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/77/e1f3a1712b5090e567b0d600f63e33/tih_rna_sample_00588_B23MVV7LT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/51178794d9e504162fcc7282988216/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e1f3a1712b5090e567b0d600f63e33/tih_rna_sample_00588_B23MVV7LT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e1f3a1712b5090e567b0d600f63e33/tih_rna_sample_00588_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/51178794d9e504162fcc7282988216/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/2b18b9be298aa465f59ec7788ec288/tih_rna_sample_00588_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)
08:53:04 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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=31800000.00/min
[540000], rate=32400000.00/min
[550000], rate=33000000.00/min
[560000], rate=33600000.00/min
[570000], rate=34200000.00/min
[580000], rate=34800000.00/min
[590000], rate=35400000.00/min
[600000], rate=36000000.00/min
[610000], rate=36600000.00/min
[620000], rate=37200000.00/min
[630000], rate=37800000.00/min
[640000], rate=38400000.00/min
[650000], rate=39000000.00/min
[660000], rate=39600000.00/min
[670000], rate=40200000.00/min
[680000], rate=40800000.00/min
[690000], rate=41400000.00/min
[700000], rate=42000000.00/min
[710000], rate=42600000.00/min
[720000], rate=43200000.00/min
[730000], rate=43800000.00/min
[740000], rate=44400000.00/min
[750000], rate=45000000.00/min
[760000], rate=45600000.00/min
[770000], rate=46200000.00/min
[780000], rate=46800000.00/min
[790000], rate=47400000.00/min
[800000], rate=48000000.00/min
[810000], rate=24300000.00/min
[820000], rate=24600000.00/min
[830000], rate=24900000.00/min
[840000], rate=25200000.00/min
[850000], rate=25500000.00/min
[860000], rate=25800000.00/min
[870000], rate=26100000.00/min
[880000], rate=26400000.00/min
[890000], rate=26700000.00/min
[900000], rate=27000000.00/min
[910000], rate=27300000.00/min
[920000], rate=27600000.00/min
[930000], rate=27900000.00/min
[940000], rate=28200000.00/min
[950000], rate=28500000.00/min
[960000], rate=28800000.00/min
[970000], rate=29100000.00/min
[980000], rate=29400000.00/min
[990000], rate=29700000.00/min
[1000000], rate=30000000.00/min
[1010000], rate=30300000.00/min
[1020000], rate=30600000.00/min
[1030000], rate=30900000.00/min
[1040000], rate=31200000.00/min
[1050000], rate=31500000.00/min
[1060000], rate=31800000.00/min
[1070000], rate=32100000.00/min
[1080000], rate=32400000.00/min
[1090000], rate=32700000.00/min
[1100000], rate=33000000.00/min
[1110000], rate=33300000.00/min
[1120000], rate=33600000.00/min
[1130000], rate=33900000.00/min
[1140000], rate=34200000.00/min
[1150000], rate=34500000.00/min
[1160000], rate=34800000.00/min
[1170000], rate=35100000.00/min
[1180000], rate=35400000.00/min
[1190000], rate=35700000.00/min
[1200000], rate=36000000.00/min
[1210000], rate=36300000.00/min
[1220000], rate=24400000.00/min
[1230000], rate=24600000.00/min
[1240000], rate=24800000.00/min
[1250000], rate=25000000.00/min
[1260000], rate=25200000.00/min
[1270000], rate=25400000.00/min
[1280000], rate=25600000.00/min
[1290000], rate=25800000.00/min
[1300000], rate=26000000.00/min
[1310000], rate=26200000.00/min
[1320000], rate=26400000.00/min
[1330000], rate=26600000.00/min
[1340000], rate=26800000.00/min
[1350000], rate=27000000.00/min
[1360000], rate=27200000.00/min
[1370000], rate=27400000.00/min
[1380000], rate=27600000.00/min
[1390000], rate=27800000.00/min
[1400000], rate=28000000.00/min
[1410000], rate=28200000.00/min
[1420000], rate=28400000.00/min
[1430000], rate=28600000.00/min
[1440000], rate=28800000.00/min
[1450000], rate=29000000.00/min
[1460000], rate=29200000.00/min
[1470000], rate=29400000.00/min
[1480000], rate=29600000.00/min
[1490000], rate=29800000.00/min
[1500000], rate=30000000.00/min
[1510000], rate=30200000.00/min
[1520000], rate=30400000.00/min
[1530000], rate=30600000.00/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=24750000.00/min
[1660000], rate=24900000.00/min
[1670000], rate=25050000.00/min
[1680000], rate=25200000.00/min
[1690000], rate=25350000.00/min
[1700000], rate=25500000.00/min
[1710000], rate=25650000.00/min
[1720000], rate=25800000.00/min
[1730000], rate=25950000.00/min
[1740000], rate=26100000.00/min
[1750000], rate=26250000.00/min
[1760000], rate=26400000.00/min
[1770000], rate=26550000.00/min
[1780000], rate=26700000.00/min
[1790000], rate=26850000.00/min
[1800000], rate=27000000.00/min
[1810000], rate=27150000.00/min
[1820000], rate=27300000.00/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=23520000.00/min
[1970000], rate=23640000.00/min
[1980000], rate=23760000.00/min
[1990000], rate=23880000.00/min
[2000000], rate=24000000.00/min
[2010000], rate=24120000.00/min
[2020000], rate=24240000.00/min
[2030000], rate=24360000.00/min
[2040000], rate=24480000.00/min
[2050000], rate=24600000.00/min
[2060000], rate=24720000.00/min
[2070000], rate=24840000.00/min
[2080000], rate=24960000.00/min
[2090000], rate=25080000.00/min
[2100000], rate=25200000.00/min
[2110000], rate=25320000.00/min
[2120000], rate=25440000.00/min
[2130000], rate=25560000.00/min
[2140000], rate=25680000.00/min
[2150000], rate=25800000.00/min
[2160000], rate=21600000.00/min
[2170000], rate=21700000.00/min
[2180000], rate=21800000.00/min
[2190000], rate=21900000.00/min
[2200000], rate=22000000.00/min
[2210000], rate=22100000.00/min
[2220000], rate=22200000.00/min
[2230000], rate=22300000.00/min
[2240000], rate=22400000.00/min
[2250000], rate=22500000.00/min
[2260000], rate=22600000.00/min
[2270000], rate=22700000.00/min
[2280000], rate=22800000.00/min
[2290000], rate=22900000.00/min
[2300000], rate=23000000.00/min
[2310000], rate=23100000.00/min
[2320000], rate=23200000.00/min
[2330000], rate=23300000.00/min
[2340000], rate=23400000.00/min
[2350000], rate=23500000.00/min
[2360000], rate=23600000.00/min
[2370000], rate=23700000.00/min
[2380000], rate=23800000.00/min
[2390000], rate=23900000.00/min
[2400000], rate=24000000.00/min
[2410000], rate=24100000.00/min
[2420000], rate=24200000.00/min
[2430000], rate=24300000.00/min
[2440000], rate=24400000.00/min
[2450000], rate=24500000.00/min
[2460000], rate=24600000.00/min
[2470000], rate=24700000.00/min
[2480000], rate=24800000.00/min
[2490000], rate=24900000.00/min
[2500000], rate=25000000.00/min
[2510000], rate=21514285.71/min
[2520000], rate=21600000.00/min
[2530000], rate=21685714.29/min
[2540000], rate=21771428.57/min
[2550000], rate=21857142.86/min
[2560000], rate=21942857.14/min
[2570000], rate=22028571.43/min
[2580000], rate=22114285.71/min
[2590000], rate=22200000.00/min
[2600000], rate=22285714.29/min
[2610000], rate=22371428.57/min
[2620000], rate=22457142.86/min
[2630000], rate=22542857.14/min
[2640000], rate=22628571.43/min
[2650000], rate=22714285.71/min
[2660000], rate=22800000.00/min
[2670000], rate=22885714.29/min
[2680000], rate=22971428.57/min
[2690000], rate=23057142.86/min
[2700000], rate=23142857.14/min
[2710000], rate=23228571.43/min
[2720000], rate=23314285.71/min
[2730000], rate=23400000.00/min
[2740000], rate=23485714.29/min
[2750000], rate=23571428.57/min
[2760000], rate=23657142.86/min
[2770000], rate=23742857.14/min
[2780000], rate=23828571.43/min
[2790000], rate=23914285.71/min
[2800000], rate=24000000.00/min
[2810000], rate=24085714.29/min
[2820000], rate=24171428.57/min
[2830000], rate=21225000.00/min
[2840000], rate=21300000.00/min
[2850000], rate=21375000.00/min
[2860000], rate=21450000.00/min
[2870000], rate=21525000.00/min
[2880000], rate=21600000.00/min
[2890000], rate=21675000.00/min
[2900000], rate=21750000.00/min
[2910000], rate=21825000.00/min
[2920000], rate=21900000.00/min
[2930000], rate=21975000.00/min
[2940000], rate=22050000.00/min
[2950000], rate=22125000.00/min
[2960000], rate=22200000.00/min
[2970000], rate=22275000.00/min
[2980000], rate=22350000.00/min
[2990000], rate=22425000.00/min
[3000000], rate=22500000.00/min
[3010000], rate=22575000.00/min
[3020000], rate=22650000.00/min
[3030000], rate=22725000.00/min
[3040000], rate=22800000.00/min
[3050000], rate=22875000.00/min
[3060000], rate=22950000.00/min
[3070000], rate=23025000.00/min
[3080000], rate=23100000.00/min
[3090000], rate=23175000.00/min
[3100000], rate=23250000.00/min
[3110000], rate=23325000.00/min
[3120000], rate=23400000.00/min
[3130000], rate=23475000.00/min
[3140000], rate=23550000.00/min
[3150000], rate=23625000.00/min
[3160000], rate=23700000.00/min
[3170000], rate=23775000.00/min
[3180000], rate=23850000.00/min
[3190000], rate=21266666.67/min
[3200000], rate=21333333.33/min
[3210000], rate=21400000.00/min
[3220000], rate=21466666.67/min
[3230000], rate=21533333.33/min
[3240000], rate=21600000.00/min
[3250000], rate=21666666.67/min
[3260000], rate=21733333.33/min
[3270000], rate=21800000.00/min
[3280000], rate=21866666.67/min
[3290000], rate=21933333.33/min
[3300000], rate=22000000.00/min
[3310000], rate=22066666.67/min
[3320000], rate=22133333.33/min
[3330000], rate=22200000.00/min
[3340000], rate=22266666.67/min
[3350000], rate=22333333.33/min
[3360000], rate=22400000.00/min
[3370000], rate=22466666.67/min
[3380000], rate=22533333.33/min
[3390000], rate=22600000.00/min
[3400000], rate=22666666.67/min
[3410000], rate=22733333.33/min
[3420000], rate=22800000.00/min
[3430000], rate=22866666.67/min
[3440000], rate=22933333.33/min
[3450000], rate=23000000.00/min
[3460000], rate=23066666.67/min
[3470000], rate=23133333.33/min
[3480000], rate=23200000.00/min
[3490000], rate=23266666.67/min
[3500000], rate=23333333.33/min
[3510000], rate=23400000.00/min
[3520000], rate=23466666.67/min
[3530000], rate=23533333.33/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=21960000.00/min
[3670000], rate=22020000.00/min
[3680000], rate=22080000.00/min
[3690000], rate=22140000.00/min
[3700000], rate=22200000.00/min
[3710000], rate=22260000.00/min
[3720000], rate=22320000.00/min
[3730000], rate=22380000.00/min
[3740000], rate=22440000.00/min
[3750000], rate=22500000.00/min
[3760000], rate=22560000.00/min
[3770000], rate=22620000.00/min
[3780000], rate=22680000.00/min
[3790000], rate=22740000.00/min
[3800000], rate=22800000.00/min
[3810000], rate=22860000.00/min
[3820000], rate=22920000.00/min
[3830000], rate=22980000.00/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=22036363.64/min
[4050000], rate=22090909.09/min
[4060000], rate=22145454.55/min
[4070000], rate=22200000.00/min
[4080000], rate=22254545.45/min
[4090000], rate=22309090.91/min
[4100000], rate=22363636.36/min
[4110000], rate=22418181.82/min
[4120000], rate=22472727.27/min
[4130000], rate=22527272.73/min
[4140000], rate=22581818.18/min
[4150000], rate=22636363.64/min
[4160000], rate=22690909.09/min
[4170000], rate=22745454.55/min
[4180000], rate=22800000.00/min
[4190000], rate=22854545.45/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=21650000.00/min
[4340000], rate=21700000.00/min
[4350000], rate=21750000.00/min
[4360000], rate=21800000.00/min
[4370000], rate=21850000.00/min
[4380000], rate=21900000.00/min
[4390000], rate=21950000.00/min
[4400000], rate=22000000.00/min
[4410000], rate=22050000.00/min
[4420000], rate=22100000.00/min
[4430000], rate=22150000.00/min
[4440000], rate=22200000.00/min
[4450000], rate=22250000.00/min
[4460000], rate=22300000.00/min
[4470000], rate=22350000.00/min
[4480000], rate=22400000.00/min
[4490000], rate=22450000.00/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=21553846.15/min
[4680000], rate=21600000.00/min
[4690000], rate=21646153.85/min
[4700000], rate=21692307.69/min
[4710000], rate=21738461.54/min
[4720000], rate=21784615.38/min
[4730000], rate=21830769.23/min
[4740000], rate=21876923.08/min
[4750000], rate=21923076.92/min
[4760000], rate=21969230.77/min
[4770000], rate=22015384.62/min
[4780000], rate=22061538.46/min
[4790000], rate=22107692.31/min
[4800000], rate=22153846.15/min
[4810000], rate=22200000.00/min
[4820000], rate=22246153.85/min
[4830000], rate=22292307.69/min
[4840000], rate=22338461.54/min
[4850000], rate=22384615.38/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=21857142.86/min
[5110000], rate=21900000.00/min
[5120000], rate=21942857.14/min
[5130000], rate=21985714.29/min
[5140000], rate=22028571.43/min
[5150000], rate=22071428.57/min
[5160000], rate=22114285.71/min
[5170000], rate=22157142.86/min
[5180000], rate=22200000.00/min
[5190000], rate=22242857.14/min
[5200000], rate=22285714.29/min
[5210000], rate=22328571.43/min
[5220000], rate=22371428.57/min
[5230000], rate=22414285.71/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=21960000.00/min
[5500000], rate=22000000.00/min
[5510000], rate=22040000.00/min
[5520000], rate=22080000.00/min
[5530000], rate=22120000.00/min
[5540000], rate=22160000.00/min
[5550000], rate=22200000.00/min
[5560000], rate=22240000.00/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=21937500.00/min
[5860000], rate=21975000.00/min
[5870000], rate=22012500.00/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=20833333.33/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=20589473.68/min
[6530000], rate=20621052.63/min
[6540000], rate=20652631.58/min
[6550000], rate=20684210.53/min
[6560000], rate=20715789.47/min
[6570000], rate=20747368.42/min
[6580000], rate=20778947.37/min
[6590000], rate=20810526.32/min
[6600000], rate=20842105.26/min
[6610000], rate=20873684.21/min
[6620000], rate=20905263.16/min
[6630000], rate=20936842.11/min
[6640000], rate=20968421.05/min
[6650000], rate=21000000.00/min
[6660000], rate=21031578.95/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=20340000.00/min
[6790000], rate=20370000.00/min
[6800000], rate=20400000.00/min
[6810000], rate=20430000.00/min
[6820000], rate=20460000.00/min
[6830000], rate=20490000.00/min
[6840000], rate=20520000.00/min
[6850000], rate=20550000.00/min
[6860000], rate=20580000.00/min
[6870000], rate=20610000.00/min
[6880000], rate=20640000.00/min
[6890000], rate=20670000.00/min
[6900000], rate=20700000.00/min
[6910000], rate=20730000.00/min
[6920000], rate=20760000.00/min
[6930000], rate=20790000.00/min
[6940000], rate=20820000.00/min
[6950000], rate=20850000.00/min
[6960000], rate=20880000.00/min
[6970000], rate=20910000.00/min
[6980000], rate=20940000.00/min
[6990000], rate=20970000.00/min
[7000000], rate=21000000.00/min
[7010000], rate=21030000.00/min
[7020000], rate=21060000.00/min
[7030000], rate=21090000.00/min
[7040000], rate=21120000.00/min
[7050000], rate=21150000.00/min
[7060000], rate=21180000.00/min
[7070000], rate=21210000.00/min
[7080000], rate=21240000.00/min
[7090000], rate=21270000.00/min
[7100000], rate=20285714.29/min
[7110000], rate=20314285.71/min
[7120000], rate=20342857.14/min
[7130000], rate=20371428.57/min
[7140000], rate=20400000.00/min
[7150000], rate=20428571.43/min
[7160000], rate=20457142.86/min
[7170000], rate=20485714.29/min
[7180000], rate=20514285.71/min
[7190000], rate=20542857.14/min
[7200000], rate=20571428.57/min
[7210000], rate=20600000.00/min
[7220000], rate=20628571.43/min
[7230000], rate=20657142.86/min
[7240000], rate=20685714.29/min
[7250000], rate=20714285.71/min
[7260000], rate=20742857.14/min
[7270000], rate=20771428.57/min
[7280000], rate=20800000.00/min
[7290000], rate=20828571.43/min
[7300000], rate=20857142.86/min
[7310000], rate=20885714.29/min
[7320000], rate=20914285.71/min
[7330000], rate=20942857.14/min
[7340000], rate=20971428.57/min
[7350000], rate=21000000.00/min
[7360000], rate=21028571.43/min
[7370000], rate=21057142.86/min
[7380000], rate=21085714.29/min
[7390000], rate=21114285.71/min
[7400000], rate=21142857.14/min
[7410000], rate=21171428.57/min
[7420000], rate=21200000.00/min
[7430000], rate=21228571.43/min
[7440000], rate=21257142.86/min
[7450000], rate=21285714.29/min
[7460000], rate=21314285.71/min
[7470000], rate=21342857.14/min
[7480000], rate=21371428.57/min
[7490000], rate=21400000.00/min
[7500000], rate=21428571.43/min
[7510000], rate=21457142.86/min
[7520000], rate=21485714.29/min
[7530000], rate=20536363.64/min
[7540000], rate=20563636.36/min
[7550000], rate=20590909.09/min
[7560000], rate=20618181.82/min
[7570000], rate=20645454.55/min
[7580000], rate=20672727.27/min
[7590000], rate=20700000.00/min
[7600000], rate=20727272.73/min
[7610000], rate=20754545.45/min
[7620000], rate=20781818.18/min
[7630000], rate=20809090.91/min
[7640000], rate=20836363.64/min
[7650000], rate=20863636.36/min
[7660000], rate=20890909.09/min
[7670000], rate=20918181.82/min
[7680000], rate=20945454.55/min
[7690000], rate=20972727.27/min
[7700000], rate=21000000.00/min
[7710000], rate=21027272.73/min
[7720000], rate=21054545.45/min
[7730000], rate=21081818.18/min
[7740000], rate=21109090.91/min
[7750000], rate=21136363.64/min
[7760000], rate=21163636.36/min
[7770000], rate=21190909.09/min
[7780000], rate=21218181.82/min
[7790000], rate=21245454.55/min
[7800000], rate=21272727.27/min
[7810000], rate=21300000.00/min
[7820000], rate=21327272.73/min
[7830000], rate=21354545.45/min
[7840000], rate=21381818.18/min
[7850000], rate=21409090.91/min
[7860000], rate=21436363.64/min
[7870000], rate=21463636.36/min
[7880000], rate=21490909.09/min
[7890000], rate=21518181.82/min
[7900000], rate=21545454.55/min
[7910000], rate=21572727.27/min
[7920000], rate=21600000.00/min
[7930000], rate=21627272.73/min
[7940000], rate=20713043.48/min
[7950000], rate=20739130.43/min
[7960000], rate=20765217.39/min
[7970000], rate=20791304.35/min
[7980000], rate=20817391.30/min
[7990000], rate=20843478.26/min
[8000000], rate=20869565.22/min
[8010000], rate=20895652.17/min
[8020000], rate=20921739.13/min
[8030000], rate=20947826.09/min
[8040000], rate=20973913.04/min
[8050000], rate=21000000.00/min
[8060000], rate=21026086.96/min
[8070000], rate=21052173.91/min
[8080000], rate=21078260.87/min
[8090000], rate=21104347.83/min
[8100000], rate=21130434.78/min
[8110000], rate=21156521.74/min
[8120000], rate=21182608.70/min
[8130000], rate=21208695.65/min
[8140000], rate=21234782.61/min
[8150000], rate=21260869.57/min
[8160000], rate=21286956.52/min
[8170000], rate=21313043.48/min
[8180000], rate=21339130.43/min
[8190000], rate=21365217.39/min
[8200000], rate=21391304.35/min
[8210000], rate=21417391.30/min
[8220000], rate=21443478.26/min
[8230000], rate=21469565.22/min
[8240000], rate=21495652.17/min
[8250000], rate=21521739.13/min
[8260000], rate=21547826.09/min
[8270000], rate=21573913.04/min
[8280000], rate=20700000.00/min
[8290000], rate=20725000.00/min
[8300000], rate=20750000.00/min
[8310000], rate=20775000.00/min
[8320000], rate=20800000.00/min
[8330000], rate=20825000.00/min
[8340000], rate=20850000.00/min
[8350000], rate=20875000.00/min
[8360000], rate=20900000.00/min
[8370000], rate=20925000.00/min
[8380000], rate=20950000.00/min
[8390000], rate=20975000.00/min
[8400000], rate=21000000.00/min
[8410000], rate=21025000.00/min
[8420000], rate=21050000.00/min
[8430000], rate=21075000.00/min
[8440000], rate=21100000.00/min
[8450000], rate=21125000.00/min
[8460000], rate=21150000.00/min
[8470000], rate=21175000.00/min
[8480000], rate=21200000.00/min
[8490000], rate=21225000.00/min
[8500000], rate=21250000.00/min
[8510000], rate=21275000.00/min
[8520000], rate=21300000.00/min
[8530000], rate=21325000.00/min
[8540000], rate=21350000.00/min
[8550000], rate=21375000.00/min
[8560000], rate=20544000.00/min
[8570000], rate=20568000.00/min
[8580000], rate=20592000.00/min
[8590000], rate=20616000.00/min
[8600000], rate=20640000.00/min
[8610000], rate=20664000.00/min
[8620000], rate=20688000.00/min
[8630000], rate=20712000.00/min
[8640000], rate=20736000.00/min
[8650000], rate=20760000.00/min
[8660000], rate=20784000.00/min
[8670000], rate=20808000.00/min
[8680000], rate=20832000.00/min
[8690000], rate=20856000.00/min
[8700000], rate=20880000.00/min
[8710000], rate=20904000.00/min
[8720000], rate=20928000.00/min
[8730000], rate=20952000.00/min
[8740000], rate=20976000.00/min
[8750000], rate=21000000.00/min
[8760000], rate=21024000.00/min
[8770000], rate=21048000.00/min
[8780000], rate=21072000.00/min
[8790000], rate=21096000.00/min
[8800000], rate=21120000.00/min
[8810000], rate=21144000.00/min
[8820000], rate=21168000.00/min
[8830000], rate=21192000.00/min
[8840000], rate=21216000.00/min
[8850000], rate=21240000.00/min
[8860000], rate=21264000.00/min
[8870000], rate=21288000.00/min
[8880000], rate=21312000.00/min
[8890000], rate=21336000.00/min
[8900000], rate=21360000.00/min
[8910000], rate=21384000.00/min
[8920000], rate=20584615.38/min
[8930000], rate=20607692.31/min
[8940000], rate=20630769.23/min
[8950000], rate=20653846.15/min
[8960000], rate=20676923.08/min
[8970000], rate=20700000.00/min
[8980000], rate=20723076.92/min
[8990000], rate=20746153.85/min
[9000000], rate=20769230.77/min
[9010000], rate=20792307.69/min
[9020000], rate=20815384.62/min
[9030000], rate=20838461.54/min
[9040000], rate=20861538.46/min
[9050000], rate=20884615.38/min
[9060000], rate=20907692.31/min
[9070000], rate=20930769.23/min
[9080000], rate=20953846.15/min
[9090000], rate=20976923.08/min
[9100000], rate=21000000.00/min
[9110000], rate=21023076.92/min
[9120000], rate=21046153.85/min
[9130000], rate=21069230.77/min
[9140000], rate=21092307.69/min
[9150000], rate=21115384.62/min
[9160000], rate=21138461.54/min
[9170000], rate=21161538.46/min
[9180000], rate=21184615.38/min
[9190000], rate=21207692.31/min
[9200000], rate=21230769.23/min
[9210000], rate=21253846.15/min
[9220000], rate=21276923.08/min
[9230000], rate=21300000.00/min
[9240000], rate=21323076.92/min
[9250000], rate=21346153.85/min
[9260000], rate=21369230.77/min
[9270000], rate=21392307.69/min
[9280000], rate=21415384.62/min
[9290000], rate=20644444.44/min
[9300000], rate=20666666.67/min
[9310000], rate=20688888.89/min
[9320000], rate=20711111.11/min
[9330000], rate=20733333.33/min
[9340000], rate=20755555.56/min
[9350000], rate=20777777.78/min
[9360000], rate=20800000.00/min
[9370000], rate=20822222.22/min
[9380000], rate=20844444.44/min
[9390000], rate=20866666.67/min
[9400000], rate=20888888.89/min
[9410000], rate=20911111.11/min
[9420000], rate=20933333.33/min
[9430000], rate=20955555.56/min
[9440000], rate=20977777.78/min
[9450000], rate=21000000.00/min
[9460000], rate=21022222.22/min
[9470000], rate=21044444.44/min
[9480000], rate=21066666.67/min
[9490000], rate=21088888.89/min
[9500000], rate=21111111.11/min
[9510000], rate=21133333.33/min
[9520000], rate=21155555.56/min
[9530000], rate=21177777.78/min
[9540000], rate=21200000.00/min
[9550000], rate=21222222.22/min
[9560000], rate=21244444.44/min
[9570000], rate=21266666.67/min
[9580000], rate=21288888.89/min
[9590000], rate=21311111.11/min
[9600000], rate=21333333.33/min
[9610000], rate=21355555.56/min
[9620000], rate=21377777.78/min
[9630000], rate=21400000.00/min
[9640000], rate=21422222.22/min
[9650000], rate=21444444.44/min
[9660000], rate=20700000.00/min
[9670000], rate=20721428.57/min
[9680000], rate=20742857.14/min
[9690000], rate=20764285.71/min
[9700000], rate=20785714.29/min
[9710000], rate=20807142.86/min
[9720000], rate=20828571.43/min
[9730000], rate=20850000.00/min
[9740000], rate=20871428.57/min
[9750000], rate=20892857.14/min
[9760000], rate=20914285.71/min
[9770000], rate=20935714.29/min
[9780000], rate=20957142.86/min
[9790000], rate=20978571.43/min
[9800000], rate=21000000.00/min
[9810000], rate=21021428.57/min
[9820000], rate=21042857.14/min
[9830000], rate=21064285.71/min
[9840000], rate=21085714.29/min
[9850000], rate=21107142.86/min
[9860000], rate=21128571.43/min
[9870000], rate=21150000.00/min
[9880000], rate=21171428.57/min
[9890000], rate=21192857.14/min
[9900000], rate=21214285.71/min
[9910000], rate=21235714.29/min
[9920000], rate=21257142.86/min
[9930000], rate=21278571.43/min
[9940000], rate=21300000.00/min
[9950000], rate=21321428.57/min
[9960000], rate=21342857.14/min
[9970000], rate=21364285.71/min
[9980000], rate=21385714.29/min
[9990000], rate=21407142.86/min
[10000000], rate=21428571.43/min
[10010000], rate=21450000.00/min
[10020000], rate=20731034.48/min
[10030000], rate=20751724.14/min
[10040000], rate=20772413.79/min
[10050000], rate=20793103.45/min
[10060000], rate=20813793.10/min
[10070000], rate=20834482.76/min
[10080000], rate=20855172.41/min
[10090000], rate=20875862.07/min
[10100000], rate=20896551.72/min
[10110000], rate=20917241.38/min
[10120000], rate=20937931.03/min
[10130000], rate=20958620.69/min
[10140000], rate=20979310.34/min
[10150000], rate=21000000.00/min
[10160000], rate=21020689.66/min
[10170000], rate=21041379.31/min
[10180000], rate=21062068.97/min
[10190000], rate=21082758.62/min
[10200000], rate=21103448.28/min
[10210000], rate=21124137.93/min
[10220000], rate=21144827.59/min
[10230000], rate=21165517.24/min
[10240000], rate=21186206.90/min
[10250000], rate=21206896.55/min
[10260000], rate=21227586.21/min
[10270000], rate=21248275.86/min
[10280000], rate=21268965.52/min
[10290000], rate=21289655.17/min
[10300000], rate=21310344.83/min
[10310000], rate=21331034.48/min
[10320000], rate=21351724.14/min
[10330000], rate=21372413.79/min
[10340000], rate=21393103.45/min
[10350000], rate=21413793.10/min
[10360000], rate=20720000.00/min
[10370000], rate=20740000.00/min
[10380000], rate=20760000.00/min
[10390000], rate=20780000.00/min
[10400000], rate=20800000.00/min
[10410000], rate=20820000.00/min
[10420000], rate=20840000.00/min
[10430000], rate=20860000.00/min
[10440000], rate=20880000.00/min
[10450000], rate=20900000.00/min
[10460000], rate=20920000.00/min
[10470000], rate=20940000.00/min
[10480000], rate=20960000.00/min
[10490000], rate=20980000.00/min
[10500000], rate=21000000.00/min
[10510000], rate=21020000.00/min
[10520000], rate=21040000.00/min
[10530000], rate=21060000.00/min
[10540000], rate=21080000.00/min
[10550000], rate=21100000.00/min
[10560000], rate=21120000.00/min
[10570000], rate=21140000.00/min
[10580000], rate=21160000.00/min
[10590000], rate=21180000.00/min
[10600000], rate=21200000.00/min
[10610000], rate=21220000.00/min
[10620000], rate=21240000.00/min
[10630000], rate=21260000.00/min
[10640000], rate=21280000.00/min
[10650000], rate=21300000.00/min
[10660000], rate=21320000.00/min
[10670000], rate=21340000.00/min
[10680000], rate=21360000.00/min
[10690000], rate=21380000.00/min
[10700000], rate=20709677.42/min
[10710000], rate=20729032.26/min
[10720000], rate=20748387.10/min
[10730000], rate=20767741.94/min
[10740000], rate=20787096.77/min
[10750000], rate=20806451.61/min
[10760000], rate=20825806.45/min
[10770000], rate=20845161.29/min
[10780000], rate=20864516.13/min
[10790000], rate=20883870.97/min
[10800000], rate=20903225.81/min
[10810000], rate=20922580.65/min
[10820000], rate=20941935.48/min
[10830000], rate=20961290.32/min
[10840000], rate=20980645.16/min
[10850000], rate=21000000.00/min
[10860000], rate=21019354.84/min
[10870000], rate=21038709.68/min
[10880000], rate=21058064.52/min
[10890000], rate=21077419.35/min
[10900000], rate=21096774.19/min
[10910000], rate=21116129.03/min
[10920000], rate=21135483.87/min
[10930000], rate=21154838.71/min
[10940000], rate=21174193.55/min
[10950000], rate=21193548.39/min
[10960000], rate=20550000.00/min
[10970000], rate=20568750.00/min
[10980000], rate=20587500.00/min
[10990000], rate=20606250.00/min
[11000000], rate=20625000.00/min
[11010000], rate=20643750.00/min
[11020000], rate=20662500.00/min
[11030000], rate=20681250.00/min
[11040000], rate=20700000.00/min
[11050000], rate=20718750.00/min
[11060000], rate=20737500.00/min
[11070000], rate=20756250.00/min
[11080000], rate=20775000.00/min
[11090000], rate=20793750.00/min
[11100000], rate=20812500.00/min
[11110000], rate=20831250.00/min
[11120000], rate=20850000.00/min
[11130000], rate=20868750.00/min
[11140000], rate=20887500.00/min
[11150000], rate=20906250.00/min
[11160000], rate=20925000.00/min
[11170000], rate=20943750.00/min
[11180000], rate=20962500.00/min
[11190000], rate=20981250.00/min
[11200000], rate=21000000.00/min
[11210000], rate=21018750.00/min
[11220000], rate=20400000.00/min
[11230000], rate=20418181.82/min
[11240000], rate=20436363.64/min
[11250000], rate=20454545.45/min
[11260000], rate=20472727.27/min
[11270000], rate=20490909.09/min
[11280000], rate=20509090.91/min
[11290000], rate=20527272.73/min 08:53:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00588_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00588_B23MVV7LT4_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.
-tih_rna_sample_00588_B23MVV7LT4_1.introns: identified 7207 cancer introns
08:53:46 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00588_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00588_B23MVV7LT4_1.cancer.introns.prelim
08:53:46 : INFO : Running: touch /tmp/nxf.AUPBSbDgvc/tih_rna_sample_00588_B23MVV7LT4_1.chckpts/prelim_introns.ok
08:53:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00588_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00588_B23MVV7LT4_1.cancer.introns
08:53:47 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00588_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00588_B23MVV7LT4_1.cancer.introns
08:53:47 : INFO : Running: touch /tmp/nxf.AUPBSbDgvc/tih_rna_sample_00588_B23MVV7LT4_1.chckpts/introns_filtered.ok
08:53:47 : INFO : -found 2817 cancer introns
08:53:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00588_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00588_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00588_B23MVV7LT4_1.introns.for_IGV.bed
08:53:47 : INFO : Creating the BED File.
08:53:52 : INFO : Saving Bed File as tih_rna_sample_00588_B23MVV7LT4_1.introns.for_IGV.bed
08:53:52 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00588_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00588_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00588_B23MVV7LT4_1.introns.for_IGV.bed
08:53:52 : INFO : Running: touch /tmp/nxf.AUPBSbDgvc/tih_rna_sample_00588_B23MVV7LT4_1.chckpts/intron_igv_bed.ok
08:53:52 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00588_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00588_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00588_B23MVV7LT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
09:10:16 : INFO : Execution Time = 16.40 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00588_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00588_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00588_B23MVV7LT4_1
09:10:16 : INFO : Running: touch /tmp/nxf.AUPBSbDgvc/tih_rna_sample_00588_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok
09:10:16 : INFO : Running: samtools sort -o tih_rna_sample_00588_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00588_B23MVV7LT4_1.cancer_intron_reads.bam
09:10:17 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00588_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00588_B23MVV7LT4_1.cancer_intron_reads.bam
09:10:17 : INFO : Running: touch /tmp/nxf.AUPBSbDgvc/tih_rna_sample_00588_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok
09:10:17 : INFO : Running: samtools sort -o tih_rna_sample_00588_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00588_B23MVV7LT4_1.gene_reads.bam