Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/66d9206e502e825117598616600ac4/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/c812a58aa1583ba385f7bb4d8c90d2/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/66d9206e502e825117598616600ac4/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/edd65c761c13bc75a05b4976c07e2f/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/66d9206e502e825117598616600ac4/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/c812a58aa1583ba385f7bb4d8c90d2/.command.run ==> STAGING COMPLETE (7 inputs) 08:55:00 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [40000], rate=2400000.00/min [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=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=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=13500000.00/min [460000], rate=13800000.00/min [470000], rate=14100000.00/min [480000], rate=14400000.00/min [490000], rate=14700000.00/min [500000], rate=15000000.00/min [510000], rate=15300000.00/min [520000], rate=15600000.00/min [530000], rate=15900000.00/min [540000], rate=16200000.00/min [550000], rate=16500000.00/min [560000], rate=16800000.00/min [570000], rate=17100000.00/min [580000], rate=17400000.00/min [590000], rate=17700000.00/min [600000], rate=18000000.00/min [610000], rate=18300000.00/min [620000], rate=18600000.00/min [630000], rate=18900000.00/min [640000], rate=19200000.00/min [650000], rate=13000000.00/min [660000], rate=13200000.00/min [670000], rate=13400000.00/min [680000], rate=13600000.00/min [690000], rate=13800000.00/min [700000], rate=14000000.00/min [710000], rate=14200000.00/min [720000], rate=14400000.00/min [730000], rate=14600000.00/min [740000], rate=14800000.00/min [750000], rate=15000000.00/min [760000], rate=15200000.00/min [770000], rate=15400000.00/min [780000], rate=15600000.00/min [790000], rate=15800000.00/min [800000], rate=16000000.00/min [810000], rate=16200000.00/min [820000], rate=16400000.00/min [830000], rate=16600000.00/min [840000], rate=16800000.00/min [850000], rate=17000000.00/min [860000], rate=17200000.00/min [870000], rate=17400000.00/min [880000], rate=17600000.00/min [890000], rate=17800000.00/min [900000], rate=13500000.00/min [910000], rate=13650000.00/min [920000], rate=13800000.00/min [930000], rate=13950000.00/min [940000], rate=14100000.00/min [950000], rate=14250000.00/min [960000], rate=14400000.00/min [970000], rate=14550000.00/min [980000], rate=14700000.00/min [990000], rate=14850000.00/min [1000000], rate=15000000.00/min [1010000], rate=15150000.00/min [1020000], rate=15300000.00/min [1030000], rate=15450000.00/min [1040000], rate=15600000.00/min [1050000], rate=15750000.00/min [1060000], rate=15900000.00/min [1070000], rate=16050000.00/min [1080000], rate=16200000.00/min [1090000], rate=16350000.00/min [1100000], rate=16500000.00/min [1110000], rate=16650000.00/min [1120000], rate=16800000.00/min [1130000], rate=16950000.00/min [1140000], rate=13680000.00/min [1150000], rate=13800000.00/min [1160000], rate=13920000.00/min [1170000], rate=14040000.00/min [1180000], rate=14160000.00/min [1190000], rate=14280000.00/min [1200000], rate=14400000.00/min [1210000], rate=14520000.00/min [1220000], rate=14640000.00/min [1230000], rate=14760000.00/min [1240000], rate=14880000.00/min [1250000], rate=15000000.00/min [1260000], rate=15120000.00/min [1270000], rate=15240000.00/min [1280000], rate=15360000.00/min [1290000], rate=15480000.00/min [1300000], rate=15600000.00/min [1310000], rate=15720000.00/min [1320000], rate=15840000.00/min [1330000], rate=15960000.00/min [1340000], rate=16080000.00/min [1350000], rate=16200000.00/min [1360000], rate=16320000.00/min [1370000], rate=13700000.00/min [1380000], rate=13800000.00/min [1390000], rate=13900000.00/min [1400000], rate=14000000.00/min [1410000], rate=14100000.00/min [1420000], rate=14200000.00/min [1430000], rate=14300000.00/min [1440000], rate=14400000.00/min [1450000], rate=14500000.00/min [1460000], rate=14600000.00/min [1470000], rate=14700000.00/min [1480000], rate=14800000.00/min [1490000], rate=14900000.00/min [1500000], rate=15000000.00/min [1510000], rate=15100000.00/min [1520000], rate=15200000.00/min [1530000], rate=15300000.00/min [1540000], rate=15400000.00/min [1550000], rate=15500000.00/min [1560000], rate=15600000.00/min [1570000], rate=15700000.00/min [1580000], rate=15800000.00/min [1590000], rate=15900000.00/min [1600000], rate=16000000.00/min [1610000], rate=16100000.00/min [1620000], rate=13885714.29/min [1630000], rate=13971428.57/min [1640000], rate=14057142.86/min [1650000], rate=14142857.14/min [1660000], rate=14228571.43/min [1670000], rate=14314285.71/min [1680000], rate=14400000.00/min [1690000], rate=14485714.29/min [1700000], rate=14571428.57/min [1710000], rate=14657142.86/min [1720000], rate=14742857.14/min [1730000], rate=14828571.43/min [1740000], rate=14914285.71/min [1750000], rate=15000000.00/min [1760000], rate=15085714.29/min [1770000], rate=15171428.57/min [1780000], rate=15257142.86/min [1790000], rate=15342857.14/min [1800000], rate=15428571.43/min [1810000], rate=15514285.71/min [1820000], rate=15600000.00/min [1830000], rate=15685714.29/min [1840000], rate=15771428.57/min [1850000], rate=15857142.86/min [1860000], rate=15942857.14/min [1870000], rate=14025000.00/min [1880000], rate=14100000.00/min [1890000], rate=14175000.00/min [1900000], rate=14250000.00/min [1910000], rate=14325000.00/min [1920000], rate=14400000.00/min [1930000], rate=14475000.00/min [1940000], rate=14550000.00/min [1950000], rate=14625000.00/min [1960000], rate=14700000.00/min [1970000], rate=14775000.00/min [1980000], rate=14850000.00/min [1990000], rate=14925000.00/min [2000000], rate=15000000.00/min [2010000], rate=15075000.00/min [2020000], rate=15150000.00/min [2030000], rate=15225000.00/min [2040000], rate=15300000.00/min [2050000], rate=15375000.00/min [2060000], rate=15450000.00/min [2070000], rate=15525000.00/min [2080000], rate=15600000.00/min [2090000], rate=15675000.00/min [2100000], rate=15750000.00/min [2110000], rate=15825000.00/min [2120000], rate=15900000.00/min [2130000], rate=15975000.00/min [2140000], rate=14266666.67/min [2150000], rate=14333333.33/min [2160000], rate=14400000.00/min [2170000], rate=14466666.67/min [2180000], rate=14533333.33/min [2190000], rate=14600000.00/min [2200000], rate=14666666.67/min [2210000], rate=14733333.33/min [2220000], rate=14800000.00/min [2230000], rate=14866666.67/min [2240000], rate=14933333.33/min [2250000], rate=15000000.00/min [2260000], rate=15066666.67/min [2270000], rate=15133333.33/min [2280000], rate=15200000.00/min [2290000], rate=15266666.67/min [2300000], rate=15333333.33/min [2310000], rate=15400000.00/min [2320000], rate=15466666.67/min [2330000], rate=15533333.33/min [2340000], rate=15600000.00/min [2350000], rate=15666666.67/min [2360000], rate=15733333.33/min [2370000], rate=15800000.00/min [2380000], rate=15866666.67/min [2390000], rate=14340000.00/min [2400000], rate=14400000.00/min [2410000], rate=14460000.00/min [2420000], rate=14520000.00/min [2430000], rate=14580000.00/min [2440000], rate=14640000.00/min [2450000], rate=14700000.00/min [2460000], rate=14760000.00/min [2470000], rate=14820000.00/min [2480000], rate=14880000.00/min [2490000], rate=14940000.00/min [2500000], rate=15000000.00/min [2510000], rate=15060000.00/min [2520000], rate=15120000.00/min [2530000], rate=15180000.00/min [2540000], rate=15240000.00/min [2550000], rate=15300000.00/min [2560000], rate=15360000.00/min [2570000], rate=15420000.00/min [2580000], rate=15480000.00/min [2590000], rate=15540000.00/min [2600000], rate=15600000.00/min [2610000], rate=15660000.00/min [2620000], rate=15720000.00/min [2630000], rate=14345454.55/min [2640000], rate=14400000.00/min [2650000], rate=14454545.45/min [2660000], rate=14509090.91/min [2670000], rate=14563636.36/min [2680000], rate=14618181.82/min [2690000], rate=14672727.27/min [2700000], rate=14727272.73/min [2710000], rate=14781818.18/min [2720000], rate=14836363.64/min [2730000], rate=14890909.09/min [2740000], rate=14945454.55/min [2750000], rate=15000000.00/min [2760000], rate=15054545.45/min [2770000], rate=15109090.91/min [2780000], rate=15163636.36/min [2790000], rate=15218181.82/min [2800000], rate=15272727.27/min [2810000], rate=15327272.73/min [2820000], rate=15381818.18/min [2830000], rate=15436363.64/min [2840000], rate=15490909.09/min [2850000], rate=15545454.55/min [2860000], rate=14300000.00/min [2870000], rate=14350000.00/min [2880000], rate=14400000.00/min [2890000], rate=14450000.00/min [2900000], rate=14500000.00/min [2910000], rate=14550000.00/min [2920000], rate=14600000.00/min [2930000], rate=14650000.00/min [2940000], rate=14700000.00/min [2950000], rate=14750000.00/min [2960000], rate=14800000.00/min [2970000], rate=14850000.00/min [2980000], rate=14900000.00/min [2990000], rate=14950000.00/min [3000000], rate=15000000.00/min [3010000], rate=15050000.00/min [3020000], rate=15100000.00/min [3030000], rate=15150000.00/min [3040000], rate=15200000.00/min [3050000], rate=15250000.00/min [3060000], rate=15300000.00/min [3070000], rate=15350000.00/min [3080000], rate=15400000.00/min [3090000], rate=15450000.00/min [3100000], rate=15500000.00/min [3110000], rate=14353846.15/min [3120000], rate=14400000.00/min [3130000], rate=14446153.85/min [3140000], rate=14492307.69/min [3150000], rate=14538461.54/min [3160000], rate=14584615.38/min [3170000], rate=14630769.23/min [3180000], rate=14676923.08/min [3190000], rate=14723076.92/min [3200000], rate=14769230.77/min [3210000], rate=14815384.62/min [3220000], rate=14861538.46/min [3230000], rate=14907692.31/min [3240000], rate=14953846.15/min [3250000], rate=15000000.00/min [3260000], rate=15046153.85/min [3270000], rate=15092307.69/min [3280000], rate=15138461.54/min [3290000], rate=15184615.38/min [3300000], rate=15230769.23/min [3310000], rate=15276923.08/min [3320000], rate=14228571.43/min [3330000], rate=14271428.57/min [3340000], rate=14314285.71/min [3350000], rate=14357142.86/min [3360000], rate=14400000.00/min [3370000], rate=14442857.14/min [3380000], rate=14485714.29/min [3390000], rate=14528571.43/min [3400000], rate=14571428.57/min [3410000], rate=14614285.71/min [3420000], rate=14657142.86/min [3430000], rate=14700000.00/min [3440000], rate=14742857.14/min [3450000], rate=14785714.29/min [3460000], rate=14828571.43/min [3470000], rate=14871428.57/min [3480000], rate=14914285.71/min [3490000], rate=14957142.86/min [3500000], rate=15000000.00/min [3510000], rate=15042857.14/min [3520000], rate=15085714.29/min [3530000], rate=15128571.43/min [3540000], rate=15171428.57/min [3550000], rate=15214285.71/min [3560000], rate=15257142.86/min [3570000], rate=15300000.00/min [3580000], rate=14320000.00/min [3590000], rate=14360000.00/min [3600000], rate=14400000.00/min [3610000], rate=14440000.00/min [3620000], rate=14480000.00/min [3630000], rate=14520000.00/min [3640000], rate=14560000.00/min [3650000], rate=14600000.00/min [3660000], rate=14640000.00/min [3670000], rate=14680000.00/min [3680000], rate=14720000.00/min [3690000], rate=14760000.00/min [3700000], rate=14800000.00/min [3710000], rate=14840000.00/min [3720000], rate=14880000.00/min [3730000], rate=14920000.00/min [3740000], rate=14960000.00/min [3750000], rate=15000000.00/min [3760000], rate=15040000.00/min [3770000], rate=15080000.00/min [3780000], rate=15120000.00/min [3790000], rate=15160000.00/min [3800000], rate=14250000.00/min [3810000], rate=14287500.00/min [3820000], rate=14325000.00/min [3830000], rate=14362500.00/min [3840000], rate=14400000.00/min [3850000], rate=14437500.00/min [3860000], rate=14475000.00/min [3870000], rate=14512500.00/min [3880000], rate=14550000.00/min [3890000], rate=14587500.00/min [3900000], rate=14625000.00/min [3910000], rate=14662500.00/min [3920000], rate=14700000.00/min [3930000], rate=14737500.00/min [3940000], rate=14775000.00/min [3950000], rate=14812500.00/min [3960000], rate=14850000.00/min [3970000], rate=14011764.71/min [3980000], rate=14047058.82/min [3990000], rate=14082352.94/min [4000000], rate=14117647.06/min [4010000], rate=14152941.18/min [4020000], rate=14188235.29/min [4030000], rate=14223529.41/min [4040000], rate=14258823.53/min [4050000], rate=14294117.65/min [4060000], rate=14329411.76/min [4070000], rate=14364705.88/min [4080000], rate=14400000.00/min [4090000], rate=14435294.12/min [4100000], rate=14470588.24/min [4110000], rate=14505882.35/min [4120000], rate=14541176.47/min [4130000], rate=13766666.67/min [4140000], rate=13800000.00/min [4150000], rate=13833333.33/min [4160000], rate=13866666.67/min [4170000], rate=13900000.00/min [4180000], rate=13933333.33/min [4190000], rate=13966666.67/min [4200000], rate=14000000.00/min [4210000], rate=14033333.33/min [4220000], rate=14066666.67/min [4230000], rate=14100000.00/min [4240000], rate=14133333.33/min [4250000], rate=14166666.67/min [4260000], rate=14200000.00/min [4270000], rate=14233333.33/min [4280000], rate=13515789.47/min [4290000], rate=13547368.42/min [4300000], rate=13578947.37/min [4310000], rate=13610526.32/min [4320000], rate=13642105.26/min [4330000], rate=13673684.21/min [4340000], rate=13705263.16/min [4350000], rate=13736842.11/min [4360000], rate=13768421.05/min [4370000], rate=13800000.00/min [4380000], rate=13831578.95/min [4390000], rate=13863157.89/min [4400000], rate=13894736.84/min [4410000], rate=13926315.79/min [4420000], rate=13957894.74/min [4430000], rate=13989473.68/min [4440000], rate=13320000.00/min [4450000], rate=13350000.00/min [4460000], rate=13380000.00/min [4470000], rate=13410000.00/min [4480000], rate=13440000.00/min [4490000], rate=13470000.00/min [4500000], rate=13500000.00/min [4510000], rate=13530000.00/min [4520000], rate=13560000.00/min [4530000], rate=13590000.00/min [4540000], rate=13620000.00/min [4550000], rate=13650000.00/min [4560000], rate=13680000.00/min [4570000], rate=13710000.00/min [4580000], rate=13085714.29/min [4590000], rate=13114285.71/min [4600000], rate=13142857.14/min [4610000], rate=13171428.57/min [4620000], rate=13200000.00/min [4630000], rate=13228571.43/min [4640000], rate=13257142.86/min [4650000], rate=13285714.29/min [4660000], rate=13314285.71/min [4670000], rate=13342857.14/min [4680000], rate=13371428.57/min [4690000], rate=13400000.00/min [4700000], rate=12818181.82/min [4710000], rate=12845454.55/min [4720000], rate=12872727.27/min [4730000], rate=12900000.00/min [4740000], rate=12927272.73/min [4750000], rate=12954545.45/min [4760000], rate=12981818.18/min [4770000], rate=13009090.91/min [4780000], rate=13036363.64/min [4790000], rate=13063636.36/min [4800000], rate=13090909.09/min [4810000], rate=12547826.09/min [4820000], rate=12573913.04/min [4830000], rate=12600000.00/min [4840000], rate=12626086.96/min [4850000], rate=12652173.91/min [4860000], rate=12678260.87/min [4870000], rate=12704347.83/min [4880000], rate=12730434.78/min [4890000], rate=12756521.74/min [4900000], rate=12782608.70/min [4910000], rate=12808695.65/min [4920000], rate=12300000.00/min [4930000], rate=12325000.00/min [4940000], rate=12350000.00/min [4950000], rate=12375000.00/min [4960000], rate=12400000.00/min [4970000], rate=12425000.00/min [4980000], rate=12450000.00/min [4990000], rate=12475000.00/min [5000000], rate=12500000.00/min [5010000], rate=12525000.00/min [5020000], rate=12550000.00/min [5030000], rate=12072000.00/min [5040000], rate=12096000.00/min [5050000], rate=12120000.00/min [5060000], rate=12144000.00/min [5070000], rate=12168000.00/min [5080000], rate=12192000.00/min [5090000], rate=12216000.00/min [5100000], rate=12240000.00/min [5110000], rate=12264000.00/min [5120000], rate=12288000.00/min [5130000], rate=12312000.00/min [5140000], rate=11861538.46/min [5150000], rate=11884615.38/min [5160000], rate=11907692.31/min [5170000], rate=11930769.23/min [5180000], rate=11953846.15/min [5190000], rate=11976923.08/min [5200000], rate=12000000.00/min [5210000], rate=12023076.92/min [5220000], rate=12046153.85/min [5230000], rate=12069230.77/min [5240000], rate=12092307.69/min [5250000], rate=12115384.62/min [5260000], rate=11688888.89/min [5270000], rate=11711111.11/min [5280000], rate=11733333.33/min [5290000], rate=11755555.56/min [5300000], rate=11777777.78/min [5310000], rate=11800000.00/min [5320000], rate=11822222.22/min [5330000], rate=11844444.44/min [5340000], rate=11866666.67/min [5350000], rate=11888888.89/min [5360000], rate=11911111.11/min [5370000], rate=11933333.33/min [5380000], rate=11955555.56/min [5390000], rate=11977777.78/min [5400000], rate=12000000.00/min [5410000], rate=12022222.22/min [5420000], rate=12044444.44/min [5430000], rate=12066666.67/min [5440000], rate=12088888.89/min [5450000], rate=12111111.11/min [5460000], rate=12133333.33/min [5470000], rate=12155555.56/min [5480000], rate=12177777.78/min [5490000], rate=12200000.00/min [5500000], rate=11785714.29/min [5510000], rate=11807142.86/min [5520000], rate=11828571.43/min [5530000], rate=11850000.00/min [5540000], rate=11871428.57/min [5550000], rate=11892857.14/min [5560000], rate=11914285.71/min [5570000], rate=11935714.29/min [5580000], rate=11957142.86/min [5590000], rate=11978571.43/min [5600000], rate=12000000.00/min [5610000], rate=12021428.57/min [5620000], rate=12042857.14/min [5630000], rate=12064285.71/min [5640000], rate=12085714.29/min [5650000], rate=12107142.86/min [5660000], rate=12128571.43/min [5670000], rate=12150000.00/min [5680000], rate=12171428.57/min [5690000], rate=12192857.14/min [5700000], rate=12214285.71/min [5710000], rate=12235714.29/min [5720000], rate=12257142.86/min [5730000], rate=12278571.43/min [5740000], rate=12300000.00/min [5750000], rate=12321428.57/min [5760000], rate=12342857.14/min [5770000], rate=12364285.71/min [5780000], rate=12385714.29/min [5790000], rate=12407142.86/min [5800000], rate=12428571.43/min [5810000], rate=12450000.00/min [5820000], rate=12041379.31/min [5830000], rate=12062068.97/min [5840000], rate=12082758.62/min [5850000], rate=12103448.28/min [5860000], rate=12124137.93/min [5870000], rate=12144827.59/min [5880000], rate=12165517.24/min [5890000], rate=12186206.90/min [5900000], rate=12206896.55/min [5910000], rate=12227586.21/min [5920000], rate=12248275.86/min [5930000], rate=12268965.52/min [5940000], rate=12289655.17/min [5950000], rate=12310344.83/min [5960000], rate=12331034.48/min [5970000], rate=12351724.14/min [5980000], rate=12372413.79/min [5990000], rate=12393103.45/min [6000000], rate=12413793.10/min [6010000], rate=12434482.76/min [6020000], rate=12455172.41/min [6030000], rate=12475862.07/min [6040000], rate=12496551.72/min [6050000], rate=12100000.00/min [6060000], rate=12120000.00/min [6070000], rate=12140000.00/min [6080000], rate=12160000.00/min [6090000], rate=12180000.00/min [6100000], rate=12200000.00/min [6110000], rate=12220000.00/min [6120000], rate=12240000.00/min [6130000], rate=12260000.00/min [6140000], rate=12280000.00/min [6150000], rate=12300000.00/min [6160000], rate=12320000.00/min [6170000], rate=12340000.00/min [6180000], rate=12360000.00/min [6190000], rate=12380000.00/min [6200000], rate=12400000.00/min [6210000], rate=12420000.00/min [6220000], rate=12440000.00/min [6230000], rate=12460000.00/min [6240000], rate=12480000.00/min [6250000], rate=12500000.00/min [6260000], rate=12520000.00/min [6270000], rate=12540000.00/min [6280000], rate=12560000.00/min [6290000], rate=12580000.00/min [6300000], rate=12193548.39/min [6310000], rate=12212903.23/min [6320000], rate=12232258.06/min [6330000], rate=12251612.90/min [6340000], rate=12270967.74/min [6350000], rate=12290322.58/min [6360000], rate=12309677.42/min [6370000], rate=12329032.26/min [6380000], rate=12348387.10/min [6390000], rate=12367741.94/min [6400000], rate=12387096.77/min [6410000], rate=12406451.61/min [6420000], rate=12425806.45/min [6430000], rate=12445161.29/min [6440000], rate=12464516.13/min [6450000], rate=12483870.97/min [6460000], rate=12503225.81/min [6470000], rate=12522580.65/min [6480000], rate=12541935.48/min [6490000], rate=12561290.32/min [6500000], rate=12580645.16/min [6510000], rate=12600000.00/min [6520000], rate=12619354.84/min [6530000], rate=12638709.68/min [6540000], rate=12658064.52/min [6550000], rate=12677419.35/min [6560000], rate=12300000.00/min [6570000], rate=12318750.00/min [6580000], rate=12337500.00/min [6590000], rate=12356250.00/min [6600000], rate=12375000.00/min [6610000], rate=12393750.00/min [6620000], rate=12412500.00/min [6630000], rate=12431250.00/min [6640000], rate=12450000.00/min [6650000], rate=12468750.00/min [6660000], rate=12487500.00/min [6670000], rate=12506250.00/min [6680000], rate=12525000.00/min [6690000], rate=12543750.00/min [6700000], rate=12562500.00/min [6710000], rate=12581250.00/min [6720000], rate=12600000.00/min [6730000], rate=12618750.00/min [6740000], rate=12637500.00/min [6750000], rate=12656250.00/min [6760000], rate=12675000.00/min [6770000], rate=12693750.00/min [6780000], rate=12712500.00/min [6790000], rate=12731250.00/min [6800000], rate=12750000.00/min [6810000], rate=12768750.00/min [6820000], rate=12400000.00/min [6830000], rate=12418181.82/min [6840000], rate=12436363.64/min [6850000], rate=12454545.45/min [6860000], rate=12472727.27/min [6870000], rate=12490909.09/min [6880000], rate=12509090.91/min [6890000], rate=12527272.73/min [6900000], rate=12545454.55/min [6910000], rate=12563636.36/min [6920000], rate=12581818.18/min [6930000], rate=12600000.00/min [6940000], rate=12618181.82/min [6950000], rate=12636363.64/min [6960000], rate=12654545.45/min [6970000], rate=12672727.27/min [6980000], rate=12690909.09/min [6990000], rate=12709090.91/min [7000000], rate=12727272.73/min [7010000], rate=12745454.55/min [7020000], rate=12763636.36/min [7030000], rate=12781818.18/min [7040000], rate=12800000.00/min [7050000], rate=12818181.82/min [7060000], rate=12836363.64/min [7070000], rate=12854545.45/min [7080000], rate=12872727.27/min [7090000], rate=12511764.71/min [7100000], rate=12529411.76/min [7110000], rate=12547058.82/min [7120000], rate=12564705.88/min [7130000], rate=12582352.94/min [7140000], rate=12600000.00/min [7150000], rate=12617647.06/min [7160000], rate=12635294.12/min [7170000], rate=12652941.18/min [7180000], rate=12670588.24/min [7190000], rate=12688235.29/min [7200000], rate=12705882.35/min [7210000], rate=12723529.41/min [7220000], rate=12741176.47/min [7230000], rate=12758823.53/min [7240000], rate=12776470.59/min [7250000], rate=12794117.65/min [7260000], rate=12811764.71/min [7270000], rate=12829411.76/min [7280000], rate=12847058.82/min [7290000], rate=12864705.88/min [7300000], rate=12882352.94/min [7310000], rate=12531428.57/min [7320000], rate=12548571.43/min [7330000], rate=12565714.29/min [7340000], rate=12582857.14/min [7350000], rate=12600000.00/min [7360000], rate=12617142.86/min [7370000], rate=12634285.71/min [7380000], rate=12651428.57/min [7390000], rate=12668571.43/min [7400000], rate=12685714.29/min [7410000], rate=12702857.14/min [7420000], rate=12720000.00/min [7430000], rate=12737142.86/min [7440000], rate=12754285.71/min [7450000], rate=12771428.57/min [7460000], rate=12788571.43/min [7470000], rate=12805714.29/min [7480000], rate=12822857.14/min [7490000], rate=12840000.00/min [7500000], rate=12857142.86/min [7510000], rate=12874285.71/min [7520000], rate=12891428.57/min [7530000], rate=12908571.43/min [7540000], rate=12925714.29/min [7550000], rate=12942857.14/min [7560000], rate=12960000.00/min [7570000], rate=12977142.86/min [7580000], rate=12633333.33/min [7590000], rate=12650000.00/min [7600000], rate=12666666.67/min [7610000], rate=12683333.33/min [7620000], rate=12700000.00/min [7630000], rate=12716666.67/min [7640000], rate=12733333.33/min [7650000], rate=12750000.00/min [7660000], rate=12766666.67/min [7670000], rate=12783333.33/min [7680000], rate=12800000.00/min [7690000], rate=12816666.67/min [7700000], rate=12833333.33/min [7710000], rate=12850000.00/min [7720000], rate=12866666.67/min [7730000], rate=12883333.33/min [7740000], rate=12900000.00/min [7750000], rate=12916666.67/min [7760000], rate=12933333.33/min [7770000], rate=12950000.00/min [7780000], rate=12966666.67/min [7790000], rate=12983333.33/min [7800000], rate=13000000.00/min [7810000], rate=13016666.67/min [7820000], rate=12681081.08/min [7830000], rate=12697297.30/min [7840000], rate=12713513.51/min [7850000], rate=12729729.73/min [7860000], rate=12745945.95/min [7870000], rate=12762162.16/min [7880000], rate=12778378.38/min [7890000], rate=12794594.59/min [7900000], rate=12810810.81/min [7910000], rate=12827027.03/min [7920000], rate=12843243.24/min [7930000], rate=12859459.46/min [7940000], rate=12875675.68/min [7950000], rate=12891891.89/min [7960000], rate=12908108.11/min [7970000], rate=12924324.32/min [7980000], rate=12940540.54/min [7990000], rate=12615789.47/min [8000000], rate=12631578.95/min [8010000], rate=12647368.42/min [8020000], rate=12663157.89/min [8030000], rate=12678947.37/min [8040000], rate=12694736.84/min [8050000], rate=12710526.32/min [8060000], rate=12726315.79/min [8070000], rate=12742105.26/min [8080000], rate=12757894.74/min [8090000], rate=12773684.21/min [8100000], rate=12789473.68/min [8110000], rate=12805263.16/min [8120000], rate=12821052.63/min [8130000], rate=12836842.11/min [8140000], rate=12852631.58/min [8150000], rate=12868421.05/min [8160000], rate=12553846.15/min [8170000], rate=12569230.77/min [8180000], rate=12584615.38/min [8190000], rate=12600000.00/min [8200000], rate=12615384.62/min [8210000], rate=12630769.23/min [8220000], rate=12646153.85/min [8230000], rate=12661538.46/min [8240000], rate=12676923.08/min [8250000], rate=12692307.69/min [8260000], rate=12707692.31/min [8270000], rate=12723076.92/min [8280000], rate=12738461.54/min [8290000], rate=12753846.15/min [8300000], rate=12769230.77/min [8310000], rate=12784615.38/min [8320000], rate=12800000.00/min [8330000], rate=12815384.62/min [8340000], rate=12830769.23/min [8350000], rate=12846153.85/min [8360000], rate=12861538.46/min [8370000], rate=12876923.08/min [8380000], rate=12892307.69/min [8390000], rate=12907692.31/min [8400000], rate=12923076.92/min [8410000], rate=12938461.54/min [8420000], rate=12630000.00/min [8430000], rate=12645000.00/min [8440000], rate=12660000.00/min [8450000], rate=12675000.00/min [8460000], rate=12690000.00/min [8470000], rate=12705000.00/min [8480000], rate=12720000.00/min [8490000], rate=12735000.00/min [8500000], rate=12750000.00/min [8510000], rate=12765000.00/min [8520000], rate=12780000.00/min [8530000], rate=12795000.00/min [8540000], rate=12810000.00/min [8550000], rate=12825000.00/min [8560000], rate=12840000.00/min [8570000], rate=12855000.00/min [8580000], rate=12870000.00/min [8590000], rate=12885000.00/min [8600000], rate=12900000.00/min [8610000], rate=12915000.00/min [8620000], rate=12930000.00/min [8630000], rate=12945000.00/min [8640000], rate=12960000.00/min [8650000], rate=12975000.00/min [8660000], rate=12990000.00/min [8670000], rate=12687804.88/min [8680000], rate=12702439.02/min [8690000], rate=12717073.17/min [8700000], rate=12731707.32/min [8710000], rate=12746341.46/min [8720000], rate=12760975.61/min [8730000], rate=12775609.76/min [8740000], rate=12790243.90/min [8750000], rate=12804878.05/min [8760000], rate=12819512.20/min [8770000], rate=12834146.34/min [8780000], rate=12848780.49/min [8790000], rate=12863414.63/min [8800000], rate=12878048.78/min [8810000], rate=12892682.93/min [8820000], rate=12907317.07/min [8830000], rate=12921951.22/min [8840000], rate=12936585.37/min [8850000], rate=12951219.51/min [8860000], rate=12965853.66/min [8870000], rate=12980487.80/min [8880000], rate=12995121.95/min [8890000], rate=13009756.10/min [8900000], rate=13024390.24/min [8910000], rate=13039024.39/min [8920000], rate=13053658.54/min [8930000], rate=13068292.68/min [8940000], rate=12771428.57/min [8950000], rate=12785714.29/min [8960000], rate=12800000.00/min [8970000], rate=12814285.71/min [8980000], rate=12828571.43/min [8990000], rate=12842857.14/min [9000000], rate=12857142.86/min [9010000], rate=12871428.57/min [9020000], rate=12885714.29/min [9030000], rate=12900000.00/min [9040000], rate=12914285.71/min [9050000], rate=12928571.43/min [9060000], rate=12942857.14/min [9070000], rate=12957142.86/min [9080000], rate=12971428.57/min [9090000], rate=12985714.29/min [9100000], rate=13000000.00/min [9110000], rate=13014285.71/min [9120000], rate=13028571.43/min [9130000], rate=13042857.14/min [9140000], rate=13057142.86/min [9150000], rate=13071428.57/min [9160000], rate=13085714.29/min [9170000], rate=13100000.00/min [9180000], rate=13114285.71/min [9190000], rate=13128571.43/min [9200000], rate=13142857.14/min [9210000], rate=13157142.86/min [9220000], rate=12865116.28/min [9230000], rate=12879069.77/min [9240000], rate=12893023.26/min [9250000], rate=12906976.74/min [9260000], rate=12920930.23/min 08:55:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer.introns.prelim Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18. -aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns: identified 8649 cancer introns 08:55:51 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer.introns.prelim 08:55:51 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 08:55:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer.introns 08:55:52 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer.introns 08:55:52 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 08:55:52 : INFO : -found 3945 cancer introns 08:55:52 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:55:52 : INFO : Creating the BED File. 08:56:00 : INFO : Saving Bed File as aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:56:01 : INFO : Execution Time = 0.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:56:01 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 08:56:01 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-b8457f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-b8457f-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b8457f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 09:25:23 : INFO : Execution Time = 29.37 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-b8457f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-b8457f-R1_A23YTGFLT4_1 09:25:23 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 09:25:23 : INFO : Running: samtools sort -o aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:25:23 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:25:23 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 09:25:24 : INFO : Running: samtools sort -o aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 132 files and 1 in-memory blocks... 09:57:18 : INFO : Execution Time = 31.91 minutes. CMD: samtools sort -o aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.bam 09:57:18 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok 09:57:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.bam Done with chr chr1. Done with chr chr2. Done with chr chr3. Done with chr chr4. Done with chr chr5. Done with chr chr6. Done with chr chr7. Done with chr chr8. Done with chr chr9. Done with chr chr10. Done with chr chr11. Done with chr chr12. Done with chr chr13. Done with chr chr14. Done with chr chr15. Done with chr chr16. Done with chr chr17. Done with chr chr18. Done with chr chr19. Done with chr chr20. Done with chr chr21. Done with chr chr22. 10:06:15 : INFO : Execution Time = 8.94 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.bam 10:06:15 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:06:15 : INFO : Running: samtools sort -o aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 4 files and 1 in-memory blocks... 10:07:27 : INFO : Execution Time = 1.20 minutes. CMD: samtools sort -o aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp 10:07:27 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:07:27 : INFO : Running: samtools index aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 10:07:35 : INFO : Execution Time = 0.13 minutes. CMD: samtools index aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 10:07:35 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:07:35 : INFO : Running: samtools index aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 10:07:35 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 10:07:35 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:07:35 : INFO : Running: create_report aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-b8457f-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-b8457f-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-b8457f-R1_A23YTGFLT4_1' 10:14:40 : INFO : Execution Time = 7.08 minutes. CMD: create_report aih-tih-sc-b8457f-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-b8457f-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-b8457f-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-b8457f-R1_A23YTGFLT4_1' 10:14:40 : INFO : Running: touch /tmp/nxf.Vh6RFApHUX/aih-tih-sc-b8457f-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok 10:14:40 : INFO : done.