Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/9974715b26386cbe22e03d563a248d/aih-tih-sc-16054b-R1_B23WHYVLT4_1.Chimeric.out.junction
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/fd/cc842db70e6f1ceb13012b8b14b011/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/9974715b26386cbe22e03d563a248d/aih-tih-sc-16054b-R1_B23WHYVLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/e3f8fc649ff395e795586b9719e337/aih-tih-sc-16054b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/cc842db70e6f1ceb13012b8b14b011/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/9974715b26386cbe22e03d563a248d/aih-tih-sc-16054b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)
09:31:06 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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=31800000.00/min
[540000], rate=32400000.00/min
[550000], rate=33000000.00/min
[560000], rate=33600000.00/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=16800000.00/min
[850000], rate=17000000.00/min
[860000], rate=17200000.00/min
[870000], rate=17400000.00/min
[880000], rate=17600000.00/min
[890000], rate=17800000.00/min
[900000], rate=18000000.00/min
[910000], rate=18200000.00/min
[920000], rate=18400000.00/min
[930000], rate=18600000.00/min
[940000], rate=18800000.00/min
[950000], rate=19000000.00/min
[960000], rate=19200000.00/min
[970000], rate=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=16950000.00/min
[1140000], rate=17100000.00/min
[1150000], rate=17250000.00/min
[1160000], rate=17400000.00/min
[1170000], rate=17550000.00/min
[1180000], rate=17700000.00/min
[1190000], rate=17850000.00/min
[1200000], rate=18000000.00/min
[1210000], rate=18150000.00/min
[1220000], rate=18300000.00/min
[1230000], rate=18450000.00/min
[1240000], rate=18600000.00/min
[1250000], rate=18750000.00/min
[1260000], rate=18900000.00/min
[1270000], rate=19050000.00/min
[1280000], rate=19200000.00/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=16920000.00/min
[1420000], rate=17040000.00/min
[1430000], rate=17160000.00/min
[1440000], rate=17280000.00/min
[1450000], rate=17400000.00/min
[1460000], rate=17520000.00/min
[1470000], rate=17640000.00/min
[1480000], rate=17760000.00/min
[1490000], rate=17880000.00/min
[1500000], rate=18000000.00/min
[1510000], rate=18120000.00/min
[1520000], rate=18240000.00/min
[1530000], rate=18360000.00/min
[1540000], rate=18480000.00/min
[1550000], rate=18600000.00/min
[1560000], rate=18720000.00/min
[1570000], rate=18840000.00/min
[1580000], rate=18960000.00/min
[1590000], rate=19080000.00/min
[1600000], rate=19200000.00/min
[1610000], rate=19320000.00/min
[1620000], rate=19440000.00/min
[1630000], rate=19560000.00/min
[1640000], rate=19680000.00/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=17000000.00/min
[1710000], rate=17100000.00/min
[1720000], rate=17200000.00/min
[1730000], rate=17300000.00/min
[1740000], rate=17400000.00/min
[1750000], rate=17500000.00/min
[1760000], rate=17600000.00/min
[1770000], rate=17700000.00/min
[1780000], rate=17800000.00/min
[1790000], rate=17900000.00/min
[1800000], rate=18000000.00/min
[1810000], rate=18100000.00/min
[1820000], rate=18200000.00/min
[1830000], rate=18300000.00/min
[1840000], rate=18400000.00/min
[1850000], rate=18500000.00/min
[1860000], rate=18600000.00/min
[1870000], rate=18700000.00/min
[1880000], rate=18800000.00/min
[1890000], rate=18900000.00/min
[1900000], rate=19000000.00/min
[1910000], rate=19100000.00/min
[1920000], rate=19200000.00/min
[1930000], rate=19300000.00/min
[1940000], rate=19400000.00/min
[1950000], rate=19500000.00/min
[1960000], rate=19600000.00/min
[1970000], rate=19700000.00/min
[1980000], rate=16971428.57/min
[1990000], rate=17057142.86/min
[2000000], rate=17142857.14/min
[2010000], rate=17228571.43/min
[2020000], rate=17314285.71/min
[2030000], rate=17400000.00/min
[2040000], rate=17485714.29/min
[2050000], rate=17571428.57/min
[2060000], rate=17657142.86/min
[2070000], rate=17742857.14/min
[2080000], rate=17828571.43/min
[2090000], rate=17914285.71/min
[2100000], rate=18000000.00/min
[2110000], rate=18085714.29/min
[2120000], rate=18171428.57/min
[2130000], rate=18257142.86/min
[2140000], rate=18342857.14/min
[2150000], rate=18428571.43/min
[2160000], rate=18514285.71/min
[2170000], rate=18600000.00/min
[2180000], rate=18685714.29/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=17025000.00/min
[2280000], rate=17100000.00/min
[2290000], rate=17175000.00/min
[2300000], rate=17250000.00/min
[2310000], rate=17325000.00/min
[2320000], rate=17400000.00/min
[2330000], rate=17475000.00/min
[2340000], rate=17550000.00/min
[2350000], rate=17625000.00/min
[2360000], rate=17700000.00/min
[2370000], rate=17775000.00/min
[2380000], rate=17850000.00/min
[2390000], rate=17925000.00/min
[2400000], rate=18000000.00/min
[2410000], rate=18075000.00/min
[2420000], rate=18150000.00/min
[2430000], rate=18225000.00/min
[2440000], rate=18300000.00/min
[2450000], rate=18375000.00/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=17066666.67/min
[2570000], rate=17133333.33/min
[2580000], rate=17200000.00/min
[2590000], rate=17266666.67/min
[2600000], rate=17333333.33/min
[2610000], rate=17400000.00/min
[2620000], rate=17466666.67/min
[2630000], rate=17533333.33/min
[2640000], rate=17600000.00/min
[2650000], rate=17666666.67/min
[2660000], rate=17733333.33/min
[2670000], rate=17800000.00/min
[2680000], rate=17866666.67/min
[2690000], rate=17933333.33/min
[2700000], rate=18000000.00/min
[2710000], rate=18066666.67/min
[2720000], rate=18133333.33/min
[2730000], rate=18200000.00/min
[2740000], rate=18266666.67/min
[2750000], rate=18333333.33/min
[2760000], rate=18400000.00/min
[2770000], rate=18466666.67/min
[2780000], rate=18533333.33/min
[2790000], rate=18600000.00/min
[2800000], rate=18666666.67/min
[2810000], rate=18733333.33/min
[2820000], rate=18800000.00/min
[2830000], rate=16980000.00/min
[2840000], rate=17040000.00/min
[2850000], rate=17100000.00/min
[2860000], rate=17160000.00/min
[2870000], rate=17220000.00/min
[2880000], rate=17280000.00/min
[2890000], rate=17340000.00/min
[2900000], rate=17400000.00/min
[2910000], rate=17460000.00/min
[2920000], rate=17520000.00/min
[2930000], rate=17580000.00/min
[2940000], rate=17640000.00/min
[2950000], rate=17700000.00/min
[2960000], rate=17760000.00/min
[2970000], rate=17820000.00/min
[2980000], rate=17880000.00/min
[2990000], rate=17940000.00/min
[3000000], rate=18000000.00/min
[3010000], rate=18060000.00/min
[3020000], rate=18120000.00/min
[3030000], rate=18180000.00/min
[3040000], rate=18240000.00/min
[3050000], rate=18300000.00/min
[3060000], rate=18360000.00/min
[3070000], rate=18420000.00/min
[3080000], rate=18480000.00/min
[3090000], rate=18540000.00/min
[3100000], rate=18600000.00/min
[3110000], rate=18660000.00/min
[3120000], rate=17018181.82/min
[3130000], rate=17072727.27/min
[3140000], rate=17127272.73/min
[3150000], rate=17181818.18/min
[3160000], rate=17236363.64/min
[3170000], rate=17290909.09/min
[3180000], rate=17345454.55/min
[3190000], rate=17400000.00/min
[3200000], rate=17454545.45/min
[3210000], rate=17509090.91/min
[3220000], rate=17563636.36/min
[3230000], rate=17618181.82/min
[3240000], rate=17672727.27/min
[3250000], rate=17727272.73/min
[3260000], rate=17781818.18/min
[3270000], rate=17836363.64/min
[3280000], rate=17890909.09/min
[3290000], rate=17945454.55/min
[3300000], rate=18000000.00/min
[3310000], rate=18054545.45/min
[3320000], rate=18109090.91/min
[3330000], rate=18163636.36/min
[3340000], rate=18218181.82/min
[3350000], rate=18272727.27/min
[3360000], rate=18327272.73/min
[3370000], rate=18381818.18/min
[3380000], rate=18436363.64/min
[3390000], rate=16950000.00/min
[3400000], rate=17000000.00/min
[3410000], rate=17050000.00/min
[3420000], rate=17100000.00/min
[3430000], rate=17150000.00/min
[3440000], rate=17200000.00/min
[3450000], rate=17250000.00/min
[3460000], rate=17300000.00/min
[3470000], rate=17350000.00/min
[3480000], rate=17400000.00/min
[3490000], rate=17450000.00/min
[3500000], rate=17500000.00/min
[3510000], rate=17550000.00/min
[3520000], rate=17600000.00/min
[3530000], rate=17650000.00/min
[3540000], rate=17700000.00/min
[3550000], rate=17750000.00/min
[3560000], rate=17800000.00/min
[3570000], rate=17850000.00/min
[3580000], rate=17900000.00/min
[3590000], rate=17950000.00/min
[3600000], rate=18000000.00/min
[3610000], rate=18050000.00/min
[3620000], rate=18100000.00/min
[3630000], rate=18150000.00/min
[3640000], rate=18200000.00/min
[3650000], rate=18250000.00/min
[3660000], rate=16892307.69/min
[3670000], rate=16938461.54/min
[3680000], rate=16984615.38/min
[3690000], rate=17030769.23/min
[3700000], rate=17076923.08/min
[3710000], rate=17123076.92/min
[3720000], rate=17169230.77/min
[3730000], rate=17215384.62/min
[3740000], rate=17261538.46/min
[3750000], rate=17307692.31/min
[3760000], rate=17353846.15/min
[3770000], rate=17400000.00/min
[3780000], rate=17446153.85/min
[3790000], rate=17492307.69/min
[3800000], rate=17538461.54/min
[3810000], rate=17584615.38/min
[3820000], rate=17630769.23/min
[3830000], rate=17676923.08/min
[3840000], rate=17723076.92/min
[3850000], rate=17769230.77/min
[3860000], rate=17815384.62/min
[3870000], rate=17861538.46/min
[3880000], rate=17907692.31/min
[3890000], rate=17953846.15/min
[3900000], rate=18000000.00/min
[3910000], rate=18046153.85/min
[3920000], rate=18092307.69/min
[3930000], rate=18138461.54/min
[3940000], rate=18184615.38/min
[3950000], rate=16928571.43/min
[3960000], rate=16971428.57/min
[3970000], rate=17014285.71/min
[3980000], rate=17057142.86/min
[3990000], rate=17100000.00/min
[4000000], rate=17142857.14/min
[4010000], rate=17185714.29/min
[4020000], rate=17228571.43/min
[4030000], rate=17271428.57/min
[4040000], rate=17314285.71/min
[4050000], rate=17357142.86/min
[4060000], rate=17400000.00/min
[4070000], rate=17442857.14/min
[4080000], rate=17485714.29/min
[4090000], rate=17528571.43/min
[4100000], rate=17571428.57/min
[4110000], rate=17614285.71/min
[4120000], rate=17657142.86/min
[4130000], rate=17700000.00/min
[4140000], rate=17742857.14/min
[4150000], rate=17785714.29/min
[4160000], rate=17828571.43/min
[4170000], rate=16680000.00/min
[4180000], rate=16720000.00/min
[4190000], rate=16760000.00/min
[4200000], rate=16800000.00/min
[4210000], rate=16840000.00/min
[4220000], rate=16880000.00/min
[4230000], rate=16920000.00/min
[4240000], rate=16960000.00/min
[4250000], rate=17000000.00/min
[4260000], rate=17040000.00/min
[4270000], rate=17080000.00/min
[4280000], rate=17120000.00/min
[4290000], rate=17160000.00/min
[4300000], rate=17200000.00/min
[4310000], rate=17240000.00/min
[4320000], rate=17280000.00/min
[4330000], rate=17320000.00/min
[4340000], rate=17360000.00/min
[4350000], rate=17400000.00/min
[4360000], rate=17440000.00/min
[4370000], rate=17480000.00/min
[4380000], rate=17520000.00/min
[4390000], rate=17560000.00/min
[4400000], rate=17600000.00/min
[4410000], rate=17640000.00/min
[4420000], rate=17680000.00/min
[4430000], rate=16612500.00/min
[4440000], rate=16650000.00/min
[4450000], rate=16687500.00/min
[4460000], rate=16725000.00/min
[4470000], rate=16762500.00/min
[4480000], rate=16800000.00/min
[4490000], rate=16837500.00/min
[4500000], rate=16875000.00/min
[4510000], rate=16912500.00/min
[4520000], rate=16950000.00/min
[4530000], rate=16987500.00/min
[4540000], rate=17025000.00/min
[4550000], rate=17062500.00/min
[4560000], rate=17100000.00/min
[4570000], rate=17137500.00/min
[4580000], rate=17175000.00/min
[4590000], rate=17212500.00/min
[4600000], rate=17250000.00/min
[4610000], rate=17287500.00/min
[4620000], rate=17325000.00/min
[4630000], rate=17362500.00/min
[4640000], rate=17400000.00/min
[4650000], rate=17437500.00/min
[4660000], rate=17475000.00/min
[4670000], rate=17512500.00/min
[4680000], rate=17550000.00/min
[4690000], rate=17587500.00/min
[4700000], rate=17625000.00/min
[4710000], rate=17662500.00/min
[4720000], rate=17700000.00/min
[4730000], rate=16694117.65/min
[4740000], rate=16729411.76/min
[4750000], rate=16764705.88/min
[4760000], rate=16800000.00/min
[4770000], rate=16835294.12/min
[4780000], rate=16870588.24/min
[4790000], rate=16905882.35/min
[4800000], rate=16941176.47/min
[4810000], rate=16976470.59/min
[4820000], rate=17011764.71/min
[4830000], rate=17047058.82/min
[4840000], rate=17082352.94/min
[4850000], rate=17117647.06/min
[4860000], rate=17152941.18/min
[4870000], rate=17188235.29/min
[4880000], rate=17223529.41/min
[4890000], rate=17258823.53/min
[4900000], rate=17294117.65/min
[4910000], rate=17329411.76/min
[4920000], rate=17364705.88/min
[4930000], rate=17400000.00/min
[4940000], rate=17435294.12/min
[4950000], rate=17470588.24/min
[4960000], rate=17505882.35/min
[4970000], rate=17541176.47/min
[4980000], rate=17576470.59/min
[4990000], rate=17611764.71/min
[5000000], rate=17647058.82/min
[5010000], rate=17682352.94/min
[5020000], rate=16733333.33/min
[5030000], rate=16766666.67/min
[5040000], rate=16800000.00/min
[5050000], rate=16833333.33/min
[5060000], rate=16866666.67/min
[5070000], rate=16900000.00/min
[5080000], rate=16933333.33/min
[5090000], rate=16966666.67/min
[5100000], rate=17000000.00/min
[5110000], rate=17033333.33/min
[5120000], rate=17066666.67/min
[5130000], rate=17100000.00/min
[5140000], rate=17133333.33/min
[5150000], rate=17166666.67/min
[5160000], rate=17200000.00/min
[5170000], rate=17233333.33/min
[5180000], rate=17266666.67/min
[5190000], rate=17300000.00/min
[5200000], rate=17333333.33/min
[5210000], rate=17366666.67/min
[5220000], rate=17400000.00/min
[5230000], rate=17433333.33/min
[5240000], rate=17466666.67/min
[5250000], rate=17500000.00/min
[5260000], rate=17533333.33/min
[5270000], rate=17566666.67/min
[5280000], rate=17600000.00/min
[5290000], rate=17633333.33/min
[5300000], rate=17666666.67/min
[5310000], rate=16768421.05/min
[5320000], rate=16800000.00/min
[5330000], rate=16831578.95/min
[5340000], rate=16863157.89/min
[5350000], rate=16894736.84/min
[5360000], rate=16926315.79/min
[5370000], rate=16957894.74/min
[5380000], rate=16989473.68/min
[5390000], rate=17021052.63/min
[5400000], rate=17052631.58/min
[5410000], rate=17084210.53/min
[5420000], rate=17115789.47/min
[5430000], rate=17147368.42/min
[5440000], rate=17178947.37/min
[5450000], rate=17210526.32/min
[5460000], rate=17242105.26/min
[5470000], rate=17273684.21/min
[5480000], rate=17305263.16/min
[5490000], rate=17336842.11/min
[5500000], rate=17368421.05/min
[5510000], rate=17400000.00/min
[5520000], rate=17431578.95/min
[5530000], rate=16590000.00/min
[5540000], rate=16620000.00/min
[5550000], rate=16650000.00/min
[5560000], rate=16680000.00/min
[5570000], rate=16710000.00/min
[5580000], rate=16740000.00/min
[5590000], rate=16770000.00/min
[5600000], rate=16800000.00/min
[5610000], rate=16830000.00/min
[5620000], rate=16860000.00/min
[5630000], rate=16890000.00/min
[5640000], rate=16920000.00/min
[5650000], rate=16950000.00/min
[5660000], rate=16980000.00/min
[5670000], rate=17010000.00/min
[5680000], rate=17040000.00/min
[5690000], rate=17070000.00/min
[5700000], rate=17100000.00/min
[5710000], rate=17130000.00/min
[5720000], rate=17160000.00/min
[5730000], rate=16371428.57/min
[5740000], rate=16400000.00/min
[5750000], rate=16428571.43/min
[5760000], rate=16457142.86/min
[5770000], rate=16485714.29/min
[5780000], rate=16514285.71/min
[5790000], rate=16542857.14/min
[5800000], rate=16571428.57/min
[5810000], rate=16600000.00/min
[5820000], rate=16628571.43/min
[5830000], rate=16657142.86/min
[5840000], rate=16685714.29/min
[5850000], rate=16714285.71/min
[5860000], rate=16742857.14/min
[5870000], rate=16771428.57/min
[5880000], rate=16800000.00/min
[5890000], rate=16828571.43/min
[5900000], rate=16090909.09/min
[5910000], rate=16118181.82/min
[5920000], rate=16145454.55/min
[5930000], rate=16172727.27/min
[5940000], rate=16200000.00/min
[5950000], rate=16227272.73/min
[5960000], rate=16254545.45/min
[5970000], rate=16281818.18/min
[5980000], rate=16309090.91/min
[5990000], rate=16336363.64/min
[6000000], rate=16363636.36/min
[6010000], rate=16390909.09/min
[6020000], rate=16418181.82/min
[6030000], rate=16445454.55/min
[6040000], rate=16472727.27/min
[6050000], rate=16500000.00/min
[6060000], rate=16527272.73/min
[6070000], rate=16554545.45/min
[6080000], rate=16581818.18/min
[6090000], rate=16609090.91/min
[6100000], rate=16636363.64/min
[6110000], rate=16663636.36/min
[6120000], rate=16690909.09/min
[6130000], rate=16718181.82/min
[6140000], rate=16745454.55/min
[6150000], rate=16772727.27/min
[6160000], rate=16800000.00/min
[6170000], rate=16827272.73/min
[6180000], rate=16854545.45/min
[6190000], rate=16147826.09/min
[6200000], rate=16173913.04/min
[6210000], rate=16200000.00/min
[6220000], rate=16226086.96/min
[6230000], rate=16252173.91/min
[6240000], rate=16278260.87/min
[6250000], rate=16304347.83/min
[6260000], rate=16330434.78/min
[6270000], rate=16356521.74/min
[6280000], rate=16382608.70/min
[6290000], rate=16408695.65/min
[6300000], rate=16434782.61/min
[6310000], rate=16460869.57/min
[6320000], rate=16486956.52/min
[6330000], rate=16513043.48/min
[6340000], rate=16539130.43/min
[6350000], rate=16565217.39/min
[6360000], rate=16591304.35/min
[6370000], rate=16617391.30/min
[6380000], rate=16643478.26/min
[6390000], rate=16669565.22/min
[6400000], rate=16695652.17/min
[6410000], rate=16721739.13/min
[6420000], rate=16747826.09/min
[6430000], rate=16773913.04/min
[6440000], rate=16800000.00/min
[6450000], rate=16125000.00/min
[6460000], rate=16150000.00/min
[6470000], rate=16175000.00/min
[6480000], rate=16200000.00/min
[6490000], rate=16225000.00/min
[6500000], rate=16250000.00/min
[6510000], rate=16275000.00/min
[6520000], rate=16300000.00/min
[6530000], rate=16325000.00/min
[6540000], rate=16350000.00/min
[6550000], rate=16375000.00/min
[6560000], rate=16400000.00/min
[6570000], rate=16425000.00/min
[6580000], rate=16450000.00/min
[6590000], rate=16475000.00/min
[6600000], rate=16500000.00/min
[6610000], rate=16525000.00/min
[6620000], rate=16550000.00/min
[6630000], rate=16575000.00/min
[6640000], rate=16600000.00/min
[6650000], rate=16625000.00/min
[6660000], rate=16650000.00/min
[6670000], rate=16675000.00/min
[6680000], rate=16700000.00/min
[6690000], rate=16725000.00/min
[6700000], rate=16750000.00/min
[6710000], rate=16775000.00/min
[6720000], rate=16800000.00/min
[6730000], rate=16825000.00/min
[6740000], rate=16850000.00/min
[6750000], rate=16875000.00/min
[6760000], rate=16900000.00/min
[6770000], rate=16925000.00/min
[6780000], rate=16950000.00/min
[6790000], rate=16296000.00/min
[6800000], rate=16320000.00/min
[6810000], rate=16344000.00/min
[6820000], rate=16368000.00/min
[6830000], rate=16392000.00/min
[6840000], rate=16416000.00/min
[6850000], rate=16440000.00/min
[6860000], rate=16464000.00/min
[6870000], rate=16488000.00/min
[6880000], rate=16512000.00/min
[6890000], rate=16536000.00/min
[6900000], rate=16560000.00/min
[6910000], rate=16584000.00/min
[6920000], rate=16608000.00/min
[6930000], rate=16632000.00/min
[6940000], rate=16656000.00/min
[6950000], rate=16680000.00/min
[6960000], rate=16704000.00/min
[6970000], rate=16728000.00/min
[6980000], rate=16752000.00/min
[6990000], rate=16776000.00/min
[7000000], rate=16800000.00/min
[7010000], rate=16824000.00/min
[7020000], rate=16848000.00/min
[7030000], rate=16872000.00/min
[7040000], rate=16896000.00/min
[7050000], rate=16920000.00/min
[7060000], rate=16944000.00/min
[7070000], rate=16968000.00/min
[7080000], rate=16338461.54/min
[7090000], rate=16361538.46/min
[7100000], rate=16384615.38/min
[7110000], rate=16407692.31/min
[7120000], rate=16430769.23/min
[7130000], rate=16453846.15/min
[7140000], rate=16476923.08/min
[7150000], rate=16500000.00/min
[7160000], rate=16523076.92/min
[7170000], rate=16546153.85/min
[7180000], rate=16569230.77/min
[7190000], rate=16592307.69/min
[7200000], rate=16615384.62/min
[7210000], rate=16638461.54/min
[7220000], rate=16661538.46/min
[7230000], rate=16684615.38/min
[7240000], rate=16707692.31/min
[7250000], rate=16730769.23/min
[7260000], rate=16753846.15/min
[7270000], rate=16776923.08/min
[7280000], rate=16800000.00/min
[7290000], rate=16823076.92/min
[7300000], rate=16846153.85/min
[7310000], rate=16869230.77/min
[7320000], rate=16892307.69/min
[7330000], rate=16915384.62/min
[7340000], rate=16938461.54/min
[7350000], rate=16961538.46/min
[7360000], rate=16355555.56/min
[7370000], rate=16377777.78/min
[7380000], rate=16400000.00/min
[7390000], rate=16422222.22/min
[7400000], rate=16444444.44/min
[7410000], rate=16466666.67/min
[7420000], rate=16488888.89/min
[7430000], rate=16511111.11/min
[7440000], rate=16533333.33/min
[7450000], rate=16555555.56/min
[7460000], rate=16577777.78/min
[7470000], rate=16600000.00/min
[7480000], rate=16622222.22/min
[7490000], rate=16644444.44/min
[7500000], rate=16666666.67/min
[7510000], rate=16688888.89/min
[7520000], rate=16711111.11/min
[7530000], rate=16733333.33/min
[7540000], rate=16755555.56/min
[7550000], rate=16777777.78/min
[7560000], rate=16800000.00/min
[7570000], rate=16822222.22/min
[7580000], rate=16844444.44/min
[7590000], rate=16866666.67/min
[7600000], rate=16888888.89/min
[7610000], rate=16911111.11/min
[7620000], rate=16933333.33/min
[7630000], rate=16955555.56/min
[7640000], rate=16977777.78/min
[7650000], rate=16392857.14/min
[7660000], rate=16414285.71/min
[7670000], rate=16435714.29/min
[7680000], rate=16457142.86/min
[7690000], rate=16478571.43/min
[7700000], rate=16500000.00/min
[7710000], rate=16521428.57/min
[7720000], rate=16542857.14/min
[7730000], rate=16564285.71/min
[7740000], rate=16585714.29/min
[7750000], rate=16607142.86/min
[7760000], rate=16628571.43/min
[7770000], rate=16650000.00/min
[7780000], rate=16671428.57/min
[7790000], rate=16692857.14/min
[7800000], rate=16714285.71/min
[7810000], rate=16735714.29/min
[7820000], rate=16757142.86/min
[7830000], rate=16778571.43/min
[7840000], rate=16800000.00/min
[7850000], rate=16821428.57/min
[7860000], rate=16842857.14/min
[7870000], rate=16864285.71/min
[7880000], rate=16885714.29/min
[7890000], rate=16324137.93/min
[7900000], rate=16344827.59/min
[7910000], rate=16365517.24/min
[7920000], rate=16386206.90/min
[7930000], rate=16406896.55/min
[7940000], rate=16427586.21/min
[7950000], rate=16448275.86/min
[7960000], rate=16468965.52/min
[7970000], rate=16489655.17/min
[7980000], rate=16510344.83/min
[7990000], rate=16531034.48/min
[8000000], rate=16551724.14/min
[8010000], rate=16572413.79/min
[8020000], rate=16593103.45/min
[8030000], rate=16613793.10/min
[8040000], rate=16634482.76/min
[8050000], rate=16655172.41/min
[8060000], rate=16675862.07/min
[8070000], rate=16696551.72/min
[8080000], rate=16717241.38/min
[8090000], rate=16737931.03/min
[8100000], rate=16758620.69/min
[8110000], rate=16779310.34/min
[8120000], rate=16800000.00/min
[8130000], rate=16820689.66/min
[8140000], rate=16841379.31/min
[8150000], rate=16862068.97/min
[8160000], rate=16882758.62/min
[8170000], rate=16340000.00/min
[8180000], rate=16360000.00/min
[8190000], rate=16380000.00/min
[8200000], rate=16400000.00/min
[8210000], rate=16420000.00/min
[8220000], rate=16440000.00/min
[8230000], rate=16460000.00/min
[8240000], rate=16480000.00/min
[8250000], rate=16500000.00/min
[8260000], rate=16520000.00/min
[8270000], rate=16540000.00/min
[8280000], rate=16560000.00/min
[8290000], rate=16580000.00/min
[8300000], rate=16600000.00/min
[8310000], rate=16620000.00/min
[8320000], rate=16640000.00/min
[8330000], rate=16660000.00/min
[8340000], rate=16680000.00/min
[8350000], rate=16700000.00/min
[8360000], rate=16720000.00/min
[8370000], rate=16740000.00/min
[8380000], rate=16760000.00/min
[8390000], rate=16780000.00/min
[8400000], rate=16800000.00/min
[8410000], rate=16820000.00/min
[8420000], rate=16840000.00/min
[8430000], rate=16860000.00/min
[8440000], rate=16880000.00/min
[8450000], rate=16900000.00/min
[8460000], rate=16920000.00/min
[8470000], rate=16393548.39/min
[8480000], rate=16412903.23/min
[8490000], rate=16432258.06/min
[8500000], rate=16451612.90/min
[8510000], rate=16470967.74/min
[8520000], rate=16490322.58/min
[8530000], rate=16509677.42/min
[8540000], rate=16529032.26/min
[8550000], rate=16548387.10/min
[8560000], rate=16567741.94/min
[8570000], rate=16587096.77/min
[8580000], rate=16606451.61/min
[8590000], rate=16625806.45/min
[8600000], rate=16645161.29/min
[8610000], rate=16664516.13/min
[8620000], rate=16683870.97/min
[8630000], rate=16703225.81/min
[8640000], rate=16722580.65/min
[8650000], rate=16741935.48/min
[8660000], rate=16761290.32/min
[8670000], rate=16780645.16/min
[8680000], rate=16800000.00/min
[8690000], rate=16819354.84/min
[8700000], rate=16838709.68/min
[8710000], rate=16858064.52/min
[8720000], rate=16877419.35/min
[8730000], rate=16896774.19/min
[8740000], rate=16916129.03/min
[8750000], rate=16406250.00/min
[8760000], rate=16425000.00/min
[8770000], rate=16443750.00/min
[8780000], rate=16462500.00/min
[8790000], rate=16481250.00/min
[8800000], rate=16500000.00/min
[8810000], rate=16518750.00/min
[8820000], rate=16537500.00/min
[8830000], rate=16556250.00/min
[8840000], rate=16575000.00/min
[8850000], rate=16593750.00/min
[8860000], rate=16612500.00/min
[8870000], rate=16631250.00/min
[8880000], rate=16650000.00/min
[8890000], rate=16668750.00/min
[8900000], rate=16687500.00/min
[8910000], rate=16706250.00/min
[8920000], rate=16725000.00/min
[8930000], rate=16743750.00/min
[8940000], rate=16762500.00/min
[8950000], rate=16781250.00/min
[8960000], rate=16800000.00/min
[8970000], rate=16818750.00/min
[8980000], rate=16837500.00/min
[8990000], rate=16856250.00/min
[9000000], rate=16875000.00/min
[9010000], rate=16893750.00/min
[9020000], rate=16912500.00/min
[9030000], rate=16418181.82/min
[9040000], rate=16436363.64/min
[9050000], rate=16454545.45/min
[9060000], rate=16472727.27/min
[9070000], rate=16490909.09/min
[9080000], rate=16509090.91/min
[9090000], rate=16527272.73/min
[9100000], rate=16545454.55/min
[9110000], rate=16563636.36/min
[9120000], rate=16581818.18/min
[9130000], rate=16600000.00/min
[9140000], rate=16618181.82/min
[9150000], rate=16636363.64/min
[9160000], rate=16654545.45/min
[9170000], rate=16672727.27/min
[9180000], rate=16690909.09/min
[9190000], rate=16709090.91/min
[9200000], rate=16727272.73/min
[9210000], rate=16745454.55/min
[9220000], rate=16763636.36/min
[9230000], rate=16781818.18/min
[9240000], rate=16800000.00/min
[9250000], rate=16818181.82/min
[9260000], rate=16836363.64/min
[9270000], rate=16854545.45/min
[9280000], rate=16872727.27/min
[9290000], rate=16890909.09/min
[9300000], rate=16909090.91/min
[9310000], rate=16927272.73/min
[9320000], rate=16945454.55/min
[9330000], rate=16464705.88/min
[9340000], rate=16482352.94/min
[9350000], rate=16500000.00/min
[9360000], rate=16517647.06/min
[9370000], rate=16535294.12/min
[9380000], rate=16552941.18/min
[9390000], rate=16570588.24/min
[9400000], rate=16588235.29/min
[9410000], rate=16605882.35/min
[9420000], rate=16623529.41/min
[9430000], rate=16641176.47/min
[9440000], rate=16658823.53/min
[9450000], rate=16676470.59/min
[9460000], rate=16694117.65/min
[9470000], rate=16711764.71/min
[9480000], rate=16729411.76/min
[9490000], rate=16747058.82/min
[9500000], rate=16764705.88/min
[9510000], rate=16782352.94/min
[9520000], rate=16800000.00/min
[9530000], rate=16817647.06/min
[9540000], rate=16835294.12/min
[9550000], rate=16852941.18/min
[9560000], rate=16870588.24/min
[9570000], rate=16888235.29/min
[9580000], rate=16905882.35/min
[9590000], rate=16923529.41/min
[9600000], rate=16941176.47/min
[9610000], rate=16958823.53/min
[9620000], rate=16976470.59/min
[9630000], rate=16508571.43/min
[9640000], rate=16525714.29/min
[9650000], rate=16542857.14/min
[9660000], rate=16560000.00/min
[9670000], rate=16577142.86/min
[9680000], rate=16594285.71/min
[9690000], rate=16611428.57/min
[9700000], rate=16628571.43/min
[9710000], rate=16645714.29/min
[9720000], rate=16662857.14/min
[9730000], rate=16680000.00/min
[9740000], rate=16697142.86/min
[9750000], rate=16714285.71/min
[9760000], rate=16731428.57/min
[9770000], rate=16748571.43/min
[9780000], rate=16765714.29/min 09:31:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-16054b-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-16054b-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-16054b-R1_B23WHYVLT4_1.introns: identified 6783 cancer introns
09:31:50 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-16054b-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-16054b-R1_B23WHYVLT4_1.cancer.introns.prelim
09:31:50 : INFO : Running: touch /tmp/nxf.I79tvYIDxR/aih-tih-sc-16054b-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok
09:31:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-16054b-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-16054b-R1_B23WHYVLT4_1.cancer.introns
09:31:50 : 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-16054b-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-16054b-R1_B23WHYVLT4_1.cancer.introns
09:31:50 : INFO : Running: touch /tmp/nxf.I79tvYIDxR/aih-tih-sc-16054b-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok
09:31:50 : INFO : -found 2652 cancer introns
09:31:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-16054b-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-16054b-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-16054b-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:31:51 : INFO : Creating the BED File.
09:31:56 : INFO : Saving Bed File as aih-tih-sc-16054b-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:31:56 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-16054b-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-16054b-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-16054b-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:31:56 : INFO : Running: touch /tmp/nxf.I79tvYIDxR/aih-tih-sc-16054b-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok
09:31:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-16054b-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-16054b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-16054b-R1_B23WHYVLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-16054b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai