Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/6c165ed8a637a13dec651605e0ee3f/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/6c165ed8a637a13dec651605e0ee3f/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/d2521bce0b275263ad0739d6d32400/aih-tih-sc-1274d4-R1_A23YTGFLT4_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/34/a79646786270854e285fec34e4ee4b/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/a79646786270854e285fec34e4ee4b/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/6c165ed8a637a13dec651605e0ee3f/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam ==> STAGING COMPLETE (7 inputs) 20:00:20 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=8100000.00/min [280000], rate=8400000.00/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=8800000.00/min [450000], rate=9000000.00/min [460000], rate=9200000.00/min [470000], rate=9400000.00/min [480000], rate=9600000.00/min [490000], rate=9800000.00/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=9600000.00/min [650000], rate=9750000.00/min [660000], rate=9900000.00/min [670000], rate=10050000.00/min [680000], rate=10200000.00/min [690000], rate=10350000.00/min [700000], rate=10500000.00/min [710000], rate=10650000.00/min [720000], rate=10800000.00/min [730000], rate=10950000.00/min [740000], rate=11100000.00/min [750000], rate=11250000.00/min [760000], rate=11400000.00/min [770000], rate=11550000.00/min [780000], rate=11700000.00/min [790000], rate=11850000.00/min [800000], rate=12000000.00/min [810000], rate=9720000.00/min [820000], rate=9840000.00/min [830000], rate=9960000.00/min [840000], rate=10080000.00/min [850000], rate=10200000.00/min [860000], rate=10320000.00/min [870000], rate=10440000.00/min [880000], rate=10560000.00/min [890000], rate=10680000.00/min [900000], rate=10800000.00/min [910000], rate=10920000.00/min [920000], rate=11040000.00/min [930000], rate=11160000.00/min [940000], rate=11280000.00/min [950000], rate=11400000.00/min [960000], rate=11520000.00/min [970000], rate=11640000.00/min [980000], rate=11760000.00/min [990000], rate=9900000.00/min [1000000], rate=10000000.00/min [1010000], rate=10100000.00/min [1020000], rate=10200000.00/min [1030000], rate=10300000.00/min [1040000], rate=10400000.00/min [1050000], rate=10500000.00/min [1060000], rate=10600000.00/min [1070000], rate=10700000.00/min [1080000], rate=10800000.00/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=10028571.43/min [1180000], rate=10114285.71/min [1190000], rate=10200000.00/min [1200000], rate=10285714.29/min [1210000], rate=10371428.57/min [1220000], rate=10457142.86/min [1230000], rate=10542857.14/min [1240000], rate=10628571.43/min [1250000], rate=10714285.71/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=10275000.00/min [1380000], rate=10350000.00/min [1390000], rate=10425000.00/min [1400000], rate=10500000.00/min [1410000], rate=10575000.00/min [1420000], rate=10650000.00/min [1430000], rate=10725000.00/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=10400000.00/min [1570000], rate=10466666.67/min [1580000], rate=10533333.33/min [1590000], rate=10600000.00/min [1600000], rate=10666666.67/min [1610000], rate=10733333.33/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=10560000.00/min [1770000], rate=10620000.00/min [1780000], rate=10680000.00/min [1790000], rate=10740000.00/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=10636363.64/min [1960000], rate=10690909.09/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=11672727.27/min [2150000], rate=11727272.73/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=11650000.00/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=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=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=11400000.00/min [2670000], rate=11442857.14/min [2680000], rate=11485714.29/min [2690000], rate=11528571.43/min [2700000], rate=11571428.57/min [2710000], rate=11614285.71/min [2720000], rate=11657142.86/min [2730000], rate=11700000.00/min [2740000], rate=11742857.14/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=11320000.00/min [2840000], rate=11360000.00/min [2850000], rate=11400000.00/min [2860000], rate=11440000.00/min [2870000], rate=11480000.00/min [2880000], rate=11520000.00/min [2890000], rate=11560000.00/min [2900000], rate=11600000.00/min [2910000], rate=11640000.00/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=11325000.00/min [3030000], rate=11362500.00/min [3040000], rate=11400000.00/min [3050000], rate=11437500.00/min [3060000], rate=11475000.00/min [3070000], rate=11512500.00/min [3080000], rate=11550000.00/min [3090000], rate=11587500.00/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=11329411.76/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=10515789.47/min [3340000], rate=10547368.42/min [3350000], rate=10578947.37/min [3360000], rate=10610526.32/min [3370000], rate=10642105.26/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=10320000.00/min [3450000], rate=10350000.00/min [3460000], rate=10380000.00/min [3470000], rate=10410000.00/min [3480000], rate=10440000.00/min [3490000], rate=10470000.00/min [3500000], rate=10500000.00/min [3510000], rate=10530000.00/min [3520000], rate=10560000.00/min [3530000], rate=10590000.00/min [3540000], rate=10620000.00/min [3550000], rate=10650000.00/min [3560000], rate=10171428.57/min [3570000], rate=10200000.00/min [3580000], rate=10228571.43/min [3590000], rate=10257142.86/min [3600000], rate=10285714.29/min [3610000], rate=10314285.71/min [3620000], rate=10342857.14/min [3630000], rate=10371428.57/min [3640000], rate=10400000.00/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=10200000.00/min [3750000], rate=10227272.73/min [3760000], rate=10254545.45/min [3770000], rate=10281818.18/min [3780000], rate=10309090.91/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=10095652.17/min [3880000], rate=10121739.13/min [3890000], rate=10147826.09/min [3900000], rate=10173913.04/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=10025000.00/min [4020000], rate=10050000.00/min [4030000], rate=10075000.00/min [4040000], rate=10100000.00/min [4050000], rate=10125000.00/min [4060000], rate=10150000.00/min [4070000], rate=10175000.00/min [4080000], rate=10200000.00/min [4090000], rate=9816000.00/min [4100000], rate=9840000.00/min [4110000], rate=9864000.00/min [4120000], rate=9888000.00/min [4130000], rate=9912000.00/min [4140000], rate=9936000.00/min [4150000], rate=9960000.00/min [4160000], rate=9984000.00/min [4170000], rate=10008000.00/min [4180000], rate=10032000.00/min [4190000], rate=10056000.00/min [4200000], rate=10080000.00/min [4210000], rate=10104000.00/min [4220000], rate=10128000.00/min [4230000], rate=10152000.00/min [4240000], rate=10176000.00/min [4250000], rate=10200000.00/min [4260000], rate=9830769.23/min [4270000], rate=9853846.15/min [4280000], rate=9876923.08/min [4290000], rate=9900000.00/min [4300000], rate=9923076.92/min [4310000], rate=9946153.85/min [4320000], rate=9969230.77/min [4330000], rate=9992307.69/min [4340000], rate=10015384.62/min [4350000], rate=10038461.54/min [4360000], rate=10061538.46/min [4370000], rate=10084615.38/min [4380000], rate=10107692.31/min [4390000], rate=10130769.23/min [4400000], rate=10153846.15/min [4410000], rate=10176923.08/min [4420000], rate=10200000.00/min [4430000], rate=9844444.44/min [4440000], rate=9866666.67/min [4450000], rate=9888888.89/min [4460000], rate=9911111.11/min [4470000], rate=9933333.33/min [4480000], rate=9955555.56/min [4490000], rate=9977777.78/min [4500000], rate=10000000.00/min [4510000], rate=10022222.22/min [4520000], rate=10044444.44/min [4530000], rate=10066666.67/min [4540000], rate=10088888.89/min [4550000], rate=10111111.11/min [4560000], rate=9771428.57/min [4570000], rate=9792857.14/min [4580000], rate=9814285.71/min [4590000], rate=9835714.29/min [4600000], rate=9857142.86/min [4610000], rate=9878571.43/min [4620000], rate=9900000.00/min [4630000], rate=9921428.57/min [4640000], rate=9942857.14/min [4650000], rate=9964285.71/min [4660000], rate=9641379.31/min [4670000], rate=9662068.97/min [4680000], rate=9682758.62/min [4690000], rate=9703448.28/min [4700000], rate=9724137.93/min [4710000], rate=9744827.59/min [4720000], rate=9765517.24/min [4730000], rate=9786206.90/min [4740000], rate=9806896.55/min [4750000], rate=9827586.21/min [4760000], rate=9848275.86/min [4770000], rate=9868965.52/min [4780000], rate=9560000.00/min [4790000], rate=9580000.00/min [4800000], rate=9600000.00/min [4810000], rate=9620000.00/min [4820000], rate=9640000.00/min [4830000], rate=9660000.00/min [4840000], rate=9680000.00/min [4850000], rate=9700000.00/min [4860000], rate=9720000.00/min [4870000], rate=9740000.00/min [4880000], rate=9760000.00/min [4890000], rate=9780000.00/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=9696774.19/min [5020000], rate=9716129.03/min [5030000], rate=9735483.87/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=9352941.18/min [5310000], rate=9370588.24/min [5320000], rate=9388235.29/min [5330000], rate=9405882.35/min [5340000], rate=9423529.41/min [5350000], rate=9441176.47/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=9291428.57/min [5430000], rate=9308571.43/min [5440000], rate=9325714.29/min [5450000], rate=9342857.14/min [5460000], rate=9360000.00/min [5470000], rate=9377142.86/min [5480000], rate=9394285.71/min [5490000], rate=9411428.57/min [5500000], rate=9428571.43/min [5510000], rate=9445714.29/min [5520000], rate=9462857.14/min [5530000], rate=9480000.00/min [5540000], rate=9233333.33/min [5550000], rate=9250000.00/min [5560000], rate=9266666.67/min [5570000], rate=9283333.33/min [5580000], rate=9300000.00/min [5590000], rate=9316666.67/min [5600000], rate=9333333.33/min [5610000], rate=9350000.00/min [5620000], rate=9366666.67/min [5630000], rate=9383333.33/min [5640000], rate=9400000.00/min [5650000], rate=9416666.67/min [5660000], rate=9178378.38/min [5670000], rate=9194594.59/min [5680000], rate=9210810.81/min [5690000], rate=9227027.03/min [5700000], rate=9243243.24/min [5710000], rate=9259459.46/min [5720000], rate=9275675.68/min [5730000], rate=9291891.89/min [5740000], rate=9063157.89/min [5750000], rate=9078947.37/min [5760000], rate=9094736.84/min [5770000], rate=9110526.32/min [5780000], rate=9126315.79/min [5790000], rate=9142105.26/min [5800000], rate=9157894.74/min [5810000], rate=9173684.21/min [5820000], rate=9189473.68/min [5830000], rate=9205263.16/min [5840000], rate=9221052.63/min [5850000], rate=9236842.11/min [5860000], rate=9015384.62/min [5870000], rate=9030769.23/min [5880000], rate=9046153.85/min [5890000], rate=9061538.46/min [5900000], rate=9076923.08/min [5910000], rate=9092307.69/min [5920000], rate=9107692.31/min [5930000], rate=9123076.92/min [5940000], rate=9138461.54/min [5950000], rate=9153846.15/min [5960000], rate=9169230.77/min [5970000], rate=9184615.38/min [5980000], rate=9200000.00/min [5990000], rate=8985000.00/min [6000000], rate=9000000.00/min [6010000], rate=9015000.00/min [6020000], rate=9030000.00/min [6030000], rate=9045000.00/min [6040000], rate=9060000.00/min [6050000], rate=9075000.00/min [6060000], rate=9090000.00/min [6070000], rate=9105000.00/min [6080000], rate=9120000.00/min [6090000], rate=9135000.00/min [6100000], rate=9150000.00/min [6110000], rate=8941463.41/min [6120000], rate=8956097.56/min [6130000], rate=8970731.71/min [6140000], rate=8985365.85/min [6150000], rate=9000000.00/min [6160000], rate=9014634.15/min [6170000], rate=9029268.29/min [6180000], rate=9043902.44/min [6190000], rate=9058536.59/min [6200000], rate=9073170.73/min [6210000], rate=9087804.88/min [6220000], rate=9102439.02/min [6230000], rate=9117073.17/min [6240000], rate=8914285.71/min [6250000], rate=8928571.43/min [6260000], rate=8942857.14/min [6270000], rate=8957142.86/min [6280000], rate=8971428.57/min [6290000], rate=8985714.29/min [6300000], rate=9000000.00/min [6310000], rate=9014285.71/min [6320000], rate=9028571.43/min [6330000], rate=9042857.14/min [6340000], rate=9057142.86/min [6350000], rate=9071428.57/min [6360000], rate=8874418.60/min [6370000], rate=8888372.09/min [6380000], rate=8902325.58/min [6390000], rate=8916279.07/min [6400000], rate=8930232.56/min [6410000], rate=8944186.05/min [6420000], rate=8958139.53/min [6430000], rate=8972093.02/min [6440000], rate=8986046.51/min [6450000], rate=9000000.00/min [6460000], rate=8809090.91/min [6470000], rate=8822727.27/min [6480000], rate=8836363.64/min [6490000], rate=8850000.00/min [6500000], rate=8863636.36/min [6510000], rate=8877272.73/min [6520000], rate=8890909.09/min [6530000], rate=8904545.45/min [6540000], rate=8918181.82/min [6550000], rate=8931818.18/min [6560000], rate=8945454.55/min [6570000], rate=8959090.91/min [6580000], rate=8972727.27/min [6590000], rate=8786666.67/min [6600000], rate=8800000.00/min [6610000], rate=8813333.33/min [6620000], rate=8826666.67/min [6630000], rate=8840000.00/min [6640000], rate=8853333.33/min [6650000], rate=8866666.67/min [6660000], rate=8880000.00/min [6670000], rate=8893333.33/min [6680000], rate=8906666.67/min [6690000], rate=8920000.00/min [6700000], rate=8933333.33/min [6710000], rate=8946666.67/min [6720000], rate=8765217.39/min [6730000], rate=8778260.87/min [6740000], rate=8791304.35/min [6750000], rate=8804347.83/min [6760000], rate=8817391.30/min [6770000], rate=8830434.78/min [6780000], rate=8843478.26/min [6790000], rate=8856521.74/min [6800000], rate=8869565.22/min [6810000], rate=8882608.70/min [6820000], rate=8895652.17/min [6830000], rate=8719148.94/min [6840000], rate=8731914.89/min [6850000], rate=8744680.85/min [6860000], rate=8757446.81/min [6870000], rate=8770212.77/min [6880000], rate=8782978.72/min [6890000], rate=8795744.68/min [6900000], rate=8808510.64/min [6910000], rate=8821276.60/min [6920000], rate=8834042.55/min [6930000], rate=8846808.51/min [6940000], rate=8859574.47/min [6950000], rate=8872340.43/min [6960000], rate=8700000.00/min [6970000], rate=8712500.00/min [6980000], rate=8725000.00/min [6990000], rate=8737500.00/min [7000000], rate=8750000.00/min [7010000], rate=8762500.00/min [7020000], rate=8775000.00/min [7030000], rate=8787500.00/min [7040000], rate=8800000.00/min [7050000], rate=8812500.00/min [7060000], rate=8825000.00/min [7070000], rate=8837500.00/min [7080000], rate=8669387.76/min [7090000], rate=8681632.65/min [7100000], rate=8693877.55/min [7110000], rate=8706122.45/min [7120000], rate=8718367.35/min [7130000], rate=8730612.24/min [7140000], rate=8742857.14/min [7150000], rate=8755102.04/min [7160000], rate=8767346.94/min [7170000], rate=8779591.84/min [7180000], rate=8791836.73/min [7190000], rate=8804081.63/min [7200000], rate=8816326.53/min [7210000], rate=8652000.00/min [7220000], rate=8664000.00/min [7230000], rate=8676000.00/min [7240000], rate=8688000.00/min [7250000], rate=8700000.00/min [7260000], rate=8712000.00/min [7270000], rate=8724000.00/min [7280000], rate=8736000.00/min [7290000], rate=8748000.00/min [7300000], rate=8760000.00/min [7310000], rate=8772000.00/min [7320000], rate=8784000.00/min [7330000], rate=8623529.41/min [7340000], rate=8635294.12/min [7350000], rate=8647058.82/min [7360000], rate=8658823.53/min [7370000], rate=8670588.24/min [7380000], rate=8682352.94/min [7390000], rate=8694117.65/min [7400000], rate=8538461.54/min [7410000], rate=8550000.00/min [7420000], rate=8561538.46/min [7430000], rate=8573076.92/min [7440000], rate=8584615.38/min [7450000], rate=8596153.85/min [7460000], rate=8607692.31/min [7470000], rate=8619230.77/min [7480000], rate=8630769.23/min [7490000], rate=8642307.69/min [7500000], rate=8653846.15/min [7510000], rate=8665384.62/min [7520000], rate=8513207.55/min [7530000], rate=8524528.30/min [7540000], rate=8535849.06/min [7550000], rate=8547169.81/min [7560000], rate=8558490.57/min [7570000], rate=8569811.32/min [7580000], rate=8581132.08/min [7590000], rate=8592452.83/min [7600000], rate=8603773.58/min [7610000], rate=8615094.34/min [7620000], rate=8626415.09/min [7630000], rate=8637735.85/min [7640000], rate=8649056.60/min [7650000], rate=8660377.36/min [7660000], rate=8671698.11/min [7670000], rate=8683018.87/min [7680000], rate=8694339.62/min [7690000], rate=8705660.38/min [7700000], rate=8716981.13/min 20:01:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-1274d4-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer.introns.prelim Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18. -aih-tih-sc-1274d4-R1_A23YTGFLT4_1.introns: identified 6129 cancer introns 20:01:29 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-1274d4-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer.introns.prelim 20:01:29 : INFO : Running: touch /tmp/nxf.m5Tq7VqLBB/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 20:01:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer.introns 20:01:30 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer.introns 20:01:30 : INFO : Running: touch /tmp/nxf.m5Tq7VqLBB/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 20:01:30 : INFO : -found 2073 cancer introns 20:01:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-1274d4-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-1274d4-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:01:30 : INFO : Creating the BED File. 20:01:43 : INFO : Saving Bed File as aih-tih-sc-1274d4-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:01:43 : INFO : Execution Time = 0.22 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-1274d4-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-1274d4-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:01:43 : INFO : Running: touch /tmp/nxf.m5Tq7VqLBB/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 20:01:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-1274d4-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-1274d4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-1274d4-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 20:22:48 : INFO : Execution Time = 21.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-1274d4-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-1274d4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-1274d4-R1_A23YTGFLT4_1 20:22:48 : INFO : Running: touch /tmp/nxf.m5Tq7VqLBB/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 20:22:49 : INFO : Running: samtools sort -o aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer_intron_reads.bam 20:22:49 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-1274d4-R1_A23YTGFLT4_1.cancer_intron_reads.bam 20:22:49 : INFO : Running: touch /tmp/nxf.m5Tq7VqLBB/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 20:22:49 : INFO : Running: samtools sort -o aih-tih-sc-1274d4-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-1274d4-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 74 files and 1 in-memory blocks...