08:43:04 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [440000], rate=26400000.00/min [450000], rate=27000000.00/min [460000], rate=27600000.00/min [470000], rate=28200000.00/min [480000], rate=28800000.00/min [490000], rate=29400000.00/min [500000], rate=30000000.00/min [510000], rate=30600000.00/min [520000], rate=31200000.00/min [530000], rate=31800000.00/min [540000], rate=32400000.00/min [550000], rate=33000000.00/min [560000], rate=33600000.00/min [570000], rate=34200000.00/min [580000], rate=34800000.00/min [590000], rate=35400000.00/min [600000], rate=36000000.00/min [610000], rate=36600000.00/min [620000], rate=37200000.00/min [630000], rate=37800000.00/min [640000], rate=38400000.00/min [650000], rate=39000000.00/min [660000], rate=39600000.00/min [670000], rate=40200000.00/min [680000], rate=40800000.00/min [690000], rate=41400000.00/min [700000], rate=42000000.00/min [710000], rate=42600000.00/min [720000], rate=43200000.00/min [730000], rate=43800000.00/min [740000], rate=44400000.00/min [750000], rate=45000000.00/min [760000], rate=45600000.00/min [770000], rate=46200000.00/min [780000], rate=46800000.00/min [790000], rate=47400000.00/min [800000], rate=48000000.00/min [810000], rate=48600000.00/min [820000], rate=49200000.00/min [830000], rate=49800000.00/min [840000], rate=50400000.00/min [850000], rate=51000000.00/min [860000], rate=51600000.00/min [870000], rate=26100000.00/min [880000], rate=26400000.00/min [890000], rate=26700000.00/min [900000], rate=27000000.00/min [910000], rate=27300000.00/min [920000], rate=27600000.00/min [930000], rate=27900000.00/min [940000], rate=28200000.00/min [950000], rate=28500000.00/min [960000], rate=28800000.00/min [970000], rate=29100000.00/min [980000], rate=29400000.00/min [990000], rate=29700000.00/min [1000000], rate=30000000.00/min [1010000], rate=30300000.00/min [1020000], rate=30600000.00/min [1030000], rate=30900000.00/min [1040000], rate=31200000.00/min [1050000], rate=31500000.00/min [1060000], rate=31800000.00/min [1070000], rate=32100000.00/min [1080000], rate=32400000.00/min [1090000], rate=32700000.00/min [1100000], rate=33000000.00/min [1110000], rate=33300000.00/min [1120000], rate=33600000.00/min [1130000], rate=33900000.00/min [1140000], rate=34200000.00/min [1150000], rate=34500000.00/min [1160000], rate=34800000.00/min [1170000], rate=35100000.00/min [1180000], rate=35400000.00/min [1190000], rate=35700000.00/min [1200000], rate=36000000.00/min [1210000], rate=36300000.00/min [1220000], rate=36600000.00/min [1230000], rate=36900000.00/min [1240000], rate=37200000.00/min [1250000], rate=25000000.00/min [1260000], rate=25200000.00/min [1270000], rate=25400000.00/min [1280000], rate=25600000.00/min [1290000], rate=25800000.00/min [1300000], rate=26000000.00/min [1310000], rate=26200000.00/min [1320000], rate=26400000.00/min [1330000], rate=26600000.00/min [1340000], rate=26800000.00/min [1350000], rate=27000000.00/min [1360000], rate=27200000.00/min [1370000], rate=27400000.00/min [1380000], rate=27600000.00/min [1390000], rate=27800000.00/min [1400000], rate=28000000.00/min [1410000], rate=28200000.00/min [1420000], rate=28400000.00/min [1430000], rate=28600000.00/min [1440000], rate=28800000.00/min [1450000], rate=29000000.00/min [1460000], rate=29200000.00/min [1470000], rate=29400000.00/min [1480000], rate=29600000.00/min [1490000], rate=29800000.00/min [1500000], rate=30000000.00/min [1510000], rate=30200000.00/min [1520000], rate=30400000.00/min [1530000], rate=30600000.00/min [1540000], rate=30800000.00/min [1550000], rate=31000000.00/min [1560000], rate=31200000.00/min [1570000], rate=31400000.00/min [1580000], rate=31600000.00/min [1590000], rate=31800000.00/min [1600000], rate=32000000.00/min [1610000], rate=32200000.00/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=25500000.00/min [1710000], rate=25650000.00/min [1720000], rate=25800000.00/min [1730000], rate=25950000.00/min [1740000], rate=26100000.00/min [1750000], rate=26250000.00/min [1760000], rate=26400000.00/min [1770000], rate=26550000.00/min [1780000], rate=26700000.00/min [1790000], rate=26850000.00/min [1800000], rate=27000000.00/min [1810000], rate=27150000.00/min [1820000], rate=27300000.00/min [1830000], rate=27450000.00/min [1840000], rate=27600000.00/min [1850000], rate=27750000.00/min [1860000], rate=27900000.00/min [1870000], rate=28050000.00/min [1880000], rate=28200000.00/min [1890000], rate=28350000.00/min [1900000], rate=28500000.00/min [1910000], rate=28650000.00/min [1920000], rate=28800000.00/min [1930000], rate=28950000.00/min [1940000], rate=29100000.00/min [1950000], rate=29250000.00/min [1960000], rate=29400000.00/min [1970000], rate=29550000.00/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=25920000.00/min [2170000], rate=26040000.00/min [2180000], rate=26160000.00/min [2190000], rate=26280000.00/min [2200000], rate=26400000.00/min [2210000], rate=26520000.00/min [2220000], rate=26640000.00/min [2230000], rate=26760000.00/min [2240000], rate=26880000.00/min [2250000], rate=27000000.00/min [2260000], rate=27120000.00/min [2270000], rate=27240000.00/min [2280000], rate=27360000.00/min [2290000], rate=27480000.00/min [2300000], rate=27600000.00/min [2310000], rate=27720000.00/min [2320000], rate=27840000.00/min [2330000], rate=27960000.00/min [2340000], rate=28080000.00/min [2350000], rate=28200000.00/min [2360000], rate=28320000.00/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=26500000.00/min [2660000], rate=26600000.00/min [2670000], rate=26700000.00/min [2680000], rate=26800000.00/min [2690000], rate=26900000.00/min [2700000], rate=27000000.00/min [2710000], rate=27100000.00/min [2720000], rate=27200000.00/min [2730000], rate=27300000.00/min [2740000], rate=27400000.00/min [2750000], rate=27500000.00/min [2760000], rate=27600000.00/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=23025000.00/min [3080000], rate=23100000.00/min [3090000], rate=23175000.00/min [3100000], rate=23250000.00/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=23066666.67/min [3470000], rate=23133333.33/min [3480000], rate=23200000.00/min [3490000], rate=23266666.67/min [3500000], rate=23333333.33/min [3510000], rate=23400000.00/min [3520000], rate=23466666.67/min [3530000], rate=23533333.33/min [3540000], rate=23600000.00/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=23160000.00/min [3870000], rate=23220000.00/min [3880000], rate=23280000.00/min [3890000], rate=23340000.00/min [3900000], rate=23400000.00/min [3910000], rate=23460000.00/min [3920000], rate=23520000.00/min [3930000], rate=23580000.00/min [3940000], rate=23640000.00/min [3950000], rate=23700000.00/min [3960000], rate=23760000.00/min [3970000], rate=23820000.00/min [3980000], rate=23880000.00/min [3990000], rate=23940000.00/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=23236363.64/min [4270000], rate=23290909.09/min [4280000], rate=23345454.55/min [4290000], rate=23400000.00/min [4300000], rate=23454545.45/min [4310000], rate=23509090.91/min [4320000], rate=23563636.36/min [4330000], rate=23618181.82/min [4340000], rate=23672727.27/min [4350000], rate=23727272.73/min [4360000], rate=23781818.18/min [4370000], rate=23836363.64/min [4380000], rate=23890909.09/min [4390000], rate=23945454.55/min [4400000], rate=24000000.00/min [4410000], rate=24054545.45/min [4420000], rate=24109090.91/min [4430000], rate=24163636.36/min [4440000], rate=24218181.82/min [4450000], rate=24272727.27/min [4460000], rate=24327272.73/min [4470000], rate=24381818.18/min [4480000], rate=24436363.64/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=23200000.00/min [4650000], rate=23250000.00/min [4660000], rate=23300000.00/min [4670000], rate=23350000.00/min [4680000], rate=23400000.00/min [4690000], rate=23450000.00/min [4700000], rate=23500000.00/min [4710000], rate=23550000.00/min [4720000], rate=23600000.00/min [4730000], rate=23650000.00/min [4740000], rate=23700000.00/min [4750000], rate=23750000.00/min [4760000], rate=23800000.00/min [4770000], rate=23850000.00/min [4780000], rate=23900000.00/min [4790000], rate=23950000.00/min [4800000], rate=24000000.00/min [4810000], rate=24050000.00/min [4820000], rate=24100000.00/min [4830000], rate=24150000.00/min [4840000], rate=24200000.00/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=23261538.46/min [5050000], rate=23307692.31/min [5060000], rate=23353846.15/min [5070000], rate=23400000.00/min [5080000], rate=23446153.85/min [5090000], rate=23492307.69/min [5100000], rate=23538461.54/min [5110000], rate=23584615.38/min [5120000], rate=23630769.23/min [5130000], rate=23676923.08/min [5140000], rate=23723076.92/min [5150000], rate=23769230.77/min [5160000], rate=23815384.62/min [5170000], rate=23861538.46/min [5180000], rate=23907692.31/min [5190000], rate=23953846.15/min [5200000], rate=24000000.00/min [5210000], rate=24046153.85/min [5220000], rate=24092307.69/min [5230000], rate=24138461.54/min [5240000], rate=24184615.38/min [5250000], rate=24230769.23/min [5260000], rate=24276923.08/min [5270000], rate=24323076.92/min [5280000], rate=24369230.77/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=23057142.86/min [5390000], rate=23100000.00/min [5400000], rate=23142857.14/min [5410000], rate=23185714.29/min [5420000], rate=23228571.43/min [5430000], rate=23271428.57/min [5440000], rate=23314285.71/min [5450000], rate=23357142.86/min [5460000], rate=23400000.00/min [5470000], rate=23442857.14/min [5480000], rate=23485714.29/min [5490000], rate=23528571.43/min [5500000], rate=23571428.57/min [5510000], rate=23614285.71/min [5520000], rate=23657142.86/min [5530000], rate=23700000.00/min [5540000], rate=23742857.14/min [5550000], rate=23785714.29/min [5560000], rate=23828571.43/min [5570000], rate=23871428.57/min [5580000], rate=23914285.71/min [5590000], rate=23957142.86/min [5600000], rate=24000000.00/min [5610000], rate=24042857.14/min [5620000], rate=24085714.29/min [5630000], rate=24128571.43/min [5640000], rate=24171428.57/min [5650000], rate=24214285.71/min [5660000], rate=24257142.86/min [5670000], rate=24300000.00/min [5680000], rate=24342857.14/min [5690000], rate=24385714.29/min [5700000], rate=22800000.00/min [5710000], rate=22840000.00/min [5720000], rate=22880000.00/min [5730000], rate=22920000.00/min [5740000], rate=22960000.00/min [5750000], rate=23000000.00/min [5760000], rate=23040000.00/min [5770000], rate=23080000.00/min [5780000], rate=23120000.00/min [5790000], rate=23160000.00/min [5800000], rate=23200000.00/min [5810000], rate=23240000.00/min [5820000], rate=23280000.00/min [5830000], rate=23320000.00/min [5840000], rate=23360000.00/min [5850000], rate=23400000.00/min [5860000], rate=23440000.00/min [5870000], rate=23480000.00/min [5880000], rate=23520000.00/min [5890000], rate=23560000.00/min [5900000], rate=23600000.00/min [5910000], rate=23640000.00/min [5920000], rate=23680000.00/min [5930000], rate=23720000.00/min [5940000], rate=23760000.00/min [5950000], rate=23800000.00/min [5960000], rate=23840000.00/min [5970000], rate=23880000.00/min [5980000], rate=23920000.00/min [5990000], rate=23960000.00/min [6000000], rate=24000000.00/min [6010000], rate=24040000.00/min [6020000], rate=24080000.00/min [6030000], rate=24120000.00/min [6040000], rate=24160000.00/min [6050000], rate=24200000.00/min [6060000], rate=24240000.00/min [6070000], rate=22762500.00/min [6080000], rate=22800000.00/min [6090000], rate=22837500.00/min [6100000], rate=22875000.00/min [6110000], rate=22912500.00/min [6120000], rate=22950000.00/min [6130000], rate=22987500.00/min [6140000], rate=23025000.00/min [6150000], rate=23062500.00/min [6160000], rate=23100000.00/min [6170000], rate=23137500.00/min [6180000], rate=23175000.00/min [6190000], rate=23212500.00/min [6200000], rate=23250000.00/min [6210000], rate=23287500.00/min [6220000], rate=23325000.00/min [6230000], rate=23362500.00/min [6240000], rate=23400000.00/min [6250000], rate=23437500.00/min [6260000], rate=23475000.00/min [6270000], rate=23512500.00/min [6280000], rate=23550000.00/min [6290000], rate=23587500.00/min [6300000], rate=23625000.00/min [6310000], rate=23662500.00/min [6320000], rate=23700000.00/min [6330000], rate=23737500.00/min [6340000], rate=23775000.00/min [6350000], rate=23812500.00/min [6360000], rate=23850000.00/min [6370000], rate=23887500.00/min [6380000], rate=23925000.00/min [6390000], rate=23962500.00/min [6400000], rate=24000000.00/min [6410000], rate=24037500.00/min [6420000], rate=24075000.00/min [6430000], rate=24112500.00/min [6440000], rate=24150000.00/min [6450000], rate=24187500.00/min [6460000], rate=24225000.00/min [6470000], rate=24262500.00/min [6480000], rate=24300000.00/min [6490000], rate=24337500.00/min [6500000], rate=22941176.47/min [6510000], rate=22976470.59/min [6520000], rate=23011764.71/min [6530000], rate=23047058.82/min [6540000], rate=23082352.94/min [6550000], rate=23117647.06/min [6560000], rate=23152941.18/min [6570000], rate=23188235.29/min [6580000], rate=23223529.41/min [6590000], rate=23258823.53/min [6600000], rate=23294117.65/min [6610000], rate=23329411.76/min [6620000], rate=23364705.88/min [6630000], rate=23400000.00/min [6640000], rate=23435294.12/min [6650000], rate=23470588.24/min [6660000], rate=23505882.35/min [6670000], rate=23541176.47/min [6680000], rate=23576470.59/min [6690000], rate=23611764.71/min [6700000], rate=23647058.82/min [6710000], rate=23682352.94/min [6720000], rate=23717647.06/min [6730000], rate=23752941.18/min [6740000], rate=23788235.29/min [6750000], rate=23823529.41/min [6760000], rate=23858823.53/min [6770000], rate=23894117.65/min [6780000], rate=23929411.76/min [6790000], rate=23964705.88/min [6800000], rate=24000000.00/min [6810000], rate=24035294.12/min [6820000], rate=24070588.24/min [6830000], rate=24105882.35/min [6840000], rate=24141176.47/min [6850000], rate=24176470.59/min [6860000], rate=24211764.71/min [6870000], rate=24247058.82/min [6880000], rate=24282352.94/min [6890000], rate=24317647.06/min [6900000], rate=24352941.18/min [6910000], rate=23033333.33/min [6920000], rate=23066666.67/min [6930000], rate=23100000.00/min [6940000], rate=23133333.33/min [6950000], rate=23166666.67/min [6960000], rate=23200000.00/min [6970000], rate=23233333.33/min [6980000], rate=23266666.67/min [6990000], rate=23300000.00/min [7000000], rate=23333333.33/min [7010000], rate=23366666.67/min [7020000], rate=23400000.00/min [7030000], rate=23433333.33/min [7040000], rate=23466666.67/min [7050000], rate=23500000.00/min [7060000], rate=23533333.33/min [7070000], rate=23566666.67/min [7080000], rate=23600000.00/min [7090000], rate=23633333.33/min [7100000], rate=23666666.67/min [7110000], rate=23700000.00/min [7120000], rate=23733333.33/min [7130000], rate=23766666.67/min [7140000], rate=23800000.00/min [7150000], rate=23833333.33/min [7160000], rate=23866666.67/min [7170000], rate=23900000.00/min [7180000], rate=23933333.33/min [7190000], rate=23966666.67/min [7200000], rate=24000000.00/min [7210000], rate=24033333.33/min [7220000], rate=24066666.67/min [7230000], rate=24100000.00/min [7240000], rate=24133333.33/min [7250000], rate=24166666.67/min [7260000], rate=24200000.00/min [7270000], rate=24233333.33/min [7280000], rate=24266666.67/min [7290000], rate=24300000.00/min [7300000], rate=23052631.58/min [7310000], rate=23084210.53/min [7320000], rate=23115789.47/min [7330000], rate=23147368.42/min [7340000], rate=23178947.37/min [7350000], rate=23210526.32/min [7360000], rate=23242105.26/min [7370000], rate=23273684.21/min [7380000], rate=23305263.16/min [7390000], rate=23336842.11/min [7400000], rate=23368421.05/min [7410000], rate=23400000.00/min [7420000], rate=23431578.95/min [7430000], rate=23463157.89/min [7440000], rate=23494736.84/min [7450000], rate=23526315.79/min [7460000], rate=23557894.74/min [7470000], rate=23589473.68/min [7480000], rate=23621052.63/min [7490000], rate=23652631.58/min [7500000], rate=23684210.53/min [7510000], rate=23715789.47/min [7520000], rate=23747368.42/min [7530000], rate=23778947.37/min [7540000], rate=23810526.32/min [7550000], rate=23842105.26/min [7560000], rate=23873684.21/min [7570000], rate=23905263.16/min [7580000], rate=23936842.11/min [7590000], rate=23968421.05/min [7600000], rate=24000000.00/min [7610000], rate=24031578.95/min [7620000], rate=24063157.89/min [7630000], rate=24094736.84/min [7640000], rate=24126315.79/min [7650000], rate=24157894.74/min [7660000], rate=24189473.68/min [7670000], rate=24221052.63/min [7680000], rate=24252631.58/min [7690000], rate=24284210.53/min [7700000], rate=24315789.47/min [7710000], rate=24347368.42/min [7720000], rate=23160000.00/min [7730000], rate=23190000.00/min [7740000], rate=23220000.00/min [7750000], rate=23250000.00/min [7760000], rate=23280000.00/min [7770000], rate=23310000.00/min [7780000], rate=23340000.00/min [7790000], rate=23370000.00/min [7800000], rate=23400000.00/min [7810000], rate=23430000.00/min [7820000], rate=23460000.00/min [7830000], rate=23490000.00/min [7840000], rate=23520000.00/min [7850000], rate=23550000.00/min [7860000], rate=23580000.00/min [7870000], rate=23610000.00/min [7880000], rate=23640000.00/min [7890000], rate=23670000.00/min [7900000], rate=23700000.00/min [7910000], rate=23730000.00/min [7920000], rate=23760000.00/min [7930000], rate=23790000.00/min [7940000], rate=23820000.00/min [7950000], rate=23850000.00/min [7960000], rate=23880000.00/min [7970000], rate=23910000.00/min [7980000], rate=23940000.00/min [7990000], rate=23970000.00/min [8000000], rate=24000000.00/min [8010000], rate=24030000.00/min [8020000], rate=24060000.00/min [8030000], rate=24090000.00/min [8040000], rate=24120000.00/min [8050000], rate=24150000.00/min [8060000], rate=24180000.00/min [8070000], rate=24210000.00/min [8080000], rate=24240000.00/min [8090000], rate=24270000.00/min [8100000], rate=24300000.00/min [8110000], rate=24330000.00/min [8120000], rate=23200000.00/min [8130000], rate=23228571.43/min [8140000], rate=23257142.86/min [8150000], rate=23285714.29/min [8160000], rate=23314285.71/min [8170000], rate=23342857.14/min [8180000], rate=23371428.57/min [8190000], rate=23400000.00/min [8200000], rate=23428571.43/min [8210000], rate=23457142.86/min [8220000], rate=23485714.29/min [8230000], rate=23514285.71/min [8240000], rate=23542857.14/min [8250000], rate=23571428.57/min [8260000], rate=23600000.00/min [8270000], rate=23628571.43/min [8280000], rate=23657142.86/min [8290000], rate=23685714.29/min [8300000], rate=23714285.71/min [8310000], rate=23742857.14/min [8320000], rate=23771428.57/min [8330000], rate=23800000.00/min [8340000], rate=23828571.43/min [8350000], rate=23857142.86/min [8360000], rate=23885714.29/min [8370000], rate=23914285.71/min [8380000], rate=23942857.14/min [8390000], rate=23971428.57/min [8400000], rate=24000000.00/min [8410000], rate=24028571.43/min [8420000], rate=24057142.86/min [8430000], rate=24085714.29/min [8440000], rate=24114285.71/min [8450000], rate=24142857.14/min [8460000], rate=24171428.57/min [8470000], rate=24200000.00/min [8480000], rate=24228571.43/min [8490000], rate=24257142.86/min [8500000], rate=24285714.29/min [8510000], rate=24314285.71/min [8520000], rate=24342857.14/min [8530000], rate=23263636.36/min [8540000], rate=23290909.09/min [8550000], rate=23318181.82/min [8560000], rate=23345454.55/min [8570000], rate=23372727.27/min [8580000], rate=23400000.00/min [8590000], rate=23427272.73/min [8600000], rate=23454545.45/min [8610000], rate=23481818.18/min [8620000], rate=23509090.91/min [8630000], rate=23536363.64/min [8640000], rate=23563636.36/min [8650000], rate=23590909.09/min [8660000], rate=23618181.82/min [8670000], rate=23645454.55/min [8680000], rate=23672727.27/min [8690000], rate=23700000.00/min [8700000], rate=23727272.73/min [8710000], rate=23754545.45/min [8720000], rate=23781818.18/min [8730000], rate=23809090.91/min [8740000], rate=23836363.64/min [8750000], rate=23863636.36/min [8760000], rate=23890909.09/min [8770000], rate=23918181.82/min [8780000], rate=23945454.55/min [8790000], rate=23972727.27/min [8800000], rate=24000000.00/min [8810000], rate=24027272.73/min [8820000], rate=24054545.45/min [8830000], rate=24081818.18/min [8840000], rate=24109090.91/min [8850000], rate=24136363.64/min [8860000], rate=24163636.36/min [8870000], rate=24190909.09/min [8880000], rate=24218181.82/min [8890000], rate=24245454.55/min [8900000], rate=24272727.27/min [8910000], rate=23243478.26/min [8920000], rate=23269565.22/min [8930000], rate=23295652.17/min [8940000], rate=23321739.13/min [8950000], rate=23347826.09/min [8960000], rate=23373913.04/min [8970000], rate=23400000.00/min [8980000], rate=23426086.96/min [8990000], rate=23452173.91/min [9000000], rate=23478260.87/min [9010000], rate=23504347.83/min [9020000], rate=23530434.78/min [9030000], rate=23556521.74/min [9040000], rate=23582608.70/min [9050000], rate=23608695.65/min [9060000], rate=23634782.61/min [9070000], rate=23660869.57/min [9080000], rate=23686956.52/min [9090000], rate=23713043.48/min [9100000], rate=23739130.43/min [9110000], rate=23765217.39/min [9120000], rate=23791304.35/min [9130000], rate=23817391.30/min [9140000], rate=23843478.26/min [9150000], rate=23869565.22/min [9160000], rate=23895652.17/min [9170000], rate=23921739.13/min [9180000], rate=23947826.09/min [9190000], rate=23973913.04/min [9200000], rate=24000000.00/min [9210000], rate=24026086.96/min 08:43:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00692_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00692_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_00692_B23MVV7LT4_1.introns: identified 4260 cancer introns 08:43:36 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00692_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00692_B23MVV7LT4_1.cancer.introns.prelim 08:43:36 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/prelim_introns.ok 08:43:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00692_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00692_B23MVV7LT4_1.cancer.introns 08:43:36 : 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_00692_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00692_B23MVV7LT4_1.cancer.introns 08:43:36 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/introns_filtered.ok 08:43:36 : INFO : -found 2193 cancer introns 08:43:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00692_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00692_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00692_B23MVV7LT4_1.introns.for_IGV.bed 08:43:36 : INFO : Creating the BED File. 08:43:41 : INFO : Saving Bed File as tih_rna_sample_00692_B23MVV7LT4_1.introns.for_IGV.bed 08:43:41 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00692_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00692_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00692_B23MVV7LT4_1.introns.for_IGV.bed 08:43:41 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 08:43:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00692_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00692_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00692_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00692_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 08:54:52 : INFO : Execution Time = 11.18 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00692_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00692_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00692_B23MVV7LT4_1 08:54:52 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 08:54:52 : INFO : Running: samtools sort -o tih_rna_sample_00692_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00692_B23MVV7LT4_1.cancer_intron_reads.bam 08:54:52 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00692_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00692_B23MVV7LT4_1.cancer_intron_reads.bam 08:54:52 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 08:54:52 : INFO : Running: samtools sort -o tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 70 files and 1 in-memory blocks... 09:07:51 : INFO : Execution Time = 12.98 minutes. CMD: samtools sort -o tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.bam 09:07:51 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 09:07:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.bam 09:12:15 : INFO : Execution Time = 4.40 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.bam 09:12:15 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:12:15 : INFO : Running: samtools sort -o tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:12:53 : INFO : Execution Time = 0.64 minutes. CMD: samtools sort -o tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 09:12:53 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:12:53 : INFO : Running: samtools index tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 09:12:58 : INFO : Execution Time = 0.07 minutes. CMD: samtools index tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 09:12:58 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/tih_rna_sample_00692_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:12:58 : INFO : Running: samtools index tih_rna_sample_00692_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 09:12:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00692_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 09:12:58 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/tih_rna_sample_00692_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:12:58 : INFO : Running: create_report tih_rna_sample_00692_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00692_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00692_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00692_B23MVV7LT4_1' 09:18:02 : INFO : Execution Time = 5.07 minutes. CMD: create_report tih_rna_sample_00692_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00692_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00692_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00692_B23MVV7LT4_1' 09:18:02 : INFO : Running: touch /tmp/nxf.I9NDIfzF06/tih_rna_sample_00692_B23MVV7LT4_1.chckpts/igv_create_html.ok 09:18:02 : INFO : done.