Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/82d3b82ba79d285fb61633dd0fb778/A673_FFPE_RNA_0001_B23LG7FLT4_3.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/82d3b82ba79d285fb61633dd0fb778/A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
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/13/c0bbf0cfa54676cc4b654af4bf5482/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/c0bbf0cfa54676cc4b654af4bf5482/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/82d3b82ba79d285fb61633dd0fb778/A673_FFPE_RNA_0001_B23LG7FLT4_3.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/3d013309291690d8fb86b67138cdef/A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)
21:23:25 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[20000], rate=1200000.00/min
[30000], rate=1800000.00/min
[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=9300000.00/min
[320000], rate=9600000.00/min
[330000], rate=9900000.00/min
[340000], rate=10200000.00/min
[350000], rate=10500000.00/min
[360000], rate=10800000.00/min
[370000], rate=11100000.00/min
[380000], rate=11400000.00/min
[390000], rate=11700000.00/min
[400000], rate=12000000.00/min
[410000], rate=12300000.00/min
[420000], rate=12600000.00/min
[430000], rate=12900000.00/min
[440000], rate=13200000.00/min
[450000], rate=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=12200000.00/min
[620000], rate=12400000.00/min
[630000], rate=12600000.00/min
[640000], rate=12800000.00/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=12450000.00/min
[840000], rate=12600000.00/min
[850000], rate=12750000.00/min
[860000], rate=12900000.00/min
[870000], rate=13050000.00/min
[880000], rate=13200000.00/min
[890000], rate=13350000.00/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=12720000.00/min
[1070000], rate=12840000.00/min
[1080000], rate=12960000.00/min
[1090000], rate=13080000.00/min
[1100000], rate=13200000.00/min
[1110000], rate=13320000.00/min
[1120000], rate=13440000.00/min
[1130000], rate=13560000.00/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=12800000.00/min
[1290000], rate=12900000.00/min
[1300000], rate=13000000.00/min
[1310000], rate=13100000.00/min
[1320000], rate=13200000.00/min
[1330000], rate=13300000.00/min
[1340000], rate=13400000.00/min
[1350000], rate=13500000.00/min
[1360000], rate=13600000.00/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=13028571.43/min
[1530000], rate=13114285.71/min
[1540000], rate=13200000.00/min
[1550000], rate=13285714.29/min
[1560000], rate=13371428.57/min
[1570000], rate=13457142.86/min
[1580000], rate=13542857.14/min
[1590000], rate=13628571.43/min
[1600000], rate=13714285.71/min
[1610000], rate=13800000.00/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=13200000.00/min
[1770000], rate=13275000.00/min
[1780000], rate=13350000.00/min
[1790000], rate=13425000.00/min
[1800000], rate=13500000.00/min
[1810000], rate=13575000.00/min
[1820000], rate=13650000.00/min
[1830000], rate=13725000.00/min
[1840000], rate=13800000.00/min
[1850000], rate=13875000.00/min
[1860000], rate=13950000.00/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=13400000.00/min
[2020000], rate=13466666.67/min
[2030000], rate=13533333.33/min
[2040000], rate=13600000.00/min
[2050000], rate=13666666.67/min
[2060000], rate=13733333.33/min
[2070000], rate=13800000.00/min
[2080000], rate=13866666.67/min
[2090000], rate=13933333.33/min
[2100000], rate=14000000.00/min
[2110000], rate=14066666.67/min
[2120000], rate=14133333.33/min
[2130000], rate=14200000.00/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=13500000.00/min
[2260000], rate=13560000.00/min
[2270000], rate=13620000.00/min
[2280000], rate=13680000.00/min
[2290000], rate=13740000.00/min
[2300000], rate=13800000.00/min
[2310000], rate=13860000.00/min
[2320000], rate=13920000.00/min
[2330000], rate=13980000.00/min
[2340000], rate=14040000.00/min
[2350000], rate=14100000.00/min
[2360000], rate=14160000.00/min
[2370000], rate=14220000.00/min
[2380000], rate=14280000.00/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=13636363.64/min
[2510000], rate=13690909.09/min
[2520000], rate=13745454.55/min
[2530000], rate=13800000.00/min
[2540000], rate=13854545.45/min
[2550000], rate=13909090.91/min
[2560000], rate=13963636.36/min
[2570000], rate=14018181.82/min
[2580000], rate=14072727.27/min
[2590000], rate=14127272.73/min
[2600000], rate=14181818.18/min
[2610000], rate=14236363.64/min
[2620000], rate=14290909.09/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=13700000.00/min
[2750000], rate=13750000.00/min
[2760000], rate=13800000.00/min
[2770000], rate=13850000.00/min
[2780000], rate=13900000.00/min
[2790000], rate=13950000.00/min
[2800000], rate=14000000.00/min
[2810000], rate=14050000.00/min
[2820000], rate=14100000.00/min
[2830000], rate=14150000.00/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=13707692.31/min
[2980000], rate=13753846.15/min
[2990000], rate=13800000.00/min
[3000000], rate=13846153.85/min
[3010000], rate=13892307.69/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=14676923.08/min
[3190000], rate=14723076.92/min
[3200000], rate=14769230.77/min
[3210000], rate=14815384.62/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=13840000.00/min
[3470000], rate=13880000.00/min
[3480000], rate=13920000.00/min
[3490000], rate=13960000.00/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=13912500.00/min
[3720000], rate=13950000.00/min
[3730000], rate=13987500.00/min
[3740000], rate=14025000.00/min
[3750000], rate=14062500.00/min
[3760000], rate=14100000.00/min
[3770000], rate=14137500.00/min
[3780000], rate=14175000.00/min
[3790000], rate=14212500.00/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=13835294.12/min
[3930000], rate=13870588.24/min
[3940000], rate=13905882.35/min
[3950000], rate=13941176.47/min
[3960000], rate=13976470.59/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=14576470.59/min
[4140000], rate=14611764.71/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=14266666.67/min
[4290000], rate=14300000.00/min
[4300000], rate=14333333.33/min
[4310000], rate=14366666.67/min
[4320000], rate=14400000.00/min
[4330000], rate=14433333.33/min
[4340000], rate=14466666.67/min
[4350000], rate=14500000.00/min
[4360000], rate=14533333.33/min
[4370000], rate=14566666.67/min
[4380000], rate=14600000.00/min
[4390000], rate=14633333.33/min
[4400000], rate=13894736.84/min
[4410000], rate=13926315.79/min
[4420000], rate=13957894.74/min
[4430000], rate=13989473.68/min
[4440000], rate=14021052.63/min
[4450000], rate=14052631.58/min
[4460000], rate=14084210.53/min
[4470000], rate=14115789.47/min
[4480000], rate=14147368.42/min
[4490000], rate=14178947.37/min
[4500000], rate=14210526.32/min
[4510000], rate=14242105.26/min
[4520000], rate=14273684.21/min
[4530000], rate=14305263.16/min
[4540000], rate=14336842.11/min
[4550000], rate=14368421.05/min
[4560000], rate=14400000.00/min
[4570000], rate=14431578.95/min
[4580000], rate=14463157.89/min
[4590000], rate=14494736.84/min
[4600000], rate=14526315.79/min
[4610000], rate=13830000.00/min
[4620000], rate=13860000.00/min
[4630000], rate=13890000.00/min
[4640000], rate=13920000.00/min
[4650000], rate=13950000.00/min
[4660000], rate=13980000.00/min
[4670000], rate=14010000.00/min
[4680000], rate=14040000.00/min
[4690000], rate=14070000.00/min
[4700000], rate=14100000.00/min
[4710000], rate=14130000.00/min
[4720000], rate=14160000.00/min
[4730000], rate=14190000.00/min
[4740000], rate=14220000.00/min
[4750000], rate=14250000.00/min
[4760000], rate=13600000.00/min
[4770000], rate=13628571.43/min
[4780000], rate=13657142.86/min
[4790000], rate=13685714.29/min
[4800000], rate=13714285.71/min
[4810000], rate=13742857.14/min
[4820000], rate=13771428.57/min
[4830000], rate=13800000.00/min
[4840000], rate=13828571.43/min
[4850000], rate=13857142.86/min
[4860000], rate=13885714.29/min
[4870000], rate=13914285.71/min
[4880000], rate=13942857.14/min
[4890000], rate=13971428.57/min
[4900000], rate=13363636.36/min
[4910000], rate=13390909.09/min
[4920000], rate=13418181.82/min
[4930000], rate=13445454.55/min
[4940000], rate=13472727.27/min
[4950000], rate=13500000.00/min
[4960000], rate=13527272.73/min
[4970000], rate=13554545.45/min
[4980000], rate=13581818.18/min
[4990000], rate=13609090.91/min
[5000000], rate=13636363.64/min
[5010000], rate=13663636.36/min
[5020000], rate=13690909.09/min
[5030000], rate=13718181.82/min
[5040000], rate=13745454.55/min
[5050000], rate=13173913.04/min
[5060000], rate=13200000.00/min
[5070000], rate=13226086.96/min
[5080000], rate=13252173.91/min
[5090000], rate=13278260.87/min
[5100000], rate=13304347.83/min
[5110000], rate=13330434.78/min
[5120000], rate=13356521.74/min
[5130000], rate=13382608.70/min
[5140000], rate=13408695.65/min
[5150000], rate=13434782.61/min
[5160000], rate=13460869.57/min
[5170000], rate=13486956.52/min
[5180000], rate=13513043.48/min
[5190000], rate=13539130.43/min
[5200000], rate=13000000.00/min
[5210000], rate=13025000.00/min
[5220000], rate=13050000.00/min
[5230000], rate=13075000.00/min
[5240000], rate=13100000.00/min
[5250000], rate=13125000.00/min
[5260000], rate=13150000.00/min
[5270000], rate=13175000.00/min
[5280000], rate=13200000.00/min
[5290000], rate=13225000.00/min
[5300000], rate=13250000.00/min
[5310000], rate=13275000.00/min
[5320000], rate=13300000.00/min
[5330000], rate=12792000.00/min
[5340000], rate=12816000.00/min
[5350000], rate=12840000.00/min
[5360000], rate=12864000.00/min
[5370000], rate=12888000.00/min
[5380000], rate=12912000.00/min
[5390000], rate=12936000.00/min
[5400000], rate=12960000.00/min
[5410000], rate=12984000.00/min
[5420000], rate=13008000.00/min
[5430000], rate=13032000.00/min
[5440000], rate=13056000.00/min
[5450000], rate=12576923.08/min
[5460000], rate=12600000.00/min
[5470000], rate=12623076.92/min
[5480000], rate=12646153.85/min
[5490000], rate=12669230.77/min
[5500000], rate=12692307.69/min
[5510000], rate=12715384.62/min
[5520000], rate=12738461.54/min
[5530000], rate=12761538.46/min
[5540000], rate=12784615.38/min
[5550000], rate=12807692.31/min
[5560000], rate=12830769.23/min
[5570000], rate=12853846.15/min
[5580000], rate=12876923.08/min
[5590000], rate=12900000.00/min
[5600000], rate=12923076.92/min
[5610000], rate=12466666.67/min
[5620000], rate=12488888.89/min
[5630000], rate=12511111.11/min
[5640000], rate=12533333.33/min
[5650000], rate=12555555.56/min
[5660000], rate=12577777.78/min
[5670000], rate=12600000.00/min
[5680000], rate=12622222.22/min
[5690000], rate=12644444.44/min
[5700000], rate=12666666.67/min
[5710000], rate=12688888.89/min
[5720000], rate=12711111.11/min
[5730000], rate=12733333.33/min
[5740000], rate=12755555.56/min
[5750000], rate=12777777.78/min
[5760000], rate=12800000.00/min
[5770000], rate=12822222.22/min
[5780000], rate=12385714.29/min
[5790000], rate=12407142.86/min
[5800000], rate=12428571.43/min
[5810000], rate=12450000.00/min
[5820000], rate=12471428.57/min
[5830000], rate=12492857.14/min
[5840000], rate=12514285.71/min
[5850000], rate=12535714.29/min
[5860000], rate=12557142.86/min
[5870000], rate=12578571.43/min
[5880000], rate=12600000.00/min
[5890000], rate=12621428.57/min
[5900000], rate=12642857.14/min
[5910000], rate=12664285.71/min
[5920000], rate=12685714.29/min
[5930000], rate=12707142.86/min
[5940000], rate=12728571.43/min
[5950000], rate=12750000.00/min
[5960000], rate=12771428.57/min
[5970000], rate=12792857.14/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=12517241.38/min
[6060000], rate=12537931.03/min
[6070000], rate=12558620.69/min
[6080000], rate=12579310.34/min
[6090000], rate=12600000.00/min
[6100000], rate=12620689.66/min
[6110000], rate=12641379.31/min
[6120000], rate=12662068.97/min
[6130000], rate=12682758.62/min
[6140000], rate=12703448.28/min
[6150000], rate=12724137.93/min
[6160000], rate=12744827.59/min
[6170000], rate=12765517.24/min
[6180000], rate=12786206.90/min
[6190000], rate=12806896.55/min
[6200000], rate=12827586.21/min
[6210000], rate=12848275.86/min
[6220000], rate=12868965.52/min
[6230000], rate=12889655.17/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=12600000.00/min
[6310000], rate=12620000.00/min
[6320000], rate=12640000.00/min
[6330000], rate=12660000.00/min
[6340000], rate=12680000.00/min
[6350000], rate=12700000.00/min
[6360000], rate=12720000.00/min
[6370000], rate=12740000.00/min
[6380000], rate=12760000.00/min
[6390000], rate=12780000.00/min
[6400000], rate=12800000.00/min
[6410000], rate=12820000.00/min
[6420000], rate=12840000.00/min
[6430000], rate=12860000.00/min
[6440000], rate=12880000.00/min
[6450000], rate=12900000.00/min
[6460000], rate=12920000.00/min
[6470000], rate=12940000.00/min
[6480000], rate=12960000.00/min
[6490000], rate=12980000.00/min
[6500000], rate=13000000.00/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=12696774.19/min
[6570000], rate=12716129.03/min
[6580000], rate=12735483.87/min
[6590000], rate=12754838.71/min
[6600000], rate=12774193.55/min
[6610000], rate=12793548.39/min
[6620000], rate=12812903.23/min
[6630000], rate=12832258.06/min
[6640000], rate=12851612.90/min
[6650000], rate=12870967.74/min
[6660000], rate=12890322.58/min
[6670000], rate=12909677.42/min
[6680000], rate=12929032.26/min
[6690000], rate=12948387.10/min
[6700000], rate=12967741.94/min
[6710000], rate=12987096.77/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=12787500.00/min
[6830000], rate=12806250.00/min
[6840000], rate=12825000.00/min
[6850000], rate=12843750.00/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=12352941.18/min
[7010000], rate=12370588.24/min
[7020000], rate=12388235.29/min
[7030000], rate=12405882.35/min
[7040000], rate=12423529.41/min
[7050000], rate=12441176.47/min
[7060000], rate=12458823.53/min
[7070000], rate=12476470.59/min
[7080000], rate=12494117.65/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=12257142.86/min
[7160000], rate=12274285.71/min
[7170000], rate=12291428.57/min
[7180000], rate=12308571.43/min
[7190000], rate=12325714.29/min
[7200000], rate=12342857.14/min
[7210000], rate=12360000.00/min
[7220000], rate=12377142.86/min
[7230000], rate=12394285.71/min
[7240000], rate=12411428.57/min
[7250000], rate=12428571.43/min
[7260000], rate=12445714.29/min
[7270000], rate=12462857.14/min
[7280000], rate=12480000.00/min
[7290000], rate=12497142.86/min
[7300000], rate=12514285.71/min
[7310000], rate=12183333.33/min
[7320000], rate=12200000.00/min
[7330000], rate=12216666.67/min
[7340000], rate=12233333.33/min
[7350000], rate=12250000.00/min
[7360000], rate=12266666.67/min
[7370000], rate=12283333.33/min
[7380000], rate=12300000.00/min
[7390000], rate=12316666.67/min
[7400000], rate=12333333.33/min
[7410000], rate=12350000.00/min
[7420000], rate=12366666.67/min
[7430000], rate=12383333.33/min
[7440000], rate=12400000.00/min
[7450000], rate=12416666.67/min
[7460000], rate=12433333.33/min
[7470000], rate=12450000.00/min
[7480000], rate=12466666.67/min
[7490000], rate=12483333.33/min
[7500000], rate=12500000.00/min
[7510000], rate=12516666.67/min
[7520000], rate=12533333.33/min
[7530000], rate=12550000.00/min
[7540000], rate=12566666.67/min
[7550000], rate=12243243.24/min
[7560000], rate=12259459.46/min
[7570000], rate=12275675.68/min
[7580000], rate=12291891.89/min
[7590000], rate=12308108.11/min
[7600000], rate=12324324.32/min
[7610000], rate=12340540.54/min
[7620000], rate=12356756.76/min
[7630000], rate=12372972.97/min
[7640000], rate=12389189.19/min
[7650000], rate=12405405.41/min
[7660000], rate=12421621.62/min
[7670000], rate=12437837.84/min
[7680000], rate=12454054.05/min
[7690000], rate=12470270.27/min
[7700000], rate=12486486.49/min
[7710000], rate=12502702.70/min
[7720000], rate=12518918.92/min
[7730000], rate=12535135.14/min
[7740000], rate=12551351.35/min
[7750000], rate=12567567.57/min
[7760000], rate=12583783.78/min
[7770000], rate=12600000.00/min
[7780000], rate=12616216.22/min
[7790000], rate=12300000.00/min
[7800000], rate=12315789.47/min
[7810000], rate=12331578.95/min
[7820000], rate=12347368.42/min
[7830000], rate=12363157.89/min
[7840000], rate=12378947.37/min
[7850000], rate=12394736.84/min
[7860000], rate=12410526.32/min
[7870000], rate=12426315.79/min
[7880000], rate=12442105.26/min
[7890000], rate=12457894.74/min
[7900000], rate=12473684.21/min
[7910000], rate=12489473.68/min
[7920000], rate=12505263.16/min
[7930000], rate=12521052.63/min
[7940000], rate=12536842.11/min
[7950000], rate=12552631.58/min
[7960000], rate=12568421.05/min
[7970000], rate=12584210.53/min
[7980000], rate=12276923.08/min
[7990000], rate=12292307.69/min
[8000000], rate=12307692.31/min
[8010000], rate=12323076.92/min
[8020000], rate=12338461.54/min
[8030000], rate=12353846.15/min
[8040000], rate=12369230.77/min
[8050000], rate=12384615.38/min
[8060000], rate=12400000.00/min
[8070000], rate=12415384.62/min
[8080000], rate=12430769.23/min
[8090000], rate=12446153.85/min
[8100000], rate=12461538.46/min
[8110000], rate=12476923.08/min
[8120000], rate=12492307.69/min
[8130000], rate=12507692.31/min
[8140000], rate=12523076.92/min
[8150000], rate=12538461.54/min
[8160000], rate=12553846.15/min
[8170000], rate=12569230.77/min
[8180000], rate=12584615.38/min
[8190000], rate=12600000.00/min
[8200000], rate=12300000.00/min
[8210000], rate=12315000.00/min
[8220000], rate=12330000.00/min
[8230000], rate=12345000.00/min
[8240000], rate=12360000.00/min
[8250000], rate=12375000.00/min
[8260000], rate=12390000.00/min
[8270000], rate=12405000.00/min
[8280000], rate=12420000.00/min
[8290000], rate=12435000.00/min
[8300000], rate=12450000.00/min
[8310000], rate=12465000.00/min
[8320000], rate=12480000.00/min
[8330000], rate=12495000.00/min
[8340000], rate=12510000.00/min
[8350000], rate=12525000.00/min
[8360000], rate=12540000.00/min
[8370000], rate=12555000.00/min
[8380000], rate=12570000.00/min
[8390000], rate=12585000.00/min
[8400000], rate=12600000.00/min
[8410000], rate=12615000.00/min
[8420000], rate=12630000.00/min
[8430000], rate=12645000.00/min
[8440000], rate=12351219.51/min
[8450000], rate=12365853.66/min
[8460000], rate=12380487.80/min
[8470000], rate=12395121.95/min
[8480000], rate=12409756.10/min
[8490000], rate=12424390.24/min
[8500000], rate=12439024.39/min
[8510000], rate=12453658.54/min
[8520000], rate=12468292.68/min
[8530000], rate=12482926.83/min
[8540000], rate=12497560.98/min
[8550000], rate=12512195.12/min
[8560000], rate=12526829.27/min
[8570000], rate=12541463.41/min
[8580000], rate=12556097.56/min
[8590000], rate=12570731.71/min
[8600000], rate=12585365.85/min
[8610000], rate=12600000.00/min
[8620000], rate=12614634.15/min
[8630000], rate=12629268.29/min
[8640000], rate=12643902.44/min
[8650000], rate=12357142.86/min
[8660000], rate=12371428.57/min
[8670000], rate=12385714.29/min
[8680000], rate=12400000.00/min
[8690000], rate=12414285.71/min
[8700000], rate=12428571.43/min
[8710000], rate=12442857.14/min
[8720000], rate=12457142.86/min
[8730000], rate=12471428.57/min
[8740000], rate=12485714.29/min
[8750000], rate=12500000.00/min
[8760000], rate=12514285.71/min
[8770000], rate=12528571.43/min
[8780000], rate=12542857.14/min
[8790000], rate=12557142.86/min
[8800000], rate=12571428.57/min
[8810000], rate=12585714.29/min
[8820000], rate=12600000.00/min
[8830000], rate=12614285.71/min
[8840000], rate=12628571.43/min
[8850000], rate=12348837.21/min
[8860000], rate=12362790.70/min
[8870000], rate=12376744.19/min
[8880000], rate=12390697.67/min
[8890000], rate=12404651.16/min
[8900000], rate=12418604.65/min
[8910000], rate=12432558.14/min
[8920000], rate=12446511.63/min
[8930000], rate=12460465.12/min
[8940000], rate=12474418.60/min
[8950000], rate=12488372.09/min
[8960000], rate=12502325.58/min
[8970000], rate=12516279.07/min
[8980000], rate=12530232.56/min
[8990000], rate=12544186.05/min
[9000000], rate=12558139.53/min
[9010000], rate=12572093.02/min
[9020000], rate=12586046.51/min
[9030000], rate=12600000.00/min
[9040000], rate=12613953.49/min
[9050000], rate=12627906.98/min
[9060000], rate=12354545.45/min
[9070000], rate=12368181.82/min
[9080000], rate=12381818.18/min
[9090000], rate=12395454.55/min
[9100000], rate=12409090.91/min
[9110000], rate=12422727.27/min
[9120000], rate=12436363.64/min
[9130000], rate=12450000.00/min
[9140000], rate=12463636.36/min
[9150000], rate=12477272.73/min
[9160000], rate=12490909.09/min
[9170000], rate=12504545.45/min
[9180000], rate=12518181.82/min
[9190000], rate=12531818.18/min
[9200000], rate=12545454.55/min
[9210000], rate=12559090.91/min
[9220000], rate=12572727.27/min
[9230000], rate=12586363.64/min
[9240000], rate=12600000.00/min
[9250000], rate=12613636.36/min
[9260000], rate=12627272.73/min
[9270000], rate=12640909.09/min
[9280000], rate=12654545.45/min
[9290000], rate=12668181.82/min
[9300000], rate=12681818.18/min
[9310000], rate=12413333.33/min
[9320000], rate=12426666.67/min
[9330000], rate=12440000.00/min
[9340000], rate=12453333.33/min
[9350000], rate=12466666.67/min
[9360000], rate=12480000.00/min
[9370000], rate=12493333.33/min
[9380000], rate=12506666.67/min
[9390000], rate=12520000.00/min
[9400000], rate=12533333.33/min
[9410000], rate=12546666.67/min
[9420000], rate=12560000.00/min
[9430000], rate=12573333.33/min
[9440000], rate=12586666.67/min
[9450000], rate=12600000.00/min
[9460000], rate=12613333.33/min
[9470000], rate=12626666.67/min
[9480000], rate=12640000.00/min
[9490000], rate=12653333.33/min
[9500000], rate=12666666.67/min
[9510000], rate=12680000.00/min
[9520000], rate=12693333.33/min
[9530000], rate=12706666.67/min
[9540000], rate=12720000.00/min
[9550000], rate=12733333.33/min
[9560000], rate=12746666.67/min
[9570000], rate=12482608.70/min
[9580000], rate=12495652.17/min
[9590000], rate=12508695.65/min
[9600000], rate=12521739.13/min
[9610000], rate=12534782.61/min
[9620000], rate=12547826.09/min
[9630000], rate=12560869.57/min
[9640000], rate=12573913.04/min
[9650000], rate=12586956.52/min
[9660000], rate=12600000.00/min
[9670000], rate=12613043.48/min
[9680000], rate=12626086.96/min
[9690000], rate=12639130.43/min
[9700000], rate=12652173.91/min
[9710000], rate=12665217.39/min
[9720000], rate=12678260.87/min
[9730000], rate=12691304.35/min
[9740000], rate=12704347.83/min
[9750000], rate=12717391.30/min
[9760000], rate=12730434.78/min
[9770000], rate=12743478.26/min
[9780000], rate=12756521.74/min
[9790000], rate=12769565.22/min
[9800000], rate=12782608.70/min
[9810000], rate=12523404.26/min
[9820000], rate=12536170.21/min
[9830000], rate=12548936.17/min
[9840000], rate=12561702.13/min
[9850000], rate=12574468.09/min
[9860000], rate=12587234.04/min
[9870000], rate=12600000.00/min
[9880000], rate=12612765.96/min
[9890000], rate=12625531.91/min
[9900000], rate=12638297.87/min
[9910000], rate=12651063.83/min
[9920000], rate=12663829.79/min
[9930000], rate=12676595.74/min
[9940000], rate=12689361.70/min
[9950000], rate=12702127.66/min
[9960000], rate=12714893.62/min 21:24:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file A673_FFPE_RNA_0001_B23LG7FLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > A673_FFPE_RNA_0001_B23LG7FLT4_3.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.
-A673_FFPE_RNA_0001_B23LG7FLT4_3.introns: identified 7289 cancer introns
21:24:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file A673_FFPE_RNA_0001_B23LG7FLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim
21:24:24 : INFO : Running: touch /tmp/nxf.sVSRoTHnn6/A673_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/prelim_introns.ok
21:24:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim --min_total_reads 5 > A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns
21:24:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim --min_total_reads 5 > A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns
21:24:24 : INFO : Running: touch /tmp/nxf.sVSRoTHnn6/A673_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/introns_filtered.ok
21:24:24 : INFO : -found 3626 cancer introns
21:24:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns A673_FFPE_RNA_0001_B23LG7FLT4_3.introns --cancer_introns A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed A673_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
21:24:25 : INFO : Creating the BED File.
21:24:34 : INFO : Saving Bed File as A673_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
21:24:34 : INFO : Execution Time = 0.17 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns A673_FFPE_RNA_0001_B23LG7FLT4_3.introns --cancer_introns A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed A673_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
21:24:34 : INFO : Running: touch /tmp/nxf.sVSRoTHnn6/A673_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/intron_igv_bed.ok
21:24:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed A673_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed --bam A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --output_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai