Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/0a6285b6dc23fa62b861ba78c6eb22/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/79b3f58b4dd235217623b237fa79d9/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
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/99/d5146afabc6c50eafa54408b8ae481/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/79b3f58b4dd235217623b237fa79d9/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/d5146afabc6c50eafa54408b8ae481/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/79b3f58b4dd235217623b237fa79d9/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)
21:03:20 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[20000], rate=1200000.00/min
[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=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=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=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=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=16200000.00/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=21300000.00/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=21120000.00/min
[1770000], rate=21240000.00/min
[1780000], rate=21360000.00/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=21100000.00/min
[2120000], rate=21200000.00/min
[2130000], rate=21300000.00/min
[2140000], rate=21400000.00/min
[2150000], rate=21500000.00/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=21085714.29/min
[2470000], rate=21171428.57/min
[2480000], rate=21257142.86/min
[2490000], rate=21342857.14/min
[2500000], rate=21428571.43/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=20775000.00/min
[2780000], rate=20850000.00/min
[2790000], rate=20925000.00/min
[2800000], rate=21000000.00/min
[2810000], rate=21075000.00/min
[2820000], rate=21150000.00/min
[2830000], rate=21225000.00/min
[2840000], rate=21300000.00/min
[2850000], rate=21375000.00/min
[2860000], rate=21450000.00/min
[2870000], rate=21525000.00/min
[2880000], rate=21600000.00/min
[2890000], rate=21675000.00/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=20666666.67/min
[3110000], rate=20733333.33/min
[3120000], rate=20800000.00/min
[3130000], rate=20866666.67/min
[3140000], rate=20933333.33/min
[3150000], rate=21000000.00/min
[3160000], rate=21066666.67/min
[3170000], rate=21133333.33/min
[3180000], rate=21200000.00/min
[3190000], rate=21266666.67/min
[3200000], rate=21333333.33/min
[3210000], rate=21400000.00/min
[3220000], rate=21466666.67/min
[3230000], rate=21533333.33/min
[3240000], rate=21600000.00/min
[3250000], rate=21666666.67/min
[3260000], rate=21733333.33/min
[3270000], rate=21800000.00/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=20340000.00/min
[3400000], rate=20400000.00/min
[3410000], rate=20460000.00/min
[3420000], rate=20520000.00/min
[3430000], rate=20580000.00/min
[3440000], rate=20640000.00/min
[3450000], rate=20700000.00/min
[3460000], rate=20760000.00/min
[3470000], rate=20820000.00/min
[3480000], rate=20880000.00/min
[3490000], rate=20940000.00/min
[3500000], rate=21000000.00/min
[3510000], rate=21060000.00/min
[3520000], rate=21120000.00/min
[3530000], rate=21180000.00/min
[3540000], rate=21240000.00/min
[3550000], rate=21300000.00/min
[3560000], rate=21360000.00/min
[3570000], rate=21420000.00/min
[3580000], rate=21480000.00/min
[3590000], rate=21540000.00/min
[3600000], rate=21600000.00/min
[3610000], rate=21660000.00/min
[3620000], rate=21720000.00/min
[3630000], rate=21780000.00/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=20290909.09/min
[3730000], rate=20345454.55/min
[3740000], rate=20400000.00/min
[3750000], rate=20454545.45/min
[3760000], rate=20509090.91/min
[3770000], rate=20563636.36/min
[3780000], rate=20618181.82/min
[3790000], rate=20672727.27/min
[3800000], rate=20727272.73/min
[3810000], rate=20781818.18/min
[3820000], rate=20836363.64/min
[3830000], rate=20890909.09/min
[3840000], rate=20945454.55/min
[3850000], rate=21000000.00/min
[3860000], rate=21054545.45/min
[3870000], rate=21109090.91/min
[3880000], rate=21163636.36/min
[3890000], rate=21218181.82/min
[3900000], rate=21272727.27/min
[3910000], rate=21327272.73/min
[3920000], rate=21381818.18/min
[3930000], rate=21436363.64/min
[3940000], rate=21490909.09/min
[3950000], rate=21545454.55/min
[3960000], rate=21600000.00/min
[3970000], rate=21654545.45/min
[3980000], rate=21709090.91/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=20350000.00/min
[4080000], rate=20400000.00/min
[4090000], rate=20450000.00/min
[4100000], rate=20500000.00/min
[4110000], rate=20550000.00/min
[4120000], rate=20600000.00/min
[4130000], rate=20650000.00/min
[4140000], rate=20700000.00/min
[4150000], rate=20750000.00/min
[4160000], rate=20800000.00/min
[4170000], rate=20850000.00/min
[4180000], rate=20900000.00/min
[4190000], rate=20950000.00/min
[4200000], rate=21000000.00/min
[4210000], rate=21050000.00/min
[4220000], rate=21100000.00/min
[4230000], rate=21150000.00/min
[4240000], rate=21200000.00/min
[4250000], rate=21250000.00/min
[4260000], rate=21300000.00/min
[4270000], rate=21350000.00/min
[4280000], rate=21400000.00/min
[4290000], rate=21450000.00/min
[4300000], rate=21500000.00/min
[4310000], rate=21550000.00/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=20400000.00/min
[4430000], rate=20446153.85/min
[4440000], rate=20492307.69/min
[4450000], rate=20538461.54/min
[4460000], rate=20584615.38/min
[4470000], rate=20630769.23/min
[4480000], rate=20676923.08/min
[4490000], rate=20723076.92/min
[4500000], rate=20769230.77/min
[4510000], rate=20815384.62/min
[4520000], rate=20861538.46/min
[4530000], rate=20907692.31/min
[4540000], rate=20953846.15/min
[4550000], rate=21000000.00/min
[4560000], rate=21046153.85/min
[4570000], rate=21092307.69/min
[4580000], rate=21138461.54/min
[4590000], rate=21184615.38/min
[4600000], rate=21230769.23/min
[4610000], rate=21276923.08/min
[4620000], rate=21323076.92/min
[4630000], rate=21369230.77/min
[4640000], rate=21415384.62/min
[4650000], rate=21461538.46/min
[4660000], rate=21507692.31/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=20442857.14/min
[4780000], rate=20485714.29/min
[4790000], rate=20528571.43/min
[4800000], rate=20571428.57/min
[4810000], rate=20614285.71/min
[4820000], rate=20657142.86/min
[4830000], rate=20700000.00/min
[4840000], rate=20742857.14/min
[4850000], rate=20785714.29/min
[4860000], rate=20828571.43/min
[4870000], rate=20871428.57/min
[4880000], rate=20914285.71/min
[4890000], rate=20957142.86/min
[4900000], rate=21000000.00/min
[4910000], rate=21042857.14/min
[4920000], rate=21085714.29/min
[4930000], rate=21128571.43/min
[4940000], rate=21171428.57/min
[4950000], rate=21214285.71/min
[4960000], rate=21257142.86/min
[4970000], rate=21300000.00/min
[4980000], rate=21342857.14/min
[4990000], rate=21385714.29/min
[5000000], rate=21428571.43/min
[5010000], rate=21471428.57/min
[5020000], rate=21514285.71/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=20320000.00/min
[5090000], rate=20360000.00/min
[5100000], rate=20400000.00/min
[5110000], rate=20440000.00/min
[5120000], rate=20480000.00/min
[5130000], rate=20520000.00/min
[5140000], rate=20560000.00/min
[5150000], rate=20600000.00/min
[5160000], rate=20640000.00/min
[5170000], rate=20680000.00/min
[5180000], rate=20720000.00/min
[5190000], rate=20760000.00/min
[5200000], rate=20800000.00/min
[5210000], rate=20840000.00/min
[5220000], rate=20880000.00/min
[5230000], rate=20920000.00/min
[5240000], rate=20960000.00/min
[5250000], rate=21000000.00/min
[5260000], rate=21040000.00/min
[5270000], rate=21080000.00/min
[5280000], rate=21120000.00/min
[5290000], rate=21160000.00/min
[5300000], rate=21200000.00/min
[5310000], rate=21240000.00/min
[5320000], rate=21280000.00/min
[5330000], rate=21320000.00/min
[5340000], rate=21360000.00/min
[5350000], rate=21400000.00/min
[5360000], rate=21440000.00/min
[5370000], rate=21480000.00/min
[5380000], rate=21520000.00/min
[5390000], rate=21560000.00/min
[5400000], rate=21600000.00/min
[5410000], rate=20287500.00/min
[5420000], rate=20325000.00/min
[5430000], rate=20362500.00/min
[5440000], rate=20400000.00/min
[5450000], rate=20437500.00/min
[5460000], rate=20475000.00/min
[5470000], rate=20512500.00/min
[5480000], rate=20550000.00/min
[5490000], rate=20587500.00/min
[5500000], rate=20625000.00/min
[5510000], rate=20662500.00/min
[5520000], rate=20700000.00/min
[5530000], rate=20737500.00/min
[5540000], rate=20775000.00/min
[5550000], rate=20812500.00/min
[5560000], rate=20850000.00/min
[5570000], rate=20887500.00/min
[5580000], rate=20925000.00/min
[5590000], rate=20962500.00/min
[5600000], rate=21000000.00/min
[5610000], rate=21037500.00/min
[5620000], rate=21075000.00/min
[5630000], rate=21112500.00/min
[5640000], rate=21150000.00/min
[5650000], rate=21187500.00/min
[5660000], rate=21225000.00/min
[5670000], rate=21262500.00/min
[5680000], rate=21300000.00/min
[5690000], rate=21337500.00/min
[5700000], rate=21375000.00/min
[5710000], rate=21412500.00/min
[5720000], rate=21450000.00/min
[5730000], rate=21487500.00/min
[5740000], rate=21525000.00/min
[5750000], rate=21562500.00/min
[5760000], rate=21600000.00/min
[5770000], rate=21637500.00/min
[5780000], rate=20400000.00/min
[5790000], rate=20435294.12/min
[5800000], rate=20470588.24/min
[5810000], rate=20505882.35/min
[5820000], rate=20541176.47/min
[5830000], rate=20576470.59/min
[5840000], rate=20611764.71/min
[5850000], rate=20647058.82/min
[5860000], rate=20682352.94/min
[5870000], rate=20717647.06/min
[5880000], rate=20752941.18/min
[5890000], rate=20788235.29/min
[5900000], rate=20823529.41/min
[5910000], rate=20858823.53/min
[5920000], rate=20894117.65/min 21:03:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > SkinN_FFPE_L02_RNA_01_B23LG7FLT4_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.
-SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns: identified 146 cancer introns
21:03:41 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns.prelim
21:03:41 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok
21:03:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns
21:03:41 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns
21:03:41 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok
21:03:41 : INFO : -found 104 cancer introns
21:03:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns --cancer_introns SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
21:03:42 : INFO : Creating the BED File.
21:03:42 : INFO : Saving Bed File as SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
21:03:42 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns --cancer_introns SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
21:03:42 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
21:03:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1
[W::hts_idx_load3] The index file is older than the data file: SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
21:06:58 : INFO : Execution Time = 3.27 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1
21:06:58 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
21:06:58 : INFO : Running: samtools sort -o SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
21:06:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
21:06:58 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
21:06:58 : INFO : Running: samtools sort -o SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.bam
[bam_sort_core] merging from 16 files and 1 in-memory blocks...
21:10:56 : INFO : Execution Time = 3.96 minutes. CMD: samtools sort -o SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.bam
21:10:56 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
21:10:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary SkinN_FFPE_L02_RNA_01_B23LG7FLT4_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.
21:11:43 : INFO : Execution Time = 0.79 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam
21:11:43 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
21:11:43 : INFO : Running: samtools sort -o SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
21:11:45 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
21:11:45 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
21:11:45 : INFO : Running: samtools index SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
21:11:45 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
21:11:45 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
21:11:45 : INFO : Running: samtools index SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
21:11:45 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
21:11:45 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
21:11:45 : INFO : Running: create_report SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1'
21:11:55 : INFO : Execution Time = 0.17 minutes. CMD: create_report SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1'
21:11:55 : INFO : Running: touch /tmp/nxf.CEBJk2HthD/SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok
21:11:55 : INFO : done.