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/4a/56b4b75017ee43faf2ab4b159e5dba/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/bc00b8bd4961ec79badbb39c1b49bf/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/56b4b75017ee43faf2ab4b159e5dba/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/bc00b8bd4961ec79badbb39c1b49bf/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/6208475b21dee22b5f7bd557f491a4/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/bc00b8bd4961ec79badbb39c1b49bf/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)
07:46:19 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[70000], rate=4200000.00/min
[80000], rate=4800000.00/min
[90000], rate=5400000.00/min
[100000], rate=6000000.00/min
[110000], rate=6600000.00/min
[120000], rate=7200000.00/min
[130000], rate=7800000.00/min
[140000], rate=8400000.00/min
[150000], rate=9000000.00/min
[160000], rate=9600000.00/min
[170000], rate=10200000.00/min
[180000], rate=10800000.00/min
[190000], rate=11400000.00/min
[200000], rate=12000000.00/min
[210000], rate=12600000.00/min
[220000], rate=13200000.00/min
[230000], rate=13800000.00/min
[240000], rate=14400000.00/min
[250000], rate=15000000.00/min
[260000], rate=15600000.00/min
[270000], rate=16200000.00/min
[280000], rate=16800000.00/min
[290000], rate=8700000.00/min
[300000], rate=9000000.00/min
[310000], rate=9300000.00/min
[320000], rate=9600000.00/min
[330000], rate=9900000.00/min
[340000], rate=10200000.00/min
[350000], rate=10500000.00/min
[360000], rate=10800000.00/min
[370000], rate=11100000.00/min
[380000], rate=11400000.00/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=10000000.00/min
[510000], rate=10200000.00/min
[520000], rate=10400000.00/min
[530000], rate=10600000.00/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=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=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=11700000.00/min
[790000], rate=11850000.00/min
[800000], rate=12000000.00/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=11520000.00/min
[970000], rate=11640000.00/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=13080000.00/min
[1100000], rate=13200000.00/min
[1110000], rate=13320000.00/min
[1120000], rate=13440000.00/min
[1130000], rate=13560000.00/min
[1140000], rate=13680000.00/min
[1150000], rate=13800000.00/min
[1160000], rate=13920000.00/min
[1170000], rate=14040000.00/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=12600000.00/min
[1270000], rate=12700000.00/min
[1280000], rate=12800000.00/min
[1290000], rate=12900000.00/min
[1300000], rate=13000000.00/min
[1310000], rate=13100000.00/min
[1320000], rate=13200000.00/min
[1330000], rate=13300000.00/min
[1340000], rate=13400000.00/min
[1350000], rate=13500000.00/min
[1360000], rate=13600000.00/min
[1370000], rate=13700000.00/min
[1380000], rate=13800000.00/min
[1390000], rate=13900000.00/min
[1400000], rate=14000000.00/min
[1410000], rate=14100000.00/min
[1420000], rate=14200000.00/min
[1430000], rate=14300000.00/min
[1440000], rate=14400000.00/min
[1450000], rate=12428571.43/min
[1460000], rate=12514285.71/min
[1470000], rate=12600000.00/min
[1480000], rate=12685714.29/min
[1490000], rate=12771428.57/min
[1500000], rate=12857142.86/min
[1510000], rate=12942857.14/min
[1520000], rate=13028571.43/min
[1530000], rate=13114285.71/min
[1540000], rate=13200000.00/min
[1550000], rate=13285714.29/min
[1560000], rate=13371428.57/min
[1570000], rate=13457142.86/min
[1580000], rate=13542857.14/min
[1590000], rate=13628571.43/min
[1600000], rate=13714285.71/min
[1610000], rate=13800000.00/min
[1620000], rate=13885714.29/min
[1630000], rate=13971428.57/min
[1640000], rate=14057142.86/min
[1650000], rate=14142857.14/min
[1660000], rate=14228571.43/min
[1670000], rate=14314285.71/min
[1680000], rate=14400000.00/min
[1690000], rate=14485714.29/min
[1700000], rate=14571428.57/min
[1710000], rate=14657142.86/min
[1720000], rate=14742857.14/min
[1730000], rate=14828571.43/min
[1740000], rate=14914285.71/min
[1750000], rate=13125000.00/min
[1760000], rate=13200000.00/min
[1770000], rate=13275000.00/min
[1780000], rate=13350000.00/min
[1790000], rate=13425000.00/min
[1800000], rate=13500000.00/min
[1810000], rate=13575000.00/min
[1820000], rate=13650000.00/min
[1830000], rate=13725000.00/min
[1840000], rate=13800000.00/min
[1850000], rate=13875000.00/min
[1860000], rate=13950000.00/min
[1870000], rate=14025000.00/min
[1880000], rate=14100000.00/min
[1890000], rate=14175000.00/min
[1900000], rate=14250000.00/min
[1910000], rate=14325000.00/min
[1920000], rate=14400000.00/min
[1930000], rate=14475000.00/min
[1940000], rate=14550000.00/min
[1950000], rate=14625000.00/min
[1960000], rate=14700000.00/min
[1970000], rate=14775000.00/min
[1980000], rate=14850000.00/min
[1990000], rate=14925000.00/min
[2000000], rate=13333333.33/min
[2010000], rate=13400000.00/min
[2020000], rate=13466666.67/min
[2030000], rate=13533333.33/min
[2040000], rate=13600000.00/min
[2050000], rate=13666666.67/min
[2060000], rate=13733333.33/min
[2070000], rate=13800000.00/min
[2080000], rate=13866666.67/min
[2090000], rate=13933333.33/min
[2100000], rate=14000000.00/min
[2110000], rate=14066666.67/min
[2120000], rate=14133333.33/min
[2130000], rate=14200000.00/min
[2140000], rate=14266666.67/min
[2150000], rate=14333333.33/min
[2160000], rate=14400000.00/min
[2170000], rate=14466666.67/min
[2180000], rate=14533333.33/min
[2190000], rate=14600000.00/min
[2200000], rate=14666666.67/min
[2210000], rate=14733333.33/min
[2220000], rate=14800000.00/min
[2230000], rate=14866666.67/min
[2240000], rate=14933333.33/min
[2250000], rate=13500000.00/min
[2260000], rate=13560000.00/min
[2270000], rate=13620000.00/min
[2280000], rate=13680000.00/min
[2290000], rate=13740000.00/min
[2300000], rate=13800000.00/min
[2310000], rate=13860000.00/min
[2320000], rate=13920000.00/min
[2330000], rate=13980000.00/min
[2340000], rate=14040000.00/min
[2350000], rate=14100000.00/min
[2360000], rate=14160000.00/min
[2370000], rate=14220000.00/min
[2380000], rate=14280000.00/min
[2390000], rate=14340000.00/min
[2400000], rate=14400000.00/min
[2410000], rate=14460000.00/min
[2420000], rate=14520000.00/min
[2430000], rate=14580000.00/min
[2440000], rate=14640000.00/min
[2450000], rate=14700000.00/min
[2460000], rate=14760000.00/min
[2470000], rate=14820000.00/min
[2480000], rate=14880000.00/min
[2490000], rate=14940000.00/min
[2500000], rate=15000000.00/min
[2510000], rate=13690909.09/min
[2520000], rate=13745454.55/min
[2530000], rate=13800000.00/min
[2540000], rate=13854545.45/min
[2550000], rate=13909090.91/min
[2560000], rate=13963636.36/min
[2570000], rate=14018181.82/min
[2580000], rate=14072727.27/min
[2590000], rate=14127272.73/min
[2600000], rate=14181818.18/min
[2610000], rate=14236363.64/min
[2620000], rate=14290909.09/min
[2630000], rate=14345454.55/min
[2640000], rate=14400000.00/min
[2650000], rate=14454545.45/min
[2660000], rate=14509090.91/min
[2670000], rate=14563636.36/min
[2680000], rate=14618181.82/min
[2690000], rate=14672727.27/min
[2700000], rate=14727272.73/min
[2710000], rate=14781818.18/min
[2720000], rate=14836363.64/min
[2730000], rate=14890909.09/min
[2740000], rate=14945454.55/min
[2750000], rate=15000000.00/min
[2760000], rate=13800000.00/min
[2770000], rate=13850000.00/min
[2780000], rate=13900000.00/min
[2790000], rate=13950000.00/min
[2800000], rate=14000000.00/min
[2810000], rate=14050000.00/min
[2820000], rate=14100000.00/min
[2830000], rate=14150000.00/min
[2840000], rate=14200000.00/min
[2850000], rate=14250000.00/min
[2860000], rate=14300000.00/min
[2870000], rate=14350000.00/min
[2880000], rate=14400000.00/min
[2890000], rate=14450000.00/min
[2900000], rate=14500000.00/min
[2910000], rate=14550000.00/min
[2920000], rate=14600000.00/min
[2930000], rate=14650000.00/min
[2940000], rate=14700000.00/min
[2950000], rate=14750000.00/min
[2960000], rate=14800000.00/min
[2970000], rate=14850000.00/min
[2980000], rate=14900000.00/min
[2990000], rate=14950000.00/min
[3000000], rate=15000000.00/min
[3010000], rate=13892307.69/min
[3020000], rate=13938461.54/min
[3030000], rate=13984615.38/min
[3040000], rate=14030769.23/min
[3050000], rate=14076923.08/min
[3060000], rate=14123076.92/min
[3070000], rate=14169230.77/min
[3080000], rate=14215384.62/min
[3090000], rate=14261538.46/min
[3100000], rate=14307692.31/min
[3110000], rate=14353846.15/min
[3120000], rate=14400000.00/min
[3130000], rate=14446153.85/min
[3140000], rate=14492307.69/min
[3150000], rate=14538461.54/min
[3160000], rate=14584615.38/min
[3170000], rate=14630769.23/min
[3180000], rate=14676923.08/min
[3190000], rate=14723076.92/min
[3200000], rate=14769230.77/min
[3210000], rate=14815384.62/min
[3220000], rate=14861538.46/min
[3230000], rate=14907692.31/min
[3240000], rate=13885714.29/min
[3250000], rate=13928571.43/min
[3260000], rate=13971428.57/min
[3270000], rate=14014285.71/min
[3280000], rate=14057142.86/min
[3290000], rate=14100000.00/min
[3300000], rate=14142857.14/min
[3310000], rate=14185714.29/min
[3320000], rate=14228571.43/min
[3330000], rate=14271428.57/min
[3340000], rate=14314285.71/min
[3350000], rate=14357142.86/min
[3360000], rate=14400000.00/min
[3370000], rate=14442857.14/min
[3380000], rate=14485714.29/min
[3390000], rate=14528571.43/min
[3400000], rate=14571428.57/min
[3410000], rate=14614285.71/min
[3420000], rate=14657142.86/min
[3430000], rate=14700000.00/min
[3440000], rate=13760000.00/min
[3450000], rate=13800000.00/min
[3460000], rate=13840000.00/min
[3470000], rate=13880000.00/min
[3480000], rate=13920000.00/min
[3490000], rate=13960000.00/min
[3500000], rate=14000000.00/min
[3510000], rate=14040000.00/min
[3520000], rate=14080000.00/min
[3530000], rate=14120000.00/min
[3540000], rate=14160000.00/min
[3550000], rate=14200000.00/min
[3560000], rate=14240000.00/min
[3570000], rate=14280000.00/min
[3580000], rate=14320000.00/min
[3590000], rate=14360000.00/min
[3600000], rate=14400000.00/min
[3610000], rate=14440000.00/min
[3620000], rate=14480000.00/min
[3630000], rate=14520000.00/min
[3640000], rate=14560000.00/min
[3650000], rate=14600000.00/min
[3660000], rate=14640000.00/min
[3670000], rate=13762500.00/min
[3680000], rate=13800000.00/min
[3690000], rate=13837500.00/min
[3700000], rate=13875000.00/min
[3710000], rate=13912500.00/min
[3720000], rate=13950000.00/min
[3730000], rate=13987500.00/min
[3740000], rate=14025000.00/min
[3750000], rate=14062500.00/min
[3760000], rate=14100000.00/min
[3770000], rate=14137500.00/min
[3780000], rate=14175000.00/min
[3790000], rate=14212500.00/min
[3800000], rate=14250000.00/min
[3810000], rate=14287500.00/min
[3820000], rate=14325000.00/min
[3830000], rate=14362500.00/min
[3840000], rate=14400000.00/min
[3850000], rate=14437500.00/min
[3860000], rate=14475000.00/min
[3870000], rate=14512500.00/min
[3880000], rate=13694117.65/min
[3890000], rate=13729411.76/min
[3900000], rate=13764705.88/min
[3910000], rate=13800000.00/min
[3920000], rate=13835294.12/min
[3930000], rate=13870588.24/min
[3940000], rate=13905882.35/min
[3950000], rate=13941176.47/min
[3960000], rate=13976470.59/min
[3970000], rate=14011764.71/min
[3980000], rate=14047058.82/min
[3990000], rate=14082352.94/min
[4000000], rate=14117647.06/min
[4010000], rate=14152941.18/min
[4020000], rate=14188235.29/min
[4030000], rate=14223529.41/min
[4040000], rate=14258823.53/min
[4050000], rate=14294117.65/min
[4060000], rate=14329411.76/min
[4070000], rate=14364705.88/min
[4080000], rate=14400000.00/min
[4090000], rate=14435294.12/min
[4100000], rate=14470588.24/min
[4110000], rate=14505882.35/min
[4120000], rate=14541176.47/min
[4130000], rate=14576470.59/min
[4140000], rate=14611764.71/min
[4150000], rate=14647058.82/min
[4160000], rate=14682352.94/min
[4170000], rate=14717647.06/min
[4180000], rate=13933333.33/min
[4190000], rate=13966666.67/min
[4200000], rate=14000000.00/min
[4210000], rate=14033333.33/min
[4220000], rate=14066666.67/min
[4230000], rate=14100000.00/min
[4240000], rate=14133333.33/min
[4250000], rate=14166666.67/min
[4260000], rate=14200000.00/min
[4270000], rate=14233333.33/min
[4280000], rate=14266666.67/min
[4290000], rate=14300000.00/min
[4300000], rate=14333333.33/min
[4310000], rate=14366666.67/min
[4320000], rate=14400000.00/min
[4330000], rate=14433333.33/min
[4340000], rate=14466666.67/min
[4350000], rate=14500000.00/min
[4360000], rate=14533333.33/min
[4370000], rate=14566666.67/min
[4380000], rate=14600000.00/min
[4390000], rate=14633333.33/min
[4400000], rate=14666666.67/min
[4410000], rate=14700000.00/min
[4420000], rate=13957894.74/min
[4430000], rate=13989473.68/min
[4440000], rate=14021052.63/min
[4450000], rate=14052631.58/min
[4460000], rate=14084210.53/min
[4470000], rate=14115789.47/min
[4480000], rate=14147368.42/min
[4490000], rate=14178947.37/min
[4500000], rate=14210526.32/min
[4510000], rate=14242105.26/min
[4520000], rate=14273684.21/min
[4530000], rate=14305263.16/min
[4540000], rate=14336842.11/min
[4550000], rate=14368421.05/min
[4560000], rate=14400000.00/min
[4570000], rate=14431578.95/min
[4580000], rate=14463157.89/min
[4590000], rate=14494736.84/min
[4600000], rate=14526315.79/min
[4610000], rate=14557894.74/min
[4620000], rate=14589473.68/min
[4630000], rate=14621052.63/min
[4640000], rate=13920000.00/min
[4650000], rate=13950000.00/min
[4660000], rate=13980000.00/min
[4670000], rate=14010000.00/min
[4680000], rate=14040000.00/min
[4690000], rate=14070000.00/min
[4700000], rate=14100000.00/min
[4710000], rate=14130000.00/min
[4720000], rate=14160000.00/min
[4730000], rate=14190000.00/min
[4740000], rate=14220000.00/min
[4750000], rate=14250000.00/min
[4760000], rate=14280000.00/min
[4770000], rate=14310000.00/min
[4780000], rate=14340000.00/min
[4790000], rate=14370000.00/min
[4800000], rate=14400000.00/min
[4810000], rate=14430000.00/min
[4820000], rate=14460000.00/min
[4830000], rate=14490000.00/min
[4840000], rate=14520000.00/min
[4850000], rate=14550000.00/min
[4860000], rate=14580000.00/min
[4870000], rate=13914285.71/min
[4880000], rate=13942857.14/min
[4890000], rate=13971428.57/min
[4900000], rate=14000000.00/min
[4910000], rate=14028571.43/min
[4920000], rate=14057142.86/min
[4930000], rate=14085714.29/min
[4940000], rate=14114285.71/min
[4950000], rate=14142857.14/min
[4960000], rate=14171428.57/min
[4970000], rate=14200000.00/min
[4980000], rate=14228571.43/min
[4990000], rate=14257142.86/min
[5000000], rate=14285714.29/min
[5010000], rate=14314285.71/min
[5020000], rate=14342857.14/min
[5030000], rate=14371428.57/min
[5040000], rate=14400000.00/min
[5050000], rate=14428571.43/min
[5060000], rate=14457142.86/min
[5070000], rate=14485714.29/min
[5080000], rate=14514285.71/min
[5090000], rate=14542857.14/min
[5100000], rate=13909090.91/min
[5110000], rate=13936363.64/min
[5120000], rate=13963636.36/min
[5130000], rate=13990909.09/min
[5140000], rate=14018181.82/min
[5150000], rate=14045454.55/min
[5160000], rate=14072727.27/min
[5170000], rate=14100000.00/min
[5180000], rate=14127272.73/min
[5190000], rate=14154545.45/min
[5200000], rate=14181818.18/min
[5210000], rate=14209090.91/min
[5220000], rate=14236363.64/min
[5230000], rate=14263636.36/min
[5240000], rate=14290909.09/min
[5250000], rate=14318181.82/min
[5260000], rate=14345454.55/min
[5270000], rate=14372727.27/min
[5280000], rate=14400000.00/min
[5290000], rate=14427272.73/min
[5300000], rate=14454545.45/min
[5310000], rate=14481818.18/min
[5320000], rate=14509090.91/min
[5330000], rate=14536363.64/min
[5340000], rate=13930434.78/min
[5350000], rate=13956521.74/min
[5360000], rate=13982608.70/min
[5370000], rate=14008695.65/min
[5380000], rate=14034782.61/min
[5390000], rate=14060869.57/min
[5400000], rate=14086956.52/min
[5410000], rate=14113043.48/min
[5420000], rate=14139130.43/min
[5430000], rate=14165217.39/min
[5440000], rate=14191304.35/min
[5450000], rate=14217391.30/min
[5460000], rate=14243478.26/min
[5470000], rate=14269565.22/min
[5480000], rate=14295652.17/min
[5490000], rate=14321739.13/min
[5500000], rate=14347826.09/min
[5510000], rate=14373913.04/min
[5520000], rate=14400000.00/min
[5530000], rate=14426086.96/min
[5540000], rate=14452173.91/min
[5550000], rate=14478260.87/min
[5560000], rate=14504347.83/min
[5570000], rate=13925000.00/min
[5580000], rate=13950000.00/min
[5590000], rate=13975000.00/min
[5600000], rate=14000000.00/min
[5610000], rate=14025000.00/min
[5620000], rate=14050000.00/min
[5630000], rate=14075000.00/min
[5640000], rate=14100000.00/min
[5650000], rate=14125000.00/min
[5660000], rate=14150000.00/min
[5670000], rate=14175000.00/min
[5680000], rate=14200000.00/min
[5690000], rate=14225000.00/min
[5700000], rate=14250000.00/min
[5710000], rate=14275000.00/min
[5720000], rate=14300000.00/min
[5730000], rate=14325000.00/min
[5740000], rate=14350000.00/min
[5750000], rate=14375000.00/min
[5760000], rate=14400000.00/min
[5770000], rate=14425000.00/min
[5780000], rate=14450000.00/min
[5790000], rate=13896000.00/min
[5800000], rate=13920000.00/min
[5810000], rate=13944000.00/min
[5820000], rate=13968000.00/min
[5830000], rate=13992000.00/min
[5840000], rate=14016000.00/min
[5850000], rate=14040000.00/min
[5860000], rate=14064000.00/min
[5870000], rate=14088000.00/min
[5880000], rate=14112000.00/min
[5890000], rate=14136000.00/min
[5900000], rate=14160000.00/min
[5910000], rate=14184000.00/min
[5920000], rate=14208000.00/min
[5930000], rate=14232000.00/min
[5940000], rate=14256000.00/min
[5950000], rate=14280000.00/min
[5960000], rate=14304000.00/min
[5970000], rate=14328000.00/min
[5980000], rate=14352000.00/min
[5990000], rate=14376000.00/min
[6000000], rate=14400000.00/min
[6010000], rate=14424000.00/min
[6020000], rate=13892307.69/min
[6030000], rate=13915384.62/min
[6040000], rate=13938461.54/min
[6050000], rate=13961538.46/min
[6060000], rate=13984615.38/min
[6070000], rate=14007692.31/min
[6080000], rate=14030769.23/min
[6090000], rate=14053846.15/min
[6100000], rate=14076923.08/min
[6110000], rate=14100000.00/min
[6120000], rate=14123076.92/min
[6130000], rate=14146153.85/min
[6140000], rate=14169230.77/min
[6150000], rate=14192307.69/min
[6160000], rate=14215384.62/min
[6170000], rate=14238461.54/min
[6180000], rate=14261538.46/min
[6190000], rate=14284615.38/min
[6200000], rate=14307692.31/min
[6210000], rate=14330769.23/min
[6220000], rate=14353846.15/min
[6230000], rate=14376923.08/min
[6240000], rate=14400000.00/min
[6250000], rate=13888888.89/min
[6260000], rate=13911111.11/min
[6270000], rate=13933333.33/min
[6280000], rate=13955555.56/min
[6290000], rate=13977777.78/min
[6300000], rate=14000000.00/min
[6310000], rate=14022222.22/min
[6320000], rate=14044444.44/min
[6330000], rate=14066666.67/min
[6340000], rate=14088888.89/min
[6350000], rate=14111111.11/min
[6360000], rate=14133333.33/min
[6370000], rate=14155555.56/min
[6380000], rate=14177777.78/min
[6390000], rate=14200000.00/min
[6400000], rate=14222222.22/min
[6410000], rate=14244444.44/min
[6420000], rate=14266666.67/min
[6430000], rate=14288888.89/min
[6440000], rate=14311111.11/min
[6450000], rate=14333333.33/min
[6460000], rate=14355555.56/min
[6470000], rate=14377777.78/min
[6480000], rate=14400000.00/min
[6490000], rate=14422222.22/min
[6500000], rate=14444444.44/min 07:46:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.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.
-EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns: identified 242 cancer introns
07:46:55 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim
07:46:55 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/prelim_introns.ok
07:46:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns
07:46:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns
07:46:55 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/introns_filtered.ok
07:46:55 : INFO : -found 156 cancer introns
07:46:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --cancer_introns EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed
07:46:56 : INFO : Creating the BED File.
07:46:57 : INFO : Saving Bed File as EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed
07:46:57 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns --cancer_introns EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed
07:46:57 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/intron_igv_bed.ok
07:46:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed --bam EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2
[W::hts_idx_load3] The index file is older than the data file: EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
07:47:52 : INFO : Execution Time = 0.91 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed --bam EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2
07:47:52 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok
07:47:52 : INFO : Running: samtools sort -o EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.bam
07:47:52 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.bam
07:47:52 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok
07:47:52 : INFO : Running: samtools sort -o EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.bam
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
07:48:54 : INFO : Execution Time = 1.03 minutes. CMD: samtools sort -o EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.bam
07:48:54 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/sort_gene_reads.ok
07:48:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.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 chr22.
07:49:11 : INFO : Execution Time = 0.28 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam
07:49:11 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
07:49:11 : INFO : Running: samtools sort -o EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp
07:49:13 : INFO : Execution Time = 0.05 minutes. CMD: samtools sort -o EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp
07:49:13 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:49:13 : INFO : Running: samtools index EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam
07:49:14 : INFO : Execution Time = 0.01 minutes. CMD: samtools index EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam
07:49:14 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
07:49:14 : INFO : Running: samtools index EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam
07:49:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools index EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam
07:49:14 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
07:49:14 : INFO : Running: create_report EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.ctat-splicing.igv.html --track-config EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
07:49:33 : INFO : Execution Time = 0.32 minutes. CMD: create_report EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.ctat-splicing.igv.html --track-config EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2'
07:49:33 : INFO : Running: touch /tmp/nxf.p5pZWKdF01/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.chckpts/igv_create_html.ok
07:49:34 : INFO : done.