Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/c3ca5c8022779ac9e9522eacf50a0f/659_cTi-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/c3ca5c8022779ac9e9522eacf50a0f/659_cTi-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/cfe6745981c23a1f520d998a16adb9/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/cfe6745981c23a1f520d998a16adb9/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/c3ca5c8022779ac9e9522eacf50a0f/659_cTi-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/ae87de345fdc8a0c4f903121810bb0/659_cTi-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai ==> STAGING COMPLETE (7 inputs) 08:45:26 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=11700000.00/min [400000], rate=12000000.00/min [410000], rate=12300000.00/min [420000], rate=12600000.00/min [430000], rate=12900000.00/min [440000], rate=13200000.00/min [450000], rate=13500000.00/min [460000], rate=13800000.00/min [470000], rate=14100000.00/min [480000], rate=14400000.00/min [490000], rate=14700000.00/min [500000], rate=15000000.00/min [510000], rate=15300000.00/min [520000], rate=15600000.00/min [530000], rate=15900000.00/min [540000], rate=10800000.00/min [550000], rate=11000000.00/min [560000], rate=11200000.00/min [570000], rate=11400000.00/min [580000], rate=11600000.00/min [590000], rate=11800000.00/min [600000], rate=12000000.00/min [610000], rate=12200000.00/min [620000], rate=12400000.00/min [630000], rate=12600000.00/min [640000], rate=12800000.00/min [650000], rate=13000000.00/min [660000], rate=13200000.00/min [670000], rate=10050000.00/min [680000], rate=10200000.00/min [690000], rate=10350000.00/min [700000], rate=10500000.00/min [710000], rate=10650000.00/min [720000], rate=10800000.00/min [730000], rate=10950000.00/min [740000], rate=11100000.00/min [750000], rate=11250000.00/min [760000], rate=11400000.00/min [770000], rate=11550000.00/min [780000], rate=9360000.00/min [790000], rate=9480000.00/min [800000], rate=9600000.00/min [810000], rate=9720000.00/min [820000], rate=9840000.00/min [830000], rate=9960000.00/min [840000], rate=10080000.00/min [850000], rate=10200000.00/min [860000], rate=10320000.00/min [870000], rate=10440000.00/min [880000], rate=10560000.00/min [890000], rate=8900000.00/min [900000], rate=9000000.00/min [910000], rate=9100000.00/min [920000], rate=9200000.00/min [930000], rate=9300000.00/min [940000], rate=9400000.00/min [950000], rate=9500000.00/min [960000], rate=9600000.00/min [970000], rate=9700000.00/min [980000], rate=9800000.00/min [990000], rate=8485714.29/min [1000000], rate=8571428.57/min [1010000], rate=8657142.86/min [1020000], rate=8742857.14/min [1030000], rate=8828571.43/min [1040000], rate=8914285.71/min [1050000], rate=9000000.00/min [1060000], rate=9085714.29/min [1070000], rate=9171428.57/min [1080000], rate=9257142.86/min [1090000], rate=9342857.14/min [1100000], rate=8250000.00/min [1110000], rate=8325000.00/min [1120000], rate=8400000.00/min [1130000], rate=8475000.00/min [1140000], rate=8550000.00/min [1150000], rate=8625000.00/min [1160000], rate=8700000.00/min [1170000], rate=8775000.00/min [1180000], rate=8850000.00/min [1190000], rate=8925000.00/min [1200000], rate=9000000.00/min [1210000], rate=9075000.00/min [1220000], rate=8133333.33/min [1230000], rate=8200000.00/min [1240000], rate=8266666.67/min [1250000], rate=8333333.33/min [1260000], rate=8400000.00/min [1270000], rate=8466666.67/min [1280000], rate=8533333.33/min [1290000], rate=8600000.00/min [1300000], rate=8666666.67/min [1310000], rate=8733333.33/min [1320000], rate=8800000.00/min [1330000], rate=7980000.00/min [1340000], rate=8040000.00/min [1350000], rate=8100000.00/min [1360000], rate=8160000.00/min [1370000], rate=8220000.00/min [1380000], rate=8280000.00/min [1390000], rate=8340000.00/min [1400000], rate=8400000.00/min [1410000], rate=8460000.00/min [1420000], rate=8520000.00/min [1430000], rate=8580000.00/min [1440000], rate=8640000.00/min [1450000], rate=7909090.91/min [1460000], rate=7963636.36/min [1470000], rate=8018181.82/min [1480000], rate=8072727.27/min [1490000], rate=8127272.73/min [1500000], rate=8181818.18/min [1510000], rate=8236363.64/min [1520000], rate=8290909.09/min [1530000], rate=8345454.55/min [1540000], rate=8400000.00/min [1550000], rate=8454545.45/min [1560000], rate=7800000.00/min [1570000], rate=7850000.00/min [1580000], rate=7900000.00/min [1590000], rate=7950000.00/min [1600000], rate=8000000.00/min [1610000], rate=8050000.00/min [1620000], rate=8100000.00/min [1630000], rate=7523076.92/min [1640000], rate=7569230.77/min [1650000], rate=7615384.62/min [1660000], rate=7661538.46/min [1670000], rate=7707692.31/min [1680000], rate=7753846.15/min [1690000], rate=7800000.00/min [1700000], rate=7846153.85/min [1710000], rate=7892307.69/min [1720000], rate=7371428.57/min [1730000], rate=7414285.71/min [1740000], rate=7457142.86/min [1750000], rate=7500000.00/min [1760000], rate=7542857.14/min [1770000], rate=7585714.29/min [1780000], rate=7628571.43/min [1790000], rate=7671428.57/min [1800000], rate=7714285.71/min [1810000], rate=7757142.86/min [1820000], rate=7800000.00/min [1830000], rate=7320000.00/min [1840000], rate=7360000.00/min [1850000], rate=7400000.00/min [1860000], rate=7440000.00/min [1870000], rate=7480000.00/min [1880000], rate=7520000.00/min [1890000], rate=7560000.00/min [1900000], rate=7600000.00/min [1910000], rate=7640000.00/min [1920000], rate=7680000.00/min [1930000], rate=7237500.00/min [1940000], rate=7275000.00/min [1950000], rate=7312500.00/min [1960000], rate=7350000.00/min [1970000], rate=7387500.00/min [1980000], rate=7425000.00/min [1990000], rate=7462500.00/min [2000000], rate=7500000.00/min [2010000], rate=7537500.00/min [2020000], rate=7575000.00/min [2030000], rate=7612500.00/min [2040000], rate=7650000.00/min [2050000], rate=7235294.12/min [2060000], rate=7270588.24/min [2070000], rate=7305882.35/min [2080000], rate=7341176.47/min [2090000], rate=7376470.59/min [2100000], rate=7411764.71/min [2110000], rate=7447058.82/min [2120000], rate=7482352.94/min [2130000], rate=7517647.06/min [2140000], rate=7552941.18/min [2150000], rate=7588235.29/min [2160000], rate=7623529.41/min [2170000], rate=7233333.33/min [2180000], rate=7266666.67/min [2190000], rate=7300000.00/min [2200000], rate=7333333.33/min [2210000], rate=7366666.67/min [2220000], rate=7400000.00/min [2230000], rate=7433333.33/min [2240000], rate=7466666.67/min [2250000], rate=7500000.00/min [2260000], rate=7533333.33/min [2270000], rate=7566666.67/min [2280000], rate=7200000.00/min [2290000], rate=7231578.95/min [2300000], rate=7263157.89/min [2310000], rate=7294736.84/min [2320000], rate=7326315.79/min [2330000], rate=7357894.74/min [2340000], rate=7389473.68/min [2350000], rate=7421052.63/min [2360000], rate=7452631.58/min [2370000], rate=7484210.53/min [2380000], rate=7515789.47/min [2390000], rate=7170000.00/min [2400000], rate=7200000.00/min [2410000], rate=7230000.00/min [2420000], rate=7260000.00/min [2430000], rate=7290000.00/min [2440000], rate=7320000.00/min [2450000], rate=7350000.00/min [2460000], rate=7380000.00/min [2470000], rate=7410000.00/min [2480000], rate=7440000.00/min [2490000], rate=7470000.00/min [2500000], rate=7142857.14/min [2510000], rate=7171428.57/min [2520000], rate=7200000.00/min [2530000], rate=7228571.43/min [2540000], rate=7257142.86/min [2550000], rate=7285714.29/min [2560000], rate=7314285.71/min [2570000], rate=7342857.14/min [2580000], rate=7371428.57/min [2590000], rate=7400000.00/min [2600000], rate=7090909.09/min [2610000], rate=7118181.82/min [2620000], rate=7145454.55/min [2630000], rate=7172727.27/min [2640000], rate=7200000.00/min [2650000], rate=7227272.73/min [2660000], rate=7254545.45/min [2670000], rate=7281818.18/min [2680000], rate=7309090.91/min [2690000], rate=7336363.64/min [2700000], rate=7363636.36/min [2710000], rate=7069565.22/min [2720000], rate=7095652.17/min [2730000], rate=7121739.13/min [2740000], rate=7147826.09/min [2750000], rate=7173913.04/min [2760000], rate=7200000.00/min [2770000], rate=7226086.96/min [2780000], rate=7252173.91/min [2790000], rate=7278260.87/min [2800000], rate=7304347.83/min [2810000], rate=7330434.78/min [2820000], rate=7356521.74/min [2830000], rate=7075000.00/min [2840000], rate=7100000.00/min [2850000], rate=7125000.00/min [2860000], rate=7150000.00/min [2870000], rate=7175000.00/min [2880000], rate=7200000.00/min [2890000], rate=7225000.00/min [2900000], rate=7250000.00/min [2910000], rate=7275000.00/min [2920000], rate=7300000.00/min [2930000], rate=7325000.00/min [2940000], rate=7350000.00/min [2950000], rate=7080000.00/min [2960000], rate=7104000.00/min [2970000], rate=7128000.00/min [2980000], rate=7152000.00/min [2990000], rate=7176000.00/min [3000000], rate=7200000.00/min [3010000], rate=7224000.00/min [3020000], rate=7248000.00/min [3030000], rate=7272000.00/min [3040000], rate=7296000.00/min [3050000], rate=7320000.00/min [3060000], rate=7061538.46/min [3070000], rate=7084615.38/min [3080000], rate=7107692.31/min [3090000], rate=7130769.23/min [3100000], rate=7153846.15/min [3110000], rate=7176923.08/min [3120000], rate=7200000.00/min [3130000], rate=7223076.92/min [3140000], rate=7246153.85/min [3150000], rate=7269230.77/min [3160000], rate=7022222.22/min [3170000], rate=7044444.44/min [3180000], rate=7066666.67/min [3190000], rate=7088888.89/min [3200000], rate=7111111.11/min [3210000], rate=7133333.33/min [3220000], rate=7155555.56/min [3230000], rate=7177777.78/min [3240000], rate=6942857.14/min [3250000], rate=6964285.71/min [3260000], rate=6985714.29/min [3270000], rate=7007142.86/min [3280000], rate=7028571.43/min [3290000], rate=7050000.00/min [3300000], rate=7071428.57/min [3310000], rate=7092857.14/min [3320000], rate=7114285.71/min [3330000], rate=7135714.29/min [3340000], rate=7157142.86/min [3350000], rate=6931034.48/min [3360000], rate=6951724.14/min [3370000], rate=6972413.79/min [3380000], rate=6993103.45/min [3390000], rate=7013793.10/min [3400000], rate=7034482.76/min [3410000], rate=7055172.41/min [3420000], rate=7075862.07/min [3430000], rate=7096551.72/min [3440000], rate=7117241.38/min [3450000], rate=7137931.03/min [3460000], rate=7158620.69/min [3470000], rate=7179310.34/min [3480000], rate=7200000.00/min [3490000], rate=7220689.66/min [3500000], rate=7241379.31/min [3510000], rate=7262068.97/min [3520000], rate=7282758.62/min [3530000], rate=7060000.00/min [3540000], rate=7080000.00/min [3550000], rate=7100000.00/min [3560000], rate=7120000.00/min [3570000], rate=7140000.00/min [3580000], rate=7160000.00/min [3590000], rate=7180000.00/min [3600000], rate=7200000.00/min [3610000], rate=7220000.00/min [3620000], rate=7240000.00/min [3630000], rate=7260000.00/min [3640000], rate=7280000.00/min [3650000], rate=7300000.00/min [3660000], rate=7320000.00/min [3670000], rate=7340000.00/min [3680000], rate=7360000.00/min [3690000], rate=7380000.00/min [3700000], rate=7400000.00/min [3710000], rate=7180645.16/min [3720000], rate=7200000.00/min [3730000], rate=7219354.84/min [3740000], rate=7238709.68/min [3750000], rate=7258064.52/min [3760000], rate=7277419.35/min [3770000], rate=7296774.19/min [3780000], rate=7316129.03/min [3790000], rate=7335483.87/min [3800000], rate=7354838.71/min [3810000], rate=7374193.55/min [3820000], rate=7393548.39/min [3830000], rate=7412903.23/min [3840000], rate=7432258.06/min [3850000], rate=7451612.90/min [3860000], rate=7470967.74/min [3870000], rate=7256250.00/min [3880000], rate=7275000.00/min [3890000], rate=7293750.00/min [3900000], rate=7312500.00/min [3910000], rate=7331250.00/min [3920000], rate=7350000.00/min [3930000], rate=7368750.00/min [3940000], rate=7387500.00/min [3950000], rate=7406250.00/min [3960000], rate=7425000.00/min [3970000], rate=7443750.00/min [3980000], rate=7462500.00/min [3990000], rate=7481250.00/min [4000000], rate=7500000.00/min [4010000], rate=7518750.00/min [4020000], rate=7537500.00/min [4030000], rate=7327272.73/min [4040000], rate=7345454.55/min [4050000], rate=7363636.36/min [4060000], rate=7381818.18/min [4070000], rate=7400000.00/min [4080000], rate=7418181.82/min [4090000], rate=7436363.64/min [4100000], rate=7454545.45/min [4110000], rate=7472727.27/min [4120000], rate=7490909.09/min [4130000], rate=7509090.91/min [4140000], rate=7527272.73/min [4150000], rate=7545454.55/min [4160000], rate=7563636.36/min [4170000], rate=7581818.18/min [4180000], rate=7600000.00/min [4190000], rate=7394117.65/min [4200000], rate=7411764.71/min [4210000], rate=7429411.76/min [4220000], rate=7447058.82/min [4230000], rate=7464705.88/min [4240000], rate=7482352.94/min [4250000], rate=7500000.00/min [4260000], rate=7517647.06/min [4270000], rate=7535294.12/min [4280000], rate=7552941.18/min [4290000], rate=7570588.24/min [4300000], rate=7588235.29/min [4310000], rate=7605882.35/min [4320000], rate=7623529.41/min [4330000], rate=7641176.47/min [4340000], rate=7658823.53/min [4350000], rate=7457142.86/min [4360000], rate=7474285.71/min [4370000], rate=7491428.57/min [4380000], rate=7508571.43/min [4390000], rate=7525714.29/min [4400000], rate=7542857.14/min [4410000], rate=7560000.00/min [4420000], rate=7577142.86/min [4430000], rate=7594285.71/min [4440000], rate=7611428.57/min [4450000], rate=7628571.43/min [4460000], rate=7645714.29/min [4470000], rate=7662857.14/min [4480000], rate=7680000.00/min [4490000], rate=7697142.86/min [4500000], rate=7500000.00/min [4510000], rate=7516666.67/min [4520000], rate=7533333.33/min [4530000], rate=7550000.00/min [4540000], rate=7566666.67/min [4550000], rate=7583333.33/min [4560000], rate=7600000.00/min [4570000], rate=7616666.67/min [4580000], rate=7633333.33/min [4590000], rate=7650000.00/min [4600000], rate=7666666.67/min [4610000], rate=7683333.33/min [4620000], rate=7700000.00/min [4630000], rate=7508108.11/min [4640000], rate=7524324.32/min [4650000], rate=7540540.54/min [4660000], rate=7556756.76/min [4670000], rate=7572972.97/min [4680000], rate=7589189.19/min [4690000], rate=7605405.41/min [4700000], rate=7621621.62/min [4710000], rate=7637837.84/min [4720000], rate=7654054.05/min [4730000], rate=7670270.27/min [4740000], rate=7686486.49/min [4750000], rate=7702702.70/min [4760000], rate=7515789.47/min [4770000], rate=7531578.95/min [4780000], rate=7547368.42/min [4790000], rate=7563157.89/min [4800000], rate=7578947.37/min [4810000], rate=7594736.84/min [4820000], rate=7610526.32/min [4830000], rate=7626315.79/min [4840000], rate=7642105.26/min [4850000], rate=7657894.74/min [4860000], rate=7673684.21/min [4870000], rate=7689473.68/min [4880000], rate=7705263.16/min [4890000], rate=7721052.63/min [4900000], rate=7736842.11/min [4910000], rate=7752631.58/min [4920000], rate=7569230.77/min [4930000], rate=7584615.38/min [4940000], rate=7600000.00/min [4950000], rate=7615384.62/min [4960000], rate=7630769.23/min [4970000], rate=7646153.85/min [4980000], rate=7661538.46/min [4990000], rate=7676923.08/min [5000000], rate=7692307.69/min [5010000], rate=7707692.31/min [5020000], rate=7723076.92/min [5030000], rate=7738461.54/min [5040000], rate=7753846.15/min [5050000], rate=7769230.77/min [5060000], rate=7590000.00/min [5070000], rate=7605000.00/min [5080000], rate=7620000.00/min [5090000], rate=7635000.00/min [5100000], rate=7650000.00/min [5110000], rate=7665000.00/min [5120000], rate=7680000.00/min [5130000], rate=7695000.00/min [5140000], rate=7710000.00/min [5150000], rate=7725000.00/min [5160000], rate=7740000.00/min [5170000], rate=7755000.00/min [5180000], rate=7770000.00/min [5190000], rate=7785000.00/min [5200000], rate=7800000.00/min [5210000], rate=7815000.00/min [5220000], rate=7830000.00/min [5230000], rate=7845000.00/min [5240000], rate=7668292.68/min [5250000], rate=7682926.83/min [5260000], rate=7697560.98/min [5270000], rate=7712195.12/min [5280000], rate=7726829.27/min [5290000], rate=7741463.41/min [5300000], rate=7756097.56/min [5310000], rate=7770731.71/min [5320000], rate=7785365.85/min [5330000], rate=7800000.00/min [5340000], rate=7814634.15/min [5350000], rate=7829268.29/min [5360000], rate=7843902.44/min [5370000], rate=7858536.59/min [5380000], rate=7873170.73/min [5390000], rate=7887804.88/min [5400000], rate=7902439.02/min [5410000], rate=7728571.43/min [5420000], rate=7742857.14/min [5430000], rate=7757142.86/min [5440000], rate=7771428.57/min [5450000], rate=7785714.29/min [5460000], rate=7800000.00/min [5470000], rate=7814285.71/min [5480000], rate=7828571.43/min [5490000], rate=7842857.14/min [5500000], rate=7857142.86/min [5510000], rate=7871428.57/min [5520000], rate=7885714.29/min [5530000], rate=7900000.00/min [5540000], rate=7914285.71/min [5550000], rate=7928571.43/min [5560000], rate=7942857.14/min [5570000], rate=7957142.86/min [5580000], rate=7786046.51/min [5590000], rate=7800000.00/min [5600000], rate=7813953.49/min [5610000], rate=7827906.98/min [5620000], rate=7841860.47/min [5630000], rate=7855813.95/min [5640000], rate=7869767.44/min [5650000], rate=7883720.93/min [5660000], rate=7897674.42/min [5670000], rate=7911627.91/min [5680000], rate=7925581.40/min [5690000], rate=7939534.88/min [5700000], rate=7953488.37/min [5710000], rate=7786363.64/min [5720000], rate=7800000.00/min [5730000], rate=7813636.36/min [5740000], rate=7827272.73/min [5750000], rate=7840909.09/min [5760000], rate=7854545.45/min [5770000], rate=7868181.82/min [5780000], rate=7881818.18/min [5790000], rate=7895454.55/min [5800000], rate=7909090.91/min [5810000], rate=7922727.27/min [5820000], rate=7936363.64/min [5830000], rate=7773333.33/min [5840000], rate=7786666.67/min [5850000], rate=7800000.00/min [5860000], rate=7813333.33/min [5870000], rate=7826666.67/min [5880000], rate=7840000.00/min [5890000], rate=7853333.33/min [5900000], rate=7866666.67/min [5910000], rate=7880000.00/min [5920000], rate=7893333.33/min [5930000], rate=7906666.67/min [5940000], rate=7920000.00/min [5950000], rate=7933333.33/min [5960000], rate=7773913.04/min [5970000], rate=7786956.52/min [5980000], rate=7800000.00/min [5990000], rate=7813043.48/min [6000000], rate=7826086.96/min [6010000], rate=7839130.43/min [6020000], rate=7852173.91/min [6030000], rate=7865217.39/min [6040000], rate=7878260.87/min [6050000], rate=7891304.35/min [6060000], rate=7904347.83/min [6070000], rate=7917391.30/min [6080000], rate=7761702.13/min [6090000], rate=7774468.09/min [6100000], rate=7787234.04/min [6110000], rate=7800000.00/min [6120000], rate=7812765.96/min [6130000], rate=7825531.91/min [6140000], rate=7838297.87/min [6150000], rate=7851063.83/min [6160000], rate=7863829.79/min [6170000], rate=7712500.00/min [6180000], rate=7725000.00/min [6190000], rate=7737500.00/min [6200000], rate=7750000.00/min [6210000], rate=7762500.00/min [6220000], rate=7775000.00/min [6230000], rate=7787500.00/min [6240000], rate=7800000.00/min [6250000], rate=7812500.00/min [6260000], rate=7825000.00/min [6270000], rate=7677551.02/min [6280000], rate=7689795.92/min [6290000], rate=7702040.82/min [6300000], rate=7714285.71/min [6310000], rate=7726530.61/min [6320000], rate=7738775.51/min [6330000], rate=7751020.41/min [6340000], rate=7763265.31/min [6350000], rate=7775510.20/min [6360000], rate=7787755.10/min [6370000], rate=7800000.00/min [6380000], rate=7812244.90/min [6390000], rate=7824489.80/min [6400000], rate=7680000.00/min [6410000], rate=7692000.00/min [6420000], rate=7704000.00/min [6430000], rate=7716000.00/min [6440000], rate=7728000.00/min [6450000], rate=7740000.00/min [6460000], rate=7752000.00/min [6470000], rate=7764000.00/min [6480000], rate=7776000.00/min [6490000], rate=7788000.00/min [6500000], rate=7800000.00/min [6510000], rate=7812000.00/min [6520000], rate=7824000.00/min [6530000], rate=7836000.00/min [6540000], rate=7848000.00/min [6550000], rate=7860000.00/min [6560000], rate=7717647.06/min [6570000], rate=7729411.76/min [6580000], rate=7741176.47/min [6590000], rate=7752941.18/min [6600000], rate=7764705.88/min [6610000], rate=7776470.59/min [6620000], rate=7788235.29/min [6630000], rate=7800000.00/min [6640000], rate=7811764.71/min [6650000], rate=7823529.41/min [6660000], rate=7835294.12/min [6670000], rate=7847058.82/min [6680000], rate=7858823.53/min [6690000], rate=7870588.24/min [6700000], rate=7882352.94/min [6710000], rate=7894117.65/min [6720000], rate=7905882.35/min [6730000], rate=7917647.06/min [6740000], rate=7929411.76/min [6750000], rate=7941176.47/min [6760000], rate=7800000.00/min [6770000], rate=7811538.46/min [6780000], rate=7823076.92/min [6790000], rate=7834615.38/min [6800000], rate=7846153.85/min [6810000], rate=7857692.31/min [6820000], rate=7869230.77/min [6830000], rate=7880769.23/min [6840000], rate=7892307.69/min [6850000], rate=7903846.15/min [6860000], rate=7915384.62/min [6870000], rate=7926923.08/min [6880000], rate=7938461.54/min [6890000], rate=7950000.00/min [6900000], rate=7961538.46/min [6910000], rate=7973076.92/min [6920000], rate=7984615.38/min [6930000], rate=7996153.85/min [6940000], rate=8007692.31/min [6950000], rate=7867924.53/min [6960000], rate=7879245.28/min [6970000], rate=7890566.04/min [6980000], rate=7901886.79/min [6990000], rate=7913207.55/min [7000000], rate=7924528.30/min [7010000], rate=7935849.06/min [7020000], rate=7947169.81/min [7030000], rate=7958490.57/min [7040000], rate=7969811.32/min [7050000], rate=7981132.08/min [7060000], rate=7992452.83/min [7070000], rate=8003773.58/min [7080000], rate=8015094.34/min [7090000], rate=8026415.09/min [7100000], rate=8037735.85/min [7110000], rate=7900000.00/min [7120000], rate=7911111.11/min [7130000], rate=7922222.22/min [7140000], rate=7933333.33/min [7150000], rate=7944444.44/min [7160000], rate=7955555.56/min [7170000], rate=7966666.67/min [7180000], rate=7977777.78/min [7190000], rate=7988888.89/min [7200000], rate=8000000.00/min [7210000], rate=8011111.11/min [7220000], rate=8022222.22/min [7230000], rate=8033333.33/min [7240000], rate=8044444.44/min [7250000], rate=8055555.56/min [7260000], rate=8066666.67/min [7270000], rate=7930909.09/min [7280000], rate=7941818.18/min [7290000], rate=7952727.27/min [7300000], rate=7963636.36/min [7310000], rate=7974545.45/min [7320000], rate=7985454.55/min [7330000], rate=7996363.64/min [7340000], rate=8007272.73/min [7350000], rate=8018181.82/min [7360000], rate=8029090.91/min [7370000], rate=8040000.00/min [7380000], rate=8050909.09/min [7390000], rate=8061818.18/min [7400000], rate=8072727.27/min [7410000], rate=8083636.36/min [7420000], rate=8094545.45/min [7430000], rate=8105454.55/min [7440000], rate=8116363.64/min [7450000], rate=7982142.86/min [7460000], rate=7992857.14/min [7470000], rate=8003571.43/min [7480000], rate=8014285.71/min [7490000], rate=8025000.00/min [7500000], rate=8035714.29/min [7510000], rate=8046428.57/min [7520000], rate=8057142.86/min [7530000], rate=8067857.14/min [7540000], rate=8078571.43/min [7550000], rate=8089285.71/min [7560000], rate=8100000.00/min [7570000], rate=8110714.29/min [7580000], rate=8121428.57/min [7590000], rate=8132142.86/min [7600000], rate=8142857.14/min [7610000], rate=8010526.32/min [7620000], rate=8021052.63/min [7630000], rate=8031578.95/min [7640000], rate=8042105.26/min [7650000], rate=8052631.58/min [7660000], rate=8063157.89/min [7670000], rate=8073684.21/min [7680000], rate=8084210.53/min [7690000], rate=8094736.84/min [7700000], rate=8105263.16/min [7710000], rate=8115789.47/min [7720000], rate=8126315.79/min [7730000], rate=8136842.11/min [7740000], rate=8147368.42/min [7750000], rate=8157894.74/min [7760000], rate=8168421.05/min [7770000], rate=8037931.03/min [7780000], rate=8048275.86/min [7790000], rate=8058620.69/min [7800000], rate=8068965.52/min [7810000], rate=8079310.34/min [7820000], rate=8089655.17/min [7830000], rate=8100000.00/min [7840000], rate=8110344.83/min [7850000], rate=8120689.66/min [7860000], rate=8131034.48/min [7870000], rate=8141379.31/min [7880000], rate=8151724.14/min [7890000], rate=8162068.97/min [7900000], rate=8172413.79/min [7910000], rate=8182758.62/min [7920000], rate=8054237.29/min [7930000], rate=8064406.78/min [7940000], rate=8074576.27/min [7950000], rate=8084745.76/min [7960000], rate=8094915.25/min [7970000], rate=8105084.75/min [7980000], rate=8115254.24/min [7990000], rate=8125423.73/min [8000000], rate=8135593.22/min [8010000], rate=8145762.71/min [8020000], rate=8155932.20/min [8030000], rate=8166101.69/min [8040000], rate=8176271.19/min [8050000], rate=8186440.68/min [8060000], rate=8196610.17/min [8070000], rate=8206779.66/min [8080000], rate=8080000.00/min [8090000], rate=8090000.00/min [8100000], rate=8100000.00/min [8110000], rate=8110000.00/min [8120000], rate=8120000.00/min [8130000], rate=8130000.00/min [8140000], rate=8140000.00/min [8150000], rate=8150000.00/min [8160000], rate=8160000.00/min [8170000], rate=8170000.00/min [8180000], rate=8180000.00/min [8190000], rate=8190000.00/min [8200000], rate=8200000.00/min [8210000], rate=8210000.00/min [8220000], rate=8220000.00/min [8230000], rate=8230000.00/min [8240000], rate=8104918.03/min [8250000], rate=8114754.10/min [8260000], rate=8124590.16/min [8270000], rate=8134426.23/min [8280000], rate=8144262.30/min [8290000], rate=8154098.36/min [8300000], rate=8163934.43/min [8310000], rate=8173770.49/min [8320000], rate=8183606.56/min [8330000], rate=8193442.62/min [8340000], rate=8203278.69/min [8350000], rate=8213114.75/min [8360000], rate=8222950.82/min [8370000], rate=8232786.89/min [8380000], rate=8242622.95/min [8390000], rate=8252459.02/min [8400000], rate=8262295.08/min [8410000], rate=8138709.68/min [8420000], rate=8148387.10/min [8430000], rate=8158064.52/min [8440000], rate=8167741.94/min [8450000], rate=8177419.35/min [8460000], rate=8187096.77/min [8470000], rate=8196774.19/min [8480000], rate=8206451.61/min [8490000], rate=8216129.03/min [8500000], rate=8225806.45/min [8510000], rate=8235483.87/min [8520000], rate=8245161.29/min [8530000], rate=8254838.71/min [8540000], rate=8264516.13/min [8550000], rate=8274193.55/min [8560000], rate=8283870.97/min [8570000], rate=8161904.76/min [8580000], rate=8171428.57/min [8590000], rate=8180952.38/min [8600000], rate=8190476.19/min [8610000], rate=8200000.00/min [8620000], rate=8209523.81/min [8630000], rate=8219047.62/min [8640000], rate=8228571.43/min [8650000], rate=8238095.24/min [8660000], rate=8247619.05/min [8670000], rate=8257142.86/min [8680000], rate=8266666.67/min [8690000], rate=8276190.48/min [8700000], rate=8285714.29/min [8710000], rate=8295238.10/min [8720000], rate=8304761.90/min [8730000], rate=8184375.00/min [8740000], rate=8193750.00/min [8750000], rate=8203125.00/min [8760000], rate=8212500.00/min [8770000], rate=8221875.00/min [8780000], rate=8231250.00/min [8790000], rate=8240625.00/min [8800000], rate=8250000.00/min [8810000], rate=8259375.00/min [8820000], rate=8268750.00/min [8830000], rate=8278125.00/min [8840000], rate=8287500.00/min [8850000], rate=8296875.00/min [8860000], rate=8306250.00/min [8870000], rate=8315625.00/min [8880000], rate=8196923.08/min [8890000], rate=8206153.85/min [8900000], rate=8215384.62/min [8910000], rate=8224615.38/min [8920000], rate=8233846.15/min [8930000], rate=8243076.92/min [8940000], rate=8252307.69/min [8950000], rate=8261538.46/min [8960000], rate=8270769.23/min [8970000], rate=8280000.00/min [8980000], rate=8289230.77/min [8990000], rate=8298461.54/min [9000000], rate=8307692.31/min [9010000], rate=8316923.08/min [9020000], rate=8326153.85/min [9030000], rate=8335384.62/min [9040000], rate=8344615.38/min [9050000], rate=8353846.15/min [9060000], rate=8236363.64/min [9070000], rate=8245454.55/min [9080000], rate=8254545.45/min [9090000], rate=8263636.36/min [9100000], rate=8272727.27/min [9110000], rate=8281818.18/min [9120000], rate=8290909.09/min [9130000], rate=8300000.00/min [9140000], rate=8309090.91/min [9150000], rate=8318181.82/min [9160000], rate=8327272.73/min [9170000], rate=8336363.64/min [9180000], rate=8345454.55/min [9190000], rate=8354545.45/min [9200000], rate=8363636.36/min [9210000], rate=8372727.27/min [9220000], rate=8381818.18/min [9230000], rate=8265671.64/min [9240000], rate=8274626.87/min [9250000], rate=8283582.09/min [9260000], rate=8292537.31/min [9270000], rate=8301492.54/min [9280000], rate=8310447.76/min [9290000], rate=8319402.99/min [9300000], rate=8328358.21/min [9310000], rate=8337313.43/min [9320000], rate=8346268.66/min [9330000], rate=8355223.88/min [9340000], rate=8364179.10/min [9350000], rate=8373134.33/min [9360000], rate=8382089.55/min [9370000], rate=8391044.78/min [9380000], rate=8400000.00/min [9390000], rate=8408955.22/min [9400000], rate=8294117.65/min [9410000], rate=8302941.18/min [9420000], rate=8311764.71/min [9430000], rate=8320588.24/min [9440000], rate=8329411.76/min [9450000], rate=8338235.29/min [9460000], rate=8347058.82/min [9470000], rate=8355882.35/min [9480000], rate=8364705.88/min [9490000], rate=8373529.41/min [9500000], rate=8382352.94/min [9510000], rate=8391176.47/min [9520000], rate=8400000.00/min [9530000], rate=8408823.53/min [9540000], rate=8417647.06/min [9550000], rate=8426470.59/min [9560000], rate=8435294.12/min [9570000], rate=8321739.13/min [9580000], rate=8330434.78/min [9590000], rate=8339130.43/min [9600000], rate=8347826.09/min [9610000], rate=8356521.74/min [9620000], rate=8365217.39/min [9630000], rate=8373913.04/min [9640000], rate=8382608.70/min [9650000], rate=8391304.35/min [9660000], rate=8400000.00/min [9670000], rate=8408695.65/min [9680000], rate=8417391.30/min [9690000], rate=8426086.96/min [9700000], rate=8434782.61/min [9710000], rate=8443478.26/min [9720000], rate=8452173.91/min [9730000], rate=8460869.57/min [9740000], rate=8469565.22/min [9750000], rate=8357142.86/min [9760000], rate=8365714.29/min [9770000], rate=8374285.71/min [9780000], rate=8382857.14/min [9790000], rate=8391428.57/min [9800000], rate=8400000.00/min [9810000], rate=8408571.43/min [9820000], rate=8417142.86/min [9830000], rate=8425714.29/min [9840000], rate=8434285.71/min [9850000], rate=8442857.14/min [9860000], rate=8451428.57/min [9870000], rate=8460000.00/min [9880000], rate=8468571.43/min [9890000], rate=8477142.86/min [9900000], rate=8485714.29/min [9910000], rate=8494285.71/min [9920000], rate=8502857.14/min [9930000], rate=8511428.57/min [9940000], rate=8400000.00/min [9950000], rate=8408450.70/min [9960000], rate=8416901.41/min [9970000], rate=8425352.11/min [9980000], rate=8433802.82/min [9990000], rate=8442253.52/min [10000000], rate=8450704.23/min [10010000], rate=8459154.93/min [10020000], rate=8467605.63/min [10030000], rate=8476056.34/min [10040000], rate=8484507.04/min [10050000], rate=8492957.75/min [10060000], rate=8501408.45/min [10070000], rate=8509859.15/min [10080000], rate=8518309.86/min [10090000], rate=8526760.56/min [10100000], rate=8416666.67/min [10110000], rate=8425000.00/min [10120000], rate=8433333.33/min [10130000], rate=8441666.67/min [10140000], rate=8450000.00/min [10150000], rate=8458333.33/min [10160000], rate=8466666.67/min [10170000], rate=8475000.00/min [10180000], rate=8483333.33/min [10190000], rate=8491666.67/min [10200000], rate=8500000.00/min [10210000], rate=8508333.33/min [10220000], rate=8516666.67/min [10230000], rate=8525000.00/min [10240000], rate=8533333.33/min [10250000], rate=8541666.67/min [10260000], rate=8550000.00/min [10270000], rate=8558333.33/min [10280000], rate=8566666.67/min [10290000], rate=8457534.25/min [10300000], rate=8465753.42/min [10310000], rate=8473972.60/min [10320000], rate=8482191.78/min [10330000], rate=8490410.96/min [10340000], rate=8498630.14/min [10350000], rate=8506849.32/min [10360000], rate=8515068.49/min [10370000], rate=8523287.67/min [10380000], rate=8531506.85/min [10390000], rate=8539726.03/min [10400000], rate=8547945.21/min [10410000], rate=8556164.38/min [10420000], rate=8564383.56/min [10430000], rate=8572602.74/min [10440000], rate=8580821.92/min [10450000], rate=8589041.10/min [10460000], rate=8597260.27/min [10470000], rate=8605479.45/min [10480000], rate=8497297.30/min [10490000], rate=8505405.41/min [10500000], rate=8513513.51/min [10510000], rate=8521621.62/min [10520000], rate=8529729.73/min [10530000], rate=8537837.84/min [10540000], rate=8545945.95/min [10550000], rate=8554054.05/min [10560000], rate=8562162.16/min [10570000], rate=8456000.00/min [10580000], rate=8464000.00/min [10590000], rate=8472000.00/min [10600000], rate=8480000.00/min [10610000], rate=8488000.00/min [10620000], rate=8496000.00/min [10630000], rate=8504000.00/min [10640000], rate=8512000.00/min [10650000], rate=8520000.00/min [10660000], rate=8528000.00/min [10670000], rate=8536000.00/min [10680000], rate=8544000.00/min 08:46:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_cTi-T1-TRNA-1_B23MHV2LT4_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. -659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns: identified 8321 cancer introns 08:46:57 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 08:46:57 : INFO : Running: touch /tmp/nxf.mXOV0Mklku/659_cTi-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 08:46:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:46:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:46:57 : INFO : Running: touch /tmp/nxf.mXOV0Mklku/659_cTi-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 08:46:57 : INFO : -found 2706 cancer introns 08:46:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:46:58 : INFO : Creating the BED File. 08:47:06 : INFO : Saving Bed File as 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:47:07 : INFO : Execution Time = 0.16 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_cTi-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:47:07 : INFO : Running: touch /tmp/nxf.mXOV0Mklku/659_cTi-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 08:47:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_cTi-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_cTi-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_cTi-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai