Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/1ee13137e8c5731227665a7e4b083a/659_Mt-T1-TRNA-1_B23WHTKLT4_1.SJ.out.tab
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/71/5e98359688d2177c85b0eb5e49f57e/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/5e98359688d2177c85b0eb5e49f57e/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/7e6869ea27d9046b0c6f5b930181c5/659_Mt-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/1ee13137e8c5731227665a7e4b083a/659_Mt-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/1ee13137e8c5731227665a7e4b083a/659_Mt-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)
08:14:43 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[30000], rate=1800000.00/min
[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=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=18000000.00/min
[610000], rate=18300000.00/min
[620000], rate=18600000.00/min
[630000], rate=18900000.00/min
[640000], rate=19200000.00/min
[650000], rate=19500000.00/min
[660000], rate=19800000.00/min
[670000], rate=20100000.00/min
[680000], rate=20400000.00/min
[690000], rate=20700000.00/min
[700000], rate=21000000.00/min
[710000], rate=21300000.00/min
[720000], rate=21600000.00/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=16800000.00/min
[850000], rate=17000000.00/min
[860000], rate=17200000.00/min
[870000], rate=17400000.00/min
[880000], rate=17600000.00/min
[890000], rate=17800000.00/min
[900000], rate=18000000.00/min
[910000], rate=18200000.00/min
[920000], rate=18400000.00/min
[930000], rate=18600000.00/min
[940000], rate=18800000.00/min
[950000], rate=19000000.00/min
[960000], rate=19200000.00/min
[970000], rate=19400000.00/min
[980000], rate=19600000.00/min
[990000], rate=19800000.00/min
[1000000], rate=20000000.00/min
[1010000], rate=20200000.00/min
[1020000], rate=20400000.00/min
[1030000], rate=20600000.00/min
[1040000], rate=20800000.00/min
[1050000], rate=21000000.00/min
[1060000], rate=21200000.00/min
[1070000], rate=21400000.00/min
[1080000], rate=21600000.00/min
[1090000], rate=16350000.00/min
[1100000], rate=16500000.00/min
[1110000], rate=16650000.00/min
[1120000], rate=16800000.00/min
[1130000], rate=16950000.00/min
[1140000], rate=17100000.00/min
[1150000], rate=17250000.00/min
[1160000], rate=17400000.00/min
[1170000], rate=17550000.00/min
[1180000], rate=17700000.00/min
[1190000], rate=17850000.00/min
[1200000], rate=18000000.00/min
[1210000], rate=18150000.00/min
[1220000], rate=18300000.00/min
[1230000], rate=18450000.00/min
[1240000], rate=18600000.00/min
[1250000], rate=18750000.00/min
[1260000], rate=18900000.00/min
[1270000], rate=19050000.00/min
[1280000], rate=19200000.00/min
[1290000], rate=19350000.00/min
[1300000], rate=19500000.00/min
[1310000], rate=19650000.00/min
[1320000], rate=19800000.00/min
[1330000], rate=19950000.00/min
[1340000], rate=20100000.00/min
[1350000], rate=20250000.00/min
[1360000], rate=20400000.00/min
[1370000], rate=20550000.00/min
[1380000], rate=20700000.00/min
[1390000], rate=20850000.00/min
[1400000], rate=21000000.00/min
[1410000], rate=21150000.00/min
[1420000], rate=17040000.00/min
[1430000], rate=17160000.00/min
[1440000], rate=17280000.00/min
[1450000], rate=17400000.00/min
[1460000], rate=17520000.00/min
[1470000], rate=17640000.00/min
[1480000], rate=17760000.00/min
[1490000], rate=17880000.00/min
[1500000], rate=18000000.00/min
[1510000], rate=18120000.00/min
[1520000], rate=18240000.00/min
[1530000], rate=18360000.00/min
[1540000], rate=18480000.00/min
[1550000], rate=18600000.00/min
[1560000], rate=18720000.00/min
[1570000], rate=18840000.00/min
[1580000], rate=18960000.00/min
[1590000], rate=19080000.00/min
[1600000], rate=19200000.00/min
[1610000], rate=19320000.00/min
[1620000], rate=19440000.00/min
[1630000], rate=19560000.00/min
[1640000], rate=19680000.00/min
[1650000], rate=19800000.00/min
[1660000], rate=19920000.00/min
[1670000], rate=20040000.00/min
[1680000], rate=20160000.00/min
[1690000], rate=20280000.00/min
[1700000], rate=20400000.00/min
[1710000], rate=20520000.00/min
[1720000], rate=20640000.00/min
[1730000], rate=20760000.00/min
[1740000], rate=20880000.00/min
[1750000], rate=21000000.00/min
[1760000], rate=17600000.00/min
[1770000], rate=17700000.00/min
[1780000], rate=17800000.00/min
[1790000], rate=17900000.00/min
[1800000], rate=18000000.00/min
[1810000], rate=18100000.00/min
[1820000], rate=18200000.00/min
[1830000], rate=18300000.00/min
[1840000], rate=18400000.00/min
[1850000], rate=18500000.00/min
[1860000], rate=18600000.00/min
[1870000], rate=18700000.00/min
[1880000], rate=18800000.00/min
[1890000], rate=18900000.00/min
[1900000], rate=19000000.00/min
[1910000], rate=19100000.00/min
[1920000], rate=19200000.00/min
[1930000], rate=19300000.00/min
[1940000], rate=19400000.00/min
[1950000], rate=19500000.00/min
[1960000], rate=19600000.00/min
[1970000], rate=19700000.00/min
[1980000], rate=19800000.00/min
[1990000], rate=19900000.00/min
[2000000], rate=20000000.00/min
[2010000], rate=20100000.00/min
[2020000], rate=20200000.00/min
[2030000], rate=20300000.00/min
[2040000], rate=20400000.00/min
[2050000], rate=20500000.00/min
[2060000], rate=20600000.00/min
[2070000], rate=20700000.00/min
[2080000], rate=20800000.00/min
[2090000], rate=20900000.00/min
[2100000], rate=21000000.00/min
[2110000], rate=18085714.29/min
[2120000], rate=18171428.57/min
[2130000], rate=18257142.86/min
[2140000], rate=18342857.14/min
[2150000], rate=18428571.43/min
[2160000], rate=18514285.71/min
[2170000], rate=18600000.00/min
[2180000], rate=18685714.29/min
[2190000], rate=18771428.57/min
[2200000], rate=18857142.86/min
[2210000], rate=18942857.14/min
[2220000], rate=19028571.43/min
[2230000], rate=19114285.71/min
[2240000], rate=19200000.00/min
[2250000], rate=19285714.29/min
[2260000], rate=19371428.57/min
[2270000], rate=19457142.86/min
[2280000], rate=19542857.14/min
[2290000], rate=19628571.43/min
[2300000], rate=19714285.71/min
[2310000], rate=19800000.00/min
[2320000], rate=19885714.29/min
[2330000], rate=19971428.57/min
[2340000], rate=20057142.86/min
[2350000], rate=20142857.14/min
[2360000], rate=20228571.43/min
[2370000], rate=20314285.71/min
[2380000], rate=20400000.00/min
[2390000], rate=20485714.29/min
[2400000], rate=20571428.57/min
[2410000], rate=20657142.86/min
[2420000], rate=20742857.14/min
[2430000], rate=20828571.43/min
[2440000], rate=20914285.71/min
[2450000], rate=21000000.00/min
[2460000], rate=18450000.00/min
[2470000], rate=18525000.00/min
[2480000], rate=18600000.00/min
[2490000], rate=18675000.00/min
[2500000], rate=18750000.00/min
[2510000], rate=18825000.00/min
[2520000], rate=18900000.00/min
[2530000], rate=18975000.00/min
[2540000], rate=19050000.00/min
[2550000], rate=19125000.00/min
[2560000], rate=19200000.00/min
[2570000], rate=19275000.00/min
[2580000], rate=19350000.00/min
[2590000], rate=19425000.00/min
[2600000], rate=19500000.00/min
[2610000], rate=19575000.00/min
[2620000], rate=19650000.00/min
[2630000], rate=19725000.00/min
[2640000], rate=19800000.00/min
[2650000], rate=19875000.00/min
[2660000], rate=19950000.00/min
[2670000], rate=20025000.00/min
[2680000], rate=20100000.00/min
[2690000], rate=20175000.00/min
[2700000], rate=20250000.00/min
[2710000], rate=20325000.00/min
[2720000], rate=20400000.00/min
[2730000], rate=20475000.00/min
[2740000], rate=20550000.00/min
[2750000], rate=20625000.00/min
[2760000], rate=20700000.00/min
[2770000], rate=18466666.67/min
[2780000], rate=18533333.33/min
[2790000], rate=18600000.00/min
[2800000], rate=18666666.67/min
[2810000], rate=18733333.33/min
[2820000], rate=18800000.00/min
[2830000], rate=18866666.67/min
[2840000], rate=18933333.33/min
[2850000], rate=19000000.00/min
[2860000], rate=19066666.67/min
[2870000], rate=19133333.33/min
[2880000], rate=19200000.00/min
[2890000], rate=19266666.67/min
[2900000], rate=19333333.33/min
[2910000], rate=19400000.00/min
[2920000], rate=19466666.67/min
[2930000], rate=19533333.33/min
[2940000], rate=19600000.00/min
[2950000], rate=19666666.67/min
[2960000], rate=19733333.33/min
[2970000], rate=19800000.00/min
[2980000], rate=19866666.67/min
[2990000], rate=19933333.33/min
[3000000], rate=20000000.00/min
[3010000], rate=20066666.67/min
[3020000], rate=20133333.33/min
[3030000], rate=20200000.00/min
[3040000], rate=20266666.67/min
[3050000], rate=20333333.33/min
[3060000], rate=20400000.00/min
[3070000], rate=20466666.67/min
[3080000], rate=20533333.33/min
[3090000], rate=20600000.00/min
[3100000], rate=18600000.00/min
[3110000], rate=18660000.00/min
[3120000], rate=18720000.00/min
[3130000], rate=18780000.00/min
[3140000], rate=18840000.00/min
[3150000], rate=18900000.00/min
[3160000], rate=18960000.00/min
[3170000], rate=19020000.00/min
[3180000], rate=19080000.00/min
[3190000], rate=19140000.00/min
[3200000], rate=19200000.00/min
[3210000], rate=19260000.00/min
[3220000], rate=19320000.00/min
[3230000], rate=19380000.00/min
[3240000], rate=19440000.00/min
[3250000], rate=19500000.00/min
[3260000], rate=19560000.00/min
[3270000], rate=19620000.00/min
[3280000], rate=19680000.00/min
[3290000], rate=19740000.00/min
[3300000], rate=19800000.00/min
[3310000], rate=19860000.00/min
[3320000], rate=19920000.00/min
[3330000], rate=19980000.00/min
[3340000], rate=20040000.00/min
[3350000], rate=20100000.00/min
[3360000], rate=20160000.00/min
[3370000], rate=20220000.00/min
[3380000], rate=20280000.00/min
[3390000], rate=18490909.09/min
[3400000], rate=18545454.55/min
[3410000], rate=18600000.00/min
[3420000], rate=18654545.45/min
[3430000], rate=18709090.91/min
[3440000], rate=18763636.36/min
[3450000], rate=18818181.82/min
[3460000], rate=18872727.27/min
[3470000], rate=18927272.73/min
[3480000], rate=18981818.18/min
[3490000], rate=19036363.64/min
[3500000], rate=19090909.09/min
[3510000], rate=19145454.55/min
[3520000], rate=19200000.00/min
[3530000], rate=19254545.45/min
[3540000], rate=19309090.91/min
[3550000], rate=19363636.36/min
[3560000], rate=19418181.82/min
[3570000], rate=19472727.27/min
[3580000], rate=19527272.73/min
[3590000], rate=19581818.18/min
[3600000], rate=19636363.64/min
[3610000], rate=19690909.09/min
[3620000], rate=19745454.55/min
[3630000], rate=19800000.00/min
[3640000], rate=19854545.45/min
[3650000], rate=19909090.91/min
[3660000], rate=19963636.36/min
[3670000], rate=20018181.82/min
[3680000], rate=20072727.27/min
[3690000], rate=20127272.73/min
[3700000], rate=20181818.18/min
[3710000], rate=20236363.64/min
[3720000], rate=18600000.00/min
[3730000], rate=18650000.00/min
[3740000], rate=18700000.00/min
[3750000], rate=18750000.00/min
[3760000], rate=18800000.00/min
[3770000], rate=18850000.00/min
[3780000], rate=18900000.00/min
[3790000], rate=18950000.00/min
[3800000], rate=19000000.00/min
[3810000], rate=19050000.00/min
[3820000], rate=19100000.00/min
[3830000], rate=19150000.00/min
[3840000], rate=19200000.00/min
[3850000], rate=19250000.00/min
[3860000], rate=19300000.00/min
[3870000], rate=19350000.00/min
[3880000], rate=19400000.00/min
[3890000], rate=19450000.00/min
[3900000], rate=19500000.00/min
[3910000], rate=19550000.00/min
[3920000], rate=19600000.00/min
[3930000], rate=19650000.00/min
[3940000], rate=19700000.00/min
[3950000], rate=19750000.00/min
[3960000], rate=19800000.00/min
[3970000], rate=19850000.00/min
[3980000], rate=19900000.00/min
[3990000], rate=19950000.00/min
[4000000], rate=20000000.00/min
[4010000], rate=20050000.00/min
[4020000], rate=20100000.00/min
[4030000], rate=20150000.00/min
[4040000], rate=20200000.00/min
[4050000], rate=20250000.00/min
[4060000], rate=20300000.00/min
[4070000], rate=18784615.38/min
[4080000], rate=18830769.23/min
[4090000], rate=18876923.08/min
[4100000], rate=18923076.92/min
[4110000], rate=18969230.77/min
[4120000], rate=19015384.62/min
[4130000], rate=19061538.46/min
[4140000], rate=19107692.31/min
[4150000], rate=19153846.15/min
[4160000], rate=19200000.00/min
[4170000], rate=19246153.85/min
[4180000], rate=19292307.69/min
[4190000], rate=19338461.54/min
[4200000], rate=19384615.38/min
[4210000], rate=19430769.23/min
[4220000], rate=19476923.08/min
[4230000], rate=19523076.92/min
[4240000], rate=19569230.77/min
[4250000], rate=19615384.62/min
[4260000], rate=19661538.46/min
[4270000], rate=19707692.31/min
[4280000], rate=19753846.15/min
[4290000], rate=19800000.00/min
[4300000], rate=19846153.85/min
[4310000], rate=19892307.69/min
[4320000], rate=19938461.54/min
[4330000], rate=19984615.38/min
[4340000], rate=20030769.23/min
[4350000], rate=20076923.08/min
[4360000], rate=20123076.92/min
[4370000], rate=20169230.77/min
[4380000], rate=20215384.62/min
[4390000], rate=20261538.46/min
[4400000], rate=20307692.31/min
[4410000], rate=20353846.15/min
[4420000], rate=18942857.14/min
[4430000], rate=18985714.29/min
[4440000], rate=19028571.43/min
[4450000], rate=19071428.57/min
[4460000], rate=19114285.71/min
[4470000], rate=19157142.86/min
[4480000], rate=19200000.00/min
[4490000], rate=19242857.14/min
[4500000], rate=19285714.29/min
[4510000], rate=19328571.43/min
[4520000], rate=19371428.57/min
[4530000], rate=19414285.71/min
[4540000], rate=19457142.86/min
[4550000], rate=19500000.00/min
[4560000], rate=19542857.14/min
[4570000], rate=19585714.29/min
[4580000], rate=19628571.43/min
[4590000], rate=19671428.57/min
[4600000], rate=19714285.71/min
[4610000], rate=19757142.86/min
[4620000], rate=19800000.00/min
[4630000], rate=19842857.14/min
[4640000], rate=19885714.29/min
[4650000], rate=19928571.43/min
[4660000], rate=19971428.57/min
[4670000], rate=20014285.71/min
[4680000], rate=20057142.86/min
[4690000], rate=20100000.00/min
[4700000], rate=20142857.14/min
[4710000], rate=20185714.29/min
[4720000], rate=20228571.43/min
[4730000], rate=20271428.57/min
[4740000], rate=20314285.71/min
[4750000], rate=20357142.86/min
[4760000], rate=20400000.00/min
[4770000], rate=19080000.00/min
[4780000], rate=19120000.00/min
[4790000], rate=19160000.00/min
[4800000], rate=19200000.00/min
[4810000], rate=19240000.00/min
[4820000], rate=19280000.00/min
[4830000], rate=19320000.00/min
[4840000], rate=19360000.00/min
[4850000], rate=19400000.00/min
[4860000], rate=19440000.00/min
[4870000], rate=19480000.00/min
[4880000], rate=19520000.00/min
[4890000], rate=19560000.00/min
[4900000], rate=19600000.00/min
[4910000], rate=19640000.00/min
[4920000], rate=19680000.00/min
[4930000], rate=19720000.00/min
[4940000], rate=19760000.00/min
[4950000], rate=19800000.00/min
[4960000], rate=19840000.00/min
[4970000], rate=19880000.00/min
[4980000], rate=19920000.00/min
[4990000], rate=19960000.00/min
[5000000], rate=20000000.00/min
[5010000], rate=20040000.00/min
[5020000], rate=20080000.00/min
[5030000], rate=20120000.00/min
[5040000], rate=20160000.00/min
[5050000], rate=20200000.00/min
[5060000], rate=20240000.00/min
[5070000], rate=20280000.00/min
[5080000], rate=19050000.00/min
[5090000], rate=19087500.00/min
[5100000], rate=19125000.00/min
[5110000], rate=19162500.00/min
[5120000], rate=19200000.00/min
[5130000], rate=19237500.00/min
[5140000], rate=19275000.00/min
[5150000], rate=19312500.00/min
[5160000], rate=19350000.00/min
[5170000], rate=19387500.00/min
[5180000], rate=19425000.00/min
[5190000], rate=19462500.00/min
[5200000], rate=19500000.00/min
[5210000], rate=19537500.00/min
[5220000], rate=19575000.00/min
[5230000], rate=19612500.00/min
[5240000], rate=19650000.00/min
[5250000], rate=19687500.00/min
[5260000], rate=19725000.00/min
[5270000], rate=19762500.00/min
[5280000], rate=19800000.00/min
[5290000], rate=19837500.00/min
[5300000], rate=19875000.00/min
[5310000], rate=19912500.00/min
[5320000], rate=19950000.00/min
[5330000], rate=19987500.00/min
[5340000], rate=20025000.00/min
[5350000], rate=20062500.00/min
[5360000], rate=20100000.00/min
[5370000], rate=20137500.00/min
[5380000], rate=20175000.00/min
[5390000], rate=20212500.00/min
[5400000], rate=20250000.00/min
[5410000], rate=20287500.00/min
[5420000], rate=20325000.00/min
[5430000], rate=19164705.88/min
[5440000], rate=19200000.00/min
[5450000], rate=19235294.12/min
[5460000], rate=19270588.24/min
[5470000], rate=19305882.35/min
[5480000], rate=19341176.47/min
[5490000], rate=19376470.59/min
[5500000], rate=19411764.71/min
[5510000], rate=19447058.82/min
[5520000], rate=19482352.94/min
[5530000], rate=19517647.06/min
[5540000], rate=19552941.18/min
[5550000], rate=19588235.29/min
[5560000], rate=19623529.41/min
[5570000], rate=19658823.53/min
[5580000], rate=19694117.65/min
[5590000], rate=19729411.76/min
[5600000], rate=19764705.88/min
[5610000], rate=19800000.00/min
[5620000], rate=19835294.12/min
[5630000], rate=19870588.24/min 08:15:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_Mt-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_Mt-T1-TRNA-1_B23WHTKLT4_1.introns: identified 1646 cancer introns
08:15:05 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim
08:15:05 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/prelim_introns.ok
08:15:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
08:15:06 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
08:15:06 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/introns_filtered.ok
08:15:06 : INFO : -found 1206 cancer introns
08:15:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
08:15:06 : INFO : Creating the BED File.
08:15:09 : INFO : Saving Bed File as 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
08:15:09 : INFO : Execution Time = 0.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
08:15:09 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/intron_igv_bed.ok
08:15:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_Mt-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_Mt-T1-TRNA-1_B23WHTKLT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
08:23:56 : INFO : Execution Time = 8.78 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_Mt-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_Mt-T1-TRNA-1_B23WHTKLT4_1
08:23:56 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok
08:23:56 : INFO : Running: samtools sort -o 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
08:23:56 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
08:23:56 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok
08:23:56 : INFO : Running: samtools sort -o 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
[bam_sort_core] merging from 43 files and 1 in-memory blocks...
08:33:49 : INFO : Execution Time = 9.89 minutes. CMD: samtools sort -o 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
08:33:49 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_gene_reads.ok
08:33:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
Done with chr chr1.
Done with chr chr2.
Done with chr chr3.
Done with chr chr4.
Done with chr chr5.
Done with chr chr6.
Done with chr chr7.
Done with chr chr8.
Done with chr chr9.
Done with chr chr10.
Done with chr chr11.
Done with chr chr12.
Done with chr chr13.
Done with chr chr14.
Done with chr chr15.
Done with chr chr16.
Done with chr chr17.
Done with chr chr18.
Done with chr chr19.
Done with chr chr20.
Done with chr chr21.
Done with chr chr22.
08:37:07 : INFO : Execution Time = 3.29 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
08:37:07 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
08:37:07 : INFO : Running: samtools sort -o 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
08:37:48 : INFO : Execution Time = 0.68 minutes. CMD: samtools sort -o 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
08:37:48 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
08:37:48 : INFO : Running: samtools index 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
08:37:51 : INFO : Execution Time = 0.06 minutes. CMD: samtools index 659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
08:37:51 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_Mt-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
08:37:52 : INFO : Running: samtools index 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
08:37:52 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
08:37:52 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_Mt-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
08:37:52 : INFO : Running: create_report 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_Mt-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_Mt-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_Mt-T1-TRNA-1_B23WHTKLT4_1'
08:42:57 : INFO : Execution Time = 5.09 minutes. CMD: create_report 659_Mt-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_Mt-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_Mt-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_Mt-T1-TRNA-1_B23WHTKLT4_1'
08:42:57 : INFO : Running: touch /tmp/nxf.eop23BLpmk/659_Mt-T1-TRNA-1_B23WHTKLT4_1.chckpts/igv_create_html.ok
08:42:57 : INFO : done.