Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/46b023ebf9ab9a87eef0626ef74b51/tih_rna_sample_00097_B23WHTKLT4_2.SJ.out.tab 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/59/cc4933821698f4e20463183641dd13/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/46b023ebf9ab9a87eef0626ef74b51/tih_rna_sample_00097_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/7c3be0c6a5745fa03b4f78ba5dda36/tih_rna_sample_00097_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/cc4933821698f4e20463183641dd13/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/46b023ebf9ab9a87eef0626ef74b51/tih_rna_sample_00097_B23WHTKLT4_2.Chimeric.out.junction ==> STAGING COMPLETE (7 inputs) 08:36:40 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=34200000.00/min [580000], rate=34800000.00/min [590000], rate=35400000.00/min [600000], rate=36000000.00/min [610000], rate=36600000.00/min [620000], rate=37200000.00/min [630000], rate=37800000.00/min [640000], rate=38400000.00/min [650000], rate=39000000.00/min [660000], rate=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=19600000.00/min [990000], rate=19800000.00/min [1000000], rate=20000000.00/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=19500000.00/min [1310000], rate=19650000.00/min [1320000], rate=19800000.00/min [1330000], rate=19950000.00/min [1340000], rate=20100000.00/min [1350000], rate=20250000.00/min [1360000], rate=20400000.00/min [1370000], rate=20550000.00/min [1380000], rate=20700000.00/min [1390000], rate=20850000.00/min [1400000], rate=21000000.00/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=19320000.00/min [1620000], rate=19440000.00/min [1630000], rate=19560000.00/min [1640000], rate=19680000.00/min [1650000], rate=19800000.00/min [1660000], rate=19920000.00/min [1670000], rate=20040000.00/min [1680000], rate=20160000.00/min [1690000], rate=20280000.00/min [1700000], rate=20400000.00/min [1710000], rate=20520000.00/min [1720000], rate=20640000.00/min [1730000], rate=20760000.00/min [1740000], rate=20880000.00/min [1750000], rate=21000000.00/min [1760000], rate=21120000.00/min [1770000], rate=21240000.00/min [1780000], rate=21360000.00/min [1790000], rate=17900000.00/min [1800000], rate=18000000.00/min [1810000], rate=18100000.00/min [1820000], rate=18200000.00/min [1830000], rate=18300000.00/min [1840000], rate=18400000.00/min [1850000], rate=18500000.00/min [1860000], rate=18600000.00/min [1870000], rate=18700000.00/min [1880000], rate=18800000.00/min [1890000], rate=18900000.00/min [1900000], rate=19000000.00/min [1910000], rate=19100000.00/min [1920000], rate=19200000.00/min [1930000], rate=19300000.00/min [1940000], rate=19400000.00/min [1950000], rate=19500000.00/min [1960000], rate=16800000.00/min [1970000], rate=16885714.29/min [1980000], rate=16971428.57/min [1990000], rate=17057142.86/min [2000000], rate=17142857.14/min [2010000], rate=17228571.43/min [2020000], rate=17314285.71/min [2030000], rate=17400000.00/min [2040000], rate=17485714.29/min [2050000], rate=17571428.57/min [2060000], rate=17657142.86/min [2070000], rate=17742857.14/min [2080000], rate=17828571.43/min [2090000], rate=17914285.71/min [2100000], rate=18000000.00/min [2110000], rate=18085714.29/min [2120000], rate=18171428.57/min [2130000], rate=15975000.00/min [2140000], rate=16050000.00/min [2150000], rate=16125000.00/min [2160000], rate=16200000.00/min [2170000], rate=16275000.00/min [2180000], rate=16350000.00/min [2190000], rate=16425000.00/min [2200000], rate=16500000.00/min [2210000], rate=16575000.00/min [2220000], rate=16650000.00/min [2230000], rate=16725000.00/min [2240000], rate=16800000.00/min [2250000], rate=16875000.00/min [2260000], rate=16950000.00/min [2270000], rate=17025000.00/min [2280000], rate=17100000.00/min [2290000], rate=17175000.00/min [2300000], rate=17250000.00/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=15933333.33/min [2400000], rate=16000000.00/min [2410000], rate=16066666.67/min [2420000], rate=16133333.33/min [2430000], rate=16200000.00/min [2440000], rate=16266666.67/min [2450000], rate=16333333.33/min [2460000], rate=16400000.00/min [2470000], rate=16466666.67/min [2480000], rate=16533333.33/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=15780000.00/min [2640000], rate=15840000.00/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=14200000.00/min [2850000], rate=14250000.00/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=13938461.54/min [3030000], rate=13984615.38/min [3040000], rate=14030769.23/min [3050000], rate=14076923.08/min [3060000], rate=14123076.92/min [3070000], rate=14169230.77/min [3080000], rate=14215384.62/min [3090000], rate=14261538.46/min [3100000], rate=14307692.31/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=13628571.43/min [3190000], rate=13671428.57/min [3200000], rate=13714285.71/min [3210000], rate=13757142.86/min [3220000], rate=13800000.00/min [3230000], rate=13842857.14/min [3240000], rate=13885714.29/min [3250000], rate=13928571.43/min [3260000], rate=13971428.57/min [3270000], rate=14014285.71/min [3280000], rate=14057142.86/min [3290000], rate=14100000.00/min [3300000], rate=14142857.14/min [3310000], rate=14185714.29/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=14000000.00/min [3510000], rate=14040000.00/min [3520000], rate=14080000.00/min [3530000], rate=14120000.00/min [3540000], rate=14160000.00/min [3550000], rate=14200000.00/min [3560000], rate=14240000.00/min [3570000], rate=14280000.00/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=14887500.00/min [3980000], rate=14925000.00/min [3990000], rate=14962500.00/min [4000000], rate=15000000.00/min [4010000], rate=15037500.00/min [4020000], rate=15075000.00/min [4030000], rate=15112500.00/min [4040000], rate=15150000.00/min [4050000], rate=15187500.00/min [4060000], rate=15225000.00/min [4070000], rate=15262500.00/min [4080000], rate=15300000.00/min [4090000], rate=14435294.12/min [4100000], rate=14470588.24/min [4110000], rate=14505882.35/min [4120000], rate=14541176.47/min [4130000], rate=14576470.59/min [4140000], rate=14611764.71/min [4150000], rate=14647058.82/min [4160000], rate=14682352.94/min [4170000], rate=14717647.06/min [4180000], rate=14752941.18/min [4190000], rate=14788235.29/min [4200000], rate=14823529.41/min [4210000], rate=14858823.53/min [4220000], rate=14894117.65/min [4230000], rate=14929411.76/min [4240000], rate=14964705.88/min [4250000], rate=15000000.00/min [4260000], rate=15035294.12/min [4270000], rate=15070588.24/min [4280000], rate=15105882.35/min [4290000], rate=15141176.47/min [4300000], rate=15176470.59/min [4310000], rate=15211764.71/min [4320000], rate=15247058.82/min [4330000], rate=15282352.94/min [4340000], rate=15317647.06/min [4350000], rate=15352941.18/min [4360000], rate=15388235.29/min [4370000], rate=15423529.41/min [4380000], rate=15458823.53/min [4390000], rate=15494117.65/min [4400000], rate=14666666.67/min [4410000], rate=14700000.00/min [4420000], rate=14733333.33/min [4430000], rate=14766666.67/min [4440000], rate=14800000.00/min [4450000], rate=14833333.33/min [4460000], rate=14866666.67/min [4470000], rate=14900000.00/min [4480000], rate=14933333.33/min [4490000], rate=14966666.67/min [4500000], rate=15000000.00/min [4510000], rate=15033333.33/min [4520000], rate=15066666.67/min [4530000], rate=15100000.00/min [4540000], rate=15133333.33/min [4550000], rate=15166666.67/min [4560000], rate=15200000.00/min [4570000], rate=15233333.33/min [4580000], rate=15266666.67/min [4590000], rate=15300000.00/min [4600000], rate=15333333.33/min [4610000], rate=15366666.67/min [4620000], rate=15400000.00/min [4630000], rate=15433333.33/min [4640000], rate=15466666.67/min [4650000], rate=15500000.00/min [4660000], rate=15533333.33/min [4670000], rate=15566666.67/min [4680000], rate=15600000.00/min [4690000], rate=15633333.33/min [4700000], rate=15666666.67/min [4710000], rate=14873684.21/min [4720000], rate=14905263.16/min [4730000], rate=14936842.11/min [4740000], rate=14968421.05/min [4750000], rate=15000000.00/min [4760000], rate=15031578.95/min [4770000], rate=15063157.89/min [4780000], rate=15094736.84/min [4790000], rate=15126315.79/min [4800000], rate=15157894.74/min [4810000], rate=15189473.68/min [4820000], rate=15221052.63/min [4830000], rate=15252631.58/min [4840000], rate=15284210.53/min [4850000], rate=15315789.47/min [4860000], rate=15347368.42/min [4870000], rate=15378947.37/min [4880000], rate=15410526.32/min [4890000], rate=15442105.26/min [4900000], rate=15473684.21/min [4910000], rate=15505263.16/min [4920000], rate=15536842.11/min [4930000], rate=15568421.05/min [4940000], rate=15600000.00/min [4950000], rate=15631578.95/min [4960000], rate=15663157.89/min [4970000], rate=15694736.84/min [4980000], rate=15726315.79/min [4990000], rate=15757894.74/min [5000000], rate=15789473.68/min [5010000], rate=15030000.00/min [5020000], rate=15060000.00/min [5030000], rate=15090000.00/min [5040000], rate=15120000.00/min [5050000], rate=15150000.00/min [5060000], rate=15180000.00/min [5070000], rate=15210000.00/min [5080000], rate=15240000.00/min [5090000], rate=15270000.00/min [5100000], rate=15300000.00/min [5110000], rate=15330000.00/min [5120000], rate=15360000.00/min [5130000], rate=15390000.00/min [5140000], rate=15420000.00/min [5150000], rate=15450000.00/min [5160000], rate=15480000.00/min [5170000], rate=15510000.00/min [5180000], rate=15540000.00/min [5190000], rate=15570000.00/min [5200000], rate=15600000.00/min [5210000], rate=15630000.00/min [5220000], rate=15660000.00/min [5230000], rate=15690000.00/min [5240000], rate=15720000.00/min [5250000], rate=15750000.00/min [5260000], rate=15780000.00/min [5270000], rate=15810000.00/min [5280000], rate=15840000.00/min [5290000], rate=15114285.71/min [5300000], rate=15142857.14/min [5310000], rate=15171428.57/min [5320000], rate=15200000.00/min [5330000], rate=15228571.43/min [5340000], rate=15257142.86/min [5350000], rate=15285714.29/min [5360000], rate=15314285.71/min [5370000], rate=15342857.14/min [5380000], rate=15371428.57/min [5390000], rate=15400000.00/min [5400000], rate=15428571.43/min [5410000], rate=15457142.86/min [5420000], rate=15485714.29/min [5430000], rate=15514285.71/min [5440000], rate=15542857.14/min [5450000], rate=15571428.57/min [5460000], rate=15600000.00/min [5470000], rate=15628571.43/min [5480000], rate=15657142.86/min [5490000], rate=15685714.29/min [5500000], rate=15714285.71/min [5510000], rate=15742857.14/min [5520000], rate=15771428.57/min [5530000], rate=15800000.00/min [5540000], rate=15828571.43/min [5550000], rate=15857142.86/min [5560000], rate=15885714.29/min [5570000], rate=15190909.09/min [5580000], rate=15218181.82/min [5590000], rate=15245454.55/min [5600000], rate=15272727.27/min [5610000], rate=15300000.00/min [5620000], rate=15327272.73/min [5630000], rate=15354545.45/min [5640000], rate=15381818.18/min [5650000], rate=15409090.91/min [5660000], rate=15436363.64/min [5670000], rate=15463636.36/min [5680000], rate=15490909.09/min [5690000], rate=15518181.82/min [5700000], rate=15545454.55/min [5710000], rate=15572727.27/min [5720000], rate=15600000.00/min [5730000], rate=15627272.73/min [5740000], rate=15654545.45/min [5750000], rate=15681818.18/min [5760000], rate=15709090.91/min [5770000], rate=15736363.64/min [5780000], rate=15763636.36/min [5790000], rate=15790909.09/min [5800000], rate=15818181.82/min [5810000], rate=15845454.55/min [5820000], rate=15182608.70/min [5830000], rate=15208695.65/min [5840000], rate=15234782.61/min [5850000], rate=15260869.57/min [5860000], rate=15286956.52/min [5870000], rate=15313043.48/min [5880000], rate=15339130.43/min [5890000], rate=15365217.39/min [5900000], rate=15391304.35/min [5910000], rate=15417391.30/min [5920000], rate=15443478.26/min [5930000], rate=15469565.22/min [5940000], rate=15495652.17/min [5950000], rate=15521739.13/min [5960000], rate=15547826.09/min [5970000], rate=15573913.04/min [5980000], rate=15600000.00/min [5990000], rate=15626086.96/min [6000000], rate=15652173.91/min [6010000], rate=15678260.87/min [6020000], rate=15704347.83/min [6030000], rate=15075000.00/min [6040000], rate=15100000.00/min [6050000], rate=15125000.00/min [6060000], rate=15150000.00/min [6070000], rate=15175000.00/min [6080000], rate=15200000.00/min [6090000], rate=15225000.00/min [6100000], rate=15250000.00/min [6110000], rate=15275000.00/min [6120000], rate=15300000.00/min [6130000], rate=15325000.00/min [6140000], rate=15350000.00/min [6150000], rate=15375000.00/min [6160000], rate=15400000.00/min [6170000], rate=15425000.00/min [6180000], rate=15450000.00/min [6190000], rate=15475000.00/min [6200000], rate=15500000.00/min [6210000], rate=15525000.00/min [6220000], rate=14928000.00/min [6230000], rate=14952000.00/min [6240000], rate=14976000.00/min [6250000], rate=15000000.00/min [6260000], rate=15024000.00/min [6270000], rate=15048000.00/min [6280000], rate=15072000.00/min [6290000], rate=15096000.00/min [6300000], rate=15120000.00/min [6310000], rate=15144000.00/min [6320000], rate=15168000.00/min [6330000], rate=15192000.00/min [6340000], rate=15216000.00/min [6350000], rate=15240000.00/min [6360000], rate=15264000.00/min [6370000], rate=15288000.00/min [6380000], rate=15312000.00/min [6390000], rate=15336000.00/min [6400000], rate=15360000.00/min [6410000], rate=15384000.00/min [6420000], rate=15408000.00/min [6430000], rate=15432000.00/min [6440000], rate=15456000.00/min [6450000], rate=15480000.00/min [6460000], rate=15504000.00/min [6470000], rate=15528000.00/min [6480000], rate=14953846.15/min [6490000], rate=14976923.08/min [6500000], rate=15000000.00/min [6510000], rate=15023076.92/min [6520000], rate=15046153.85/min [6530000], rate=15069230.77/min [6540000], rate=15092307.69/min [6550000], rate=15115384.62/min [6560000], rate=15138461.54/min [6570000], rate=15161538.46/min [6580000], rate=15184615.38/min [6590000], rate=15207692.31/min [6600000], rate=15230769.23/min [6610000], rate=15253846.15/min [6620000], rate=15276923.08/min [6630000], rate=15300000.00/min [6640000], rate=15323076.92/min [6650000], rate=15346153.85/min [6660000], rate=15369230.77/min [6670000], rate=15392307.69/min [6680000], rate=15415384.62/min [6690000], rate=15438461.54/min [6700000], rate=15461538.46/min [6710000], rate=15484615.38/min [6720000], rate=15507692.31/min [6730000], rate=14955555.56/min [6740000], rate=14977777.78/min [6750000], rate=15000000.00/min [6760000], rate=15022222.22/min [6770000], rate=15044444.44/min [6780000], rate=15066666.67/min [6790000], rate=15088888.89/min [6800000], rate=15111111.11/min [6810000], rate=15133333.33/min [6820000], rate=15155555.56/min [6830000], rate=15177777.78/min [6840000], rate=15200000.00/min [6850000], rate=15222222.22/min [6860000], rate=15244444.44/min [6870000], rate=15266666.67/min [6880000], rate=15288888.89/min [6890000], rate=15311111.11/min [6900000], rate=15333333.33/min [6910000], rate=15355555.56/min [6920000], rate=15377777.78/min [6930000], rate=15400000.00/min [6940000], rate=15422222.22/min [6950000], rate=15444444.44/min [6960000], rate=15466666.67/min [6970000], rate=15488888.89/min [6980000], rate=15511111.11/min [6990000], rate=15533333.33/min [7000000], rate=15555555.56/min [7010000], rate=15021428.57/min [7020000], rate=15042857.14/min [7030000], rate=15064285.71/min [7040000], rate=15085714.29/min [7050000], rate=15107142.86/min [7060000], rate=15128571.43/min [7070000], rate=15150000.00/min [7080000], rate=15171428.57/min [7090000], rate=15192857.14/min [7100000], rate=15214285.71/min [7110000], rate=15235714.29/min [7120000], rate=15257142.86/min [7130000], rate=15278571.43/min [7140000], rate=15300000.00/min [7150000], rate=15321428.57/min [7160000], rate=15342857.14/min [7170000], rate=15364285.71/min [7180000], rate=15385714.29/min [7190000], rate=14875862.07/min [7200000], rate=14896551.72/min [7210000], rate=14917241.38/min [7220000], rate=14937931.03/min [7230000], rate=14958620.69/min [7240000], rate=14979310.34/min [7250000], rate=15000000.00/min [7260000], rate=15020689.66/min [7270000], rate=15041379.31/min [7280000], rate=15062068.97/min [7290000], rate=15082758.62/min [7300000], rate=15103448.28/min [7310000], rate=15124137.93/min [7320000], rate=15144827.59/min [7330000], rate=15165517.24/min [7340000], rate=15186206.90/min [7350000], rate=15206896.55/min [7360000], rate=15227586.21/min [7370000], rate=14740000.00/min [7380000], rate=14760000.00/min [7390000], rate=14780000.00/min [7400000], rate=14800000.00/min [7410000], rate=14820000.00/min [7420000], rate=14840000.00/min [7430000], rate=14860000.00/min [7440000], rate=14880000.00/min [7450000], rate=14900000.00/min [7460000], rate=14920000.00/min [7470000], rate=14940000.00/min [7480000], rate=14960000.00/min [7490000], rate=14980000.00/min [7500000], rate=15000000.00/min [7510000], rate=15020000.00/min [7520000], rate=15040000.00/min [7530000], rate=15060000.00/min [7540000], rate=15080000.00/min [7550000], rate=14612903.23/min [7560000], rate=14632258.06/min [7570000], rate=14651612.90/min [7580000], rate=14670967.74/min [7590000], rate=14690322.58/min [7600000], rate=14709677.42/min [7610000], rate=14729032.26/min [7620000], rate=14748387.10/min [7630000], rate=14767741.94/min [7640000], rate=14787096.77/min [7650000], rate=14806451.61/min [7660000], rate=14825806.45/min [7670000], rate=14845161.29/min [7680000], rate=14864516.13/min [7690000], rate=14883870.97/min [7700000], rate=14903225.81/min [7710000], rate=14922580.65/min [7720000], rate=14941935.48/min [7730000], rate=14961290.32/min [7740000], rate=14512500.00/min [7750000], rate=14531250.00/min [7760000], rate=14550000.00/min [7770000], rate=14568750.00/min [7780000], rate=14587500.00/min [7790000], rate=14606250.00/min [7800000], rate=14625000.00/min [7810000], rate=14643750.00/min [7820000], rate=14662500.00/min [7830000], rate=14681250.00/min [7840000], rate=14700000.00/min [7850000], rate=14718750.00/min [7860000], rate=14737500.00/min [7870000], rate=14756250.00/min [7880000], rate=14775000.00/min [7890000], rate=14793750.00/min [7900000], rate=14812500.00/min [7910000], rate=14381818.18/min [7920000], rate=14400000.00/min [7930000], rate=14418181.82/min [7940000], rate=14436363.64/min [7950000], rate=14454545.45/min [7960000], rate=14472727.27/min [7970000], rate=14490909.09/min [7980000], rate=14509090.91/min [7990000], rate=14527272.73/min [8000000], rate=14545454.55/min [8010000], rate=14563636.36/min [8020000], rate=14581818.18/min [8030000], rate=14600000.00/min [8040000], rate=14618181.82/min [8050000], rate=14205882.35/min [8060000], rate=14223529.41/min [8070000], rate=14241176.47/min [8080000], rate=14258823.53/min [8090000], rate=14276470.59/min [8100000], rate=14294117.65/min [8110000], rate=14311764.71/min [8120000], rate=14329411.76/min [8130000], rate=14347058.82/min [8140000], rate=14364705.88/min [8150000], rate=14382352.94/min [8160000], rate=14400000.00/min [8170000], rate=14417647.06/min [8180000], rate=14435294.12/min [8190000], rate=14452941.18/min [8200000], rate=14470588.24/min [8210000], rate=14488235.29/min [8220000], rate=14091428.57/min [8230000], rate=14108571.43/min [8240000], rate=14125714.29/min [8250000], rate=14142857.14/min [8260000], rate=14160000.00/min [8270000], rate=14177142.86/min [8280000], rate=14194285.71/min [8290000], rate=14211428.57/min [8300000], rate=14228571.43/min [8310000], rate=14245714.29/min [8320000], rate=14262857.14/min [8330000], rate=14280000.00/min [8340000], rate=14297142.86/min [8350000], rate=14314285.71/min [8360000], rate=14331428.57/min [8370000], rate=14348571.43/min [8380000], rate=14365714.29/min [8390000], rate=14382857.14/min [8400000], rate=14000000.00/min [8410000], rate=14016666.67/min [8420000], rate=14033333.33/min [8430000], rate=14050000.00/min [8440000], rate=14066666.67/min [8450000], rate=14083333.33/min [8460000], rate=14100000.00/min [8470000], rate=14116666.67/min [8480000], rate=14133333.33/min [8490000], rate=14150000.00/min [8500000], rate=14166666.67/min [8510000], rate=14183333.33/min [8520000], rate=14200000.00/min [8530000], rate=14216666.67/min [8540000], rate=14233333.33/min [8550000], rate=14250000.00/min [8560000], rate=14266666.67/min [8570000], rate=14283333.33/min [8580000], rate=14300000.00/min [8590000], rate=13929729.73/min [8600000], rate=13945945.95/min [8610000], rate=13962162.16/min [8620000], rate=13978378.38/min [8630000], rate=13994594.59/min [8640000], rate=14010810.81/min [8650000], rate=14027027.03/min [8660000], rate=14043243.24/min [8670000], rate=14059459.46/min [8680000], rate=14075675.68/min [8690000], rate=14091891.89/min [8700000], rate=14108108.11/min [8710000], rate=14124324.32/min [8720000], rate=14140540.54/min [8730000], rate=14156756.76/min [8740000], rate=14172972.97/min [8750000], rate=14189189.19/min [8760000], rate=14205405.41/min [8770000], rate=13847368.42/min [8780000], rate=13863157.89/min [8790000], rate=13878947.37/min [8800000], rate=13894736.84/min [8810000], rate=13910526.32/min [8820000], rate=13926315.79/min [8830000], rate=13942105.26/min [8840000], rate=13957894.74/min [8850000], rate=13973684.21/min [8860000], rate=13989473.68/min [8870000], rate=14005263.16/min [8880000], rate=14021052.63/min [8890000], rate=14036842.11/min [8900000], rate=14052631.58/min [8910000], rate=14068421.05/min [8920000], rate=14084210.53/min [8930000], rate=14100000.00/min [8940000], rate=13753846.15/min [8950000], rate=13769230.77/min [8960000], rate=13784615.38/min [8970000], rate=13800000.00/min [8980000], rate=13815384.62/min [8990000], rate=13830769.23/min [9000000], rate=13846153.85/min [9010000], rate=13861538.46/min [9020000], rate=13876923.08/min [9030000], rate=13892307.69/min [9040000], rate=13907692.31/min [9050000], rate=13923076.92/min [9060000], rate=13938461.54/min [9070000], rate=13953846.15/min [9080000], rate=13969230.77/min [9090000], rate=13984615.38/min [9100000], rate=14000000.00/min [9110000], rate=14015384.62/min [9120000], rate=13680000.00/min [9130000], rate=13695000.00/min [9140000], rate=13710000.00/min [9150000], rate=13725000.00/min [9160000], rate=13740000.00/min [9170000], rate=13755000.00/min [9180000], rate=13770000.00/min [9190000], rate=13785000.00/min [9200000], rate=13800000.00/min [9210000], rate=13815000.00/min [9220000], rate=13830000.00/min [9230000], rate=13845000.00/min [9240000], rate=13860000.00/min [9250000], rate=13875000.00/min [9260000], rate=13890000.00/min [9270000], rate=13905000.00/min [9280000], rate=13920000.00/min [9290000], rate=13935000.00/min [9300000], rate=13609756.10/min [9310000], rate=13624390.24/min [9320000], rate=13639024.39/min [9330000], rate=13653658.54/min [9340000], rate=13668292.68/min [9350000], rate=13682926.83/min [9360000], rate=13697560.98/min [9370000], rate=13712195.12/min [9380000], rate=13726829.27/min [9390000], rate=13741463.41/min [9400000], rate=13756097.56/min [9410000], rate=13770731.71/min [9420000], rate=13785365.85/min [9430000], rate=13800000.00/min [9440000], rate=13814634.15/min [9450000], rate=13829268.29/min [9460000], rate=13843902.44/min [9470000], rate=13858536.59/min [9480000], rate=13542857.14/min [9490000], rate=13557142.86/min [9500000], rate=13571428.57/min [9510000], rate=13585714.29/min [9520000], rate=13600000.00/min [9530000], rate=13614285.71/min [9540000], rate=13628571.43/min [9550000], rate=13642857.14/min [9560000], rate=13657142.86/min [9570000], rate=13671428.57/min [9580000], rate=13685714.29/min [9590000], rate=13700000.00/min [9600000], rate=13714285.71/min [9610000], rate=13728571.43/min [9620000], rate=13742857.14/min [9630000], rate=13757142.86/min [9640000], rate=13771428.57/min [9650000], rate=13465116.28/min [9660000], rate=13479069.77/min [9670000], rate=13493023.26/min [9680000], rate=13506976.74/min [9690000], rate=13520930.23/min [9700000], rate=13534883.72/min [9710000], rate=13548837.21/min [9720000], rate=13562790.70/min [9730000], rate=13576744.19/min [9740000], rate=13590697.67/min [9750000], rate=13604651.16/min [9760000], rate=13618604.65/min [9770000], rate=13632558.14/min [9780000], rate=13646511.63/min [9790000], rate=13660465.12/min [9800000], rate=13674418.60/min [9810000], rate=13688372.09/min [9820000], rate=13390909.09/min [9830000], rate=13404545.45/min [9840000], rate=13418181.82/min [9850000], rate=13431818.18/min [9860000], rate=13445454.55/min [9870000], rate=13459090.91/min [9880000], rate=13472727.27/min [9890000], rate=13486363.64/min [9900000], rate=13500000.00/min [9910000], rate=13513636.36/min [9920000], rate=13527272.73/min [9930000], rate=13540909.09/min [9940000], rate=13554545.45/min [9950000], rate=13568181.82/min [9960000], rate=13581818.18/min [9970000], rate=13595454.55/min [9980000], rate=13609090.91/min [9990000], rate=13622727.27/min [10000000], rate=13333333.33/min [10010000], rate=13346666.67/min [10020000], rate=13360000.00/min [10030000], rate=13373333.33/min [10040000], rate=13386666.67/min [10050000], rate=13400000.00/min [10060000], rate=13413333.33/min [10070000], rate=13426666.67/min [10080000], rate=13440000.00/min [10090000], rate=13453333.33/min [10100000], rate=13466666.67/min [10110000], rate=13480000.00/min [10120000], rate=13493333.33/min [10130000], rate=13506666.67/min [10140000], rate=13520000.00/min [10150000], rate=13533333.33/min [10160000], rate=13546666.67/min [10170000], rate=13560000.00/min [10180000], rate=13573333.33/min [10190000], rate=13291304.35/min [10200000], rate=13304347.83/min [10210000], rate=13317391.30/min [10220000], rate=13330434.78/min [10230000], rate=13343478.26/min [10240000], rate=13356521.74/min 08:37:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00097_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00097_B23WHTKLT4_2.cancer.introns.prelim Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18. -tih_rna_sample_00097_B23WHTKLT4_2.introns: identified 5615 cancer introns 08:37:38 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00097_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00097_B23WHTKLT4_2.cancer.introns.prelim 08:37:38 : INFO : Running: touch /tmp/nxf.3XASX4GpSz/tih_rna_sample_00097_B23WHTKLT4_2.chckpts/prelim_introns.ok 08:37:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00097_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00097_B23WHTKLT4_2.cancer.introns 08:37:38 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00097_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00097_B23WHTKLT4_2.cancer.introns 08:37:38 : INFO : Running: touch /tmp/nxf.3XASX4GpSz/tih_rna_sample_00097_B23WHTKLT4_2.chckpts/introns_filtered.ok 08:37:38 : INFO : -found 2855 cancer introns 08:37:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00097_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00097_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00097_B23WHTKLT4_2.introns.for_IGV.bed 08:37:39 : INFO : Creating the BED File. 08:37:48 : INFO : Saving Bed File as tih_rna_sample_00097_B23WHTKLT4_2.introns.for_IGV.bed 08:37:48 : INFO : Execution Time = 0.16 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00097_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00097_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00097_B23WHTKLT4_2.introns.for_IGV.bed 08:37:48 : INFO : Running: touch /tmp/nxf.3XASX4GpSz/tih_rna_sample_00097_B23WHTKLT4_2.chckpts/intron_igv_bed.ok 08:37:48 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00097_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00097_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00097_B23WHTKLT4_2 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00097_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam.bai 09:05:42 : INFO : Execution Time = 27.89 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00097_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00097_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00097_B23WHTKLT4_2 09:05:42 : INFO : Running: touch /tmp/nxf.3XASX4GpSz/tih_rna_sample_00097_B23WHTKLT4_2.chckpts/reads_alignments_extracted.ok 09:05:42 : INFO : Running: samtools sort -o tih_rna_sample_00097_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00097_B23WHTKLT4_2.cancer_intron_reads.bam 09:05:42 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00097_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00097_B23WHTKLT4_2.cancer_intron_reads.bam 09:05:42 : INFO : Running: touch /tmp/nxf.3XASX4GpSz/tih_rna_sample_00097_B23WHTKLT4_2.chckpts/sort_cancer_intron_reads.ok 09:05:42 : INFO : Running: samtools sort -o tih_rna_sample_00097_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00097_B23WHTKLT4_2.gene_reads.bam