 : INFO : Execution Time = 0.28 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:09:11 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 09:09:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-6c4b48-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 09:44:51 : INFO : Execution Time = 35.68 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-6c4b48-R1_A23YTGFLT4_1 09:44:51 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 09:44:51 : INFO : Running: samtools sort -o aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:44:53 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:44:53 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 09:44:53 : INFO : Running: samtools sort -o aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 145 files and 1 in-memory blocks... 10:19:45 : INFO : Execution Time = 34.87 minutes. CMD: samtools sort -o aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.bam 10:19:45 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok 10:19:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.bam 10:30:25 : INFO : Execution Time = 10.67 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.bam 10:30:25 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:30:25 : INFO : Running: samtools sort -o aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 4 files and 1 in-memory blocks... 10:31:42 : INFO : Execution Time = 1.28 minutes. CMD: samtools sort -o aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp 10:31:42 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:31:42 : INFO : Running: samtools index aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 10:31:50 : INFO : Execution Time = 0.14 minutes. CMD: samtools index aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 10:31:50 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:31:50 : INFO : Running: samtools index aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 10:31:50 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 10:31:50 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:31:50 : INFO : Running: create_report aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-6c4b48-R1_A23YTGFLT4_1' [W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi 10:39:09 : INFO : Execution Time = 7.32 minutes. CMD: create_report aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-6c4b48-R1_A23YTGFLT4_1' 10:39:09 : INFO : Running: touch /tmp/nxf.gb4wHAPMHg/aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok 10:39:09 : INFO : done.