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/9d/938abe7f19a8b6af90edbca74e3d06/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/b3b63b00d3d7a0958420df488a393a/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/accf6489903581f6a7d8f23fd46c03/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/938abe7f19a8b6af90edbca74e3d06/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/b3b63b00d3d7a0958420df488a393a/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/938abe7f19a8b6af90edbca74e3d06/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)
08:16:29 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[80000], rate=4800000.00/min
[90000], rate=5400000.00/min
[100000], rate=6000000.00/min
[110000], rate=6600000.00/min
[120000], rate=7200000.00/min
[130000], rate=7800000.00/min
[140000], rate=8400000.00/min
[150000], rate=9000000.00/min
[160000], rate=9600000.00/min
[170000], rate=10200000.00/min
[180000], rate=10800000.00/min
[190000], rate=11400000.00/min
[200000], rate=12000000.00/min
[210000], rate=12600000.00/min
[220000], rate=13200000.00/min
[230000], rate=13800000.00/min
[240000], rate=14400000.00/min
[250000], rate=15000000.00/min
[260000], rate=15600000.00/min
[270000], rate=16200000.00/min
[280000], rate=16800000.00/min
[290000], rate=17400000.00/min
[300000], rate=18000000.00/min
[310000], rate=18600000.00/min
[320000], rate=19200000.00/min
[330000], rate=19800000.00/min
[340000], rate=20400000.00/min
[350000], rate=21000000.00/min
[360000], rate=21600000.00/min
[370000], rate=22200000.00/min
[380000], rate=22800000.00/min
[390000], rate=23400000.00/min
[400000], rate=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=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=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=18800000.00/min
[950000], rate=19000000.00/min
[960000], rate=19200000.00/min
[970000], rate=19400000.00/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=19350000.00/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=24150000.00/min
[1620000], rate=24300000.00/min
[1630000], rate=24450000.00/min
[1640000], rate=24600000.00/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=21480000.00/min
[1800000], rate=21600000.00/min
[1810000], rate=21720000.00/min
[1820000], rate=21840000.00/min
[1830000], rate=21960000.00/min
[1840000], rate=22080000.00/min
[1850000], rate=22200000.00/min
[1860000], rate=22320000.00/min
[1870000], rate=22440000.00/min
[1880000], rate=22560000.00/min
[1890000], rate=22680000.00/min
[1900000], rate=22800000.00/min
[1910000], rate=22920000.00/min
[1920000], rate=23040000.00/min
[1930000], rate=23160000.00/min
[1940000], rate=23280000.00/min
[1950000], rate=23400000.00/min
[1960000], rate=19600000.00/min
[1970000], rate=19700000.00/min
[1980000], rate=19800000.00/min
[1990000], rate=19900000.00/min
[2000000], rate=20000000.00/min
[2010000], rate=20100000.00/min
[2020000], rate=20200000.00/min
[2030000], rate=20300000.00/min
[2040000], rate=20400000.00/min
[2050000], rate=20500000.00/min
[2060000], rate=20600000.00/min
[2070000], rate=20700000.00/min
[2080000], rate=20800000.00/min
[2090000], rate=20900000.00/min
[2100000], rate=21000000.00/min
[2110000], rate=21100000.00/min
[2120000], rate=21200000.00/min
[2130000], rate=21300000.00/min
[2140000], rate=21400000.00/min
[2150000], rate=21500000.00/min
[2160000], rate=21600000.00/min
[2170000], rate=21700000.00/min
[2180000], rate=21800000.00/min
[2190000], rate=18771428.57/min
[2200000], rate=18857142.86/min
[2210000], rate=18942857.14/min
[2220000], rate=19028571.43/min
[2230000], rate=19114285.71/min
[2240000], rate=19200000.00/min
[2250000], rate=19285714.29/min
[2260000], rate=19371428.57/min
[2270000], rate=19457142.86/min
[2280000], rate=19542857.14/min
[2290000], rate=19628571.43/min
[2300000], rate=19714285.71/min
[2310000], rate=19800000.00/min
[2320000], rate=19885714.29/min
[2330000], rate=19971428.57/min
[2340000], rate=20057142.86/min
[2350000], rate=20142857.14/min
[2360000], rate=20228571.43/min
[2370000], rate=20314285.71/min
[2380000], rate=20400000.00/min
[2390000], rate=20485714.29/min
[2400000], rate=20571428.57/min
[2410000], rate=20657142.86/min
[2420000], rate=20742857.14/min
[2430000], rate=20828571.43/min
[2440000], rate=20914285.71/min
[2450000], rate=21000000.00/min
[2460000], rate=18450000.00/min
[2470000], rate=18525000.00/min
[2480000], rate=18600000.00/min
[2490000], rate=18675000.00/min
[2500000], rate=18750000.00/min
[2510000], rate=18825000.00/min
[2520000], rate=18900000.00/min
[2530000], rate=18975000.00/min
[2540000], rate=19050000.00/min
[2550000], rate=19125000.00/min
[2560000], rate=19200000.00/min
[2570000], rate=19275000.00/min
[2580000], rate=19350000.00/min
[2590000], rate=19425000.00/min
[2600000], rate=19500000.00/min
[2610000], rate=19575000.00/min
[2620000], rate=19650000.00/min
[2630000], rate=19725000.00/min
[2640000], rate=19800000.00/min
[2650000], rate=19875000.00/min
[2660000], rate=19950000.00/min
[2670000], rate=20025000.00/min
[2680000], rate=20100000.00/min
[2690000], rate=20175000.00/min
[2700000], rate=20250000.00/min
[2710000], rate=20325000.00/min
[2720000], rate=20400000.00/min
[2730000], rate=20475000.00/min
[2740000], rate=20550000.00/min
[2750000], rate=20625000.00/min
[2760000], rate=20700000.00/min
[2770000], rate=20775000.00/min
[2780000], rate=20850000.00/min
[2790000], rate=20925000.00/min
[2800000], rate=21000000.00/min
[2810000], rate=21075000.00/min
[2820000], rate=18800000.00/min
[2830000], rate=18866666.67/min
[2840000], rate=18933333.33/min
[2850000], rate=19000000.00/min
[2860000], rate=19066666.67/min
[2870000], rate=19133333.33/min
[2880000], rate=19200000.00/min
[2890000], rate=19266666.67/min
[2900000], rate=19333333.33/min
[2910000], rate=19400000.00/min
[2920000], rate=19466666.67/min
[2930000], rate=19533333.33/min
[2940000], rate=19600000.00/min
[2950000], rate=19666666.67/min
[2960000], rate=19733333.33/min
[2970000], rate=19800000.00/min
[2980000], rate=19866666.67/min
[2990000], rate=19933333.33/min
[3000000], rate=20000000.00/min
[3010000], rate=20066666.67/min
[3020000], rate=20133333.33/min
[3030000], rate=20200000.00/min
[3040000], rate=20266666.67/min
[3050000], rate=20333333.33/min
[3060000], rate=20400000.00/min
[3070000], rate=20466666.67/min
[3080000], rate=20533333.33/min
[3090000], rate=20600000.00/min
[3100000], rate=20666666.67/min
[3110000], rate=20733333.33/min
[3120000], rate=20800000.00/min
[3130000], rate=20866666.67/min
[3140000], rate=20933333.33/min
[3150000], rate=21000000.00/min
[3160000], rate=21066666.67/min
[3170000], rate=21133333.33/min
[3180000], rate=21200000.00/min
[3190000], rate=21266666.67/min
[3200000], rate=21333333.33/min
[3210000], rate=21400000.00/min
[3220000], rate=21466666.67/min
[3230000], rate=19380000.00/min
[3240000], rate=19440000.00/min
[3250000], rate=19500000.00/min
[3260000], rate=19560000.00/min
[3270000], rate=19620000.00/min
[3280000], rate=19680000.00/min
[3290000], rate=19740000.00/min
[3300000], rate=19800000.00/min
[3310000], rate=19860000.00/min
[3320000], rate=19920000.00/min
[3330000], rate=19980000.00/min
[3340000], rate=20040000.00/min
[3350000], rate=20100000.00/min
[3360000], rate=20160000.00/min
[3370000], rate=20220000.00/min
[3380000], rate=20280000.00/min
[3390000], rate=20340000.00/min
[3400000], rate=20400000.00/min
[3410000], rate=20460000.00/min
[3420000], rate=20520000.00/min
[3430000], rate=20580000.00/min
[3440000], rate=20640000.00/min
[3450000], rate=20700000.00/min
[3460000], rate=20760000.00/min
[3470000], rate=20820000.00/min
[3480000], rate=20880000.00/min
[3490000], rate=20940000.00/min
[3500000], rate=21000000.00/min
[3510000], rate=21060000.00/min
[3520000], rate=21120000.00/min
[3530000], rate=21180000.00/min
[3540000], rate=21240000.00/min
[3550000], rate=21300000.00/min
[3560000], rate=21360000.00/min
[3570000], rate=21420000.00/min
[3580000], rate=21480000.00/min
[3590000], rate=21540000.00/min
[3600000], rate=21600000.00/min
[3610000], rate=21660000.00/min
[3620000], rate=21720000.00/min
[3630000], rate=21780000.00/min
[3640000], rate=21840000.00/min
[3650000], rate=21900000.00/min
[3660000], rate=19963636.36/min
[3670000], rate=20018181.82/min
[3680000], rate=20072727.27/min
[3690000], rate=20127272.73/min
[3700000], rate=20181818.18/min
[3710000], rate=20236363.64/min
[3720000], rate=20290909.09/min
[3730000], rate=20345454.55/min
[3740000], rate=20400000.00/min
[3750000], rate=20454545.45/min
[3760000], rate=20509090.91/min
[3770000], rate=20563636.36/min
[3780000], rate=20618181.82/min
[3790000], rate=20672727.27/min
[3800000], rate=20727272.73/min
[3810000], rate=20781818.18/min
[3820000], rate=20836363.64/min
[3830000], rate=20890909.09/min
[3840000], rate=20945454.55/min
[3850000], rate=21000000.00/min
[3860000], rate=21054545.45/min
[3870000], rate=21109090.91/min
[3880000], rate=21163636.36/min
[3890000], rate=21218181.82/min
[3900000], rate=21272727.27/min
[3910000], rate=21327272.73/min
[3920000], rate=21381818.18/min
[3930000], rate=21436363.64/min
[3940000], rate=21490909.09/min
[3950000], rate=21545454.55/min
[3960000], rate=21600000.00/min
[3970000], rate=21654545.45/min
[3980000], rate=21709090.91/min
[3990000], rate=21763636.36/min
[4000000], rate=21818181.82/min
[4010000], rate=21872727.27/min
[4020000], rate=21927272.73/min
[4030000], rate=21981818.18/min
[4040000], rate=20200000.00/min
[4050000], rate=20250000.00/min
[4060000], rate=20300000.00/min
[4070000], rate=20350000.00/min
[4080000], rate=20400000.00/min
[4090000], rate=20450000.00/min
[4100000], rate=20500000.00/min
[4110000], rate=20550000.00/min
[4120000], rate=20600000.00/min
[4130000], rate=20650000.00/min
[4140000], rate=20700000.00/min
[4150000], rate=20750000.00/min
[4160000], rate=20800000.00/min
[4170000], rate=20850000.00/min
[4180000], rate=20900000.00/min
[4190000], rate=20950000.00/min
[4200000], rate=21000000.00/min
[4210000], rate=21050000.00/min
[4220000], rate=21100000.00/min
[4230000], rate=21150000.00/min
[4240000], rate=21200000.00/min
[4250000], rate=21250000.00/min
[4260000], rate=21300000.00/min
[4270000], rate=21350000.00/min
[4280000], rate=21400000.00/min
[4290000], rate=21450000.00/min
[4300000], rate=21500000.00/min
[4310000], rate=21550000.00/min
[4320000], rate=21600000.00/min
[4330000], rate=19984615.38/min
[4340000], rate=20030769.23/min
[4350000], rate=20076923.08/min
[4360000], rate=20123076.92/min
[4370000], rate=20169230.77/min
[4380000], rate=20215384.62/min
[4390000], rate=20261538.46/min
[4400000], rate=20307692.31/min
[4410000], rate=20353846.15/min
[4420000], rate=20400000.00/min
[4430000], rate=20446153.85/min
[4440000], rate=20492307.69/min
[4450000], rate=20538461.54/min
[4460000], rate=20584615.38/min
[4470000], rate=20630769.23/min
[4480000], rate=20676923.08/min
[4490000], rate=20723076.92/min
[4500000], rate=20769230.77/min
[4510000], rate=20815384.62/min
[4520000], rate=20861538.46/min
[4530000], rate=20907692.31/min
[4540000], rate=20953846.15/min
[4550000], rate=21000000.00/min
[4560000], rate=21046153.85/min
[4570000], rate=21092307.69/min
[4580000], rate=21138461.54/min
[4590000], rate=21184615.38/min
[4600000], rate=21230769.23/min
[4610000], rate=21276923.08/min
[4620000], rate=21323076.92/min
[4630000], rate=21369230.77/min
[4640000], rate=21415384.62/min
[4650000], rate=21461538.46/min
[4660000], rate=21507692.31/min
[4670000], rate=20014285.71/min
[4680000], rate=20057142.86/min
[4690000], rate=20100000.00/min
[4700000], rate=20142857.14/min
[4710000], rate=20185714.29/min
[4720000], rate=20228571.43/min
[4730000], rate=20271428.57/min
[4740000], rate=20314285.71/min
[4750000], rate=20357142.86/min
[4760000], rate=20400000.00/min
[4770000], rate=20442857.14/min
[4780000], rate=20485714.29/min
[4790000], rate=20528571.43/min
[4800000], rate=20571428.57/min
[4810000], rate=20614285.71/min
[4820000], rate=20657142.86/min
[4830000], rate=20700000.00/min
[4840000], rate=20742857.14/min
[4850000], rate=20785714.29/min
[4860000], rate=20828571.43/min
[4870000], rate=20871428.57/min
[4880000], rate=20914285.71/min
[4890000], rate=20957142.86/min
[4900000], rate=21000000.00/min
[4910000], rate=21042857.14/min
[4920000], rate=21085714.29/min
[4930000], rate=21128571.43/min
[4940000], rate=21171428.57/min
[4950000], rate=21214285.71/min
[4960000], rate=21257142.86/min
[4970000], rate=21300000.00/min
[4980000], rate=21342857.14/min
[4990000], rate=21385714.29/min
[5000000], rate=21428571.43/min
[5010000], rate=21471428.57/min
[5020000], rate=21514285.71/min
[5030000], rate=21557142.86/min
[5040000], rate=21600000.00/min
[5050000], rate=21642857.14/min
[5060000], rate=21685714.29/min
[5070000], rate=21728571.43/min
[5080000], rate=21771428.57/min
[5090000], rate=21814285.71/min
[5100000], rate=20400000.00/min
[5110000], rate=20440000.00/min
[5120000], rate=20480000.00/min
[5130000], rate=20520000.00/min
[5140000], rate=20560000.00/min
[5150000], rate=20600000.00/min
[5160000], rate=20640000.00/min
[5170000], rate=20680000.00/min
[5180000], rate=20720000.00/min
[5190000], rate=20760000.00/min
[5200000], rate=20800000.00/min
[5210000], rate=20840000.00/min
[5220000], rate=20880000.00/min
[5230000], rate=20920000.00/min
[5240000], rate=20960000.00/min
[5250000], rate=21000000.00/min
[5260000], rate=21040000.00/min
[5270000], rate=21080000.00/min
[5280000], rate=21120000.00/min
[5290000], rate=21160000.00/min
[5300000], rate=21200000.00/min
[5310000], rate=21240000.00/min
[5320000], rate=21280000.00/min
[5330000], rate=21320000.00/min
[5340000], rate=21360000.00/min
[5350000], rate=21400000.00/min
[5360000], rate=21440000.00/min
[5370000], rate=21480000.00/min
[5380000], rate=21520000.00/min
[5390000], rate=21560000.00/min
[5400000], rate=21600000.00/min
[5410000], rate=21640000.00/min
[5420000], rate=21680000.00/min
[5430000], rate=21720000.00/min
[5440000], rate=21760000.00/min
[5450000], rate=21800000.00/min
[5460000], rate=21840000.00/min
[5470000], rate=21880000.00/min
[5480000], rate=21920000.00/min
[5490000], rate=20587500.00/min
[5500000], rate=20625000.00/min
[5510000], rate=20662500.00/min
[5520000], rate=20700000.00/min
[5530000], rate=20737500.00/min
[5540000], rate=20775000.00/min
[5550000], rate=20812500.00/min
[5560000], rate=20850000.00/min
[5570000], rate=20887500.00/min
[5580000], rate=20925000.00/min
[5590000], rate=20962500.00/min
[5600000], rate=21000000.00/min
[5610000], rate=21037500.00/min
[5620000], rate=21075000.00/min
[5630000], rate=21112500.00/min
[5640000], rate=21150000.00/min
[5650000], rate=21187500.00/min
[5660000], rate=21225000.00/min
[5670000], rate=21262500.00/min
[5680000], rate=21300000.00/min
[5690000], rate=21337500.00/min
[5700000], rate=21375000.00/min
[5710000], rate=21412500.00/min
[5720000], rate=21450000.00/min
[5730000], rate=21487500.00/min
[5740000], rate=21525000.00/min
[5750000], rate=21562500.00/min
[5760000], rate=21600000.00/min
[5770000], rate=21637500.00/min
[5780000], rate=21675000.00/min
[5790000], rate=21712500.00/min
[5800000], rate=21750000.00/min
[5810000], rate=21787500.00/min
[5820000], rate=21825000.00/min
[5830000], rate=21862500.00/min
[5840000], rate=21900000.00/min
[5850000], rate=20647058.82/min
[5860000], rate=20682352.94/min
[5870000], rate=20717647.06/min
[5880000], rate=20752941.18/min
[5890000], rate=20788235.29/min
[5900000], rate=20823529.41/min
[5910000], rate=20858823.53/min
[5920000], rate=20894117.65/min
[5930000], rate=20929411.76/min
[5940000], rate=20964705.88/min
[5950000], rate=21000000.00/min
[5960000], rate=21035294.12/min
[5970000], rate=21070588.24/min
[5980000], rate=21105882.35/min
[5990000], rate=21141176.47/min
[6000000], rate=21176470.59/min
[6010000], rate=21211764.71/min
[6020000], rate=21247058.82/min
[6030000], rate=21282352.94/min
[6040000], rate=21317647.06/min
[6050000], rate=21352941.18/min
[6060000], rate=21388235.29/min
[6070000], rate=21423529.41/min
[6080000], rate=21458823.53/min
[6090000], rate=21494117.65/min
[6100000], rate=21529411.76/min
[6110000], rate=21564705.88/min
[6120000], rate=21600000.00/min
[6130000], rate=21635294.12/min
[6140000], rate=21670588.24/min
[6150000], rate=21705882.35/min
[6160000], rate=21741176.47/min
[6170000], rate=21776470.59/min
[6180000], rate=21811764.71/min
[6190000], rate=21847058.82/min
[6200000], rate=21882352.94/min
[6210000], rate=21917647.06/min
[6220000], rate=21952941.18/min
[6230000], rate=21988235.29/min
[6240000], rate=22023529.41/min
[6250000], rate=22058823.53/min
[6260000], rate=20866666.67/min
[6270000], rate=20900000.00/min
[6280000], rate=20933333.33/min
[6290000], rate=20966666.67/min
[6300000], rate=21000000.00/min
[6310000], rate=21033333.33/min
[6320000], rate=21066666.67/min
[6330000], rate=21100000.00/min
[6340000], rate=21133333.33/min
[6350000], rate=21166666.67/min
[6360000], rate=21200000.00/min
[6370000], rate=21233333.33/min
[6380000], rate=21266666.67/min
[6390000], rate=21300000.00/min
[6400000], rate=21333333.33/min
[6410000], rate=21366666.67/min
[6420000], rate=21400000.00/min
[6430000], rate=21433333.33/min
[6440000], rate=21466666.67/min
[6450000], rate=21500000.00/min
[6460000], rate=21533333.33/min
[6470000], rate=21566666.67/min
[6480000], rate=21600000.00/min
[6490000], rate=21633333.33/min
[6500000], rate=21666666.67/min
[6510000], rate=21700000.00/min
[6520000], rate=21733333.33/min
[6530000], rate=21766666.67/min
[6540000], rate=21800000.00/min
[6550000], rate=21833333.33/min
[6560000], rate=21866666.67/min
[6570000], rate=21900000.00/min
[6580000], rate=21933333.33/min
[6590000], rate=21966666.67/min
[6600000], rate=22000000.00/min
[6610000], rate=22033333.33/min
[6620000], rate=22066666.67/min
[6630000], rate=22100000.00/min
[6640000], rate=22133333.33/min
[6650000], rate=22166666.67/min
[6660000], rate=22200000.00/min
[6670000], rate=21063157.89/min
[6680000], rate=21094736.84/min
[6690000], rate=21126315.79/min
[6700000], rate=21157894.74/min
[6710000], rate=21189473.68/min
[6720000], rate=21221052.63/min
[6730000], rate=21252631.58/min
[6740000], rate=21284210.53/min
[6750000], rate=21315789.47/min
[6760000], rate=21347368.42/min
[6770000], rate=21378947.37/min
[6780000], rate=21410526.32/min
[6790000], rate=21442105.26/min
[6800000], rate=21473684.21/min
[6810000], rate=21505263.16/min
[6820000], rate=21536842.11/min
[6830000], rate=21568421.05/min
[6840000], rate=21600000.00/min
[6850000], rate=21631578.95/min
[6860000], rate=21663157.89/min
[6870000], rate=21694736.84/min
[6880000], rate=21726315.79/min
[6890000], rate=21757894.74/min
[6900000], rate=21789473.68/min
[6910000], rate=21821052.63/min
[6920000], rate=21852631.58/min
[6930000], rate=21884210.53/min
[6940000], rate=21915789.47/min
[6950000], rate=21947368.42/min
[6960000], rate=21978947.37/min
[6970000], rate=22010526.32/min
[6980000], rate=22042105.26/min
[6990000], rate=22073684.21/min
[7000000], rate=22105263.16/min
[7010000], rate=22136842.11/min
[7020000], rate=22168421.05/min
[7030000], rate=22200000.00/min
[7040000], rate=22231578.95/min
[7050000], rate=22263157.89/min
[7060000], rate=22294736.84/min
[7070000], rate=22326315.79/min
[7080000], rate=21240000.00/min
[7090000], rate=21270000.00/min
[7100000], rate=21300000.00/min
[7110000], rate=21330000.00/min
[7120000], rate=21360000.00/min
[7130000], rate=21390000.00/min
[7140000], rate=21420000.00/min
[7150000], rate=21450000.00/min
[7160000], rate=21480000.00/min
[7170000], rate=21510000.00/min
[7180000], rate=21540000.00/min
[7190000], rate=21570000.00/min
[7200000], rate=21600000.00/min
[7210000], rate=21630000.00/min
[7220000], rate=21660000.00/min
[7230000], rate=21690000.00/min
[7240000], rate=21720000.00/min
[7250000], rate=21750000.00/min
[7260000], rate=21780000.00/min
[7270000], rate=21810000.00/min
[7280000], rate=21840000.00/min 08:16:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-18a6f2-R1_B23WHYVLT4_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-18a6f2-R1_B23WHYVLT4_1.introns: identified 2898 cancer introns
08:16:56 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer.introns.prelim
08:16:56 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok
08:16:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer.introns
08:16:56 : 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-18a6f2-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer.introns
08:16:56 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok
08:16:56 : INFO : -found 1367 cancer introns
08:16:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns.for_IGV.bed
08:16:56 : INFO : Creating the BED File.
08:16:59 : INFO : Saving Bed File as aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns.for_IGV.bed
08:16:59 : INFO : Execution Time = 0.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns.for_IGV.bed
08:16:59 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok
08:16:59 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-18a6f2-R1_B23WHYVLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
08:26:00 : INFO : Execution Time = 9.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-18a6f2-R1_B23WHYVLT4_1
08:26:00 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/reads_alignments_extracted.ok
08:26:00 : INFO : Running: samtools sort -o aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer_intron_reads.bam
08:26:01 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer_intron_reads.bam
08:26:01 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/sort_cancer_intron_reads.ok
08:26:01 : INFO : Running: samtools sort -o aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.bam
[bam_sort_core] merging from 55 files and 1 in-memory blocks...
08:38:53 : INFO : Execution Time = 12.87 minutes. CMD: samtools sort -o aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.bam
08:38:53 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/sort_gene_reads.ok
08:38:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-18a6f2-R1_B23WHYVLT4_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.
08:44:44 : INFO : Execution Time = 5.85 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.bam
08:44:44 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
08:44:44 : INFO : Running: samtools sort -o aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
08:45:16 : INFO : Execution Time = 0.53 minutes. CMD: samtools sort -o aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp
08:45:16 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
08:45:16 : INFO : Running: samtools index aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam
08:45:20 : INFO : Execution Time = 0.06 minutes. CMD: samtools index aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam
08:45:20 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
08:45:20 : INFO : Running: samtools index aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam
08:45:20 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam
08:45:20 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
08:45:20 : INFO : Running: create_report aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1'
08:49:51 : INFO : Execution Time = 4.52 minutes. CMD: create_report aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1'
08:49:51 : INFO : Running: touch /tmp/nxf.X8C2qAnglf/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.chckpts/igv_create_html.ok
08:49:51 : INFO : done.