08:04:56 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=17400000.00/min [300000], rate=18000000.00/min [310000], rate=18600000.00/min [320000], rate=19200000.00/min [330000], rate=19800000.00/min [340000], rate=20400000.00/min [350000], rate=21000000.00/min [360000], rate=21600000.00/min [370000], rate=22200000.00/min [380000], rate=22800000.00/min [390000], rate=23400000.00/min [400000], rate=24000000.00/min [410000], rate=24600000.00/min [420000], rate=25200000.00/min [430000], rate=25800000.00/min [440000], rate=26400000.00/min [450000], rate=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=14400000.00/min [730000], rate=14600000.00/min [740000], rate=14800000.00/min [750000], rate=15000000.00/min [760000], rate=15200000.00/min [770000], rate=15400000.00/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=15000000.00/min [1010000], rate=15150000.00/min [1020000], rate=15300000.00/min [1030000], rate=15450000.00/min [1040000], rate=15600000.00/min [1050000], rate=15750000.00/min [1060000], rate=15900000.00/min [1070000], rate=16050000.00/min [1080000], rate=16200000.00/min [1090000], rate=16350000.00/min [1100000], rate=16500000.00/min [1110000], rate=16650000.00/min [1120000], rate=16800000.00/min [1130000], rate=16950000.00/min [1140000], rate=17100000.00/min [1150000], rate=17250000.00/min [1160000], rate=17400000.00/min [1170000], rate=17550000.00/min [1180000], rate=17700000.00/min [1190000], rate=17850000.00/min [1200000], rate=18000000.00/min [1210000], rate=18150000.00/min [1220000], rate=18300000.00/min [1230000], rate=18450000.00/min [1240000], rate=18600000.00/min [1250000], rate=18750000.00/min [1260000], rate=18900000.00/min [1270000], rate=19050000.00/min [1280000], rate=15360000.00/min [1290000], rate=15480000.00/min [1300000], rate=15600000.00/min [1310000], rate=15720000.00/min [1320000], rate=15840000.00/min [1330000], rate=15960000.00/min [1340000], rate=16080000.00/min [1350000], rate=16200000.00/min [1360000], rate=16320000.00/min [1370000], rate=16440000.00/min [1380000], rate=16560000.00/min [1390000], rate=16680000.00/min [1400000], rate=16800000.00/min [1410000], rate=16920000.00/min [1420000], rate=17040000.00/min [1430000], rate=17160000.00/min [1440000], rate=17280000.00/min [1450000], rate=17400000.00/min [1460000], rate=17520000.00/min [1470000], rate=17640000.00/min [1480000], rate=17760000.00/min [1490000], rate=17880000.00/min [1500000], rate=18000000.00/min [1510000], rate=18120000.00/min [1520000], rate=18240000.00/min [1530000], rate=18360000.00/min [1540000], rate=18480000.00/min [1550000], rate=18600000.00/min [1560000], rate=15600000.00/min [1570000], rate=15700000.00/min [1580000], rate=15800000.00/min [1590000], rate=15900000.00/min [1600000], rate=16000000.00/min [1610000], rate=16100000.00/min [1620000], rate=16200000.00/min [1630000], rate=16300000.00/min [1640000], rate=16400000.00/min [1650000], rate=16500000.00/min [1660000], rate=16600000.00/min [1670000], rate=16700000.00/min [1680000], rate=16800000.00/min [1690000], rate=16900000.00/min [1700000], rate=17000000.00/min [1710000], rate=17100000.00/min [1720000], rate=17200000.00/min [1730000], rate=17300000.00/min [1740000], rate=17400000.00/min [1750000], rate=17500000.00/min [1760000], rate=17600000.00/min [1770000], rate=17700000.00/min [1780000], rate=17800000.00/min [1790000], rate=17900000.00/min [1800000], rate=18000000.00/min [1810000], rate=18100000.00/min [1820000], rate=18200000.00/min [1830000], rate=18300000.00/min [1840000], rate=18400000.00/min [1850000], rate=18500000.00/min [1860000], rate=18600000.00/min [1870000], rate=18700000.00/min [1880000], rate=18800000.00/min [1890000], rate=18900000.00/min [1900000], rate=19000000.00/min [1910000], rate=19100000.00/min [1920000], rate=19200000.00/min [1930000], rate=19300000.00/min [1940000], rate=19400000.00/min [1950000], rate=19500000.00/min [1960000], rate=16800000.00/min [1970000], rate=16885714.29/min [1980000], rate=16971428.57/min [1990000], rate=17057142.86/min [2000000], rate=17142857.14/min [2010000], rate=17228571.43/min [2020000], rate=17314285.71/min [2030000], rate=17400000.00/min [2040000], rate=17485714.29/min [2050000], rate=17571428.57/min [2060000], rate=17657142.86/min [2070000], rate=17742857.14/min [2080000], rate=17828571.43/min [2090000], rate=17914285.71/min [2100000], rate=18000000.00/min [2110000], rate=18085714.29/min [2120000], rate=18171428.57/min [2130000], rate=18257142.86/min [2140000], rate=18342857.14/min [2150000], rate=18428571.43/min [2160000], rate=18514285.71/min [2170000], rate=18600000.00/min [2180000], rate=18685714.29/min [2190000], rate=18771428.57/min [2200000], rate=18857142.86/min [2210000], rate=18942857.14/min [2220000], rate=19028571.43/min [2230000], rate=19114285.71/min [2240000], rate=19200000.00/min [2250000], rate=19285714.29/min [2260000], rate=19371428.57/min [2270000], rate=19457142.86/min [2280000], rate=19542857.14/min [2290000], rate=19628571.43/min [2300000], rate=19714285.71/min [2310000], rate=19800000.00/min [2320000], rate=19885714.29/min [2330000], rate=19971428.57/min [2340000], rate=20057142.86/min [2350000], rate=17625000.00/min [2360000], rate=17700000.00/min [2370000], rate=17775000.00/min [2380000], rate=17850000.00/min [2390000], rate=17925000.00/min [2400000], rate=18000000.00/min [2410000], rate=18075000.00/min [2420000], rate=18150000.00/min [2430000], rate=18225000.00/min [2440000], rate=18300000.00/min [2450000], rate=18375000.00/min [2460000], rate=18450000.00/min [2470000], rate=18525000.00/min [2480000], rate=18600000.00/min [2490000], rate=18675000.00/min [2500000], rate=18750000.00/min [2510000], rate=18825000.00/min [2520000], rate=18900000.00/min [2530000], rate=18975000.00/min [2540000], rate=19050000.00/min [2550000], rate=19125000.00/min [2560000], rate=19200000.00/min [2570000], rate=19275000.00/min [2580000], rate=19350000.00/min [2590000], rate=19425000.00/min [2600000], rate=19500000.00/min [2610000], rate=19575000.00/min [2620000], rate=19650000.00/min [2630000], rate=19725000.00/min [2640000], rate=19800000.00/min [2650000], rate=19875000.00/min [2660000], rate=19950000.00/min [2670000], rate=20025000.00/min [2680000], rate=20100000.00/min [2690000], rate=20175000.00/min [2700000], rate=20250000.00/min [2710000], rate=20325000.00/min [2720000], rate=18133333.33/min [2730000], rate=18200000.00/min [2740000], rate=18266666.67/min [2750000], rate=18333333.33/min [2760000], rate=18400000.00/min [2770000], rate=18466666.67/min [2780000], rate=18533333.33/min [2790000], rate=18600000.00/min [2800000], rate=18666666.67/min [2810000], rate=18733333.33/min [2820000], rate=18800000.00/min [2830000], rate=18866666.67/min [2840000], rate=18933333.33/min [2850000], rate=19000000.00/min [2860000], rate=19066666.67/min [2870000], rate=19133333.33/min [2880000], rate=19200000.00/min [2890000], rate=19266666.67/min [2900000], rate=19333333.33/min [2910000], rate=19400000.00/min [2920000], rate=19466666.67/min [2930000], rate=19533333.33/min [2940000], rate=19600000.00/min [2950000], rate=19666666.67/min [2960000], rate=19733333.33/min [2970000], rate=19800000.00/min [2980000], rate=19866666.67/min [2990000], rate=19933333.33/min [3000000], rate=20000000.00/min [3010000], rate=20066666.67/min [3020000], rate=20133333.33/min [3030000], rate=20200000.00/min [3040000], rate=20266666.67/min [3050000], rate=20333333.33/min [3060000], rate=20400000.00/min [3070000], rate=20466666.67/min [3080000], rate=20533333.33/min [3090000], rate=20600000.00/min [3100000], rate=20666666.67/min [3110000], rate=18660000.00/min [3120000], rate=18720000.00/min [3130000], rate=18780000.00/min [3140000], rate=18840000.00/min [3150000], rate=18900000.00/min [3160000], rate=18960000.00/min [3170000], rate=19020000.00/min [3180000], rate=19080000.00/min [3190000], rate=19140000.00/min [3200000], rate=19200000.00/min [3210000], rate=19260000.00/min [3220000], rate=19320000.00/min [3230000], rate=19380000.00/min [3240000], rate=19440000.00/min [3250000], rate=19500000.00/min [3260000], rate=19560000.00/min [3270000], rate=19620000.00/min [3280000], rate=19680000.00/min [3290000], rate=19740000.00/min [3300000], rate=19800000.00/min [3310000], rate=19860000.00/min [3320000], rate=19920000.00/min [3330000], rate=19980000.00/min [3340000], rate=20040000.00/min [3350000], rate=20100000.00/min [3360000], rate=20160000.00/min [3370000], rate=20220000.00/min [3380000], rate=20280000.00/min [3390000], rate=20340000.00/min [3400000], rate=20400000.00/min [3410000], rate=20460000.00/min [3420000], rate=20520000.00/min [3430000], rate=20580000.00/min [3440000], rate=20640000.00/min [3450000], rate=20700000.00/min [3460000], rate=20760000.00/min [3470000], rate=20820000.00/min [3480000], rate=20880000.00/min [3490000], rate=20940000.00/min [3500000], rate=21000000.00/min [3510000], rate=19145454.55/min [3520000], rate=19200000.00/min [3530000], rate=19254545.45/min [3540000], rate=19309090.91/min [3550000], rate=19363636.36/min [3560000], rate=19418181.82/min [3570000], rate=19472727.27/min [3580000], rate=19527272.73/min [3590000], rate=19581818.18/min [3600000], rate=19636363.64/min [3610000], rate=19690909.09/min [3620000], rate=19745454.55/min [3630000], rate=19800000.00/min [3640000], rate=19854545.45/min [3650000], rate=19909090.91/min [3660000], rate=19963636.36/min [3670000], rate=20018181.82/min [3680000], rate=20072727.27/min [3690000], rate=20127272.73/min [3700000], rate=20181818.18/min [3710000], rate=20236363.64/min [3720000], rate=20290909.09/min [3730000], rate=20345454.55/min [3740000], rate=20400000.00/min [3750000], rate=20454545.45/min [3760000], rate=20509090.91/min [3770000], rate=20563636.36/min [3780000], rate=20618181.82/min [3790000], rate=20672727.27/min [3800000], rate=20727272.73/min [3810000], rate=20781818.18/min [3820000], rate=20836363.64/min [3830000], rate=20890909.09/min [3840000], rate=20945454.55/min [3850000], rate=21000000.00/min [3860000], rate=21054545.45/min [3870000], rate=19350000.00/min [3880000], rate=19400000.00/min [3890000], rate=19450000.00/min [3900000], rate=19500000.00/min [3910000], rate=19550000.00/min [3920000], rate=19600000.00/min [3930000], rate=19650000.00/min [3940000], rate=19700000.00/min [3950000], rate=19750000.00/min [3960000], rate=19800000.00/min [3970000], rate=19850000.00/min [3980000], rate=19900000.00/min [3990000], rate=19950000.00/min [4000000], rate=20000000.00/min [4010000], rate=20050000.00/min [4020000], rate=20100000.00/min [4030000], rate=20150000.00/min [4040000], rate=20200000.00/min [4050000], rate=20250000.00/min [4060000], rate=20300000.00/min [4070000], rate=20350000.00/min [4080000], rate=20400000.00/min [4090000], rate=20450000.00/min [4100000], rate=20500000.00/min [4110000], rate=20550000.00/min [4120000], rate=20600000.00/min [4130000], rate=19061538.46/min [4140000], rate=19107692.31/min [4150000], rate=19153846.15/min [4160000], rate=19200000.00/min [4170000], rate=19246153.85/min [4180000], rate=19292307.69/min [4190000], rate=19338461.54/min [4200000], rate=19384615.38/min [4210000], rate=19430769.23/min [4220000], rate=19476923.08/min [4230000], rate=19523076.92/min [4240000], rate=19569230.77/min [4250000], rate=19615384.62/min [4260000], rate=19661538.46/min [4270000], rate=19707692.31/min [4280000], rate=19753846.15/min [4290000], rate=19800000.00/min [4300000], rate=19846153.85/min [4310000], rate=19892307.69/min [4320000], rate=19938461.54/min [4330000], rate=19984615.38/min [4340000], rate=20030769.23/min [4350000], rate=20076923.08/min [4360000], rate=20123076.92/min [4370000], rate=20169230.77/min [4380000], rate=20215384.62/min [4390000], rate=20261538.46/min [4400000], rate=20307692.31/min [4410000], rate=20353846.15/min [4420000], rate=18942857.14/min [4430000], rate=18985714.29/min [4440000], rate=19028571.43/min [4450000], rate=19071428.57/min [4460000], rate=19114285.71/min [4470000], rate=19157142.86/min [4480000], rate=19200000.00/min [4490000], rate=19242857.14/min [4500000], rate=19285714.29/min [4510000], rate=19328571.43/min [4520000], rate=19371428.57/min [4530000], rate=19414285.71/min [4540000], rate=19457142.86/min [4550000], rate=19500000.00/min [4560000], rate=19542857.14/min [4570000], rate=19585714.29/min [4580000], rate=19628571.43/min [4590000], rate=19671428.57/min [4600000], rate=19714285.71/min [4610000], rate=19757142.86/min [4620000], rate=19800000.00/min [4630000], rate=19842857.14/min [4640000], rate=19885714.29/min [4650000], rate=19928571.43/min [4660000], rate=19971428.57/min [4670000], rate=20014285.71/min [4680000], rate=20057142.86/min [4690000], rate=20100000.00/min [4700000], rate=20142857.14/min [4710000], rate=20185714.29/min [4720000], rate=18880000.00/min [4730000], rate=18920000.00/min [4740000], rate=18960000.00/min [4750000], rate=19000000.00/min [4760000], rate=19040000.00/min [4770000], rate=19080000.00/min [4780000], rate=19120000.00/min [4790000], rate=19160000.00/min [4800000], rate=19200000.00/min [4810000], rate=19240000.00/min [4820000], rate=19280000.00/min [4830000], rate=19320000.00/min [4840000], rate=19360000.00/min [4850000], rate=19400000.00/min [4860000], rate=19440000.00/min [4870000], rate=19480000.00/min [4880000], rate=19520000.00/min [4890000], rate=19560000.00/min [4900000], rate=19600000.00/min [4910000], rate=19640000.00/min [4920000], rate=19680000.00/min [4930000], rate=19720000.00/min [4940000], rate=19760000.00/min [4950000], rate=19800000.00/min [4960000], rate=19840000.00/min [4970000], rate=19880000.00/min [4980000], rate=19920000.00/min [4990000], rate=19960000.00/min [5000000], rate=20000000.00/min [5010000], rate=20040000.00/min [5020000], rate=20080000.00/min [5030000], rate=20120000.00/min [5040000], rate=18900000.00/min [5050000], rate=18937500.00/min [5060000], rate=18975000.00/min [5070000], rate=19012500.00/min [5080000], rate=19050000.00/min [5090000], rate=19087500.00/min [5100000], rate=19125000.00/min [5110000], rate=19162500.00/min [5120000], rate=19200000.00/min [5130000], rate=19237500.00/min [5140000], rate=19275000.00/min [5150000], rate=19312500.00/min [5160000], rate=19350000.00/min [5170000], rate=19387500.00/min [5180000], rate=19425000.00/min [5190000], rate=19462500.00/min [5200000], rate=19500000.00/min [5210000], rate=19537500.00/min [5220000], rate=19575000.00/min [5230000], rate=19612500.00/min [5240000], rate=19650000.00/min [5250000], rate=19687500.00/min [5260000], rate=19725000.00/min [5270000], rate=19762500.00/min [5280000], rate=19800000.00/min [5290000], rate=19837500.00/min [5300000], rate=19875000.00/min [5310000], rate=19912500.00/min [5320000], rate=18776470.59/min [5330000], rate=18811764.71/min [5340000], rate=18847058.82/min [5350000], rate=18882352.94/min [5360000], rate=18917647.06/min [5370000], rate=18952941.18/min [5380000], rate=18988235.29/min [5390000], rate=19023529.41/min [5400000], rate=19058823.53/min [5410000], rate=19094117.65/min [5420000], rate=19129411.76/min [5430000], rate=19164705.88/min [5440000], rate=19200000.00/min [5450000], rate=19235294.12/min [5460000], rate=19270588.24/min [5470000], rate=19305882.35/min [5480000], rate=19341176.47/min [5490000], rate=19376470.59/min [5500000], rate=19411764.71/min [5510000], rate=19447058.82/min [5520000], rate=19482352.94/min [5530000], rate=19517647.06/min [5540000], rate=19552941.18/min [5550000], rate=19588235.29/min [5560000], rate=19623529.41/min [5570000], rate=19658823.53/min [5580000], rate=19694117.65/min [5590000], rate=19729411.76/min [5600000], rate=19764705.88/min [5610000], rate=19800000.00/min [5620000], rate=19835294.12/min [5630000], rate=18766666.67/min [5640000], rate=18800000.00/min [5650000], rate=18833333.33/min [5660000], rate=18866666.67/min [5670000], rate=18900000.00/min [5680000], rate=18933333.33/min [5690000], rate=18966666.67/min [5700000], rate=19000000.00/min [5710000], rate=19033333.33/min [5720000], rate=19066666.67/min [5730000], rate=19100000.00/min [5740000], rate=19133333.33/min [5750000], rate=19166666.67/min [5760000], rate=19200000.00/min [5770000], rate=19233333.33/min [5780000], rate=19266666.67/min [5790000], rate=19300000.00/min [5800000], rate=19333333.33/min [5810000], rate=19366666.67/min [5820000], rate=19400000.00/min [5830000], rate=19433333.33/min [5840000], rate=19466666.67/min [5850000], rate=19500000.00/min [5860000], rate=19533333.33/min [5870000], rate=19566666.67/min [5880000], rate=19600000.00/min [5890000], rate=19633333.33/min [5900000], rate=19666666.67/min [5910000], rate=19700000.00/min [5920000], rate=19733333.33/min [5930000], rate=19766666.67/min [5940000], rate=19800000.00/min [5950000], rate=18789473.68/min [5960000], rate=18821052.63/min [5970000], rate=18852631.58/min [5980000], rate=18884210.53/min [5990000], rate=18915789.47/min [6000000], rate=18947368.42/min [6010000], rate=18978947.37/min [6020000], rate=19010526.32/min [6030000], rate=19042105.26/min [6040000], rate=19073684.21/min [6050000], rate=19105263.16/min [6060000], rate=19136842.11/min [6070000], rate=19168421.05/min [6080000], rate=19200000.00/min [6090000], rate=19231578.95/min [6100000], rate=19263157.89/min [6110000], rate=19294736.84/min [6120000], rate=19326315.79/min [6130000], rate=19357894.74/min [6140000], rate=19389473.68/min [6150000], rate=19421052.63/min [6160000], rate=19452631.58/min [6170000], rate=19484210.53/min [6180000], rate=19515789.47/min [6190000], rate=19547368.42/min [6200000], rate=19578947.37/min [6210000], rate=19610526.32/min [6220000], rate=19642105.26/min [6230000], rate=19673684.21/min [6240000], rate=19705263.16/min [6250000], rate=18750000.00/min [6260000], rate=18780000.00/min [6270000], rate=18810000.00/min [6280000], rate=18840000.00/min [6290000], rate=18870000.00/min [6300000], rate=18900000.00/min [6310000], rate=18930000.00/min [6320000], rate=18960000.00/min [6330000], rate=18990000.00/min [6340000], rate=19020000.00/min [6350000], rate=19050000.00/min [6360000], rate=19080000.00/min [6370000], rate=19110000.00/min [6380000], rate=19140000.00/min [6390000], rate=19170000.00/min [6400000], rate=19200000.00/min [6410000], rate=19230000.00/min [6420000], rate=19260000.00/min [6430000], rate=19290000.00/min [6440000], rate=19320000.00/min [6450000], rate=19350000.00/min [6460000], rate=19380000.00/min [6470000], rate=19410000.00/min [6480000], rate=19440000.00/min [6490000], rate=18542857.14/min [6500000], rate=18571428.57/min [6510000], rate=18600000.00/min [6520000], rate=18628571.43/min [6530000], rate=18657142.86/min [6540000], rate=18685714.29/min [6550000], rate=18714285.71/min [6560000], rate=18742857.14/min [6570000], rate=18771428.57/min [6580000], rate=18800000.00/min [6590000], rate=18828571.43/min [6600000], rate=18857142.86/min [6610000], rate=18885714.29/min [6620000], rate=18914285.71/min [6630000], rate=18942857.14/min 08:05:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00667_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00667_B23MVV7LT4_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. -tih_rna_sample_00667_B23MVV7LT4_1.introns: identified 1868 cancer introns 08:05:25 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00667_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00667_B23MVV7LT4_1.cancer.introns.prelim 08:05:25 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/prelim_introns.ok 08:05:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00667_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00667_B23MVV7LT4_1.cancer.introns 08:05:26 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00667_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00667_B23MVV7LT4_1.cancer.introns 08:05:26 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/introns_filtered.ok 08:05:26 : INFO : -found 1090 cancer introns 08:05:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00667_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00667_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00667_B23MVV7LT4_1.introns.for_IGV.bed 08:05:26 : INFO : Creating the BED File. 08:05:29 : INFO : Saving Bed File as tih_rna_sample_00667_B23MVV7LT4_1.introns.for_IGV.bed 08:05:29 : INFO : Execution Time = 0.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00667_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00667_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00667_B23MVV7LT4_1.introns.for_IGV.bed 08:05:29 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 08:05:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00667_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00667_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00667_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00667_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 08:08:44 : INFO : Execution Time = 3.24 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00667_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00667_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00667_B23MVV7LT4_1 08:08:44 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 08:08:44 : INFO : Running: samtools sort -o tih_rna_sample_00667_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00667_B23MVV7LT4_1.cancer_intron_reads.bam 08:08:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o tih_rna_sample_00667_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00667_B23MVV7LT4_1.cancer_intron_reads.bam 08:08:44 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 08:08:44 : INFO : Running: samtools sort -o tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 16 files and 1 in-memory blocks... 08:12:11 : INFO : Execution Time = 3.44 minutes. CMD: samtools sort -o tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.bam 08:12:11 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 08:12:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.bam 08:13:29 : INFO : Execution Time = 1.30 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.bam 08:13:29 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 08:13:29 : INFO : Running: samtools sort -o tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 08:13:42 : INFO : Execution Time = 0.22 minutes. CMD: samtools sort -o tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 08:13:42 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:13:42 : INFO : Running: samtools index tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 08:13:44 : INFO : Execution Time = 0.03 minutes. CMD: samtools index tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 08:13:44 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/tih_rna_sample_00667_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 08:13:44 : INFO : Running: samtools index tih_rna_sample_00667_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 08:13:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00667_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 08:13:44 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/tih_rna_sample_00667_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 08:13:44 : INFO : Running: create_report tih_rna_sample_00667_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00667_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00667_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00667_B23MVV7LT4_1' 08:15:16 : INFO : Execution Time = 1.54 minutes. CMD: create_report tih_rna_sample_00667_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00667_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00667_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00667_B23MVV7LT4_1' 08:15:16 : INFO : Running: touch /tmp/nxf.gOljgiwqm8/tih_rna_sample_00667_B23MVV7LT4_1.chckpts/igv_create_html.ok 08:15:16 : INFO : done.