Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/a16369d4f9602cc89265d7b34ba17c/659_ciJ-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/6fb8ef780865c3d88239b108874389/659_ciJ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai 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/6e/486b47f6a5167e4cda40513659598c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/a16369d4f9602cc89265d7b34ba17c/659_ciJ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/a16369d4f9602cc89265d7b34ba17c/659_ciJ-T1-TRNA-1_B23WHTKLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/486b47f6a5167e4cda40513659598c/.command.run ==> STAGING COMPLETE (7 inputs) 08:54:53 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [40000], rate=2400000.00/min [50000], rate=3000000.00/min [60000], rate=3600000.00/min [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=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=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=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=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=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=16200000.00/min [820000], rate=16400000.00/min [830000], rate=16600000.00/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=14700000.00/min [990000], rate=14850000.00/min [1000000], rate=15000000.00/min [1010000], rate=15150000.00/min [1020000], rate=15300000.00/min [1030000], rate=15450000.00/min [1040000], rate=15600000.00/min [1050000], rate=15750000.00/min [1060000], rate=15900000.00/min [1070000], rate=16050000.00/min [1080000], rate=16200000.00/min [1090000], rate=16350000.00/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=14160000.00/min [1190000], rate=14280000.00/min [1200000], rate=14400000.00/min [1210000], rate=14520000.00/min [1220000], rate=14640000.00/min [1230000], rate=14760000.00/min [1240000], rate=14880000.00/min [1250000], rate=15000000.00/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=12257142.86/min [1440000], rate=12342857.14/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=12000000.00/min [1610000], rate=12075000.00/min [1620000], rate=12150000.00/min [1630000], rate=12225000.00/min [1640000], rate=12300000.00/min [1650000], rate=12375000.00/min [1660000], rate=12450000.00/min [1670000], rate=12525000.00/min [1680000], rate=12600000.00/min [1690000], rate=12675000.00/min [1700000], rate=12750000.00/min [1710000], rate=12825000.00/min [1720000], rate=12900000.00/min [1730000], rate=12975000.00/min [1740000], rate=13050000.00/min [1750000], rate=13125000.00/min [1760000], rate=11733333.33/min [1770000], rate=11800000.00/min [1780000], rate=11866666.67/min [1790000], rate=11933333.33/min [1800000], rate=12000000.00/min [1810000], rate=12066666.67/min [1820000], rate=12133333.33/min [1830000], rate=12200000.00/min [1840000], rate=12266666.67/min [1850000], rate=12333333.33/min [1860000], rate=12400000.00/min [1870000], rate=12466666.67/min [1880000], rate=12533333.33/min [1890000], rate=12600000.00/min [1900000], rate=12666666.67/min [1910000], rate=12733333.33/min [1920000], rate=12800000.00/min [1930000], rate=12866666.67/min [1940000], rate=11640000.00/min [1950000], rate=11700000.00/min [1960000], rate=11760000.00/min [1970000], rate=11820000.00/min [1980000], rate=11880000.00/min [1990000], rate=11940000.00/min [2000000], rate=12000000.00/min [2010000], rate=12060000.00/min [2020000], rate=12120000.00/min [2030000], rate=12180000.00/min [2040000], rate=12240000.00/min [2050000], rate=12300000.00/min [2060000], rate=12360000.00/min [2070000], rate=12420000.00/min [2080000], rate=12480000.00/min [2090000], rate=12540000.00/min [2100000], rate=11454545.45/min [2110000], rate=11509090.91/min [2120000], rate=11563636.36/min [2130000], rate=11618181.82/min [2140000], rate=11672727.27/min [2150000], rate=11727272.73/min [2160000], rate=11781818.18/min [2170000], rate=11836363.64/min [2180000], rate=11890909.09/min [2190000], rate=11945454.55/min [2200000], rate=12000000.00/min [2210000], rate=12054545.45/min [2220000], rate=12109090.91/min [2230000], rate=12163636.36/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=11650000.00/min [2340000], rate=11700000.00/min [2350000], rate=11750000.00/min [2360000], rate=11800000.00/min [2370000], rate=11850000.00/min [2380000], rate=11900000.00/min [2390000], rate=11950000.00/min [2400000], rate=12000000.00/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=11538461.54/min [2510000], rate=11584615.38/min [2520000], rate=11630769.23/min [2530000], rate=11676923.08/min [2540000], rate=11723076.92/min [2550000], rate=11769230.77/min [2560000], rate=11815384.62/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=11400000.00/min [2670000], rate=11442857.14/min [2680000], rate=11485714.29/min [2690000], rate=11528571.43/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=10462500.00/min [2800000], rate=10500000.00/min [2810000], rate=10537500.00/min [2820000], rate=10575000.00/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=10270588.24/min [2920000], rate=10305882.35/min [2930000], rate=10341176.47/min [2940000], rate=10376470.59/min [2950000], rate=10411764.71/min [2960000], rate=10447058.82/min [2970000], rate=10482352.94/min [2980000], rate=10517647.06/min [2990000], rate=10552941.18/min [3000000], rate=10588235.29/min [3010000], rate=10623529.41/min [3020000], rate=10658823.53/min [3030000], rate=10100000.00/min [3040000], rate=10133333.33/min [3050000], rate=10166666.67/min [3060000], rate=10200000.00/min [3070000], rate=10233333.33/min [3080000], rate=10266666.67/min [3090000], rate=10300000.00/min [3100000], rate=10333333.33/min [3110000], rate=10366666.67/min [3120000], rate=10400000.00/min [3130000], rate=10433333.33/min [3140000], rate=10466666.67/min [3150000], rate=10500000.00/min [3160000], rate=10533333.33/min [3170000], rate=10010526.32/min [3180000], rate=10042105.26/min [3190000], rate=10073684.21/min [3200000], rate=10105263.16/min [3210000], rate=10136842.11/min [3220000], rate=10168421.05/min [3230000], rate=10200000.00/min [3240000], rate=10231578.95/min [3250000], rate=10263157.89/min [3260000], rate=10294736.84/min [3270000], rate=10326315.79/min [3280000], rate=10357894.74/min [3290000], rate=10389473.68/min [3300000], rate=10421052.63/min [3310000], rate=10452631.58/min [3320000], rate=9960000.00/min [3330000], rate=9990000.00/min [3340000], rate=10020000.00/min [3350000], rate=10050000.00/min [3360000], rate=10080000.00/min [3370000], rate=10110000.00/min [3380000], rate=10140000.00/min [3390000], rate=10170000.00/min [3400000], rate=10200000.00/min [3410000], rate=10230000.00/min [3420000], rate=10260000.00/min [3430000], rate=10290000.00/min [3440000], rate=10320000.00/min [3450000], rate=9857142.86/min [3460000], rate=9885714.29/min [3470000], rate=9914285.71/min [3480000], rate=9942857.14/min [3490000], rate=9971428.57/min [3500000], rate=10000000.00/min [3510000], rate=10028571.43/min [3520000], rate=10057142.86/min [3530000], rate=10085714.29/min [3540000], rate=10114285.71/min [3550000], rate=10142857.14/min [3560000], rate=10171428.57/min [3570000], rate=10200000.00/min [3580000], rate=10228571.43/min [3590000], rate=9790909.09/min [3600000], rate=9818181.82/min [3610000], rate=9845454.55/min [3620000], rate=9872727.27/min [3630000], rate=9900000.00/min [3640000], rate=9927272.73/min [3650000], rate=9954545.45/min [3660000], rate=9981818.18/min [3670000], rate=10009090.91/min [3680000], rate=10036363.64/min [3690000], rate=10063636.36/min [3700000], rate=10090909.09/min [3710000], rate=10118181.82/min [3720000], rate=10145454.55/min [3730000], rate=10172727.27/min [3740000], rate=9756521.74/min [3750000], rate=9782608.70/min [3760000], rate=9808695.65/min [3770000], rate=9834782.61/min [3780000], rate=9860869.57/min [3790000], rate=9886956.52/min [3800000], rate=9913043.48/min [3810000], rate=9939130.43/min [3820000], rate=9965217.39/min [3830000], rate=9991304.35/min [3840000], rate=10017391.30/min [3850000], rate=10043478.26/min [3860000], rate=10069565.22/min [3870000], rate=9675000.00/min [3880000], rate=9700000.00/min [3890000], rate=9725000.00/min [3900000], rate=9750000.00/min [3910000], rate=9775000.00/min [3920000], rate=9800000.00/min [3930000], rate=9825000.00/min [3940000], rate=9850000.00/min [3950000], rate=9875000.00/min [3960000], rate=9900000.00/min [3970000], rate=9925000.00/min [3980000], rate=9950000.00/min [3990000], rate=9975000.00/min [4000000], rate=10000000.00/min [4010000], rate=9624000.00/min [4020000], rate=9648000.00/min [4030000], rate=9672000.00/min [4040000], rate=9696000.00/min [4050000], rate=9720000.00/min [4060000], rate=9744000.00/min [4070000], rate=9768000.00/min [4080000], rate=9792000.00/min [4090000], rate=9816000.00/min [4100000], rate=9840000.00/min [4110000], rate=9864000.00/min [4120000], rate=9888000.00/min [4130000], rate=9530769.23/min [4140000], rate=9553846.15/min [4150000], rate=9576923.08/min [4160000], rate=9600000.00/min [4170000], rate=9623076.92/min [4180000], rate=9646153.85/min [4190000], rate=9669230.77/min [4200000], rate=9692307.69/min [4210000], rate=9715384.62/min [4220000], rate=9738461.54/min [4230000], rate=9761538.46/min [4240000], rate=9784615.38/min [4250000], rate=9444444.44/min [4260000], rate=9466666.67/min [4270000], rate=9488888.89/min [4280000], rate=9511111.11/min [4290000], rate=9533333.33/min [4300000], rate=9555555.56/min [4310000], rate=9577777.78/min [4320000], rate=9600000.00/min [4330000], rate=9278571.43/min [4340000], rate=9300000.00/min [4350000], rate=9321428.57/min [4360000], rate=9342857.14/min [4370000], rate=9364285.71/min [4380000], rate=9385714.29/min [4390000], rate=9407142.86/min [4400000], rate=9428571.43/min [4410000], rate=9450000.00/min [4420000], rate=9471428.57/min [4430000], rate=9165517.24/min [4440000], rate=9186206.90/min [4450000], rate=9206896.55/min [4460000], rate=9227586.21/min [4470000], rate=9248275.86/min [4480000], rate=9268965.52/min [4490000], rate=9289655.17/min [4500000], rate=9310344.83/min [4510000], rate=9331034.48/min [4520000], rate=9351724.14/min [4530000], rate=9372413.79/min [4540000], rate=9393103.45/min [4550000], rate=9413793.10/min [4560000], rate=9434482.76/min [4570000], rate=9140000.00/min [4580000], rate=9160000.00/min [4590000], rate=9180000.00/min [4600000], rate=9200000.00/min [4610000], rate=9220000.00/min [4620000], rate=9240000.00/min [4630000], rate=9260000.00/min [4640000], rate=9280000.00/min [4650000], rate=9300000.00/min [4660000], rate=9320000.00/min [4670000], rate=9340000.00/min [4680000], rate=9360000.00/min [4690000], rate=9380000.00/min [4700000], rate=9400000.00/min [4710000], rate=9420000.00/min [4720000], rate=9440000.00/min [4730000], rate=9460000.00/min [4740000], rate=9480000.00/min [4750000], rate=9500000.00/min [4760000], rate=9520000.00/min [4770000], rate=9540000.00/min [4780000], rate=9560000.00/min [4790000], rate=9580000.00/min [4800000], rate=9290322.58/min [4810000], rate=9309677.42/min [4820000], rate=9329032.26/min [4830000], rate=9348387.10/min [4840000], rate=9367741.94/min [4850000], rate=9387096.77/min [4860000], rate=9406451.61/min [4870000], rate=9425806.45/min [4880000], rate=9445161.29/min [4890000], rate=9464516.13/min [4900000], rate=9483870.97/min [4910000], rate=9503225.81/min [4920000], rate=9522580.65/min [4930000], rate=9541935.48/min [4940000], rate=9561290.32/min [4950000], rate=9580645.16/min [4960000], rate=9600000.00/min [4970000], rate=9619354.84/min [4980000], rate=9638709.68/min [4990000], rate=9658064.52/min [5000000], rate=9677419.35/min [5010000], rate=9393750.00/min [5020000], rate=9412500.00/min [5030000], rate=9431250.00/min [5040000], rate=9450000.00/min [5050000], rate=9468750.00/min [5060000], rate=9487500.00/min [5070000], rate=9506250.00/min [5080000], rate=9525000.00/min [5090000], rate=9543750.00/min [5100000], rate=9562500.00/min [5110000], rate=9581250.00/min [5120000], rate=9600000.00/min [5130000], rate=9618750.00/min [5140000], rate=9637500.00/min [5150000], rate=9656250.00/min [5160000], rate=9675000.00/min [5170000], rate=9693750.00/min [5180000], rate=9418181.82/min [5190000], rate=9436363.64/min [5200000], rate=9454545.45/min [5210000], rate=9472727.27/min [5220000], rate=9490909.09/min [5230000], rate=9509090.91/min [5240000], rate=9527272.73/min [5250000], rate=9545454.55/min [5260000], rate=9563636.36/min [5270000], rate=9581818.18/min [5280000], rate=9600000.00/min [5290000], rate=9618181.82/min [5300000], rate=9636363.64/min [5310000], rate=9654545.45/min [5320000], rate=9672727.27/min [5330000], rate=9690909.09/min [5340000], rate=9709090.91/min [5350000], rate=9727272.73/min [5360000], rate=9458823.53/min [5370000], rate=9476470.59/min [5380000], rate=9494117.65/min [5390000], rate=9511764.71/min [5400000], rate=9529411.76/min [5410000], rate=9547058.82/min [5420000], rate=9564705.88/min [5430000], rate=9582352.94/min [5440000], rate=9600000.00/min [5450000], rate=9617647.06/min [5460000], rate=9635294.12/min [5470000], rate=9652941.18/min [5480000], rate=9670588.24/min [5490000], rate=9688235.29/min [5500000], rate=9705882.35/min [5510000], rate=9445714.29/min [5520000], rate=9462857.14/min [5530000], rate=9480000.00/min [5540000], rate=9497142.86/min [5550000], rate=9514285.71/min [5560000], rate=9531428.57/min [5570000], rate=9548571.43/min [5580000], rate=9565714.29/min [5590000], rate=9582857.14/min [5600000], rate=9600000.00/min [5610000], rate=9617142.86/min [5620000], rate=9634285.71/min [5630000], rate=9651428.57/min [5640000], rate=9668571.43/min [5650000], rate=9685714.29/min [5660000], rate=9702857.14/min [5670000], rate=9720000.00/min [5680000], rate=9737142.86/min [5690000], rate=9754285.71/min [5700000], rate=9500000.00/min [5710000], rate=9516666.67/min [5720000], rate=9533333.33/min [5730000], rate=9550000.00/min [5740000], rate=9566666.67/min [5750000], rate=9583333.33/min [5760000], rate=9600000.00/min [5770000], rate=9616666.67/min [5780000], rate=9633333.33/min [5790000], rate=9650000.00/min [5800000], rate=9666666.67/min [5810000], rate=9683333.33/min [5820000], rate=9700000.00/min [5830000], rate=9716666.67/min [5840000], rate=9733333.33/min [5850000], rate=9750000.00/min [5860000], rate=9766666.67/min [5870000], rate=9783333.33/min [5880000], rate=9800000.00/min [5890000], rate=9816666.67/min [5900000], rate=9833333.33/min [5910000], rate=9850000.00/min [5920000], rate=9600000.00/min [5930000], rate=9616216.22/min [5940000], rate=9632432.43/min [5950000], rate=9648648.65/min [5960000], rate=9664864.86/min [5970000], rate=9681081.08/min [5980000], rate=9697297.30/min [5990000], rate=9713513.51/min [6000000], rate=9729729.73/min [6010000], rate=9745945.95/min [6020000], rate=9762162.16/min [6030000], rate=9778378.38/min [6040000], rate=9794594.59/min [6050000], rate=9810810.81/min [6060000], rate=9827027.03/min [6070000], rate=9843243.24/min [6080000], rate=9859459.46/min [6090000], rate=9875675.68/min [6100000], rate=9891891.89/min [6110000], rate=9908108.11/min [6120000], rate=9663157.89/min [6130000], rate=9678947.37/min [6140000], rate=9694736.84/min [6150000], rate=9710526.32/min [6160000], rate=9726315.79/min [6170000], rate=9742105.26/min [6180000], rate=9757894.74/min [6190000], rate=9773684.21/min [6200000], rate=9789473.68/min [6210000], rate=9805263.16/min [6220000], rate=9821052.63/min [6230000], rate=9836842.11/min [6240000], rate=9852631.58/min [6250000], rate=9868421.05/min [6260000], rate=9884210.53/min [6270000], rate=9900000.00/min [6280000], rate=9915789.47/min [6290000], rate=9931578.95/min [6300000], rate=9947368.42/min [6310000], rate=9963157.89/min [6320000], rate=9978947.37/min [6330000], rate=9994736.84/min [6340000], rate=10010526.32/min [6350000], rate=9769230.77/min [6360000], rate=9784615.38/min [6370000], rate=9800000.00/min [6380000], rate=9815384.62/min [6390000], rate=9830769.23/min [6400000], rate=9846153.85/min [6410000], rate=9861538.46/min [6420000], rate=9876923.08/min [6430000], rate=9892307.69/min [6440000], rate=9907692.31/min [6450000], rate=9923076.92/min [6460000], rate=9938461.54/min [6470000], rate=9953846.15/min [6480000], rate=9969230.77/min [6490000], rate=9984615.38/min [6500000], rate=10000000.00/min [6510000], rate=10015384.62/min [6520000], rate=10030769.23/min [6530000], rate=10046153.85/min [6540000], rate=10061538.46/min [6550000], rate=10076923.08/min [6560000], rate=10092307.69/min [6570000], rate=9855000.00/min [6580000], rate=9870000.00/min [6590000], rate=9885000.00/min [6600000], rate=9900000.00/min [6610000], rate=9915000.00/min [6620000], rate=9930000.00/min [6630000], rate=9945000.00/min [6640000], rate=9960000.00/min [6650000], rate=9975000.00/min [6660000], rate=9990000.00/min [6670000], rate=10005000.00/min [6680000], rate=10020000.00/min [6690000], rate=10035000.00/min [6700000], rate=10050000.00/min [6710000], rate=10065000.00/min [6720000], rate=10080000.00/min [6730000], rate=10095000.00/min [6740000], rate=10110000.00/min [6750000], rate=10125000.00/min [6760000], rate=10140000.00/min [6770000], rate=10155000.00/min [6780000], rate=10170000.00/min [6790000], rate=10185000.00/min [6800000], rate=9951219.51/min [6810000], rate=9965853.66/min [6820000], rate=9980487.80/min [6830000], rate=9995121.95/min [6840000], rate=10009756.10/min [6850000], rate=10024390.24/min [6860000], rate=10039024.39/min [6870000], rate=10053658.54/min [6880000], rate=10068292.68/min [6890000], rate=10082926.83/min [6900000], rate=10097560.98/min [6910000], rate=10112195.12/min [6920000], rate=10126829.27/min [6930000], rate=10141463.41/min [6940000], rate=10156097.56/min [6950000], rate=10170731.71/min [6960000], rate=10185365.85/min [6970000], rate=10200000.00/min [6980000], rate=10214634.15/min [6990000], rate=10229268.29/min [7000000], rate=10243902.44/min [7010000], rate=10258536.59/min [7020000], rate=10273170.73/min [7030000], rate=10042857.14/min [7040000], rate=10057142.86/min [7050000], rate=10071428.57/min [7060000], rate=10085714.29/min [7070000], rate=10100000.00/min [7080000], rate=10114285.71/min [7090000], rate=10128571.43/min [7100000], rate=10142857.14/min [7110000], rate=10157142.86/min [7120000], rate=10171428.57/min [7130000], rate=10185714.29/min [7140000], rate=10200000.00/min [7150000], rate=10214285.71/min [7160000], rate=10228571.43/min [7170000], rate=10242857.14/min [7180000], rate=10257142.86/min [7190000], rate=10271428.57/min [7200000], rate=10285714.29/min [7210000], rate=10300000.00/min [7220000], rate=10314285.71/min [7230000], rate=10328571.43/min [7240000], rate=10342857.14/min [7250000], rate=10116279.07/min [7260000], rate=10130232.56/min [7270000], rate=10144186.05/min [7280000], rate=10158139.53/min [7290000], rate=10172093.02/min [7300000], rate=10186046.51/min [7310000], rate=10200000.00/min [7320000], rate=10213953.49/min [7330000], rate=10227906.98/min [7340000], rate=10241860.47/min [7350000], rate=10255813.95/min [7360000], rate=10269767.44/min [7370000], rate=10283720.93/min [7380000], rate=10297674.42/min [7390000], rate=10311627.91/min [7400000], rate=10325581.40/min [7410000], rate=10339534.88/min [7420000], rate=10353488.37/min [7430000], rate=10367441.86/min [7440000], rate=10381395.35/min [7450000], rate=10395348.84/min [7460000], rate=10409302.33/min [7470000], rate=10423255.81/min [7480000], rate=10437209.30/min [7490000], rate=10213636.36/min [7500000], rate=10227272.73/min [7510000], rate=10240909.09/min [7520000], rate=10254545.45/min [7530000], rate=10268181.82/min [7540000], rate=10281818.18/min [7550000], rate=10295454.55/min [7560000], rate=10309090.91/min [7570000], rate=10322727.27/min [7580000], rate=10336363.64/min [7590000], rate=10350000.00/min [7600000], rate=10363636.36/min [7610000], rate=10377272.73/min [7620000], rate=10390909.09/min [7630000], rate=10404545.45/min [7640000], rate=10418181.82/min [7650000], rate=10431818.18/min [7660000], rate=10445454.55/min [7670000], rate=10459090.91/min [7680000], rate=10472727.27/min [7690000], rate=10486363.64/min [7700000], rate=10500000.00/min [7710000], rate=10513636.36/min [7720000], rate=10527272.73/min [7730000], rate=10540909.09/min [7740000], rate=10320000.00/min [7750000], rate=10333333.33/min [7760000], rate=10346666.67/min [7770000], rate=10360000.00/min [7780000], rate=10373333.33/min [7790000], rate=10386666.67/min [7800000], rate=10400000.00/min [7810000], rate=10413333.33/min [7820000], rate=10426666.67/min [7830000], rate=10440000.00/min [7840000], rate=10453333.33/min [7850000], rate=10466666.67/min [7860000], rate=10480000.00/min [7870000], rate=10493333.33/min [7880000], rate=10506666.67/min [7890000], rate=10520000.00/min [7900000], rate=10533333.33/min [7910000], rate=10546666.67/min [7920000], rate=10560000.00/min [7930000], rate=10573333.33/min [7940000], rate=10586666.67/min [7950000], rate=10600000.00/min [7960000], rate=10613333.33/min [7970000], rate=10626666.67/min [7980000], rate=10408695.65/min [7990000], rate=10421739.13/min [8000000], rate=10434782.61/min [8010000], rate=10447826.09/min [8020000], rate=10460869.57/min [8030000], rate=10473913.04/min [8040000], rate=10486956.52/min [8050000], rate=10500000.00/min [8060000], rate=10513043.48/min [8070000], rate=10526086.96/min [8080000], rate=10539130.43/min [8090000], rate=10552173.91/min [8100000], rate=10565217.39/min [8110000], rate=10578260.87/min [8120000], rate=10591304.35/min [8130000], rate=10604347.83/min [8140000], rate=10617391.30/min [8150000], rate=10630434.78/min [8160000], rate=10643478.26/min [8170000], rate=10656521.74/min [8180000], rate=10669565.22/min [8190000], rate=10682608.70/min [8200000], rate=10695652.17/min [8210000], rate=10708695.65/min [8220000], rate=10493617.02/min [8230000], rate=10506382.98/min [8240000], rate=10519148.94/min [8250000], rate=10531914.89/min [8260000], rate=10544680.85/min [8270000], rate=10557446.81/min [8280000], rate=10570212.77/min [8290000], rate=10582978.72/min [8300000], rate=10595744.68/min [8310000], rate=10608510.64/min [8320000], rate=10621276.60/min [8330000], rate=10634042.55/min [8340000], rate=10646808.51/min [8350000], rate=10659574.47/min [8360000], rate=10672340.43/min [8370000], rate=10685106.38/min [8380000], rate=10697872.34/min [8390000], rate=10710638.30/min [8400000], rate=10723404.26/min [8410000], rate=10736170.21/min [8420000], rate=10748936.17/min [8430000], rate=10761702.13/min [8440000], rate=10774468.09/min [8450000], rate=10787234.04/min [8460000], rate=10800000.00/min [8470000], rate=10587500.00/min [8480000], rate=10600000.00/min [8490000], rate=10612500.00/min [8500000], rate=10625000.00/min [8510000], rate=10637500.00/min [8520000], rate=10650000.00/min [8530000], rate=10662500.00/min [8540000], rate=10675000.00/min [8550000], rate=10687500.00/min [8560000], rate=10700000.00/min [8570000], rate=10712500.00/min [8580000], rate=10725000.00/min [8590000], rate=10737500.00/min [8600000], rate=10750000.00/min [8610000], rate=10762500.00/min [8620000], rate=10775000.00/min [8630000], rate=10787500.00/min [8640000], rate=10800000.00/min [8650000], rate=10591836.73/min [8660000], rate=10604081.63/min [8670000], rate=10616326.53/min [8680000], rate=10628571.43/min [8690000], rate=10640816.33/min [8700000], rate=10653061.22/min [8710000], rate=10665306.12/min [8720000], rate=10677551.02/min [8730000], rate=10689795.92/min [8740000], rate=10702040.82/min [8750000], rate=10714285.71/min [8760000], rate=10726530.61/min [8770000], rate=10738775.51/min [8780000], rate=10751020.41/min [8790000], rate=10763265.31/min [8800000], rate=10775510.20/min [8810000], rate=10787755.10/min [8820000], rate=10800000.00/min [8830000], rate=10812244.90/min [8840000], rate=10824489.80/min [8850000], rate=10836734.69/min [8860000], rate=10848979.59/min [8870000], rate=10644000.00/min [8880000], rate=10656000.00/min [8890000], rate=10668000.00/min [8900000], rate=10680000.00/min [8910000], rate=10692000.00/min [8920000], rate=10704000.00/min [8930000], rate=10716000.00/min [8940000], rate=10728000.00/min [8950000], rate=10740000.00/min [8960000], rate=10752000.00/min [8970000], rate=10764000.00/min [8980000], rate=10776000.00/min [8990000], rate=10788000.00/min [9000000], rate=10800000.00/min [9010000], rate=10812000.00/min [9020000], rate=10824000.00/min [9030000], rate=10836000.00/min [9040000], rate=10848000.00/min [9050000], rate=10860000.00/min 08:55:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18. -659_ciJ-T1-TRNA-1_B23WHTKLT4_1.introns: identified 4964 cancer introns 08:55:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim 08:55:55 : INFO : Running: touch /tmp/nxf.eNucFGp6ku/659_ciJ-T1-TRNA-1_B23WHTKLT4_1.chckpts/prelim_introns.ok 08:55:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer.introns 08:55:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer.introns 08:55:55 : INFO : Running: touch /tmp/nxf.eNucFGp6ku/659_ciJ-T1-TRNA-1_B23WHTKLT4_1.chckpts/introns_filtered.ok 08:55:55 : INFO : -found 2851 cancer introns 08:55:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed 08:55:56 : INFO : Creating the BED File. 08:56:04 : INFO : Saving Bed File as 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed 08:56:04 : INFO : Execution Time = 0.15 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed 08:56:04 : INFO : Running: touch /tmp/nxf.eNucFGp6ku/659_ciJ-T1-TRNA-1_B23WHTKLT4_1.chckpts/intron_igv_bed.ok 08:56:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_ciJ-T1-TRNA-1_B23WHTKLT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai 09:16:30 : INFO : Execution Time = 20.42 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_ciJ-T1-TRNA-1_B23WHTKLT4_1 09:16:30 : INFO : Running: touch /tmp/nxf.eNucFGp6ku/659_ciJ-T1-TRNA-1_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok 09:16:30 : INFO : Running: samtools sort -o 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam 09:16:30 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam 09:16:30 : INFO : Running: touch /tmp/nxf.eNucFGp6ku/659_ciJ-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok 09:16:30 : INFO : Running: samtools sort -o 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam