Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/8104b4b0ab7c8cc196aedf761ae43a/aih-tih-sc-92d360-R1_A23YTGFLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/d5b425fcd3b78ab10a22d6315b8378/aih-tih-sc-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
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/e7/8ed558e081aaa0d195a2c80030172c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/8104b4b0ab7c8cc196aedf761ae43a/aih-tih-sc-92d360-R1_A23YTGFLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/8ed558e081aaa0d195a2c80030172c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/8104b4b0ab7c8cc196aedf761ae43a/aih-tih-sc-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)
20:33:56 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[140000], rate=8400000.00/min
[150000], rate=9000000.00/min
[160000], rate=9600000.00/min
[170000], rate=10200000.00/min
[180000], rate=10800000.00/min
[190000], rate=11400000.00/min
[200000], rate=12000000.00/min
[210000], rate=12600000.00/min
[220000], rate=13200000.00/min
[230000], rate=13800000.00/min
[240000], rate=14400000.00/min
[250000], rate=15000000.00/min
[260000], rate=15600000.00/min
[270000], rate=16200000.00/min
[280000], rate=16800000.00/min
[290000], rate=17400000.00/min
[300000], rate=18000000.00/min
[310000], rate=18600000.00/min
[320000], rate=19200000.00/min
[330000], rate=19800000.00/min
[340000], rate=20400000.00/min
[350000], rate=21000000.00/min
[360000], rate=21600000.00/min
[370000], rate=22200000.00/min
[380000], rate=22800000.00/min
[390000], rate=23400000.00/min
[400000], rate=24000000.00/min
[410000], rate=24600000.00/min
[420000], rate=25200000.00/min
[430000], rate=25800000.00/min
[440000], rate=26400000.00/min
[450000], rate=27000000.00/min
[460000], rate=27600000.00/min
[470000], rate=28200000.00/min
[480000], rate=28800000.00/min
[490000], rate=29400000.00/min
[500000], rate=30000000.00/min
[510000], rate=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=19500000.00/min
[660000], rate=19800000.00/min
[670000], rate=20100000.00/min
[680000], rate=20400000.00/min
[690000], rate=20700000.00/min
[700000], rate=21000000.00/min
[710000], rate=21300000.00/min
[720000], rate=21600000.00/min
[730000], rate=21900000.00/min
[740000], rate=22200000.00/min
[750000], rate=22500000.00/min
[760000], rate=22800000.00/min
[770000], rate=23100000.00/min
[780000], rate=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=18000000.00/min
[910000], rate=18200000.00/min
[920000], rate=18400000.00/min
[930000], rate=18600000.00/min
[940000], rate=18800000.00/min
[950000], rate=19000000.00/min
[960000], rate=19200000.00/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=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=15200000.00/min
[1530000], rate=15300000.00/min
[1540000], rate=15400000.00/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=12675000.00/min
[1700000], rate=12750000.00/min
[1710000], rate=12825000.00/min
[1720000], rate=12900000.00/min
[1730000], rate=12975000.00/min
[1740000], rate=13050000.00/min
[1750000], rate=13125000.00/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=13200000.00/min
[1990000], rate=13266666.67/min
[2000000], rate=13333333.33/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=15000000.00/min
[2510000], rate=15060000.00/min
[2520000], rate=15120000.00/min
[2530000], rate=15180000.00/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=14850000.00/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=14828571.43/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=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=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=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=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=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=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=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=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=14557894.74/min
[4620000], rate=14589473.68/min
[4630000], rate=14621052.63/min
[4640000], rate=14652631.58/min
[4650000], rate=14684210.53/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=14280000.00/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=13772727.27/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=13565217.39/min
[5210000], rate=13591304.35/min
[5220000], rate=13617391.30/min
[5230000], rate=13643478.26/min
[5240000], rate=13669565.22/min
[5250000], rate=13695652.17/min
[5260000], rate=13721739.13/min
[5270000], rate=13747826.09/min
[5280000], rate=13773913.04/min
[5290000], rate=13800000.00/min
[5300000], rate=13826086.96/min
[5310000], rate=13852173.91/min
[5320000], rate=13878260.87/min
[5330000], rate=13904347.83/min
[5340000], rate=13930434.78/min
[5350000], rate=13375000.00/min
[5360000], rate=13400000.00/min
[5370000], rate=13425000.00/min
[5380000], rate=13450000.00/min
[5390000], rate=13475000.00/min
[5400000], rate=13500000.00/min
[5410000], rate=13525000.00/min
[5420000], rate=13550000.00/min
[5430000], rate=13575000.00/min
[5440000], rate=13600000.00/min
[5450000], rate=13625000.00/min
[5460000], rate=13650000.00/min
[5470000], rate=13675000.00/min
[5480000], rate=13700000.00/min
[5490000], rate=13725000.00/min
[5500000], rate=13750000.00/min
[5510000], rate=13775000.00/min
[5520000], rate=13800000.00/min
[5530000], rate=13825000.00/min
[5540000], rate=13850000.00/min
[5550000], rate=13875000.00/min
[5560000], rate=13900000.00/min
[5570000], rate=13925000.00/min
[5580000], rate=13950000.00/min
[5590000], rate=13975000.00/min
[5600000], rate=14000000.00/min
[5610000], rate=14025000.00/min
[5620000], rate=14050000.00/min
[5630000], rate=14075000.00/min
[5640000], rate=13536000.00/min
[5650000], rate=13560000.00/min
[5660000], rate=13584000.00/min
[5670000], rate=13608000.00/min
[5680000], rate=13632000.00/min
[5690000], rate=13656000.00/min
[5700000], rate=13680000.00/min
[5710000], rate=13704000.00/min
[5720000], rate=13728000.00/min
[5730000], rate=13752000.00/min
[5740000], rate=13776000.00/min
[5750000], rate=13800000.00/min
[5760000], rate=13824000.00/min
[5770000], rate=13848000.00/min
[5780000], rate=13872000.00/min
[5790000], rate=13896000.00/min
[5800000], rate=13920000.00/min
[5810000], rate=13944000.00/min
[5820000], rate=13968000.00/min
[5830000], rate=13992000.00/min
[5840000], rate=14016000.00/min
[5850000], rate=14040000.00/min
[5860000], rate=14064000.00/min
[5870000], rate=14088000.00/min
[5880000], rate=14112000.00/min
[5890000], rate=14136000.00/min
[5900000], rate=14160000.00/min
[5910000], rate=14184000.00/min
[5920000], rate=14208000.00/min
[5930000], rate=13684615.38/min
[5940000], rate=13707692.31/min
[5950000], rate=13730769.23/min
[5960000], rate=13753846.15/min
[5970000], rate=13776923.08/min
[5980000], rate=13800000.00/min
[5990000], rate=13823076.92/min
[6000000], rate=13846153.85/min
[6010000], rate=13869230.77/min
[6020000], rate=13892307.69/min
[6030000], rate=13915384.62/min
[6040000], rate=13938461.54/min
[6050000], rate=13961538.46/min
[6060000], rate=13984615.38/min
[6070000], rate=14007692.31/min
[6080000], rate=14030769.23/min
[6090000], rate=14053846.15/min
[6100000], rate=14076923.08/min
[6110000], rate=14100000.00/min
[6120000], rate=14123076.92/min
[6130000], rate=14146153.85/min
[6140000], rate=14169230.77/min
[6150000], rate=14192307.69/min
[6160000], rate=14215384.62/min
[6170000], rate=14238461.54/min
[6180000], rate=14261538.46/min
[6190000], rate=13755555.56/min
[6200000], rate=13777777.78/min
[6210000], rate=13800000.00/min
[6220000], rate=13822222.22/min
[6230000], rate=13844444.44/min
[6240000], rate=13866666.67/min
[6250000], rate=13888888.89/min
[6260000], rate=13911111.11/min
[6270000], rate=13933333.33/min
[6280000], rate=13955555.56/min
[6290000], rate=13977777.78/min
[6300000], rate=14000000.00/min
[6310000], rate=14022222.22/min
[6320000], rate=14044444.44/min
[6330000], rate=14066666.67/min
[6340000], rate=14088888.89/min
[6350000], rate=14111111.11/min
[6360000], rate=14133333.33/min
[6370000], rate=14155555.56/min
[6380000], rate=14177777.78/min
[6390000], rate=14200000.00/min
[6400000], rate=14222222.22/min
[6410000], rate=14244444.44/min
[6420000], rate=14266666.67/min
[6430000], rate=14288888.89/min
[6440000], rate=14311111.11/min
[6450000], rate=14333333.33/min
[6460000], rate=14355555.56/min
[6470000], rate=14377777.78/min
[6480000], rate=14400000.00/min
[6490000], rate=13907142.86/min
[6500000], rate=13928571.43/min
[6510000], rate=13950000.00/min
[6520000], rate=13971428.57/min
[6530000], rate=13992857.14/min
[6540000], rate=14014285.71/min
[6550000], rate=14035714.29/min
[6560000], rate=14057142.86/min
[6570000], rate=14078571.43/min
[6580000], rate=14100000.00/min
[6590000], rate=14121428.57/min
[6600000], rate=14142857.14/min
[6610000], rate=14164285.71/min
[6620000], rate=14185714.29/min
[6630000], rate=14207142.86/min
[6640000], rate=14228571.43/min
[6650000], rate=14250000.00/min
[6660000], rate=14271428.57/min
[6670000], rate=14292857.14/min
[6680000], rate=14314285.71/min
[6690000], rate=14335714.29/min
[6700000], rate=14357142.86/min
[6710000], rate=14378571.43/min
[6720000], rate=14400000.00/min
[6730000], rate=14421428.57/min
[6740000], rate=14442857.14/min
[6750000], rate=14464285.71/min
[6760000], rate=14485714.29/min
[6770000], rate=14507142.86/min
[6780000], rate=14027586.21/min
[6790000], rate=14048275.86/min
[6800000], rate=14068965.52/min
[6810000], rate=14089655.17/min
[6820000], rate=14110344.83/min
[6830000], rate=14131034.48/min
[6840000], rate=14151724.14/min
[6850000], rate=14172413.79/min
[6860000], rate=14193103.45/min
[6870000], rate=14213793.10/min
[6880000], rate=14234482.76/min
[6890000], rate=14255172.41/min
[6900000], rate=14275862.07/min
[6910000], rate=14296551.72/min
[6920000], rate=14317241.38/min
[6930000], rate=14337931.03/min
[6940000], rate=14358620.69/min
[6950000], rate=14379310.34/min
[6960000], rate=14400000.00/min
[6970000], rate=14420689.66/min
[6980000], rate=14441379.31/min
[6990000], rate=14462068.97/min
[7000000], rate=14482758.62/min
[7010000], rate=14503448.28/min
[7020000], rate=14524137.93/min
[7030000], rate=14544827.59/min
[7040000], rate=14565517.24/min
[7050000], rate=14586206.90/min
[7060000], rate=14606896.55/min
[7070000], rate=14140000.00/min
[7080000], rate=14160000.00/min
[7090000], rate=14180000.00/min
[7100000], rate=14200000.00/min
[7110000], rate=14220000.00/min
[7120000], rate=14240000.00/min
[7130000], rate=14260000.00/min
[7140000], rate=14280000.00/min
[7150000], rate=14300000.00/min
[7160000], rate=14320000.00/min
[7170000], rate=14340000.00/min
[7180000], rate=14360000.00/min
[7190000], rate=14380000.00/min
[7200000], rate=14400000.00/min
[7210000], rate=14420000.00/min
[7220000], rate=14440000.00/min
[7230000], rate=14460000.00/min
[7240000], rate=14480000.00/min
[7250000], rate=14500000.00/min
[7260000], rate=14520000.00/min
[7270000], rate=14540000.00/min
[7280000], rate=14560000.00/min
[7290000], rate=14580000.00/min
[7300000], rate=14600000.00/min
[7310000], rate=14620000.00/min
[7320000], rate=14640000.00/min
[7330000], rate=14660000.00/min
[7340000], rate=14680000.00/min
[7350000], rate=14700000.00/min
[7360000], rate=14245161.29/min
[7370000], rate=14264516.13/min
[7380000], rate=14283870.97/min
[7390000], rate=14303225.81/min
[7400000], rate=14322580.65/min
[7410000], rate=14341935.48/min
[7420000], rate=14361290.32/min
[7430000], rate=14380645.16/min
[7440000], rate=14400000.00/min
[7450000], rate=14419354.84/min
[7460000], rate=14438709.68/min
[7470000], rate=14458064.52/min
[7480000], rate=14477419.35/min
[7490000], rate=14496774.19/min
[7500000], rate=14516129.03/min
[7510000], rate=14535483.87/min
[7520000], rate=14554838.71/min
[7530000], rate=14574193.55/min
[7540000], rate=14593548.39/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=14325000.00/min
[7650000], rate=14343750.00/min
[7660000], rate=14362500.00/min
[7670000], rate=14381250.00/min
[7680000], rate=14400000.00/min
[7690000], rate=14418750.00/min
[7700000], rate=14437500.00/min
[7710000], rate=14456250.00/min
[7720000], rate=14475000.00/min
[7730000], rate=14493750.00/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=14831250.00/min
[7920000], rate=14850000.00/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=14636363.64/min
[8060000], rate=14654545.45/min
[8070000], rate=14672727.27/min
[8080000], rate=14690909.09/min
[8090000], rate=14709090.91/min
[8100000], rate=14727272.73/min
[8110000], rate=14745454.55/min
[8120000], rate=14763636.36/min
[8130000], rate=14781818.18/min
[8140000], rate=14800000.00/min
[8150000], rate=14818181.82/min
[8160000], rate=14836363.64/min
[8170000], rate=14854545.45/min
[8180000], rate=14872727.27/min
[8190000], rate=14890909.09/min
[8200000], rate=14909090.91/min
[8210000], rate=14488235.29/min
[8220000], rate=14505882.35/min
[8230000], rate=14523529.41/min
[8240000], rate=14541176.47/min
[8250000], rate=14558823.53/min
[8260000], rate=14576470.59/min
[8270000], rate=14594117.65/min
[8280000], rate=14611764.71/min
[8290000], rate=14629411.76/min
[8300000], rate=14647058.82/min
[8310000], rate=14664705.88/min
[8320000], rate=14682352.94/min
[8330000], rate=14700000.00/min
[8340000], rate=14717647.06/min
[8350000], rate=14735294.12/min
[8360000], rate=14752941.18/min
[8370000], rate=14770588.24/min
[8380000], rate=14788235.29/min
[8390000], rate=14805882.35/min
[8400000], rate=14823529.41/min
[8410000], rate=14841176.47/min
[8420000], rate=14858823.53/min
[8430000], rate=14876470.59/min
[8440000], rate=14468571.43/min
[8450000], rate=14485714.29/min
[8460000], rate=14502857.14/min
[8470000], rate=14520000.00/min
[8480000], rate=14537142.86/min
[8490000], rate=14554285.71/min
[8500000], rate=14571428.57/min
[8510000], rate=14588571.43/min
[8520000], rate=14605714.29/min
[8530000], rate=14622857.14/min
[8540000], rate=14640000.00/min
[8550000], rate=14657142.86/min
[8560000], rate=14674285.71/min
[8570000], rate=14691428.57/min
[8580000], rate=14708571.43/min
[8590000], rate=14725714.29/min
[8600000], rate=14742857.14/min
[8610000], rate=14350000.00/min
[8620000], rate=14366666.67/min
[8630000], rate=14383333.33/min
[8640000], rate=14400000.00/min
[8650000], rate=14416666.67/min
[8660000], rate=14433333.33/min 20:34:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-92d360-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-92d360-R1_A23YTGFLT4_1.introns: identified 4776 cancer introns
20:34:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns.prelim
20:34:44 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok
20:34:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns
20:34:44 : 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-92d360-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns
20:34:44 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok
20:34:44 : INFO : -found 1742 cancer introns
20:34:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed
20:34:45 : INFO : Creating the BED File.
20:34:50 : INFO : Saving Bed File as aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed
20:34:50 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed
20:34:50 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok
20:34:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-92d360-R1_A23YTGFLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
20:50:06 : INFO : Execution Time = 15.26 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-92d360-R1_A23YTGFLT4_1
20:50:06 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok
20:50:06 : INFO : Running: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.bam
20:50:06 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.bam
20:50:06 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok
20:50:06 : INFO : Running: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.bam
[bam_sort_core] merging from 68 files and 1 in-memory blocks...
21:06:30 : INFO : Execution Time = 16.40 minutes. CMD: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.bam
21:06:30 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok
21:06:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-92d360-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.
Done with chr chrX.
21:11:04 : INFO : Execution Time = 4.57 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.bam
21:11:04 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
21:11:04 : INFO : Running: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
21:11:57 : INFO : Execution Time = 0.88 minutes. CMD: samtools sort -o aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp
21:11:57 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
21:11:57 : INFO : Running: samtools index aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam
21:12:03 : INFO : Execution Time = 0.09 minutes. CMD: samtools index aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam
21:12:03 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-92d360-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
21:12:03 : INFO : Running: samtools index aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam
21:12:03 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam
21:12:03 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-92d360-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
21:12:03 : INFO : Running: create_report aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-92d360-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-92d360-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-92d360-R1_A23YTGFLT4_1'
21:17:32 : INFO : Execution Time = 5.49 minutes. CMD: create_report aih-tih-sc-92d360-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-92d360-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-92d360-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-92d360-R1_A23YTGFLT4_1'
21:17:32 : INFO : Running: touch /tmp/nxf.8v8Akx0rTS/aih-tih-sc-92d360-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok
21:17:32 : INFO : done.