08:32:42 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[130000], rate=7800000.00/min
[140000], rate=8400000.00/min
[150000], rate=9000000.00/min
[160000], rate=9600000.00/min
[170000], rate=10200000.00/min
[180000], rate=10800000.00/min
[190000], rate=11400000.00/min
[200000], rate=12000000.00/min
[210000], rate=12600000.00/min
[220000], rate=13200000.00/min
[230000], rate=13800000.00/min
[240000], rate=14400000.00/min
[250000], rate=15000000.00/min
[260000], rate=15600000.00/min
[270000], rate=16200000.00/min
[280000], rate=16800000.00/min
[290000], rate=17400000.00/min
[300000], rate=18000000.00/min
[310000], rate=18600000.00/min
[320000], rate=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=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=17100000.00/min
[580000], rate=17400000.00/min
[590000], rate=17700000.00/min
[600000], rate=18000000.00/min
[610000], rate=18300000.00/min
[620000], rate=18600000.00/min
[630000], rate=18900000.00/min
[640000], rate=19200000.00/min
[650000], rate=19500000.00/min
[660000], rate=19800000.00/min
[670000], rate=20100000.00/min
[680000], rate=20400000.00/min
[690000], rate=20700000.00/min
[700000], rate=21000000.00/min
[710000], rate=21300000.00/min
[720000], rate=21600000.00/min
[730000], rate=21900000.00/min
[740000], rate=22200000.00/min
[750000], rate=22500000.00/min
[760000], rate=22800000.00/min
[770000], rate=23100000.00/min
[780000], rate=23400000.00/min
[790000], rate=23700000.00/min
[800000], rate=24000000.00/min
[810000], rate=24300000.00/min
[820000], rate=24600000.00/min
[830000], rate=24900000.00/min
[840000], rate=25200000.00/min
[850000], rate=25500000.00/min
[860000], rate=25800000.00/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=20200000.00/min
[1020000], rate=20400000.00/min
[1030000], rate=20600000.00/min
[1040000], rate=20800000.00/min
[1050000], rate=21000000.00/min
[1060000], rate=21200000.00/min
[1070000], rate=21400000.00/min
[1080000], rate=21600000.00/min
[1090000], rate=21800000.00/min
[1100000], rate=22000000.00/min
[1110000], rate=22200000.00/min
[1120000], rate=22400000.00/min
[1130000], rate=22600000.00/min
[1140000], rate=22800000.00/min
[1150000], rate=23000000.00/min
[1160000], rate=23200000.00/min
[1170000], rate=23400000.00/min
[1180000], rate=23600000.00/min
[1190000], rate=23800000.00/min
[1200000], rate=24000000.00/min
[1210000], rate=24200000.00/min
[1220000], rate=24400000.00/min
[1230000], rate=24600000.00/min
[1240000], rate=24800000.00/min
[1250000], rate=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=21150000.00/min
[1420000], rate=21300000.00/min
[1430000], rate=21450000.00/min
[1440000], rate=21600000.00/min
[1450000], rate=21750000.00/min
[1460000], rate=21900000.00/min
[1470000], rate=22050000.00/min
[1480000], rate=22200000.00/min
[1490000], rate=22350000.00/min
[1500000], rate=22500000.00/min
[1510000], rate=22650000.00/min
[1520000], rate=22800000.00/min
[1530000], rate=22950000.00/min
[1540000], rate=23100000.00/min
[1550000], rate=23250000.00/min
[1560000], rate=23400000.00/min
[1570000], rate=23550000.00/min
[1580000], rate=23700000.00/min
[1590000], rate=23850000.00/min
[1600000], rate=24000000.00/min
[1610000], rate=24150000.00/min
[1620000], rate=24300000.00/min
[1630000], rate=24450000.00/min
[1640000], rate=24600000.00/min
[1650000], rate=24750000.00/min
[1660000], rate=24900000.00/min
[1670000], rate=25050000.00/min
[1680000], rate=25200000.00/min
[1690000], rate=25350000.00/min
[1700000], rate=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=22200000.00/min
[1860000], rate=22320000.00/min
[1870000], rate=22440000.00/min
[1880000], rate=22560000.00/min
[1890000], rate=22680000.00/min
[1900000], rate=22800000.00/min
[1910000], rate=22920000.00/min
[1920000], rate=23040000.00/min
[1930000], rate=23160000.00/min
[1940000], rate=23280000.00/min
[1950000], rate=23400000.00/min
[1960000], rate=23520000.00/min
[1970000], rate=23640000.00/min
[1980000], rate=23760000.00/min
[1990000], rate=23880000.00/min
[2000000], rate=24000000.00/min
[2010000], rate=24120000.00/min
[2020000], rate=24240000.00/min
[2030000], rate=24360000.00/min
[2040000], rate=24480000.00/min
[2050000], rate=24600000.00/min
[2060000], rate=24720000.00/min
[2070000], rate=24840000.00/min
[2080000], rate=24960000.00/min
[2090000], rate=25080000.00/min
[2100000], rate=25200000.00/min
[2110000], rate=25320000.00/min
[2120000], rate=25440000.00/min
[2130000], rate=25560000.00/min
[2140000], rate=25680000.00/min
[2150000], rate=25800000.00/min
[2160000], rate=25920000.00/min
[2170000], rate=26040000.00/min
[2180000], rate=21800000.00/min
[2190000], rate=21900000.00/min
[2200000], rate=22000000.00/min
[2210000], rate=22100000.00/min
[2220000], rate=22200000.00/min
[2230000], rate=22300000.00/min
[2240000], rate=22400000.00/min
[2250000], rate=22500000.00/min
[2260000], rate=22600000.00/min
[2270000], rate=22700000.00/min
[2280000], rate=22800000.00/min
[2290000], rate=22900000.00/min
[2300000], rate=23000000.00/min
[2310000], rate=23100000.00/min
[2320000], rate=23200000.00/min
[2330000], rate=23300000.00/min
[2340000], rate=23400000.00/min
[2350000], rate=23500000.00/min
[2360000], rate=23600000.00/min
[2370000], rate=23700000.00/min
[2380000], rate=23800000.00/min
[2390000], rate=23900000.00/min
[2400000], rate=24000000.00/min
[2410000], rate=24100000.00/min
[2420000], rate=24200000.00/min
[2430000], rate=24300000.00/min
[2440000], rate=24400000.00/min
[2450000], rate=24500000.00/min
[2460000], rate=24600000.00/min
[2470000], rate=24700000.00/min
[2480000], rate=24800000.00/min
[2490000], rate=24900000.00/min
[2500000], rate=25000000.00/min
[2510000], rate=25100000.00/min
[2520000], rate=25200000.00/min
[2530000], rate=25300000.00/min
[2540000], rate=25400000.00/min
[2550000], rate=25500000.00/min
[2560000], rate=25600000.00/min
[2570000], rate=25700000.00/min
[2580000], rate=25800000.00/min
[2590000], rate=22200000.00/min
[2600000], rate=22285714.29/min
[2610000], rate=22371428.57/min
[2620000], rate=22457142.86/min
[2630000], rate=22542857.14/min
[2640000], rate=22628571.43/min
[2650000], rate=22714285.71/min
[2660000], rate=22800000.00/min
[2670000], rate=22885714.29/min
[2680000], rate=22971428.57/min
[2690000], rate=23057142.86/min
[2700000], rate=23142857.14/min
[2710000], rate=23228571.43/min
[2720000], rate=23314285.71/min
[2730000], rate=23400000.00/min
[2740000], rate=23485714.29/min
[2750000], rate=23571428.57/min
[2760000], rate=23657142.86/min
[2770000], rate=23742857.14/min
[2780000], rate=23828571.43/min
[2790000], rate=23914285.71/min
[2800000], rate=24000000.00/min
[2810000], rate=24085714.29/min
[2820000], rate=24171428.57/min
[2830000], rate=24257142.86/min
[2840000], rate=24342857.14/min
[2850000], rate=24428571.43/min
[2860000], rate=24514285.71/min
[2870000], rate=24600000.00/min
[2880000], rate=24685714.29/min
[2890000], rate=24771428.57/min
[2900000], rate=24857142.86/min
[2910000], rate=24942857.14/min
[2920000], rate=25028571.43/min
[2930000], rate=25114285.71/min
[2940000], rate=25200000.00/min
[2950000], rate=25285714.29/min
[2960000], rate=25371428.57/min
[2970000], rate=25457142.86/min
[2980000], rate=25542857.14/min
[2990000], rate=25628571.43/min
[3000000], rate=25714285.71/min
[3010000], rate=25800000.00/min
[3020000], rate=22650000.00/min
[3030000], rate=22725000.00/min
[3040000], rate=22800000.00/min
[3050000], rate=22875000.00/min
[3060000], rate=22950000.00/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=25950000.00/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=25560000.00/min
[4270000], rate=25620000.00/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=25309090.91/min
[4650000], rate=25363636.36/min
[4660000], rate=25418181.82/min
[4670000], rate=25472727.27/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=25200000.00/min
[5050000], rate=25250000.00/min
[5060000], rate=25300000.00/min
[5070000], rate=25350000.00/min
[5080000], rate=25400000.00/min
[5090000], rate=25450000.00/min
[5100000], rate=25500000.00/min
[5110000], rate=25550000.00/min
[5120000], rate=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=24830769.23/min
[5390000], rate=24876923.08/min
[5400000], rate=24923076.92/min
[5410000], rate=24969230.77/min
[5420000], rate=25015384.62/min
[5430000], rate=25061538.46/min
[5440000], rate=25107692.31/min
[5450000], rate=25153846.15/min
[5460000], rate=25200000.00/min
[5470000], rate=25246153.85/min
[5480000], rate=25292307.69/min
[5490000], rate=25338461.54/min
[5500000], rate=25384615.38/min
[5510000], rate=25430769.23/min
[5520000], rate=25476923.08/min
[5530000], rate=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=24428571.43/min
[5710000], rate=24471428.57/min
[5720000], rate=24514285.71/min
[5730000], rate=24557142.86/min
[5740000], rate=24600000.00/min
[5750000], rate=24642857.14/min
[5760000], rate=24685714.29/min
[5770000], rate=24728571.43/min
[5780000], rate=24771428.57/min
[5790000], rate=24814285.71/min
[5800000], rate=24857142.86/min
[5810000], rate=24900000.00/min
[5820000], rate=24942857.14/min
[5830000], rate=24985714.29/min
[5840000], rate=25028571.43/min
[5850000], rate=25071428.57/min
[5860000], rate=25114285.71/min
[5870000], rate=25157142.86/min
[5880000], rate=25200000.00/min
[5890000], rate=25242857.14/min
[5900000], rate=25285714.29/min
[5910000], rate=25328571.43/min
[5920000], rate=25371428.57/min
[5930000], rate=25414285.71/min
[5940000], rate=25457142.86/min
[5950000], rate=25500000.00/min
[5960000], rate=25542857.14/min
[5970000], rate=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=24280000.00/min
[6080000], rate=24320000.00/min
[6090000], rate=24360000.00/min
[6100000], rate=24400000.00/min
[6110000], rate=24440000.00/min
[6120000], rate=24480000.00/min
[6130000], rate=24520000.00/min
[6140000], rate=24560000.00/min
[6150000], rate=24600000.00/min
[6160000], rate=24640000.00/min
[6170000], rate=24680000.00/min
[6180000], rate=24720000.00/min
[6190000], rate=24760000.00/min
[6200000], rate=24800000.00/min
[6210000], rate=24840000.00/min
[6220000], rate=24880000.00/min
[6230000], rate=24920000.00/min
[6240000], rate=24960000.00/min
[6250000], rate=25000000.00/min
[6260000], rate=25040000.00/min
[6270000], rate=25080000.00/min
[6280000], rate=25120000.00/min
[6290000], rate=25160000.00/min
[6300000], rate=25200000.00/min
[6310000], rate=25240000.00/min
[6320000], rate=25280000.00/min
[6330000], rate=25320000.00/min
[6340000], rate=25360000.00/min
[6350000], rate=25400000.00/min
[6360000], rate=25440000.00/min
[6370000], rate=25480000.00/min
[6380000], rate=25520000.00/min
[6390000], rate=25560000.00/min
[6400000], rate=25600000.00/min
[6410000], rate=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=24375000.00/min
[6510000], rate=24412500.00/min
[6520000], rate=24450000.00/min
[6530000], rate=24487500.00/min
[6540000], rate=24525000.00/min
[6550000], rate=24562500.00/min
[6560000], rate=24600000.00/min
[6570000], rate=24637500.00/min
[6580000], rate=24675000.00/min
[6590000], rate=24712500.00/min
[6600000], rate=24750000.00/min 08:33:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_6i-T1-TRNA-1_B23WHTKLT4_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_6i-T1-TRNA-1_B23WHTKLT4_1.introns: identified 1696 cancer introns
08:33:03 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim
08:33:03 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/prelim_introns.ok
08:33:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
08:33:04 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
08:33:04 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/introns_filtered.ok
08:33:04 : INFO : -found 1210 cancer introns
08:33:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
08:33:04 : INFO : Creating the BED File.
08:33:07 : INFO : Saving Bed File as 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
08:33:07 : INFO : Execution Time = 0.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
08:33:07 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/intron_igv_bed.ok
08:33:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_6i-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_6i-T1-TRNA-1_B23WHTKLT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
08:39:16 : INFO : Execution Time = 6.15 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_6i-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_6i-T1-TRNA-1_B23WHTKLT4_1
08:39:16 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok
08:39:16 : INFO : Running: samtools sort -o 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
08:39:16 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
08:39:16 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok
08:39:16 : INFO : Running: samtools sort -o 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
[bam_sort_core] merging from 41 files and 1 in-memory blocks...
08:46:47 : INFO : Execution Time = 7.51 minutes. CMD: samtools sort -o 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
08:46:47 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_gene_reads.ok
08:46:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
08:49:40 : INFO : Execution Time = 2.89 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
08:49:40 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
08:49:40 : INFO : Running: samtools sort -o 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
08:50:11 : INFO : Execution Time = 0.52 minutes. CMD: samtools sort -o 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
08:50:11 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
08:50:11 : INFO : Running: samtools index 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
08:50:14 : INFO : Execution Time = 0.06 minutes. CMD: samtools index 659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
08:50:14 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_6i-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
08:50:15 : INFO : Running: samtools index 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
08:50:15 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
08:50:15 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_6i-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
08:50:15 : INFO : Running: create_report 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_6i-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_6i-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_6i-T1-TRNA-1_B23WHTKLT4_1'
08:54:46 : INFO : Execution Time = 4.53 minutes. CMD: create_report 659_6i-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_6i-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_6i-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_6i-T1-TRNA-1_B23WHTKLT4_1'
08:54:46 : INFO : Running: touch /tmp/nxf.6KebQNYjrS/659_6i-T1-TRNA-1_B23WHTKLT4_1.chckpts/igv_create_html.ok
08:54:46 : INFO : done.