09:08:03 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [50000], rate=3000000.00/min [60000], rate=3600000.00/min [70000], rate=4200000.00/min [80000], rate=4800000.00/min [90000], rate=5400000.00/min [100000], rate=6000000.00/min [110000], rate=6600000.00/min [120000], rate=7200000.00/min [130000], rate=7800000.00/min [140000], rate=8400000.00/min [150000], rate=9000000.00/min [160000], rate=9600000.00/min [170000], rate=10200000.00/min [180000], rate=10800000.00/min [190000], rate=11400000.00/min [200000], rate=12000000.00/min [210000], rate=12600000.00/min [220000], rate=13200000.00/min [230000], rate=13800000.00/min [240000], rate=14400000.00/min [250000], rate=15000000.00/min [260000], rate=7800000.00/min [270000], rate=8100000.00/min [280000], rate=8400000.00/min [290000], rate=8700000.00/min [300000], rate=9000000.00/min [310000], rate=9300000.00/min [320000], rate=9600000.00/min [330000], rate=9900000.00/min [340000], rate=10200000.00/min [350000], rate=10500000.00/min [360000], rate=10800000.00/min [370000], rate=11100000.00/min [380000], rate=11400000.00/min [390000], rate=11700000.00/min [400000], rate=12000000.00/min [410000], rate=12300000.00/min [420000], rate=12600000.00/min [430000], rate=12900000.00/min [440000], rate=13200000.00/min [450000], rate=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=11400000.00/min [580000], rate=11600000.00/min [590000], rate=11800000.00/min [600000], rate=12000000.00/min [610000], rate=12200000.00/min [620000], rate=12400000.00/min [630000], rate=12600000.00/min [640000], rate=12800000.00/min [650000], rate=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=10500000.00/min [710000], rate=10650000.00/min [720000], rate=10800000.00/min [730000], rate=10950000.00/min [740000], rate=11100000.00/min [750000], rate=11250000.00/min [760000], rate=11400000.00/min [770000], rate=11550000.00/min [780000], rate=11700000.00/min [790000], rate=11850000.00/min [800000], rate=12000000.00/min [810000], rate=12150000.00/min [820000], rate=12300000.00/min [830000], rate=12450000.00/min [840000], rate=12600000.00/min [850000], rate=12750000.00/min [860000], rate=10320000.00/min [870000], rate=10440000.00/min [880000], rate=10560000.00/min [890000], rate=10680000.00/min [900000], rate=10800000.00/min [910000], rate=10920000.00/min [920000], rate=11040000.00/min [930000], rate=11160000.00/min [940000], rate=11280000.00/min [950000], rate=11400000.00/min [960000], rate=11520000.00/min [970000], rate=11640000.00/min [980000], rate=11760000.00/min [990000], rate=11880000.00/min [1000000], rate=10000000.00/min [1010000], rate=10100000.00/min [1020000], rate=10200000.00/min [1030000], rate=10300000.00/min [1040000], rate=10400000.00/min [1050000], rate=10500000.00/min [1060000], rate=10600000.00/min [1070000], rate=10700000.00/min [1080000], rate=10800000.00/min [1090000], rate=10900000.00/min [1100000], rate=11000000.00/min [1110000], rate=11100000.00/min [1120000], rate=11200000.00/min [1130000], rate=11300000.00/min [1140000], rate=11400000.00/min [1150000], rate=11500000.00/min [1160000], rate=11600000.00/min [1170000], rate=11700000.00/min [1180000], rate=11800000.00/min [1190000], rate=11900000.00/min [1200000], rate=12000000.00/min [1210000], rate=12100000.00/min [1220000], rate=10457142.86/min [1230000], rate=10542857.14/min [1240000], rate=10628571.43/min [1250000], rate=10714285.71/min [1260000], rate=10800000.00/min [1270000], rate=10885714.29/min [1280000], rate=10971428.57/min [1290000], rate=11057142.86/min [1300000], rate=11142857.14/min [1310000], rate=11228571.43/min [1320000], rate=11314285.71/min [1330000], rate=11400000.00/min [1340000], rate=11485714.29/min [1350000], rate=11571428.57/min [1360000], rate=11657142.86/min [1370000], rate=11742857.14/min [1380000], rate=11828571.43/min [1390000], rate=11914285.71/min [1400000], rate=10500000.00/min [1410000], rate=10575000.00/min [1420000], rate=10650000.00/min [1430000], rate=10725000.00/min [1440000], rate=10800000.00/min [1450000], rate=10875000.00/min [1460000], rate=10950000.00/min [1470000], rate=11025000.00/min [1480000], rate=11100000.00/min [1490000], rate=11175000.00/min [1500000], rate=11250000.00/min [1510000], rate=11325000.00/min [1520000], rate=11400000.00/min [1530000], rate=11475000.00/min [1540000], rate=10266666.67/min [1550000], rate=10333333.33/min [1560000], rate=10400000.00/min [1570000], rate=10466666.67/min [1580000], rate=10533333.33/min [1590000], rate=10600000.00/min [1600000], rate=10666666.67/min [1610000], rate=10733333.33/min [1620000], rate=10800000.00/min [1630000], rate=10866666.67/min [1640000], rate=10933333.33/min [1650000], rate=11000000.00/min [1660000], rate=11066666.67/min [1670000], rate=11133333.33/min [1680000], rate=10080000.00/min [1690000], rate=10140000.00/min [1700000], rate=10200000.00/min [1710000], rate=10260000.00/min [1720000], rate=10320000.00/min [1730000], rate=10380000.00/min [1740000], rate=10440000.00/min [1750000], rate=10500000.00/min [1760000], rate=10560000.00/min [1770000], rate=10620000.00/min [1780000], rate=10680000.00/min [1790000], rate=10740000.00/min [1800000], rate=9818181.82/min [1810000], rate=9872727.27/min [1820000], rate=9927272.73/min [1830000], rate=9981818.18/min [1840000], rate=10036363.64/min [1850000], rate=10090909.09/min [1860000], rate=10145454.55/min [1870000], rate=10200000.00/min [1880000], rate=10254545.45/min [1890000], rate=10309090.91/min [1900000], rate=10363636.36/min [1910000], rate=10418181.82/min [1920000], rate=10472727.27/min [1930000], rate=10527272.73/min [1940000], rate=9700000.00/min [1950000], rate=9750000.00/min [1960000], rate=9800000.00/min [1970000], rate=9850000.00/min [1980000], rate=9900000.00/min [1990000], rate=9950000.00/min [2000000], rate=10000000.00/min [2010000], rate=10050000.00/min [2020000], rate=10100000.00/min [2030000], rate=10150000.00/min [2040000], rate=10200000.00/min [2050000], rate=10250000.00/min [2060000], rate=10300000.00/min [2070000], rate=10350000.00/min [2080000], rate=9600000.00/min [2090000], rate=9646153.85/min [2100000], rate=9692307.69/min [2110000], rate=9738461.54/min [2120000], rate=9784615.38/min [2130000], rate=9830769.23/min [2140000], rate=9876923.08/min [2150000], rate=9923076.92/min [2160000], rate=9969230.77/min [2170000], rate=10015384.62/min [2180000], rate=10061538.46/min [2190000], rate=10107692.31/min [2200000], rate=10153846.15/min [2210000], rate=10200000.00/min [2220000], rate=10246153.85/min [2230000], rate=9557142.86/min [2240000], rate=9600000.00/min [2250000], rate=9642857.14/min [2260000], rate=9685714.29/min [2270000], rate=9728571.43/min [2280000], rate=9771428.57/min [2290000], rate=9814285.71/min [2300000], rate=9857142.86/min [2310000], rate=9900000.00/min [2320000], rate=9942857.14/min [2330000], rate=9985714.29/min [2340000], rate=10028571.43/min [2350000], rate=10071428.57/min [2360000], rate=10114285.71/min [2370000], rate=9480000.00/min [2380000], rate=9520000.00/min [2390000], rate=9560000.00/min [2400000], rate=9600000.00/min [2410000], rate=9640000.00/min [2420000], rate=9680000.00/min [2430000], rate=9720000.00/min [2440000], rate=9760000.00/min [2450000], rate=9800000.00/min [2460000], rate=9840000.00/min [2470000], rate=9880000.00/min [2480000], rate=9920000.00/min [2490000], rate=9960000.00/min [2500000], rate=10000000.00/min [2510000], rate=10040000.00/min [2520000], rate=10080000.00/min [2530000], rate=10120000.00/min [2540000], rate=10160000.00/min [2550000], rate=10200000.00/min [2560000], rate=10240000.00/min [2570000], rate=10280000.00/min [2580000], rate=10320000.00/min [2590000], rate=10360000.00/min [2600000], rate=9750000.00/min [2610000], rate=9787500.00/min [2620000], rate=9825000.00/min [2630000], rate=9862500.00/min [2640000], rate=9900000.00/min [2650000], rate=9937500.00/min [2660000], rate=9975000.00/min [2670000], rate=10012500.00/min [2680000], rate=10050000.00/min [2690000], rate=10087500.00/min [2700000], rate=10125000.00/min [2710000], rate=10162500.00/min [2720000], rate=10200000.00/min [2730000], rate=10237500.00/min [2740000], rate=10275000.00/min [2750000], rate=10312500.00/min [2760000], rate=10350000.00/min [2770000], rate=10387500.00/min [2780000], rate=10425000.00/min [2790000], rate=10462500.00/min [2800000], rate=10500000.00/min [2810000], rate=9917647.06/min [2820000], rate=9952941.18/min [2830000], rate=9988235.29/min [2840000], rate=10023529.41/min [2850000], rate=10058823.53/min [2860000], rate=10094117.65/min [2870000], rate=10129411.76/min [2880000], rate=10164705.88/min [2890000], rate=10200000.00/min [2900000], rate=10235294.12/min [2910000], rate=10270588.24/min [2920000], rate=10305882.35/min [2930000], rate=10341176.47/min [2940000], rate=9800000.00/min [2950000], rate=9833333.33/min [2960000], rate=9866666.67/min [2970000], rate=9900000.00/min [2980000], rate=9933333.33/min [2990000], rate=9966666.67/min [3000000], rate=10000000.00/min [3010000], rate=10033333.33/min [3020000], rate=10066666.67/min [3030000], rate=10100000.00/min [3040000], rate=10133333.33/min [3050000], rate=10166666.67/min [3060000], rate=10200000.00/min [3070000], rate=10233333.33/min [3080000], rate=10266666.67/min [3090000], rate=10300000.00/min [3100000], rate=10333333.33/min [3110000], rate=10366666.67/min [3120000], rate=10400000.00/min [3130000], rate=10433333.33/min [3140000], rate=10466666.67/min [3150000], rate=10500000.00/min [3160000], rate=10533333.33/min [3170000], rate=10566666.67/min [3180000], rate=10042105.26/min [3190000], rate=10073684.21/min [3200000], rate=10105263.16/min [3210000], rate=10136842.11/min [3220000], rate=10168421.05/min [3230000], rate=10200000.00/min [3240000], rate=10231578.95/min [3250000], rate=10263157.89/min [3260000], rate=10294736.84/min [3270000], rate=10326315.79/min [3280000], rate=10357894.74/min [3290000], rate=10389473.68/min [3300000], rate=10421052.63/min [3310000], rate=10452631.58/min [3320000], rate=10484210.53/min [3330000], rate=10515789.47/min [3340000], rate=10547368.42/min [3350000], rate=10578947.37/min [3360000], rate=10610526.32/min [3370000], rate=10642105.26/min [3380000], rate=10673684.21/min [3390000], rate=10705263.16/min [3400000], rate=10200000.00/min [3410000], rate=10230000.00/min [3420000], rate=10260000.00/min [3430000], rate=10290000.00/min [3440000], rate=10320000.00/min [3450000], rate=10350000.00/min [3460000], rate=10380000.00/min [3470000], rate=10410000.00/min [3480000], rate=10440000.00/min [3490000], rate=10470000.00/min [3500000], rate=10500000.00/min [3510000], rate=10530000.00/min [3520000], rate=10560000.00/min [3530000], rate=10590000.00/min [3540000], rate=10620000.00/min [3550000], rate=10650000.00/min [3560000], rate=10680000.00/min [3570000], rate=10710000.00/min [3580000], rate=10228571.43/min [3590000], rate=10257142.86/min [3600000], rate=10285714.29/min [3610000], rate=10314285.71/min [3620000], rate=10342857.14/min [3630000], rate=10371428.57/min [3640000], rate=10400000.00/min [3650000], rate=10428571.43/min [3660000], rate=10457142.86/min [3670000], rate=10485714.29/min [3680000], rate=10514285.71/min [3690000], rate=10542857.14/min [3700000], rate=10571428.57/min [3710000], rate=10600000.00/min [3720000], rate=10628571.43/min [3730000], rate=10657142.86/min [3740000], rate=10685714.29/min [3750000], rate=10714285.71/min [3760000], rate=10742857.14/min [3770000], rate=10771428.57/min [3780000], rate=10800000.00/min [3790000], rate=10828571.43/min [3800000], rate=10363636.36/min [3810000], rate=10390909.09/min [3820000], rate=10418181.82/min [3830000], rate=10445454.55/min [3840000], rate=10472727.27/min [3850000], rate=10500000.00/min [3860000], rate=10527272.73/min [3870000], rate=10554545.45/min [3880000], rate=10581818.18/min [3890000], rate=10609090.91/min [3900000], rate=10636363.64/min [3910000], rate=10663636.36/min [3920000], rate=10690909.09/min [3930000], rate=10718181.82/min [3940000], rate=10745454.55/min [3950000], rate=10772727.27/min [3960000], rate=10800000.00/min [3970000], rate=10827272.73/min [3980000], rate=10854545.45/min [3990000], rate=10881818.18/min [4000000], rate=10909090.91/min [4010000], rate=10460869.57/min [4020000], rate=10486956.52/min [4030000], rate=10513043.48/min [4040000], rate=10539130.43/min [4050000], rate=10565217.39/min [4060000], rate=10591304.35/min [4070000], rate=10617391.30/min [4080000], rate=10643478.26/min [4090000], rate=10669565.22/min [4100000], rate=10695652.17/min [4110000], rate=10721739.13/min [4120000], rate=10747826.09/min [4130000], rate=10773913.04/min [4140000], rate=10800000.00/min [4150000], rate=10826086.96/min [4160000], rate=10852173.91/min [4170000], rate=10878260.87/min [4180000], rate=10904347.83/min [4190000], rate=10475000.00/min [4200000], rate=10500000.00/min [4210000], rate=10525000.00/min [4220000], rate=10550000.00/min [4230000], rate=10575000.00/min [4240000], rate=10600000.00/min [4250000], rate=10625000.00/min [4260000], rate=10650000.00/min [4270000], rate=10675000.00/min [4280000], rate=10700000.00/min [4290000], rate=10725000.00/min [4300000], rate=10750000.00/min [4310000], rate=10775000.00/min [4320000], rate=10800000.00/min [4330000], rate=10825000.00/min [4340000], rate=10850000.00/min [4350000], rate=10875000.00/min [4360000], rate=10900000.00/min [4370000], rate=10925000.00/min [4380000], rate=10950000.00/min [4390000], rate=10975000.00/min [4400000], rate=11000000.00/min [4410000], rate=11025000.00/min [4420000], rate=11050000.00/min [4430000], rate=10632000.00/min [4440000], rate=10656000.00/min [4450000], rate=10680000.00/min [4460000], rate=10704000.00/min [4470000], rate=10728000.00/min [4480000], rate=10752000.00/min [4490000], rate=10776000.00/min [4500000], rate=10800000.00/min [4510000], rate=10824000.00/min [4520000], rate=10848000.00/min [4530000], rate=10872000.00/min [4540000], rate=10896000.00/min [4550000], rate=10920000.00/min [4560000], rate=10944000.00/min [4570000], rate=10968000.00/min [4580000], rate=10992000.00/min [4590000], rate=11016000.00/min [4600000], rate=11040000.00/min [4610000], rate=11064000.00/min [4620000], rate=11088000.00/min [4630000], rate=11112000.00/min [4640000], rate=11136000.00/min [4650000], rate=11160000.00/min [4660000], rate=11184000.00/min [4670000], rate=11208000.00/min [4680000], rate=10800000.00/min [4690000], rate=10823076.92/min [4700000], rate=10846153.85/min [4710000], rate=10869230.77/min [4720000], rate=10892307.69/min [4730000], rate=10915384.62/min [4740000], rate=10938461.54/min [4750000], rate=10961538.46/min [4760000], rate=10984615.38/min [4770000], rate=11007692.31/min [4780000], rate=11030769.23/min [4790000], rate=11053846.15/min [4800000], rate=11076923.08/min [4810000], rate=11100000.00/min [4820000], rate=11123076.92/min [4830000], rate=11146153.85/min [4840000], rate=11169230.77/min [4850000], rate=11192307.69/min [4860000], rate=11215384.62/min [4870000], rate=11238461.54/min [4880000], rate=11261538.46/min [4890000], rate=11284615.38/min [4900000], rate=11307692.31/min [4910000], rate=10911111.11/min [4920000], rate=10933333.33/min [4930000], rate=10955555.56/min [4940000], rate=10977777.78/min [4950000], rate=11000000.00/min [4960000], rate=11022222.22/min [4970000], rate=11044444.44/min [4980000], rate=11066666.67/min [4990000], rate=11088888.89/min [5000000], rate=11111111.11/min [5010000], rate=11133333.33/min [5020000], rate=11155555.56/min [5030000], rate=11177777.78/min [5040000], rate=11200000.00/min [5050000], rate=11222222.22/min [5060000], rate=11244444.44/min [5070000], rate=11266666.67/min [5080000], rate=10885714.29/min [5090000], rate=10907142.86/min [5100000], rate=10928571.43/min [5110000], rate=10950000.00/min [5120000], rate=10971428.57/min [5130000], rate=10992857.14/min [5140000], rate=11014285.71/min [5150000], rate=11035714.29/min [5160000], rate=11057142.86/min [5170000], rate=11078571.43/min [5180000], rate=11100000.00/min [5190000], rate=11121428.57/min [5200000], rate=11142857.14/min [5210000], rate=11164285.71/min [5220000], rate=11185714.29/min [5230000], rate=11207142.86/min [5240000], rate=10841379.31/min [5250000], rate=10862068.97/min [5260000], rate=10882758.62/min [5270000], rate=10903448.28/min [5280000], rate=10924137.93/min [5290000], rate=10944827.59/min [5300000], rate=10965517.24/min [5310000], rate=10986206.90/min [5320000], rate=11006896.55/min [5330000], rate=11027586.21/min [5340000], rate=11048275.86/min [5350000], rate=11068965.52/min [5360000], rate=11089655.17/min [5370000], rate=11110344.83/min [5380000], rate=11131034.48/min [5390000], rate=11151724.14/min [5400000], rate=11172413.79/min [5410000], rate=11193103.45/min [5420000], rate=10840000.00/min [5430000], rate=10860000.00/min [5440000], rate=10880000.00/min [5450000], rate=10900000.00/min [5460000], rate=10920000.00/min [5470000], rate=10940000.00/min [5480000], rate=10960000.00/min [5490000], rate=10980000.00/min [5500000], rate=11000000.00/min [5510000], rate=11020000.00/min [5520000], rate=11040000.00/min [5530000], rate=11060000.00/min [5540000], rate=11080000.00/min [5550000], rate=11100000.00/min [5560000], rate=11120000.00/min [5570000], rate=11140000.00/min [5580000], rate=10800000.00/min [5590000], rate=10819354.84/min [5600000], rate=10838709.68/min [5610000], rate=10858064.52/min [5620000], rate=10877419.35/min [5630000], rate=10896774.19/min [5640000], rate=10916129.03/min [5650000], rate=10935483.87/min [5660000], rate=10954838.71/min [5670000], rate=10974193.55/min [5680000], rate=10993548.39/min [5690000], rate=11012903.23/min [5700000], rate=11032258.06/min [5710000], rate=11051612.90/min [5720000], rate=11070967.74/min [5730000], rate=11090322.58/min [5740000], rate=11109677.42/min [5750000], rate=11129032.26/min [5760000], rate=11148387.10/min [5770000], rate=10818750.00/min [5780000], rate=10837500.00/min [5790000], rate=10856250.00/min [5800000], rate=10875000.00/min [5810000], rate=10893750.00/min [5820000], rate=10912500.00/min [5830000], rate=10931250.00/min [5840000], rate=10950000.00/min [5850000], rate=10968750.00/min [5860000], rate=10987500.00/min [5870000], rate=11006250.00/min [5880000], rate=11025000.00/min [5890000], rate=11043750.00/min [5900000], rate=11062500.00/min [5910000], rate=11081250.00/min [5920000], rate=11100000.00/min [5930000], rate=11118750.00/min [5940000], rate=11137500.00/min [5950000], rate=11156250.00/min [5960000], rate=11175000.00/min [5970000], rate=11193750.00/min [5980000], rate=11212500.00/min [5990000], rate=10890909.09/min [6000000], rate=10909090.91/min [6010000], rate=10927272.73/min [6020000], rate=10945454.55/min [6030000], rate=10963636.36/min [6040000], rate=10981818.18/min [6050000], rate=11000000.00/min [6060000], rate=11018181.82/min [6070000], rate=11036363.64/min [6080000], rate=11054545.45/min [6090000], rate=11072727.27/min [6100000], rate=11090909.09/min [6110000], rate=11109090.91/min [6120000], rate=11127272.73/min [6130000], rate=11145454.55/min [6140000], rate=11163636.36/min [6150000], rate=11181818.18/min [6160000], rate=11200000.00/min [6170000], rate=11218181.82/min [6180000], rate=11236363.64/min [6190000], rate=11254545.45/min [6200000], rate=11272727.27/min [6210000], rate=11290909.09/min [6220000], rate=11309090.91/min [6230000], rate=11327272.73/min [6240000], rate=11345454.55/min [6250000], rate=11363636.36/min [6260000], rate=11381818.18/min [6270000], rate=11064705.88/min [6280000], rate=11082352.94/min [6290000], rate=11100000.00/min [6300000], rate=11117647.06/min [6310000], rate=11135294.12/min [6320000], rate=11152941.18/min [6330000], rate=11170588.24/min [6340000], rate=11188235.29/min [6350000], rate=11205882.35/min [6360000], rate=11223529.41/min [6370000], rate=11241176.47/min [6380000], rate=11258823.53/min [6390000], rate=11276470.59/min [6400000], rate=11294117.65/min [6410000], rate=11311764.71/min [6420000], rate=11329411.76/min [6430000], rate=11347058.82/min [6440000], rate=11364705.88/min [6450000], rate=11382352.94/min [6460000], rate=11400000.00/min [6470000], rate=11417647.06/min [6480000], rate=11435294.12/min [6490000], rate=11452941.18/min [6500000], rate=11470588.24/min [6510000], rate=11488235.29/min [6520000], rate=11505882.35/min [6530000], rate=11194285.71/min [6540000], rate=11211428.57/min [6550000], rate=11228571.43/min [6560000], rate=11245714.29/min [6570000], rate=11262857.14/min [6580000], rate=11280000.00/min [6590000], rate=11297142.86/min [6600000], rate=11314285.71/min [6610000], rate=11331428.57/min [6620000], rate=11348571.43/min [6630000], rate=11365714.29/min [6640000], rate=11382857.14/min [6650000], rate=11400000.00/min [6660000], rate=11417142.86/min [6670000], rate=11434285.71/min [6680000], rate=11451428.57/min [6690000], rate=11468571.43/min [6700000], rate=11485714.29/min [6710000], rate=11502857.14/min [6720000], rate=11520000.00/min [6730000], rate=11537142.86/min [6740000], rate=11554285.71/min [6750000], rate=11571428.57/min [6760000], rate=11588571.43/min [6770000], rate=11283333.33/min [6780000], rate=11300000.00/min [6790000], rate=11316666.67/min [6800000], rate=11333333.33/min [6810000], rate=11350000.00/min [6820000], rate=11366666.67/min [6830000], rate=11383333.33/min [6840000], rate=11400000.00/min [6850000], rate=11416666.67/min [6860000], rate=11433333.33/min [6870000], rate=11450000.00/min [6880000], rate=11466666.67/min [6890000], rate=11483333.33/min [6900000], rate=11500000.00/min [6910000], rate=11516666.67/min [6920000], rate=11533333.33/min [6930000], rate=11550000.00/min [6940000], rate=11566666.67/min [6950000], rate=11583333.33/min [6960000], rate=11600000.00/min [6970000], rate=11302702.70/min [6980000], rate=11318918.92/min [6990000], rate=11335135.14/min [7000000], rate=11351351.35/min [7010000], rate=11367567.57/min [7020000], rate=11383783.78/min [7030000], rate=11400000.00/min [7040000], rate=11416216.22/min [7050000], rate=11432432.43/min [7060000], rate=11448648.65/min [7070000], rate=11464864.86/min [7080000], rate=11481081.08/min [7090000], rate=11497297.30/min [7100000], rate=11513513.51/min [7110000], rate=11529729.73/min [7120000], rate=11545945.95/min [7130000], rate=11562162.16/min [7140000], rate=11578378.38/min [7150000], rate=11594594.59/min [7160000], rate=11610810.81/min [7170000], rate=11627027.03/min [7180000], rate=11643243.24/min [7190000], rate=11352631.58/min [7200000], rate=11368421.05/min [7210000], rate=11384210.53/min [7220000], rate=11400000.00/min [7230000], rate=11415789.47/min [7240000], rate=11431578.95/min [7250000], rate=11447368.42/min [7260000], rate=11463157.89/min [7270000], rate=11478947.37/min [7280000], rate=11494736.84/min [7290000], rate=11510526.32/min [7300000], rate=11526315.79/min [7310000], rate=11542105.26/min [7320000], rate=11557894.74/min [7330000], rate=11573684.21/min [7340000], rate=11589473.68/min [7350000], rate=11605263.16/min [7360000], rate=11621052.63/min [7370000], rate=11636842.11/min [7380000], rate=11652631.58/min [7390000], rate=11668421.05/min [7400000], rate=11684210.53/min [7410000], rate=11700000.00/min [7420000], rate=11715789.47/min [7430000], rate=11731578.95/min [7440000], rate=11446153.85/min [7450000], rate=11461538.46/min [7460000], rate=11476923.08/min [7470000], rate=11492307.69/min [7480000], rate=11507692.31/min [7490000], rate=11523076.92/min [7500000], rate=11538461.54/min [7510000], rate=11553846.15/min [7520000], rate=11569230.77/min [7530000], rate=11584615.38/min [7540000], rate=11600000.00/min [7550000], rate=11615384.62/min [7560000], rate=11630769.23/min [7570000], rate=11646153.85/min [7580000], rate=11661538.46/min [7590000], rate=11676923.08/min [7600000], rate=11692307.69/min [7610000], rate=11707692.31/min [7620000], rate=11723076.92/min [7630000], rate=11738461.54/min [7640000], rate=11753846.15/min [7650000], rate=11475000.00/min [7660000], rate=11490000.00/min [7670000], rate=11505000.00/min [7680000], rate=11520000.00/min [7690000], rate=11535000.00/min [7700000], rate=11550000.00/min [7710000], rate=11565000.00/min [7720000], rate=11580000.00/min [7730000], rate=11595000.00/min [7740000], rate=11610000.00/min [7750000], rate=11625000.00/min [7760000], rate=11640000.00/min [7770000], rate=11655000.00/min [7780000], rate=11670000.00/min [7790000], rate=11685000.00/min [7800000], rate=11700000.00/min [7810000], rate=11715000.00/min [7820000], rate=11730000.00/min [7830000], rate=11745000.00/min [7840000], rate=11760000.00/min [7850000], rate=11775000.00/min [7860000], rate=11790000.00/min [7870000], rate=11805000.00/min [7880000], rate=11531707.32/min [7890000], rate=11546341.46/min [7900000], rate=11560975.61/min [7910000], rate=11575609.76/min [7920000], rate=11590243.90/min [7930000], rate=11604878.05/min [7940000], rate=11619512.20/min [7950000], rate=11634146.34/min [7960000], rate=11648780.49/min [7970000], rate=11663414.63/min [7980000], rate=11678048.78/min [7990000], rate=11692682.93/min [8000000], rate=11707317.07/min [8010000], rate=11721951.22/min [8020000], rate=11736585.37/min [8030000], rate=11751219.51/min [8040000], rate=11765853.66/min [8050000], rate=11780487.80/min [8060000], rate=11795121.95/min [8070000], rate=11809756.10/min [8080000], rate=11824390.24/min [8090000], rate=11839024.39/min [8100000], rate=11853658.54/min [8110000], rate=11868292.68/min [8120000], rate=11600000.00/min [8130000], rate=11614285.71/min [8140000], rate=11628571.43/min [8150000], rate=11642857.14/min [8160000], rate=11657142.86/min [8170000], rate=11671428.57/min [8180000], rate=11685714.29/min [8190000], rate=11700000.00/min [8200000], rate=11714285.71/min [8210000], rate=11728571.43/min [8220000], rate=11742857.14/min [8230000], rate=11757142.86/min [8240000], rate=11771428.57/min [8250000], rate=11785714.29/min [8260000], rate=11800000.00/min [8270000], rate=11814285.71/min [8280000], rate=11828571.43/min [8290000], rate=11842857.14/min [8300000], rate=11857142.86/min [8310000], rate=11871428.57/min [8320000], rate=11885714.29/min [8330000], rate=11900000.00/min [8340000], rate=11914285.71/min [8350000], rate=11928571.43/min [8360000], rate=11665116.28/min [8370000], rate=11679069.77/min [8380000], rate=11693023.26/min [8390000], rate=11706976.74/min [8400000], rate=11720930.23/min [8410000], rate=11734883.72/min [8420000], rate=11748837.21/min [8430000], rate=11762790.70/min [8440000], rate=11776744.19/min [8450000], rate=11790697.67/min [8460000], rate=11804651.16/min [8470000], rate=11818604.65/min [8480000], rate=11832558.14/min [8490000], rate=11846511.63/min [8500000], rate=11860465.12/min [8510000], rate=11874418.60/min [8520000], rate=11888372.09/min [8530000], rate=11902325.58/min [8540000], rate=11916279.07/min [8550000], rate=11930232.56/min [8560000], rate=11672727.27/min [8570000], rate=11686363.64/min [8580000], rate=11700000.00/min [8590000], rate=11713636.36/min [8600000], rate=11727272.73/min [8610000], rate=11740909.09/min [8620000], rate=11754545.45/min [8630000], rate=11768181.82/min [8640000], rate=11781818.18/min [8650000], rate=11795454.55/min [8660000], rate=11809090.91/min [8670000], rate=11822727.27/min [8680000], rate=11836363.64/min [8690000], rate=11850000.00/min [8700000], rate=11863636.36/min [8710000], rate=11877272.73/min [8720000], rate=11626666.67/min [8730000], rate=11640000.00/min [8740000], rate=11653333.33/min [8750000], rate=11666666.67/min [8760000], rate=11680000.00/min [8770000], rate=11693333.33/min [8780000], rate=11706666.67/min [8790000], rate=11720000.00/min [8800000], rate=11733333.33/min [8810000], rate=11746666.67/min [8820000], rate=11760000.00/min [8830000], rate=11773333.33/min [8840000], rate=11786666.67/min [8850000], rate=11800000.00/min [8860000], rate=11813333.33/min [8870000], rate=11826666.67/min [8880000], rate=11582608.70/min [8890000], rate=11595652.17/min [8900000], rate=11608695.65/min [8910000], rate=11621739.13/min [8920000], rate=11634782.61/min [8930000], rate=11647826.09/min [8940000], rate=11660869.57/min [8950000], rate=11673913.04/min [8960000], rate=11686956.52/min [8970000], rate=11700000.00/min [8980000], rate=11713043.48/min [8990000], rate=11726086.96/min [9000000], rate=11739130.43/min [9010000], rate=11502127.66/min [9020000], rate=11514893.62/min [9030000], rate=11527659.57/min [9040000], rate=11540425.53/min [9050000], rate=11553191.49/min [9060000], rate=11565957.45/min [9070000], rate=11578723.40/min [9080000], rate=11591489.36/min [9090000], rate=11604255.32/min [9100000], rate=11617021.28/min [9110000], rate=11629787.23/min [9120000], rate=11642553.19/min [9130000], rate=11655319.15/min [9140000], rate=11668085.11/min [9150000], rate=11437500.00/min [9160000], rate=11450000.00/min [9170000], rate=11462500.00/min [9180000], rate=11475000.00/min [9190000], rate=11487500.00/min [9200000], rate=11500000.00/min [9210000], rate=11512500.00/min [9220000], rate=11525000.00/min [9230000], rate=11537500.00/min [9240000], rate=11550000.00/min [9250000], rate=11562500.00/min [9260000], rate=11338775.51/min [9270000], rate=11351020.41/min [9280000], rate=11363265.31/min [9290000], rate=11375510.20/min [9300000], rate=11387755.10/min [9310000], rate=11400000.00/min [9320000], rate=11412244.90/min [9330000], rate=11424489.80/min [9340000], rate=11436734.69/min [9350000], rate=11448979.59/min [9360000], rate=11461224.49/min [9370000], rate=11473469.39/min [9380000], rate=11485714.29/min [9390000], rate=11268000.00/min [9400000], rate=11280000.00/min [9410000], rate=11292000.00/min [9420000], rate=11304000.00/min [9430000], rate=11316000.00/min [9440000], rate=11328000.00/min [9450000], rate=11340000.00/min [9460000], rate=11352000.00/min [9470000], rate=11364000.00/min [9480000], rate=11376000.00/min [9490000], rate=11388000.00/min [9500000], rate=11400000.00/min [9510000], rate=11412000.00/min [9520000], rate=11200000.00/min [9530000], rate=11211764.71/min [9540000], rate=11223529.41/min [9550000], rate=11235294.12/min [9560000], rate=11247058.82/min [9570000], rate=11258823.53/min [9580000], rate=11270588.24/min [9590000], rate=11282352.94/min [9600000], rate=11294117.65/min [9610000], rate=11305882.35/min [9620000], rate=11317647.06/min [9630000], rate=11329411.76/min [9640000], rate=11341176.47/min [9650000], rate=11134615.38/min [9660000], rate=11146153.85/min [9670000], rate=11157692.31/min [9680000], rate=11169230.77/min [9690000], rate=11180769.23/min [9700000], rate=11192307.69/min [9710000], rate=11203846.15/min [9720000], rate=11215384.62/min [9730000], rate=11226923.08/min [9740000], rate=11238461.54/min [9750000], rate=11250000.00/min [9760000], rate=11261538.46/min [9770000], rate=11273076.92/min [9780000], rate=11284615.38/min [9790000], rate=11296153.85/min [9800000], rate=11307692.31/min [9810000], rate=11105660.38/min [9820000], rate=11116981.13/min [9830000], rate=11128301.89/min [9840000], rate=11139622.64/min [9850000], rate=11150943.40/min [9860000], rate=11162264.15/min [9870000], rate=11173584.91/min [9880000], rate=11184905.66/min [9890000], rate=11196226.42/min [9900000], rate=11207547.17/min [9910000], rate=11218867.92/min [9920000], rate=11230188.68/min [9930000], rate=11241509.43/min [9940000], rate=11252830.19/min [9950000], rate=11264150.94/min [9960000], rate=11275471.70/min 09:09:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bGW-T1-TRNA-1_B23MHV2LT4_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. -659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns: identified 7763 cancer introns 09:09:14 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 09:09:14 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 09:09:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 09:09:14 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 09:09:14 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 09:09:14 : INFO : -found 2630 cancer introns 09:09:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 09:09:15 : INFO : Creating the BED File. 09:09:21 : INFO : Saving Bed File as 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 09:09:21 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 09:09:21 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 09:09:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 09:36:40 : INFO : Execution Time = 27.31 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1 09:36:40 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 09:36:40 : INFO : Running: samtools sort -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:36:41 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:36:41 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 09:36:41 : INFO : Running: samtools sort -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam [bam_sort_core] merging from 108 files and 1 in-memory blocks... 10:04:19 : INFO : Execution Time = 27.63 minutes. CMD: samtools sort -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam 10:04:19 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_gene_reads.ok 10:04:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 10:13:20 : INFO : Execution Time = 9.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 10:13:20 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:13:20 : INFO : Running: samtools sort -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:14:11 : INFO : Execution Time = 0.85 minutes. CMD: samtools sort -o 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp 10:14:11 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:14:11 : INFO : Running: samtools index 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 10:14:16 : INFO : Execution Time = 0.09 minutes. CMD: samtools index 659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 10:14:16 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:14:17 : INFO : Running: samtools index 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 10:14:17 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 10:14:17 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bGW-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:14:17 : INFO : Running: create_report 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bGW-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bGW-T1-TRNA-1_B23MHV2LT4_1' 10:20:31 : INFO : Execution Time = 6.24 minutes. CMD: create_report 659_bGW-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bGW-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bGW-T1-TRNA-1_B23MHV2LT4_1' 10:20:31 : INFO : Running: touch /tmp/nxf.v8xVFtg26g/659_bGW-T1-TRNA-1_B23MHV2LT4_1.chckpts/igv_create_html.ok 10:20:31 : INFO : done.