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/c1/3e34abccd85a52eb9095a499b1e1fa/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/f3cd8145eac896f42d606440633efa/tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/f3cd8145eac896f42d606440633efa/tih_rna_sample_00146_B23WHTKLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/cfbc4ab5b2a73c739a299563ce9dcb/tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/3e34abccd85a52eb9095a499b1e1fa/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/f3cd8145eac896f42d606440633efa/tih_rna_sample_00146_B23WHTKLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)
08:50:35 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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=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=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=17700000.00/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=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=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=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=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=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=14500000.00/min
[1460000], rate=14600000.00/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=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=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=11820000.00/min
[1980000], rate=11880000.00/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=10600000.00/min
[2130000], rate=10650000.00/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=10430769.23/min
[2270000], rate=10476923.08/min
[2280000], rate=10523076.92/min
[2290000], rate=10569230.77/min
[2300000], rate=10615384.62/min
[2310000], rate=10661538.46/min
[2320000], rate=10707692.31/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=10285714.29/min
[2410000], rate=10328571.43/min
[2420000], rate=10371428.57/min
[2430000], rate=10414285.71/min
[2440000], rate=10457142.86/min
[2450000], rate=10500000.00/min
[2460000], rate=10542857.14/min
[2470000], rate=10585714.29/min
[2480000], rate=10628571.43/min
[2490000], rate=10671428.57/min
[2500000], rate=10714285.71/min
[2510000], rate=10040000.00/min
[2520000], rate=10080000.00/min
[2530000], rate=10120000.00/min
[2540000], rate=10160000.00/min
[2550000], rate=10200000.00/min
[2560000], rate=10240000.00/min
[2570000], rate=10280000.00/min
[2580000], rate=10320000.00/min
[2590000], rate=10360000.00/min
[2600000], rate=10400000.00/min
[2610000], rate=9787500.00/min
[2620000], rate=9825000.00/min
[2630000], rate=9862500.00/min
[2640000], rate=9900000.00/min
[2650000], rate=9937500.00/min
[2660000], rate=9975000.00/min
[2670000], rate=10012500.00/min
[2680000], rate=10050000.00/min
[2690000], rate=10087500.00/min
[2700000], rate=10125000.00/min
[2710000], rate=10162500.00/min
[2720000], rate=10200000.00/min
[2730000], rate=10237500.00/min
[2740000], rate=9670588.24/min
[2750000], rate=9705882.35/min
[2760000], rate=9741176.47/min
[2770000], rate=9776470.59/min
[2780000], rate=9811764.71/min
[2790000], rate=9847058.82/min
[2800000], rate=9882352.94/min
[2810000], rate=9917647.06/min
[2820000], rate=9952941.18/min
[2830000], rate=9988235.29/min
[2840000], rate=10023529.41/min
[2850000], rate=10058823.53/min
[2860000], rate=10094117.65/min
[2870000], rate=10129411.76/min
[2880000], rate=9600000.00/min
[2890000], rate=9633333.33/min
[2900000], rate=9666666.67/min
[2910000], rate=9700000.00/min
[2920000], rate=9733333.33/min
[2930000], rate=9766666.67/min
[2940000], rate=9800000.00/min
[2950000], rate=9833333.33/min
[2960000], rate=9866666.67/min
[2970000], rate=9900000.00/min
[2980000], rate=9933333.33/min
[2990000], rate=9966666.67/min
[3000000], rate=10000000.00/min
[3010000], rate=9505263.16/min
[3020000], rate=9536842.11/min
[3030000], rate=9568421.05/min
[3040000], rate=9600000.00/min
[3050000], rate=9631578.95/min
[3060000], rate=9663157.89/min
[3070000], rate=9694736.84/min
[3080000], rate=9726315.79/min
[3090000], rate=9757894.74/min
[3100000], rate=9789473.68/min
[3110000], rate=9821052.63/min
[3120000], rate=9852631.58/min
[3130000], rate=9884210.53/min
[3140000], rate=9915789.47/min
[3150000], rate=9450000.00/min
[3160000], rate=9480000.00/min
[3170000], rate=9510000.00/min
[3180000], rate=9540000.00/min
[3190000], rate=9570000.00/min
[3200000], rate=9600000.00/min
[3210000], rate=9630000.00/min
[3220000], rate=9660000.00/min
[3230000], rate=9690000.00/min
[3240000], rate=9720000.00/min
[3250000], rate=9750000.00/min
[3260000], rate=9780000.00/min
[3270000], rate=9810000.00/min
[3280000], rate=9371428.57/min
[3290000], rate=9400000.00/min
[3300000], rate=9428571.43/min
[3310000], rate=9457142.86/min
[3320000], rate=9485714.29/min
[3330000], rate=9514285.71/min
[3340000], rate=9542857.14/min
[3350000], rate=9571428.57/min
[3360000], rate=9600000.00/min
[3370000], rate=9628571.43/min
[3380000], rate=9657142.86/min
[3390000], rate=9685714.29/min
[3400000], rate=9714285.71/min
[3410000], rate=9742857.14/min
[3420000], rate=9771428.57/min
[3430000], rate=9354545.45/min
[3440000], rate=9381818.18/min
[3450000], rate=9409090.91/min
[3460000], rate=9436363.64/min
[3470000], rate=9463636.36/min
[3480000], rate=9490909.09/min
[3490000], rate=9518181.82/min
[3500000], rate=9545454.55/min
[3510000], rate=9572727.27/min
[3520000], rate=9600000.00/min
[3530000], rate=9627272.73/min
[3540000], rate=9654545.45/min
[3550000], rate=9681818.18/min
[3560000], rate=9709090.91/min
[3570000], rate=9736363.64/min
[3580000], rate=9763636.36/min
[3590000], rate=9790909.09/min
[3600000], rate=9818181.82/min
[3610000], rate=9845454.55/min
[3620000], rate=9872727.27/min
[3630000], rate=9469565.22/min
[3640000], rate=9495652.17/min
[3650000], rate=9521739.13/min
[3660000], rate=9547826.09/min
[3670000], rate=9573913.04/min
[3680000], rate=9600000.00/min
[3690000], rate=9626086.96/min
[3700000], rate=9652173.91/min
[3710000], rate=9678260.87/min
[3720000], rate=9704347.83/min
[3730000], rate=9730434.78/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=9525000.00/min
[3820000], rate=9550000.00/min
[3830000], rate=9575000.00/min
[3840000], rate=9600000.00/min
[3850000], rate=9625000.00/min
[3860000], rate=9650000.00/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=9552000.00/min
[3990000], rate=9576000.00/min
[4000000], rate=9600000.00/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=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=9761538.46/min
[4240000], rate=9784615.38/min
[4250000], rate=9807692.31/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=10223076.92/min
[4440000], rate=10246153.85/min
[4450000], rate=10269230.77/min
[4460000], rate=10292307.69/min
[4470000], rate=10315384.62/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=10133333.33/min
[4570000], rate=10155555.56/min
[4580000], rate=10177777.78/min
[4590000], rate=10200000.00/min
[4600000], rate=10222222.22/min
[4610000], rate=10244444.44/min
[4620000], rate=10266666.67/min
[4630000], rate=10288888.89/min
[4640000], rate=10311111.11/min
[4650000], rate=10333333.33/min
[4660000], rate=10355555.56/min
[4670000], rate=10377777.78/min
[4680000], rate=10400000.00/min
[4690000], rate=10422222.22/min
[4700000], rate=10444444.44/min
[4710000], rate=10092857.14/min
[4720000], rate=10114285.71/min
[4730000], rate=10135714.29/min
[4740000], rate=10157142.86/min
[4750000], rate=10178571.43/min
[4760000], rate=10200000.00/min
[4770000], rate=10221428.57/min
[4780000], rate=10242857.14/min
[4790000], rate=10264285.71/min
[4800000], rate=10285714.29/min
[4810000], rate=10307142.86/min
[4820000], rate=10328571.43/min
[4830000], rate=10350000.00/min
[4840000], rate=10371428.57/min
[4850000], rate=10392857.14/min
[4860000], rate=10414285.71/min
[4870000], rate=10075862.07/min
[4880000], rate=10096551.72/min
[4890000], rate=10117241.38/min
[4900000], rate=10137931.03/min
[4910000], rate=10158620.69/min
[4920000], rate=10179310.34/min
[4930000], rate=10200000.00/min
[4940000], rate=10220689.66/min
[4950000], rate=10241379.31/min
[4960000], rate=10262068.97/min
[4970000], rate=10282758.62/min
[4980000], rate=10303448.28/min
[4990000], rate=10324137.93/min
[5000000], rate=10344827.59/min
[5010000], rate=10365517.24/min
[5020000], rate=10040000.00/min
[5030000], rate=10060000.00/min
[5040000], rate=10080000.00/min
[5050000], rate=10100000.00/min
[5060000], rate=10120000.00/min
[5070000], rate=10140000.00/min
[5080000], rate=10160000.00/min
[5090000], rate=10180000.00/min
[5100000], rate=10200000.00/min
[5110000], rate=10220000.00/min
[5120000], rate=10240000.00/min
[5130000], rate=10260000.00/min
[5140000], rate=10280000.00/min
[5150000], rate=10300000.00/min
[5160000], rate=10320000.00/min
[5170000], rate=10340000.00/min
[5180000], rate=10360000.00/min
[5190000], rate=10380000.00/min
[5200000], rate=10064516.13/min
[5210000], rate=10083870.97/min
[5220000], rate=10103225.81/min
[5230000], rate=10122580.65/min
[5240000], rate=10141935.48/min
[5250000], rate=10161290.32/min
[5260000], rate=10180645.16/min
[5270000], rate=10200000.00/min
[5280000], rate=10219354.84/min
[5290000], rate=10238709.68/min
[5300000], rate=10258064.52/min
[5310000], rate=10277419.35/min
[5320000], rate=10296774.19/min
[5330000], rate=10316129.03/min
[5340000], rate=10335483.87/min
[5350000], rate=10354838.71/min
[5360000], rate=10374193.55/min
[5370000], rate=10393548.39/min
[5380000], rate=10087500.00/min
[5390000], rate=10106250.00/min
[5400000], rate=10125000.00/min
[5410000], rate=10143750.00/min
[5420000], rate=10162500.00/min
[5430000], rate=10181250.00/min
[5440000], rate=10200000.00/min
[5450000], rate=10218750.00/min
[5460000], rate=10237500.00/min
[5470000], rate=10256250.00/min
[5480000], rate=10275000.00/min
[5490000], rate=10293750.00/min
[5500000], rate=10312500.00/min
[5510000], rate=10331250.00/min
[5520000], rate=10350000.00/min
[5530000], rate=10368750.00/min
[5540000], rate=10387500.00/min
[5550000], rate=10406250.00/min
[5560000], rate=10425000.00/min
[5570000], rate=10443750.00/min
[5580000], rate=10462500.00/min
[5590000], rate=10481250.00/min
[5600000], rate=10500000.00/min
[5610000], rate=10518750.00/min
[5620000], rate=10218181.82/min
[5630000], rate=10236363.64/min
[5640000], rate=10254545.45/min
[5650000], rate=10272727.27/min
[5660000], rate=10290909.09/min
[5670000], rate=10309090.91/min
[5680000], rate=10327272.73/min
[5690000], rate=10345454.55/min
[5700000], rate=10363636.36/min
[5710000], rate=10381818.18/min
[5720000], rate=10400000.00/min
[5730000], rate=10418181.82/min
[5740000], rate=10436363.64/min
[5750000], rate=10454545.45/min
[5760000], rate=10472727.27/min
[5770000], rate=10490909.09/min
[5780000], rate=10509090.91/min
[5790000], rate=10527272.73/min
[5800000], rate=10545454.55/min
[5810000], rate=10563636.36/min
[5820000], rate=10581818.18/min
[5830000], rate=10600000.00/min
[5840000], rate=10618181.82/min
[5850000], rate=10323529.41/min
[5860000], rate=10341176.47/min
[5870000], rate=10358823.53/min
[5880000], rate=10376470.59/min
[5890000], rate=10394117.65/min
[5900000], rate=10411764.71/min
[5910000], rate=10429411.76/min
[5920000], rate=10447058.82/min
[5930000], rate=10464705.88/min
[5940000], rate=10482352.94/min
[5950000], rate=10500000.00/min
[5960000], rate=10517647.06/min
[5970000], rate=10535294.12/min
[5980000], rate=10552941.18/min
[5990000], rate=10570588.24/min
[6000000], rate=10588235.29/min
[6010000], rate=10605882.35/min
[6020000], rate=10623529.41/min
[6030000], rate=10641176.47/min
[6040000], rate=10658823.53/min
[6050000], rate=10676470.59/min
[6060000], rate=10694117.65/min
[6070000], rate=10405714.29/min
[6080000], rate=10422857.14/min
[6090000], rate=10440000.00/min
[6100000], rate=10457142.86/min
[6110000], rate=10474285.71/min
[6120000], rate=10491428.57/min
[6130000], rate=10508571.43/min
[6140000], rate=10525714.29/min
[6150000], rate=10542857.14/min
[6160000], rate=10560000.00/min
[6170000], rate=10577142.86/min
[6180000], rate=10594285.71/min
[6190000], rate=10611428.57/min
[6200000], rate=10628571.43/min
[6210000], rate=10645714.29/min
[6220000], rate=10662857.14/min
[6230000], rate=10680000.00/min
[6240000], rate=10697142.86/min
[6250000], rate=10714285.71/min
[6260000], rate=10731428.57/min
[6270000], rate=10748571.43/min
[6280000], rate=10765714.29/min
[6290000], rate=10483333.33/min
[6300000], rate=10500000.00/min
[6310000], rate=10516666.67/min
[6320000], rate=10533333.33/min
[6330000], rate=10550000.00/min
[6340000], rate=10566666.67/min
[6350000], rate=10583333.33/min
[6360000], rate=10600000.00/min
[6370000], rate=10616666.67/min
[6380000], rate=10633333.33/min
[6390000], rate=10650000.00/min
[6400000], rate=10666666.67/min
[6410000], rate=10683333.33/min
[6420000], rate=10700000.00/min
[6430000], rate=10716666.67/min
[6440000], rate=10733333.33/min
[6450000], rate=10750000.00/min
[6460000], rate=10475675.68/min
[6470000], rate=10491891.89/min
[6480000], rate=10508108.11/min
[6490000], rate=10524324.32/min
[6500000], rate=10540540.54/min
[6510000], rate=10556756.76/min
[6520000], rate=10572972.97/min
[6530000], rate=10589189.19/min
[6540000], rate=10605405.41/min
[6550000], rate=10621621.62/min
[6560000], rate=10637837.84/min
[6570000], rate=10654054.05/min
[6580000], rate=10670270.27/min
[6590000], rate=10686486.49/min
[6600000], rate=10421052.63/min
[6610000], rate=10436842.11/min
[6620000], rate=10452631.58/min
[6630000], rate=10468421.05/min
[6640000], rate=10484210.53/min
[6650000], rate=10500000.00/min
[6660000], rate=10515789.47/min
[6670000], rate=10531578.95/min
[6680000], rate=10547368.42/min
[6690000], rate=10563157.89/min
[6700000], rate=10578947.37/min
[6710000], rate=10594736.84/min
[6720000], rate=10610526.32/min
[6730000], rate=10353846.15/min
[6740000], rate=10369230.77/min
[6750000], rate=10384615.38/min
[6760000], rate=10400000.00/min
[6770000], rate=10415384.62/min
[6780000], rate=10430769.23/min
[6790000], rate=10446153.85/min
[6800000], rate=10461538.46/min
[6810000], rate=10476923.08/min
[6820000], rate=10492307.69/min
[6830000], rate=10507692.31/min
[6840000], rate=10523076.92/min
[6850000], rate=10538461.54/min
[6860000], rate=10553846.15/min
[6870000], rate=10305000.00/min
[6880000], rate=10320000.00/min
[6890000], rate=10335000.00/min
[6900000], rate=10350000.00/min
[6910000], rate=10365000.00/min
[6920000], rate=10380000.00/min
[6930000], rate=10395000.00/min
[6940000], rate=10410000.00/min
[6950000], rate=10425000.00/min
[6960000], rate=10440000.00/min
[6970000], rate=10455000.00/min
[6980000], rate=10470000.00/min
[6990000], rate=10485000.00/min
[7000000], rate=10500000.00/min
[7010000], rate=10515000.00/min
[7020000], rate=10530000.00/min
[7030000], rate=10545000.00/min
[7040000], rate=10560000.00/min
[7050000], rate=10575000.00/min
[7060000], rate=10590000.00/min
[7070000], rate=10605000.00/min
[7080000], rate=10360975.61/min
[7090000], rate=10375609.76/min
[7100000], rate=10390243.90/min
[7110000], rate=10404878.05/min
[7120000], rate=10419512.20/min
[7130000], rate=10434146.34/min
[7140000], rate=10448780.49/min
[7150000], rate=10463414.63/min
[7160000], rate=10478048.78/min
[7170000], rate=10492682.93/min
[7180000], rate=10507317.07/min
[7190000], rate=10521951.22/min
[7200000], rate=10536585.37/min
[7210000], rate=10551219.51/min
[7220000], rate=10565853.66/min
[7230000], rate=10580487.80/min
[7240000], rate=10595121.95/min
[7250000], rate=10609756.10/min
[7260000], rate=10624390.24/min
[7270000], rate=10639024.39/min
[7280000], rate=10653658.54/min
[7290000], rate=10668292.68/min
[7300000], rate=10682926.83/min
[7310000], rate=10697560.98/min
[7320000], rate=10712195.12/min
[7330000], rate=10471428.57/min
[7340000], rate=10485714.29/min
[7350000], rate=10500000.00/min
[7360000], rate=10514285.71/min
[7370000], rate=10528571.43/min
[7380000], rate=10542857.14/min
[7390000], rate=10557142.86/min
[7400000], rate=10571428.57/min
[7410000], rate=10585714.29/min
[7420000], rate=10600000.00/min
[7430000], rate=10614285.71/min
[7440000], rate=10628571.43/min
[7450000], rate=10642857.14/min
[7460000], rate=10657142.86/min
[7470000], rate=10671428.57/min
[7480000], rate=10685714.29/min
[7490000], rate=10700000.00/min
[7500000], rate=10714285.71/min
[7510000], rate=10728571.43/min
[7520000], rate=10742857.14/min
[7530000], rate=10757142.86/min
[7540000], rate=10520930.23/min
[7550000], rate=10534883.72/min
[7560000], rate=10548837.21/min
[7570000], rate=10562790.70/min
[7580000], rate=10576744.19/min
[7590000], rate=10590697.67/min
[7600000], rate=10604651.16/min
[7610000], rate=10618604.65/min
[7620000], rate=10632558.14/min
[7630000], rate=10646511.63/min
[7640000], rate=10660465.12/min
[7650000], rate=10674418.60/min
[7660000], rate=10688372.09/min
[7670000], rate=10702325.58/min
[7680000], rate=10716279.07/min
[7690000], rate=10730232.56/min
[7700000], rate=10500000.00/min
[7710000], rate=10513636.36/min
[7720000], rate=10527272.73/min
[7730000], rate=10540909.09/min
[7740000], rate=10554545.45/min
[7750000], rate=10568181.82/min
[7760000], rate=10581818.18/min
[7770000], rate=10595454.55/min
[7780000], rate=10609090.91/min
[7790000], rate=10622727.27/min
[7800000], rate=10636363.64/min
[7810000], rate=10650000.00/min
[7820000], rate=10663636.36/min
[7830000], rate=10677272.73/min
[7840000], rate=10690909.09/min
[7850000], rate=10704545.45/min
[7860000], rate=10718181.82/min
[7870000], rate=10731818.18/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=10640000.00/min
[7990000], rate=10653333.33/min
[8000000], rate=10666666.67/min
[8010000], rate=10680000.00/min
[8020000], rate=10693333.33/min
[8030000], rate=10706666.67/min
[8040000], rate=10720000.00/min
[8050000], rate=10733333.33/min
[8060000], rate=10746666.67/min
[8070000], rate=10760000.00/min
[8080000], rate=10773333.33/min
[8090000], rate=10786666.67/min
[8100000], rate=10800000.00/min
[8110000], rate=10813333.33/min
[8120000], rate=10826666.67/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=10721739.13/min
[8230000], rate=10734782.61/min
[8240000], rate=10747826.09/min
[8250000], rate=10760869.57/min
[8260000], rate=10773913.04/min
[8270000], rate=10786956.52/min
[8280000], rate=10800000.00/min
[8290000], rate=10813043.48/min
[8300000], rate=10826086.96/min
[8310000], rate=10839130.43/min
[8320000], rate=10852173.91/min
[8330000], rate=10865217.39/min
[8340000], rate=10878260.87/min
[8350000], rate=10891304.35/min
[8360000], rate=10904347.83/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=10812765.96/min
[8480000], rate=10825531.91/min
[8490000], rate=10838297.87/min
[8500000], rate=10851063.83/min
[8510000], rate=10863829.79/min
[8520000], rate=10876595.74/min 08:51:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00146_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00146_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.
-tih_rna_sample_00146_B23WHTKLT4_1.introns: identified 6528 cancer introns
08:51:35 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00146_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns.prelim
08:51:35 : INFO : Running: touch /tmp/nxf.hcAwnpJQDw/tih_rna_sample_00146_B23WHTKLT4_1.chckpts/prelim_introns.ok
08:51:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns
08:51:35 : 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_00146_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns
08:51:35 : INFO : Running: touch /tmp/nxf.hcAwnpJQDw/tih_rna_sample_00146_B23WHTKLT4_1.chckpts/introns_filtered.ok
08:51:35 : INFO : -found 3336 cancer introns
08:51:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00146_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00146_B23WHTKLT4_1.introns.for_IGV.bed
08:51:36 : INFO : Creating the BED File.
08:51:53 : INFO : Saving Bed File as tih_rna_sample_00146_B23WHTKLT4_1.introns.for_IGV.bed
08:51:54 : INFO : Execution Time = 0.30 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00146_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00146_B23WHTKLT4_1.introns.for_IGV.bed
08:51:54 : INFO : Running: touch /tmp/nxf.hcAwnpJQDw/tih_rna_sample_00146_B23WHTKLT4_1.chckpts/intron_igv_bed.ok
08:51:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00146_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00146_B23WHTKLT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
09:18:43 : INFO : Execution Time = 26.82 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00146_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00146_B23WHTKLT4_1
09:18:43 : INFO : Running: touch /tmp/nxf.hcAwnpJQDw/tih_rna_sample_00146_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok
09:18:43 : INFO : Running: samtools sort -o tih_rna_sample_00146_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00146_B23WHTKLT4_1.cancer_intron_reads.bam
09:18:44 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o tih_rna_sample_00146_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00146_B23WHTKLT4_1.cancer_intron_reads.bam
09:18:44 : INFO : Running: touch /tmp/nxf.hcAwnpJQDw/tih_rna_sample_00146_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok
09:18:44 : INFO : Running: samtools sort -o tih_rna_sample_00146_B23WHTKLT4_1.gene_reads.sorted.bam tih_rna_sample_00146_B23WHTKLT4_1.gene_reads.bam