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/fa/12bab6e944ec7005ed4fbfcfe5523b/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/cd114c1560772e904029e18f9157cc/tih_rna_sample_00649_B23MVV7LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/cd114c1560772e904029e18f9157cc/tih_rna_sample_00649_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/cd114c1560772e904029e18f9157cc/tih_rna_sample_00649_B23MVV7LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/47a0eb2b7fafb4b1fcdb75de626181/tih_rna_sample_00649_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/12bab6e944ec7005ed4fbfcfe5523b/.command.run ==> STAGING COMPLETE (7 inputs) 09:26:19 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [190000], rate=11400000.00/min [200000], rate=12000000.00/min [210000], rate=12600000.00/min [220000], rate=13200000.00/min [230000], rate=13800000.00/min [240000], rate=14400000.00/min [250000], rate=15000000.00/min [260000], rate=15600000.00/min [270000], rate=16200000.00/min [280000], rate=16800000.00/min [290000], rate=17400000.00/min [300000], rate=18000000.00/min [310000], rate=18600000.00/min [320000], rate=19200000.00/min [330000], rate=19800000.00/min [340000], rate=20400000.00/min [350000], rate=21000000.00/min [360000], rate=21600000.00/min [370000], rate=22200000.00/min [380000], rate=22800000.00/min [390000], rate=23400000.00/min [400000], rate=24000000.00/min [410000], rate=24600000.00/min [420000], rate=25200000.00/min [430000], rate=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=16200000.00/min [550000], rate=16500000.00/min [560000], rate=16800000.00/min [570000], rate=17100000.00/min [580000], rate=17400000.00/min [590000], rate=17700000.00/min [600000], rate=18000000.00/min [610000], rate=18300000.00/min [620000], rate=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=13400000.00/min [680000], rate=13600000.00/min [690000], rate=13800000.00/min [700000], rate=14000000.00/min [710000], rate=14200000.00/min [720000], rate=14400000.00/min [730000], rate=14600000.00/min [740000], rate=14800000.00/min [750000], rate=15000000.00/min [760000], rate=15200000.00/min [770000], rate=15400000.00/min [780000], rate=15600000.00/min [790000], rate=15800000.00/min [800000], rate=16000000.00/min [810000], rate=12150000.00/min [820000], rate=12300000.00/min [830000], rate=12450000.00/min [840000], rate=12600000.00/min [850000], rate=12750000.00/min [860000], rate=12900000.00/min [870000], rate=13050000.00/min [880000], rate=13200000.00/min [890000], rate=13350000.00/min [900000], rate=13500000.00/min [910000], rate=13650000.00/min [920000], rate=13800000.00/min [930000], rate=13950000.00/min [940000], rate=14100000.00/min [950000], rate=14250000.00/min [960000], rate=14400000.00/min [970000], rate=14550000.00/min [980000], rate=11760000.00/min [990000], rate=11880000.00/min [1000000], rate=12000000.00/min [1010000], rate=12120000.00/min [1020000], rate=12240000.00/min [1030000], rate=12360000.00/min [1040000], rate=12480000.00/min [1050000], rate=12600000.00/min [1060000], rate=12720000.00/min [1070000], rate=12840000.00/min [1080000], rate=12960000.00/min [1090000], rate=10900000.00/min [1100000], rate=11000000.00/min [1110000], rate=11100000.00/min [1120000], rate=11200000.00/min [1130000], rate=11300000.00/min [1140000], rate=11400000.00/min [1150000], rate=11500000.00/min [1160000], rate=11600000.00/min [1170000], rate=11700000.00/min [1180000], rate=11800000.00/min [1190000], rate=11900000.00/min [1200000], rate=12000000.00/min [1210000], rate=12100000.00/min [1220000], rate=12200000.00/min [1230000], rate=12300000.00/min [1240000], rate=12400000.00/min [1250000], rate=12500000.00/min [1260000], rate=10800000.00/min [1270000], rate=10885714.29/min [1280000], rate=10971428.57/min [1290000], rate=11057142.86/min [1300000], rate=11142857.14/min [1310000], rate=11228571.43/min [1320000], rate=11314285.71/min [1330000], rate=11400000.00/min [1340000], rate=11485714.29/min [1350000], rate=11571428.57/min [1360000], rate=11657142.86/min [1370000], rate=11742857.14/min [1380000], rate=11828571.43/min [1390000], rate=11914285.71/min [1400000], rate=12000000.00/min [1410000], rate=12085714.29/min [1420000], rate=12171428.57/min [1430000], rate=12257142.86/min [1440000], rate=10800000.00/min [1450000], rate=10875000.00/min [1460000], rate=10950000.00/min [1470000], rate=11025000.00/min [1480000], rate=11100000.00/min [1490000], rate=11175000.00/min [1500000], rate=11250000.00/min [1510000], rate=11325000.00/min [1520000], rate=11400000.00/min [1530000], rate=11475000.00/min [1540000], rate=11550000.00/min [1550000], rate=11625000.00/min [1560000], rate=11700000.00/min [1570000], rate=11775000.00/min [1580000], rate=11850000.00/min [1590000], rate=11925000.00/min [1600000], rate=12000000.00/min [1610000], rate=12075000.00/min [1620000], rate=10800000.00/min [1630000], rate=10866666.67/min [1640000], rate=10933333.33/min [1650000], rate=11000000.00/min [1660000], rate=11066666.67/min [1670000], rate=11133333.33/min [1680000], rate=11200000.00/min [1690000], rate=11266666.67/min [1700000], rate=11333333.33/min [1710000], rate=11400000.00/min [1720000], rate=11466666.67/min [1730000], rate=11533333.33/min [1740000], rate=11600000.00/min [1750000], rate=11666666.67/min [1760000], rate=11733333.33/min [1770000], rate=11800000.00/min [1780000], rate=11866666.67/min [1790000], rate=11933333.33/min [1800000], rate=10800000.00/min [1810000], rate=10860000.00/min [1820000], rate=10920000.00/min [1830000], rate=10980000.00/min [1840000], rate=11040000.00/min [1850000], rate=11100000.00/min [1860000], rate=11160000.00/min [1870000], rate=11220000.00/min [1880000], rate=11280000.00/min [1890000], rate=11340000.00/min [1900000], rate=11400000.00/min [1910000], rate=11460000.00/min [1920000], rate=11520000.00/min [1930000], rate=11580000.00/min [1940000], rate=11640000.00/min [1950000], rate=11700000.00/min [1960000], rate=11760000.00/min [1970000], rate=10745454.55/min [1980000], rate=10800000.00/min [1990000], rate=10854545.45/min [2000000], rate=10909090.91/min [2010000], rate=10963636.36/min [2020000], rate=11018181.82/min [2030000], rate=11072727.27/min [2040000], rate=11127272.73/min [2050000], rate=11181818.18/min [2060000], rate=11236363.64/min [2070000], rate=11290909.09/min [2080000], rate=11345454.55/min [2090000], rate=11400000.00/min [2100000], rate=11454545.45/min [2110000], rate=11509090.91/min [2120000], rate=11563636.36/min [2130000], rate=11618181.82/min [2140000], rate=10700000.00/min [2150000], rate=10750000.00/min [2160000], rate=10800000.00/min [2170000], rate=10850000.00/min [2180000], rate=10900000.00/min [2190000], rate=10950000.00/min [2200000], rate=11000000.00/min [2210000], rate=11050000.00/min [2220000], rate=11100000.00/min [2230000], rate=11150000.00/min [2240000], rate=11200000.00/min [2250000], rate=11250000.00/min [2260000], rate=11300000.00/min [2270000], rate=11350000.00/min [2280000], rate=11400000.00/min [2290000], rate=11450000.00/min [2300000], rate=11500000.00/min [2310000], rate=11550000.00/min [2320000], rate=11600000.00/min [2330000], rate=10753846.15/min [2340000], rate=10800000.00/min [2350000], rate=10846153.85/min [2360000], rate=10892307.69/min [2370000], rate=10938461.54/min [2380000], rate=10984615.38/min [2390000], rate=11030769.23/min [2400000], rate=11076923.08/min [2410000], rate=11123076.92/min [2420000], rate=11169230.77/min [2430000], rate=11215384.62/min [2440000], rate=11261538.46/min [2450000], rate=11307692.31/min [2460000], rate=11353846.15/min [2470000], rate=11400000.00/min [2480000], rate=11446153.85/min [2490000], rate=11492307.69/min [2500000], rate=10714285.71/min [2510000], rate=10757142.86/min [2520000], rate=10800000.00/min [2530000], rate=10842857.14/min [2540000], rate=10885714.29/min [2550000], rate=10928571.43/min [2560000], rate=10971428.57/min [2570000], rate=11014285.71/min [2580000], rate=11057142.86/min [2590000], rate=11100000.00/min [2600000], rate=11142857.14/min [2610000], rate=11185714.29/min [2620000], rate=11228571.43/min [2630000], rate=11271428.57/min [2640000], rate=11314285.71/min [2650000], rate=11357142.86/min [2660000], rate=10640000.00/min [2670000], rate=10680000.00/min [2680000], rate=10720000.00/min [2690000], rate=10760000.00/min [2700000], rate=10800000.00/min [2710000], rate=10840000.00/min [2720000], rate=10880000.00/min [2730000], rate=10920000.00/min [2740000], rate=10960000.00/min [2750000], rate=11000000.00/min [2760000], rate=11040000.00/min [2770000], rate=11080000.00/min [2780000], rate=11120000.00/min [2790000], rate=11160000.00/min [2800000], rate=11200000.00/min [2810000], rate=11240000.00/min [2820000], rate=11280000.00/min [2830000], rate=10612500.00/min [2840000], rate=10650000.00/min [2850000], rate=10687500.00/min [2860000], rate=10725000.00/min [2870000], rate=10762500.00/min [2880000], rate=10800000.00/min [2890000], rate=10837500.00/min [2900000], rate=10875000.00/min [2910000], rate=10912500.00/min [2920000], rate=10950000.00/min [2930000], rate=10987500.00/min [2940000], rate=11025000.00/min [2950000], rate=11062500.00/min [2960000], rate=11100000.00/min [2970000], rate=11137500.00/min [2980000], rate=11175000.00/min [2990000], rate=11212500.00/min [3000000], rate=11250000.00/min [3010000], rate=11287500.00/min [3020000], rate=10658823.53/min [3030000], rate=10694117.65/min [3040000], rate=10729411.76/min [3050000], rate=10764705.88/min [3060000], rate=10800000.00/min [3070000], rate=10835294.12/min [3080000], rate=10870588.24/min [3090000], rate=10905882.35/min [3100000], rate=10941176.47/min [3110000], rate=10976470.59/min [3120000], rate=11011764.71/min [3130000], rate=11047058.82/min [3140000], rate=11082352.94/min [3150000], rate=11117647.06/min [3160000], rate=11152941.18/min [3170000], rate=11188235.29/min [3180000], rate=11223529.41/min [3190000], rate=11258823.53/min [3200000], rate=11294117.65/min [3210000], rate=10700000.00/min [3220000], rate=10733333.33/min [3230000], rate=10766666.67/min [3240000], rate=10800000.00/min [3250000], rate=10833333.33/min [3260000], rate=10866666.67/min [3270000], rate=10900000.00/min [3280000], rate=10933333.33/min [3290000], rate=10966666.67/min [3300000], rate=11000000.00/min [3310000], rate=11033333.33/min [3320000], rate=11066666.67/min [3330000], rate=11100000.00/min [3340000], rate=11133333.33/min [3350000], rate=11166666.67/min [3360000], rate=11200000.00/min [3370000], rate=11233333.33/min [3380000], rate=10673684.21/min [3390000], rate=10705263.16/min [3400000], rate=10736842.11/min [3410000], rate=10768421.05/min [3420000], rate=10800000.00/min [3430000], rate=10831578.95/min [3440000], rate=10863157.89/min [3450000], rate=10894736.84/min [3460000], rate=10926315.79/min [3470000], rate=10957894.74/min [3480000], rate=10989473.68/min [3490000], rate=11021052.63/min [3500000], rate=11052631.58/min [3510000], rate=11084210.53/min [3520000], rate=11115789.47/min [3530000], rate=11147368.42/min [3540000], rate=10620000.00/min [3550000], rate=10650000.00/min [3560000], rate=10680000.00/min [3570000], rate=10710000.00/min [3580000], rate=10740000.00/min [3590000], rate=10770000.00/min [3600000], rate=10800000.00/min [3610000], rate=10830000.00/min [3620000], rate=10860000.00/min [3630000], rate=10890000.00/min [3640000], rate=10920000.00/min [3650000], rate=10950000.00/min [3660000], rate=10980000.00/min [3670000], rate=11010000.00/min [3680000], rate=11040000.00/min [3690000], rate=11070000.00/min [3700000], rate=11100000.00/min [3710000], rate=11130000.00/min [3720000], rate=11160000.00/min [3730000], rate=10657142.86/min [3740000], rate=10685714.29/min [3750000], rate=10714285.71/min [3760000], rate=10742857.14/min [3770000], rate=10771428.57/min [3780000], rate=10800000.00/min [3790000], rate=10828571.43/min [3800000], rate=10857142.86/min [3810000], rate=10885714.29/min [3820000], rate=10914285.71/min [3830000], rate=10942857.14/min [3840000], rate=10971428.57/min [3850000], rate=11000000.00/min [3860000], rate=11028571.43/min [3870000], rate=11057142.86/min [3880000], rate=11085714.29/min [3890000], rate=10609090.91/min [3900000], rate=10636363.64/min [3910000], rate=10663636.36/min [3920000], rate=10690909.09/min [3930000], rate=10718181.82/min [3940000], rate=10745454.55/min [3950000], rate=10772727.27/min [3960000], rate=10800000.00/min [3970000], rate=10827272.73/min [3980000], rate=10854545.45/min [3990000], rate=10881818.18/min [4000000], rate=10909090.91/min [4010000], rate=10936363.64/min [4020000], rate=10963636.36/min [4030000], rate=10990909.09/min [4040000], rate=11018181.82/min [4050000], rate=11045454.55/min [4060000], rate=11072727.27/min [4070000], rate=11100000.00/min [4080000], rate=10643478.26/min [4090000], rate=10669565.22/min [4100000], rate=10695652.17/min [4110000], rate=10721739.13/min [4120000], rate=10747826.09/min [4130000], rate=10773913.04/min [4140000], rate=10800000.00/min [4150000], rate=10826086.96/min [4160000], rate=10852173.91/min [4170000], rate=10878260.87/min [4180000], rate=10904347.83/min [4190000], rate=10930434.78/min [4200000], rate=10956521.74/min [4210000], rate=10982608.70/min [4220000], rate=11008695.65/min [4230000], rate=11034782.61/min [4240000], rate=11060869.57/min [4250000], rate=10625000.00/min [4260000], rate=10650000.00/min [4270000], rate=10675000.00/min [4280000], rate=10700000.00/min [4290000], rate=10725000.00/min [4300000], rate=10750000.00/min [4310000], rate=10775000.00/min [4320000], rate=10800000.00/min [4330000], rate=10825000.00/min [4340000], rate=10850000.00/min [4350000], rate=10875000.00/min [4360000], rate=10900000.00/min [4370000], rate=10925000.00/min [4380000], rate=10950000.00/min [4390000], rate=10975000.00/min [4400000], rate=11000000.00/min [4410000], rate=11025000.00/min [4420000], rate=11050000.00/min [4430000], rate=10632000.00/min [4440000], rate=10656000.00/min [4450000], rate=10680000.00/min [4460000], rate=10704000.00/min [4470000], rate=10728000.00/min [4480000], rate=10752000.00/min [4490000], rate=10776000.00/min [4500000], rate=10800000.00/min [4510000], rate=10824000.00/min [4520000], rate=10848000.00/min [4530000], rate=10872000.00/min [4540000], rate=10896000.00/min [4550000], rate=10920000.00/min [4560000], rate=10944000.00/min [4570000], rate=10968000.00/min [4580000], rate=10992000.00/min [4590000], rate=11016000.00/min [4600000], rate=11040000.00/min [4610000], rate=10638461.54/min [4620000], rate=10661538.46/min [4630000], rate=10684615.38/min [4640000], rate=10707692.31/min [4650000], rate=10730769.23/min [4660000], rate=10753846.15/min [4670000], rate=10776923.08/min [4680000], rate=10800000.00/min [4690000], rate=10823076.92/min [4700000], rate=10846153.85/min [4710000], rate=10869230.77/min [4720000], rate=10892307.69/min [4730000], rate=10915384.62/min [4740000], rate=10938461.54/min [4750000], rate=10961538.46/min [4760000], rate=10984615.38/min [4770000], rate=11007692.31/min [4780000], rate=10622222.22/min [4790000], rate=10644444.44/min [4800000], rate=10666666.67/min [4810000], rate=10688888.89/min [4820000], rate=10711111.11/min [4830000], rate=10733333.33/min [4840000], rate=10755555.56/min [4850000], rate=10777777.78/min [4860000], rate=10800000.00/min [4870000], rate=10822222.22/min [4880000], rate=10844444.44/min [4890000], rate=10866666.67/min [4900000], rate=10888888.89/min [4910000], rate=10911111.11/min [4920000], rate=10933333.33/min [4930000], rate=10955555.56/min [4940000], rate=10977777.78/min [4950000], rate=11000000.00/min [4960000], rate=11022222.22/min [4970000], rate=11044444.44/min [4980000], rate=11066666.67/min [4990000], rate=10692857.14/min [5000000], rate=10714285.71/min [5010000], rate=10735714.29/min [5020000], rate=10757142.86/min [5030000], rate=10778571.43/min [5040000], rate=10800000.00/min [5050000], rate=10821428.57/min [5060000], rate=10842857.14/min [5070000], rate=10864285.71/min [5080000], rate=10885714.29/min [5090000], rate=10907142.86/min [5100000], rate=10928571.43/min [5110000], rate=10950000.00/min [5120000], rate=10971428.57/min [5130000], rate=10992857.14/min [5140000], rate=11014285.71/min [5150000], rate=11035714.29/min [5160000], rate=11057142.86/min [5170000], rate=11078571.43/min [5180000], rate=11100000.00/min [5190000], rate=11121428.57/min [5200000], rate=11142857.14/min [5210000], rate=11164285.71/min [5220000], rate=11185714.29/min [5230000], rate=10820689.66/min [5240000], rate=10841379.31/min [5250000], rate=10862068.97/min [5260000], rate=10882758.62/min [5270000], rate=10903448.28/min [5280000], rate=10924137.93/min [5290000], rate=10944827.59/min [5300000], rate=10965517.24/min [5310000], rate=10986206.90/min [5320000], rate=11006896.55/min [5330000], rate=11027586.21/min [5340000], rate=11048275.86/min [5350000], rate=11068965.52/min [5360000], rate=11089655.17/min [5370000], rate=11110344.83/min [5380000], rate=11131034.48/min [5390000], rate=11151724.14/min [5400000], rate=11172413.79/min [5410000], rate=11193103.45/min [5420000], rate=11213793.10/min [5430000], rate=11234482.76/min [5440000], rate=11255172.41/min [5450000], rate=11275862.07/min [5460000], rate=10920000.00/min [5470000], rate=10940000.00/min [5480000], rate=10960000.00/min [5490000], rate=10980000.00/min [5500000], rate=11000000.00/min [5510000], rate=11020000.00/min [5520000], rate=11040000.00/min [5530000], rate=11060000.00/min [5540000], rate=11080000.00/min [5550000], rate=11100000.00/min [5560000], rate=11120000.00/min [5570000], rate=11140000.00/min [5580000], rate=11160000.00/min [5590000], rate=11180000.00/min [5600000], rate=11200000.00/min [5610000], rate=11220000.00/min [5620000], rate=11240000.00/min [5630000], rate=11260000.00/min [5640000], rate=11280000.00/min [5650000], rate=11300000.00/min [5660000], rate=11320000.00/min [5670000], rate=11340000.00/min [5680000], rate=11360000.00/min [5690000], rate=11380000.00/min [5700000], rate=11400000.00/min [5710000], rate=11420000.00/min [5720000], rate=11070967.74/min [5730000], rate=11090322.58/min [5740000], rate=11109677.42/min [5750000], rate=11129032.26/min [5760000], rate=11148387.10/min [5770000], rate=11167741.94/min [5780000], rate=11187096.77/min [5790000], rate=11206451.61/min [5800000], rate=11225806.45/min [5810000], rate=11245161.29/min [5820000], rate=11264516.13/min [5830000], rate=11283870.97/min [5840000], rate=11303225.81/min [5850000], rate=11322580.65/min [5860000], rate=11341935.48/min [5870000], rate=11361290.32/min [5880000], rate=11380645.16/min [5890000], rate=11400000.00/min [5900000], rate=11419354.84/min [5910000], rate=11081250.00/min [5920000], rate=11100000.00/min [5930000], rate=11118750.00/min [5940000], rate=11137500.00/min [5950000], rate=11156250.00/min [5960000], rate=11175000.00/min [5970000], rate=11193750.00/min [5980000], rate=11212500.00/min [5990000], rate=11231250.00/min [6000000], rate=11250000.00/min [6010000], rate=11268750.00/min [6020000], rate=11287500.00/min [6030000], rate=11306250.00/min [6040000], rate=11325000.00/min [6050000], rate=11343750.00/min [6060000], rate=11362500.00/min [6070000], rate=11381250.00/min [6080000], rate=11400000.00/min [6090000], rate=11072727.27/min [6100000], rate=11090909.09/min [6110000], rate=11109090.91/min [6120000], rate=11127272.73/min [6130000], rate=11145454.55/min [6140000], rate=11163636.36/min [6150000], rate=11181818.18/min [6160000], rate=11200000.00/min [6170000], rate=11218181.82/min [6180000], rate=11236363.64/min [6190000], rate=11254545.45/min [6200000], rate=11272727.27/min [6210000], rate=11290909.09/min [6220000], rate=11309090.91/min [6230000], rate=11327272.73/min [6240000], rate=11345454.55/min [6250000], rate=11363636.36/min [6260000], rate=11381818.18/min [6270000], rate=11400000.00/min [6280000], rate=11418181.82/min [6290000], rate=11100000.00/min [6300000], rate=11117647.06/min [6310000], rate=11135294.12/min [6320000], rate=11152941.18/min [6330000], rate=11170588.24/min [6340000], rate=11188235.29/min [6350000], rate=11205882.35/min [6360000], rate=11223529.41/min [6370000], rate=11241176.47/min [6380000], rate=11258823.53/min [6390000], rate=11276470.59/min [6400000], rate=11294117.65/min [6410000], rate=11311764.71/min [6420000], rate=11329411.76/min [6430000], rate=11347058.82/min [6440000], rate=11364705.88/min [6450000], rate=11382352.94/min [6460000], rate=11400000.00/min [6470000], rate=11417647.06/min [6480000], rate=11435294.12/min [6490000], rate=11452941.18/min [6500000], rate=11470588.24/min [6510000], rate=11488235.29/min [6520000], rate=11505882.35/min [6530000], rate=11194285.71/min [6540000], rate=11211428.57/min [6550000], rate=11228571.43/min [6560000], rate=11245714.29/min [6570000], rate=11262857.14/min [6580000], rate=11280000.00/min [6590000], rate=11297142.86/min [6600000], rate=11314285.71/min [6610000], rate=11331428.57/min [6620000], rate=11348571.43/min [6630000], rate=11365714.29/min [6640000], rate=11382857.14/min [6650000], rate=11400000.00/min [6660000], rate=11417142.86/min [6670000], rate=11434285.71/min [6680000], rate=11451428.57/min [6690000], rate=11468571.43/min [6700000], rate=11485714.29/min [6710000], rate=11502857.14/min [6720000], rate=11520000.00/min [6730000], rate=11537142.86/min [6740000], rate=11554285.71/min [6750000], rate=11571428.57/min [6760000], rate=11588571.43/min [6770000], rate=11605714.29/min [6780000], rate=11622857.14/min [6790000], rate=11640000.00/min [6800000], rate=11657142.86/min [6810000], rate=11674285.71/min [6820000], rate=11691428.57/min [6830000], rate=11708571.43/min [6840000], rate=11725714.29/min [6850000], rate=11742857.14/min [6860000], rate=11433333.33/min [6870000], rate=11450000.00/min [6880000], rate=11466666.67/min [6890000], rate=11483333.33/min [6900000], rate=11500000.00/min [6910000], rate=11516666.67/min [6920000], rate=11533333.33/min [6930000], rate=11550000.00/min [6940000], rate=11566666.67/min [6950000], rate=11583333.33/min [6960000], rate=11600000.00/min [6970000], rate=11616666.67/min [6980000], rate=11633333.33/min [6990000], rate=11650000.00/min [7000000], rate=11666666.67/min [7010000], rate=11683333.33/min [7020000], rate=11700000.00/min [7030000], rate=11716666.67/min [7040000], rate=11733333.33/min [7050000], rate=11750000.00/min [7060000], rate=11766666.67/min [7070000], rate=11464864.86/min [7080000], rate=11481081.08/min [7090000], rate=11497297.30/min [7100000], rate=11513513.51/min [7110000], rate=11529729.73/min [7120000], rate=11545945.95/min [7130000], rate=11562162.16/min [7140000], rate=11578378.38/min [7150000], rate=11594594.59/min [7160000], rate=11610810.81/min [7170000], rate=11627027.03/min [7180000], rate=11643243.24/min [7190000], rate=11659459.46/min [7200000], rate=11675675.68/min [7210000], rate=11691891.89/min [7220000], rate=11708108.11/min [7230000], rate=11724324.32/min [7240000], rate=11740540.54/min [7250000], rate=11756756.76/min [7260000], rate=11772972.97/min [7270000], rate=11789189.19/min [7280000], rate=11805405.41/min [7290000], rate=11821621.62/min [7300000], rate=11837837.84/min [7310000], rate=11854054.05/min [7320000], rate=11870270.27/min [7330000], rate=11886486.49/min [7340000], rate=11589473.68/min [7350000], rate=11605263.16/min [7360000], rate=11621052.63/min [7370000], rate=11636842.11/min [7380000], rate=11652631.58/min [7390000], rate=11668421.05/min [7400000], rate=11684210.53/min [7410000], rate=11700000.00/min [7420000], rate=11715789.47/min [7430000], rate=11731578.95/min [7440000], rate=11747368.42/min [7450000], rate=11763157.89/min [7460000], rate=11778947.37/min [7470000], rate=11794736.84/min [7480000], rate=11810526.32/min [7490000], rate=11826315.79/min [7500000], rate=11842105.26/min [7510000], rate=11857894.74/min [7520000], rate=11873684.21/min [7530000], rate=11889473.68/min [7540000], rate=11905263.16/min [7550000], rate=11921052.63/min [7560000], rate=11936842.11/min [7570000], rate=11952631.58/min [7580000], rate=11968421.05/min [7590000], rate=11676923.08/min [7600000], rate=11692307.69/min [7610000], rate=11707692.31/min [7620000], rate=11723076.92/min [7630000], rate=11738461.54/min [7640000], rate=11753846.15/min [7650000], rate=11769230.77/min [7660000], rate=11784615.38/min [7670000], rate=11800000.00/min [7680000], rate=11815384.62/min [7690000], rate=11830769.23/min [7700000], rate=11846153.85/min [7710000], rate=11861538.46/min [7720000], rate=11876923.08/min [7730000], rate=11892307.69/min [7740000], rate=11907692.31/min [7750000], rate=11923076.92/min [7760000], rate=11938461.54/min [7770000], rate=11953846.15/min [7780000], rate=11969230.77/min [7790000], rate=11984615.38/min [7800000], rate=12000000.00/min [7810000], rate=12015384.62/min [7820000], rate=12030769.23/min [7830000], rate=12046153.85/min [7840000], rate=12061538.46/min [7850000], rate=12076923.08/min [7860000], rate=11790000.00/min [7870000], rate=11805000.00/min [7880000], rate=11820000.00/min [7890000], rate=11835000.00/min [7900000], rate=11850000.00/min [7910000], rate=11865000.00/min [7920000], rate=11880000.00/min [7930000], rate=11895000.00/min [7940000], rate=11910000.00/min [7950000], rate=11925000.00/min [7960000], rate=11940000.00/min [7970000], rate=11955000.00/min [7980000], rate=11970000.00/min [7990000], rate=11985000.00/min [8000000], rate=12000000.00/min [8010000], rate=12015000.00/min [8020000], rate=12030000.00/min [8030000], rate=12045000.00/min [8040000], rate=12060000.00/min [8050000], rate=12075000.00/min [8060000], rate=12090000.00/min [8070000], rate=12105000.00/min [8080000], rate=12120000.00/min [8090000], rate=12135000.00/min [8100000], rate=12150000.00/min [8110000], rate=12165000.00/min [8120000], rate=11882926.83/min [8130000], rate=11897560.98/min [8140000], rate=11912195.12/min [8150000], rate=11926829.27/min [8160000], rate=11941463.41/min [8170000], rate=11956097.56/min [8180000], rate=11970731.71/min [8190000], rate=11985365.85/min [8200000], rate=12000000.00/min [8210000], rate=12014634.15/min [8220000], rate=12029268.29/min [8230000], rate=12043902.44/min [8240000], rate=12058536.59/min [8250000], rate=12073170.73/min [8260000], rate=12087804.88/min [8270000], rate=12102439.02/min [8280000], rate=12117073.17/min [8290000], rate=12131707.32/min [8300000], rate=12146341.46/min [8310000], rate=12160975.61/min [8320000], rate=12175609.76/min [8330000], rate=12190243.90/min [8340000], rate=12204878.05/min [8350000], rate=12219512.20/min [8360000], rate=12234146.34/min [8370000], rate=12248780.49/min [8380000], rate=11971428.57/min [8390000], rate=11985714.29/min [8400000], rate=12000000.00/min [8410000], rate=12014285.71/min [8420000], rate=12028571.43/min [8430000], rate=12042857.14/min [8440000], rate=12057142.86/min [8450000], rate=12071428.57/min [8460000], rate=12085714.29/min [8470000], rate=12100000.00/min [8480000], rate=12114285.71/min [8490000], rate=12128571.43/min [8500000], rate=12142857.14/min [8510000], rate=12157142.86/min [8520000], rate=12171428.57/min [8530000], rate=12185714.29/min [8540000], rate=12200000.00/min [8550000], rate=12214285.71/min [8560000], rate=12228571.43/min [8570000], rate=12242857.14/min [8580000], rate=12257142.86/min [8590000], rate=12271428.57/min [8600000], rate=12285714.29/min [8610000], rate=12300000.00/min [8620000], rate=12314285.71/min [8630000], rate=12328571.43/min [8640000], rate=12342857.14/min [8650000], rate=12069767.44/min [8660000], rate=12083720.93/min [8670000], rate=12097674.42/min [8680000], rate=12111627.91/min [8690000], rate=12125581.40/min [8700000], rate=12139534.88/min [8710000], rate=12153488.37/min [8720000], rate=12167441.86/min [8730000], rate=12181395.35/min [8740000], rate=12195348.84/min [8750000], rate=12209302.33/min [8760000], rate=12223255.81/min [8770000], rate=12237209.30/min [8780000], rate=12251162.79/min [8790000], rate=12265116.28/min [8800000], rate=12279069.77/min [8810000], rate=12293023.26/min [8820000], rate=12306976.74/min [8830000], rate=12320930.23/min [8840000], rate=12334883.72/min [8850000], rate=12348837.21/min [8860000], rate=12362790.70/min [8870000], rate=12376744.19/min [8880000], rate=12390697.67/min [8890000], rate=12404651.16/min [8900000], rate=12418604.65/min [8910000], rate=12150000.00/min [8920000], rate=12163636.36/min [8930000], rate=12177272.73/min [8940000], rate=12190909.09/min [8950000], rate=12204545.45/min [8960000], rate=12218181.82/min [8970000], rate=12231818.18/min [8980000], rate=12245454.55/min [8990000], rate=12259090.91/min [9000000], rate=12272727.27/min [9010000], rate=12286363.64/min [9020000], rate=12300000.00/min [9030000], rate=12313636.36/min [9040000], rate=12327272.73/min [9050000], rate=12340909.09/min [9060000], rate=12354545.45/min [9070000], rate=12368181.82/min [9080000], rate=12381818.18/min [9090000], rate=12395454.55/min [9100000], rate=12409090.91/min [9110000], rate=12422727.27/min [9120000], rate=12436363.64/min [9130000], rate=12450000.00/min [9140000], rate=12463636.36/min [9150000], rate=12477272.73/min [9160000], rate=12213333.33/min [9170000], rate=12226666.67/min [9180000], rate=12240000.00/min [9190000], rate=12253333.33/min [9200000], rate=12266666.67/min [9210000], rate=12280000.00/min [9220000], rate=12293333.33/min [9230000], rate=12306666.67/min [9240000], rate=12320000.00/min [9250000], rate=12333333.33/min [9260000], rate=12346666.67/min [9270000], rate=12360000.00/min [9280000], rate=12373333.33/min [9290000], rate=12386666.67/min [9300000], rate=12400000.00/min [9310000], rate=12413333.33/min [9320000], rate=12426666.67/min [9330000], rate=12440000.00/min [9340000], rate=12453333.33/min [9350000], rate=12466666.67/min [9360000], rate=12480000.00/min [9370000], rate=12493333.33/min [9380000], rate=12506666.67/min [9390000], rate=12520000.00/min [9400000], rate=12533333.33/min [9410000], rate=12546666.67/min [9420000], rate=12560000.00/min [9430000], rate=12300000.00/min [9440000], rate=12313043.48/min [9450000], rate=12326086.96/min [9460000], rate=12339130.43/min [9470000], rate=12352173.91/min [9480000], rate=12365217.39/min [9490000], rate=12378260.87/min [9500000], rate=12391304.35/min [9510000], rate=12404347.83/min [9520000], rate=12417391.30/min [9530000], rate=12430434.78/min [9540000], rate=12443478.26/min [9550000], rate=12456521.74/min [9560000], rate=12469565.22/min [9570000], rate=12482608.70/min [9580000], rate=12495652.17/min [9590000], rate=12508695.65/min [9600000], rate=12521739.13/min [9610000], rate=12534782.61/min [9620000], rate=12547826.09/min [9630000], rate=12560869.57/min [9640000], rate=12573913.04/min [9650000], rate=12319148.94/min [9660000], rate=12331914.89/min [9670000], rate=12344680.85/min [9680000], rate=12357446.81/min [9690000], rate=12370212.77/min [9700000], rate=12382978.72/min [9710000], rate=12395744.68/min [9720000], rate=12408510.64/min [9730000], rate=12421276.60/min [9740000], rate=12434042.55/min [9750000], rate=12446808.51/min [9760000], rate=12459574.47/min [9770000], rate=12472340.43/min [9780000], rate=12485106.38/min [9790000], rate=12497872.34/min [9800000], rate=12510638.30/min [9810000], rate=12523404.26/min [9820000], rate=12536170.21/min [9830000], rate=12548936.17/min [9840000], rate=12561702.13/min [9850000], rate=12574468.09/min [9860000], rate=12587234.04/min [9870000], rate=12600000.00/min [9880000], rate=12612765.96/min [9890000], rate=12625531.91/min [9900000], rate=12375000.00/min [9910000], rate=12387500.00/min [9920000], rate=12400000.00/min [9930000], rate=12412500.00/min [9940000], rate=12425000.00/min [9950000], rate=12437500.00/min [9960000], rate=12450000.00/min [9970000], rate=12462500.00/min [9980000], rate=12475000.00/min [9990000], rate=12487500.00/min [10000000], rate=12500000.00/min [10010000], rate=12512500.00/min [10020000], rate=12525000.00/min [10030000], rate=12537500.00/min [10040000], rate=12550000.00/min [10050000], rate=12562500.00/min [10060000], rate=12575000.00/min [10070000], rate=12587500.00/min [10080000], rate=12600000.00/min [10090000], rate=12612500.00/min [10100000], rate=12625000.00/min [10110000], rate=12637500.00/min [10120000], rate=12650000.00/min [10130000], rate=12662500.00/min [10140000], rate=12675000.00/min [10150000], rate=12687500.00/min [10160000], rate=12440816.33/min [10170000], rate=12453061.22/min [10180000], rate=12465306.12/min [10190000], rate=12477551.02/min [10200000], rate=12489795.92/min [10210000], rate=12502040.82/min [10220000], rate=12514285.71/min [10230000], rate=12526530.61/min [10240000], rate=12538775.51/min [10250000], rate=12551020.41/min [10260000], rate=12563265.31/min [10270000], rate=12575510.20/min [10280000], rate=12587755.10/min [10290000], rate=12600000.00/min [10300000], rate=12612244.90/min [10310000], rate=12624489.80/min 09:27:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00649_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00649_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_00649_B23MVV7LT4_1.introns: identified 8332 cancer introns 09:27:21 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00649_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00649_B23MVV7LT4_1.cancer.introns.prelim 09:27:21 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/prelim_introns.ok 09:27:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00649_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00649_B23MVV7LT4_1.cancer.introns 09:27:21 : 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_00649_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00649_B23MVV7LT4_1.cancer.introns 09:27:21 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/introns_filtered.ok 09:27:21 : INFO : -found 3593 cancer introns 09:27:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00649_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00649_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00649_B23MVV7LT4_1.introns.for_IGV.bed 09:27:21 : INFO : Creating the BED File. 09:27:29 : INFO : Saving Bed File as tih_rna_sample_00649_B23MVV7LT4_1.introns.for_IGV.bed 09:27:29 : INFO : Execution Time = 0.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00649_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00649_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00649_B23MVV7LT4_1.introns.for_IGV.bed 09:27:29 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 09:27:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00649_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00649_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00649_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00649_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 09:57:32 : INFO : Execution Time = 30.04 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00649_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00649_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00649_B23MVV7LT4_1 09:57:32 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 09:57:32 : INFO : Running: samtools sort -o tih_rna_sample_00649_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00649_B23MVV7LT4_1.cancer_intron_reads.bam 09:57:33 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00649_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00649_B23MVV7LT4_1.cancer_intron_reads.bam 09:57:33 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 09:57:33 : INFO : Running: samtools sort -o tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 146 files and 1 in-memory blocks... 10:31:13 : INFO : Execution Time = 33.67 minutes. CMD: samtools sort -o tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.bam 10:31:13 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 10:31:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.bam Done with chr chr1. Done with chr chr2. Done with chr chr3. Done with chr chr4. Done with chr chr5. Done with chr chr6. Done with chr chr7. Done with chr chr8. Done with chr chr9. Done with chr chr10. Done with chr chr11. Done with chr chr12. Done with chr chr13. Done with chr chr14. Done with chr chr15. Done with chr chr16. Done with chr chr17. Done with chr chr18. Done with chr chr19. Done with chr chr20. Done with chr chr21. Done with chr chr22. Done with chr chrX. 10:40:43 : INFO : Execution Time = 9.51 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.bam 10:40:43 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:40:43 : INFO : Running: samtools sort -o tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:41:35 : INFO : Execution Time = 0.85 minutes. CMD: samtools sort -o tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 10:41:35 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:41:35 : INFO : Running: samtools index tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 10:41:41 : INFO : Execution Time = 0.10 minutes. CMD: samtools index tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 10:41:41 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/tih_rna_sample_00649_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:41:41 : INFO : Running: samtools index tih_rna_sample_00649_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 10:41:41 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00649_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 10:41:41 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/tih_rna_sample_00649_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:41:41 : INFO : Running: create_report tih_rna_sample_00649_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00649_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00649_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00649_B23MVV7LT4_1' [W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi 10:48:29 : INFO : Execution Time = 6.79 minutes. CMD: create_report tih_rna_sample_00649_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00649_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00649_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00649_B23MVV7LT4_1' 10:48:29 : INFO : Running: touch /tmp/nxf.XnStS3Ckf3/tih_rna_sample_00649_B23MVV7LT4_1.chckpts/igv_create_html.ok 10:48:29 : INFO : done.