Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/69b1a07291cf51ce7508a88b401932/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.Chimeric.out.junction
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/d1/8b7cb5b6a23c017f15a69b348572cc/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/69b1a07291cf51ce7508a88b401932/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/69b1a07291cf51ce7508a88b401932/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/8b7cb5b6a23c017f15a69b348572cc/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/36f8a0d70e84ce6522504bce00e7ae/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)
08:26:01 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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=23400000.00/min
[400000], rate=24000000.00/min
[410000], rate=24600000.00/min
[420000], rate=25200000.00/min
[430000], rate=25800000.00/min
[440000], rate=26400000.00/min
[450000], rate=27000000.00/min
[460000], rate=27600000.00/min
[470000], rate=28200000.00/min
[480000], rate=28800000.00/min
[490000], rate=29400000.00/min
[500000], rate=30000000.00/min
[510000], rate=30600000.00/min
[520000], rate=31200000.00/min
[530000], rate=31800000.00/min
[540000], rate=32400000.00/min
[550000], rate=33000000.00/min
[560000], rate=33600000.00/min
[570000], rate=34200000.00/min
[580000], rate=34800000.00/min
[590000], rate=35400000.00/min
[600000], rate=36000000.00/min
[610000], rate=36600000.00/min
[620000], rate=37200000.00/min
[630000], rate=37800000.00/min
[640000], rate=38400000.00/min
[650000], rate=39000000.00/min
[660000], rate=39600000.00/min
[670000], rate=40200000.00/min
[680000], rate=40800000.00/min
[690000], rate=41400000.00/min
[700000], rate=42000000.00/min
[710000], rate=42600000.00/min
[720000], rate=43200000.00/min
[730000], rate=43800000.00/min
[740000], rate=44400000.00/min
[750000], rate=45000000.00/min
[760000], rate=22800000.00/min
[770000], rate=23100000.00/min
[780000], rate=23400000.00/min
[790000], rate=23700000.00/min
[800000], rate=24000000.00/min
[810000], rate=24300000.00/min
[820000], rate=24600000.00/min
[830000], rate=24900000.00/min
[840000], rate=25200000.00/min
[850000], rate=25500000.00/min
[860000], rate=25800000.00/min
[870000], rate=26100000.00/min
[880000], rate=26400000.00/min
[890000], rate=26700000.00/min
[900000], rate=27000000.00/min
[910000], rate=27300000.00/min
[920000], rate=27600000.00/min
[930000], rate=27900000.00/min
[940000], rate=28200000.00/min
[950000], rate=28500000.00/min
[960000], rate=28800000.00/min
[970000], rate=29100000.00/min
[980000], rate=29400000.00/min
[990000], rate=29700000.00/min
[1000000], rate=30000000.00/min
[1010000], rate=30300000.00/min
[1020000], rate=30600000.00/min
[1030000], rate=30900000.00/min
[1040000], rate=31200000.00/min
[1050000], rate=31500000.00/min
[1060000], rate=31800000.00/min
[1070000], rate=32100000.00/min
[1080000], rate=32400000.00/min
[1090000], rate=32700000.00/min
[1100000], rate=33000000.00/min
[1110000], rate=33300000.00/min
[1120000], rate=33600000.00/min
[1130000], rate=33900000.00/min
[1140000], rate=34200000.00/min
[1150000], rate=34500000.00/min
[1160000], rate=34800000.00/min
[1170000], rate=35100000.00/min
[1180000], rate=35400000.00/min
[1190000], rate=35700000.00/min
[1200000], rate=24000000.00/min
[1210000], rate=24200000.00/min
[1220000], rate=24400000.00/min
[1230000], rate=24600000.00/min
[1240000], rate=24800000.00/min
[1250000], rate=25000000.00/min
[1260000], rate=25200000.00/min
[1270000], rate=25400000.00/min
[1280000], rate=25600000.00/min
[1290000], rate=25800000.00/min
[1300000], rate=26000000.00/min
[1310000], rate=26200000.00/min
[1320000], rate=26400000.00/min
[1330000], rate=26600000.00/min
[1340000], rate=26800000.00/min
[1350000], rate=27000000.00/min
[1360000], rate=27200000.00/min
[1370000], rate=27400000.00/min
[1380000], rate=27600000.00/min
[1390000], rate=27800000.00/min
[1400000], rate=28000000.00/min
[1410000], rate=28200000.00/min
[1420000], rate=28400000.00/min
[1430000], rate=28600000.00/min
[1440000], rate=28800000.00/min
[1450000], rate=29000000.00/min
[1460000], rate=29200000.00/min
[1470000], rate=29400000.00/min
[1480000], rate=29600000.00/min
[1490000], rate=29800000.00/min
[1500000], rate=30000000.00/min
[1510000], rate=30200000.00/min
[1520000], rate=30400000.00/min
[1530000], rate=30600000.00/min
[1540000], rate=30800000.00/min
[1550000], rate=31000000.00/min
[1560000], rate=31200000.00/min
[1570000], rate=23550000.00/min
[1580000], rate=23700000.00/min
[1590000], rate=23850000.00/min
[1600000], rate=24000000.00/min
[1610000], rate=24150000.00/min
[1620000], rate=24300000.00/min
[1630000], rate=24450000.00/min
[1640000], rate=24600000.00/min
[1650000], rate=24750000.00/min
[1660000], rate=24900000.00/min
[1670000], rate=25050000.00/min
[1680000], rate=25200000.00/min
[1690000], rate=25350000.00/min
[1700000], rate=25500000.00/min
[1710000], rate=25650000.00/min
[1720000], rate=25800000.00/min
[1730000], rate=25950000.00/min
[1740000], rate=26100000.00/min
[1750000], rate=26250000.00/min
[1760000], rate=26400000.00/min
[1770000], rate=26550000.00/min
[1780000], rate=26700000.00/min
[1790000], rate=26850000.00/min
[1800000], rate=27000000.00/min
[1810000], rate=27150000.00/min
[1820000], rate=27300000.00/min
[1830000], rate=27450000.00/min
[1840000], rate=27600000.00/min
[1850000], rate=27750000.00/min
[1860000], rate=27900000.00/min
[1870000], rate=28050000.00/min
[1880000], rate=28200000.00/min
[1890000], rate=28350000.00/min
[1900000], rate=28500000.00/min
[1910000], rate=28650000.00/min
[1920000], rate=28800000.00/min
[1930000], rate=28950000.00/min
[1940000], rate=29100000.00/min
[1950000], rate=29250000.00/min
[1960000], rate=29400000.00/min
[1970000], rate=29550000.00/min
[1980000], rate=23760000.00/min
[1990000], rate=23880000.00/min
[2000000], rate=24000000.00/min
[2010000], rate=24120000.00/min
[2020000], rate=24240000.00/min
[2030000], rate=24360000.00/min
[2040000], rate=24480000.00/min
[2050000], rate=24600000.00/min
[2060000], rate=24720000.00/min
[2070000], rate=24840000.00/min
[2080000], rate=24960000.00/min
[2090000], rate=25080000.00/min
[2100000], rate=25200000.00/min
[2110000], rate=25320000.00/min
[2120000], rate=25440000.00/min
[2130000], rate=25560000.00/min
[2140000], rate=25680000.00/min
[2150000], rate=25800000.00/min
[2160000], rate=25920000.00/min
[2170000], rate=26040000.00/min
[2180000], rate=26160000.00/min
[2190000], rate=26280000.00/min
[2200000], rate=26400000.00/min
[2210000], rate=26520000.00/min
[2220000], rate=26640000.00/min
[2230000], rate=26760000.00/min
[2240000], rate=26880000.00/min
[2250000], rate=27000000.00/min
[2260000], rate=27120000.00/min
[2270000], rate=27240000.00/min
[2280000], rate=27360000.00/min
[2290000], rate=27480000.00/min
[2300000], rate=27600000.00/min
[2310000], rate=27720000.00/min
[2320000], rate=27840000.00/min
[2330000], rate=27960000.00/min
[2340000], rate=28080000.00/min
[2350000], rate=28200000.00/min
[2360000], rate=28320000.00/min
[2370000], rate=28440000.00/min
[2380000], rate=23800000.00/min
[2390000], rate=23900000.00/min
[2400000], rate=24000000.00/min
[2410000], rate=24100000.00/min
[2420000], rate=24200000.00/min
[2430000], rate=24300000.00/min
[2440000], rate=24400000.00/min
[2450000], rate=24500000.00/min
[2460000], rate=24600000.00/min
[2470000], rate=24700000.00/min
[2480000], rate=24800000.00/min
[2490000], rate=24900000.00/min
[2500000], rate=25000000.00/min
[2510000], rate=25100000.00/min
[2520000], rate=25200000.00/min
[2530000], rate=25300000.00/min
[2540000], rate=25400000.00/min
[2550000], rate=25500000.00/min
[2560000], rate=25600000.00/min
[2570000], rate=25700000.00/min
[2580000], rate=25800000.00/min
[2590000], rate=25900000.00/min
[2600000], rate=26000000.00/min
[2610000], rate=26100000.00/min
[2620000], rate=26200000.00/min
[2630000], rate=26300000.00/min
[2640000], rate=26400000.00/min
[2650000], rate=26500000.00/min
[2660000], rate=26600000.00/min
[2670000], rate=26700000.00/min
[2680000], rate=26800000.00/min
[2690000], rate=26900000.00/min
[2700000], rate=27000000.00/min
[2710000], rate=27100000.00/min
[2720000], rate=27200000.00/min
[2730000], rate=27300000.00/min
[2740000], rate=23485714.29/min
[2750000], rate=23571428.57/min
[2760000], rate=23657142.86/min
[2770000], rate=23742857.14/min
[2780000], rate=23828571.43/min
[2790000], rate=23914285.71/min
[2800000], rate=24000000.00/min
[2810000], rate=24085714.29/min
[2820000], rate=24171428.57/min
[2830000], rate=24257142.86/min
[2840000], rate=24342857.14/min
[2850000], rate=24428571.43/min
[2860000], rate=24514285.71/min
[2870000], rate=24600000.00/min
[2880000], rate=24685714.29/min
[2890000], rate=24771428.57/min
[2900000], rate=24857142.86/min
[2910000], rate=24942857.14/min
[2920000], rate=25028571.43/min
[2930000], rate=25114285.71/min
[2940000], rate=25200000.00/min
[2950000], rate=25285714.29/min
[2960000], rate=25371428.57/min
[2970000], rate=25457142.86/min
[2980000], rate=25542857.14/min
[2990000], rate=25628571.43/min
[3000000], rate=25714285.71/min
[3010000], rate=25800000.00/min
[3020000], rate=25885714.29/min
[3030000], rate=25971428.57/min
[3040000], rate=26057142.86/min
[3050000], rate=26142857.14/min
[3060000], rate=26228571.43/min
[3070000], rate=26314285.71/min
[3080000], rate=23100000.00/min
[3090000], rate=23175000.00/min
[3100000], rate=23250000.00/min
[3110000], rate=23325000.00/min
[3120000], rate=23400000.00/min
[3130000], rate=23475000.00/min
[3140000], rate=23550000.00/min
[3150000], rate=23625000.00/min
[3160000], rate=23700000.00/min
[3170000], rate=23775000.00/min
[3180000], rate=23850000.00/min
[3190000], rate=23925000.00/min
[3200000], rate=24000000.00/min
[3210000], rate=24075000.00/min
[3220000], rate=24150000.00/min
[3230000], rate=24225000.00/min
[3240000], rate=24300000.00/min
[3250000], rate=24375000.00/min
[3260000], rate=24450000.00/min
[3270000], rate=24525000.00/min
[3280000], rate=24600000.00/min
[3290000], rate=24675000.00/min
[3300000], rate=24750000.00/min
[3310000], rate=24825000.00/min
[3320000], rate=24900000.00/min
[3330000], rate=24975000.00/min
[3340000], rate=25050000.00/min
[3350000], rate=25125000.00/min
[3360000], rate=25200000.00/min
[3370000], rate=25275000.00/min
[3380000], rate=25350000.00/min
[3390000], rate=25425000.00/min
[3400000], rate=25500000.00/min
[3410000], rate=25575000.00/min
[3420000], rate=25650000.00/min
[3430000], rate=25725000.00/min
[3440000], rate=25800000.00/min
[3450000], rate=25875000.00/min
[3460000], rate=25950000.00/min
[3470000], rate=26025000.00/min
[3480000], rate=26100000.00/min
[3490000], rate=26175000.00/min
[3500000], rate=26250000.00/min
[3510000], rate=26325000.00/min
[3520000], rate=23466666.67/min
[3530000], rate=23533333.33/min
[3540000], rate=23600000.00/min
[3550000], rate=23666666.67/min
[3560000], rate=23733333.33/min
[3570000], rate=23800000.00/min
[3580000], rate=23866666.67/min
[3590000], rate=23933333.33/min
[3600000], rate=24000000.00/min
[3610000], rate=24066666.67/min
[3620000], rate=24133333.33/min
[3630000], rate=24200000.00/min
[3640000], rate=24266666.67/min
[3650000], rate=24333333.33/min
[3660000], rate=24400000.00/min
[3670000], rate=24466666.67/min
[3680000], rate=24533333.33/min
[3690000], rate=24600000.00/min
[3700000], rate=24666666.67/min
[3710000], rate=24733333.33/min
[3720000], rate=24800000.00/min
[3730000], rate=24866666.67/min
[3740000], rate=24933333.33/min
[3750000], rate=25000000.00/min
[3760000], rate=25066666.67/min
[3770000], rate=25133333.33/min
[3780000], rate=25200000.00/min
[3790000], rate=25266666.67/min
[3800000], rate=25333333.33/min
[3810000], rate=25400000.00/min
[3820000], rate=25466666.67/min
[3830000], rate=25533333.33/min
[3840000], rate=25600000.00/min
[3850000], rate=25666666.67/min
[3860000], rate=25733333.33/min
[3870000], rate=25800000.00/min
[3880000], rate=25866666.67/min
[3890000], rate=25933333.33/min
[3900000], rate=26000000.00/min
[3910000], rate=26066666.67/min
[3920000], rate=23520000.00/min
[3930000], rate=23580000.00/min
[3940000], rate=23640000.00/min
[3950000], rate=23700000.00/min
[3960000], rate=23760000.00/min
[3970000], rate=23820000.00/min
[3980000], rate=23880000.00/min
[3990000], rate=23940000.00/min
[4000000], rate=24000000.00/min
[4010000], rate=24060000.00/min
[4020000], rate=24120000.00/min
[4030000], rate=24180000.00/min
[4040000], rate=24240000.00/min
[4050000], rate=24300000.00/min
[4060000], rate=24360000.00/min
[4070000], rate=24420000.00/min
[4080000], rate=24480000.00/min
[4090000], rate=24540000.00/min
[4100000], rate=24600000.00/min
[4110000], rate=24660000.00/min
[4120000], rate=24720000.00/min
[4130000], rate=24780000.00/min
[4140000], rate=24840000.00/min
[4150000], rate=24900000.00/min
[4160000], rate=24960000.00/min
[4170000], rate=25020000.00/min
[4180000], rate=25080000.00/min
[4190000], rate=25140000.00/min
[4200000], rate=25200000.00/min
[4210000], rate=25260000.00/min
[4220000], rate=25320000.00/min
[4230000], rate=25380000.00/min
[4240000], rate=25440000.00/min
[4250000], rate=25500000.00/min
[4260000], rate=23236363.64/min
[4270000], rate=23290909.09/min
[4280000], rate=23345454.55/min
[4290000], rate=23400000.00/min
[4300000], rate=23454545.45/min
[4310000], rate=23509090.91/min
[4320000], rate=23563636.36/min
[4330000], rate=23618181.82/min
[4340000], rate=23672727.27/min
[4350000], rate=23727272.73/min
[4360000], rate=23781818.18/min
[4370000], rate=23836363.64/min
[4380000], rate=23890909.09/min
[4390000], rate=23945454.55/min
[4400000], rate=24000000.00/min
[4410000], rate=24054545.45/min
[4420000], rate=24109090.91/min
[4430000], rate=24163636.36/min
[4440000], rate=24218181.82/min
[4450000], rate=24272727.27/min
[4460000], rate=24327272.73/min
[4470000], rate=24381818.18/min
[4480000], rate=24436363.64/min
[4490000], rate=24490909.09/min
[4500000], rate=24545454.55/min
[4510000], rate=24600000.00/min
[4520000], rate=24654545.45/min
[4530000], rate=24709090.91/min
[4540000], rate=24763636.36/min
[4550000], rate=24818181.82/min
[4560000], rate=24872727.27/min
[4570000], rate=24927272.73/min
[4580000], rate=22900000.00/min
[4590000], rate=22950000.00/min
[4600000], rate=23000000.00/min
[4610000], rate=23050000.00/min
[4620000], rate=23100000.00/min
[4630000], rate=23150000.00/min
[4640000], rate=23200000.00/min
[4650000], rate=23250000.00/min
[4660000], rate=23300000.00/min
[4670000], rate=23350000.00/min
[4680000], rate=23400000.00/min
[4690000], rate=23450000.00/min
[4700000], rate=23500000.00/min
[4710000], rate=23550000.00/min
[4720000], rate=23600000.00/min
[4730000], rate=23650000.00/min
[4740000], rate=23700000.00/min
[4750000], rate=23750000.00/min
[4760000], rate=23800000.00/min
[4770000], rate=23850000.00/min
[4780000], rate=23900000.00/min
[4790000], rate=23950000.00/min
[4800000], rate=24000000.00/min
[4810000], rate=24050000.00/min
[4820000], rate=24100000.00/min
[4830000], rate=24150000.00/min
[4840000], rate=24200000.00/min
[4850000], rate=24250000.00/min
[4860000], rate=24300000.00/min
[4870000], rate=24350000.00/min
[4880000], rate=24400000.00/min
[4890000], rate=24450000.00/min
[4900000], rate=24500000.00/min
[4910000], rate=24550000.00/min
[4920000], rate=24600000.00/min
[4930000], rate=24650000.00/min
[4940000], rate=24700000.00/min
[4950000], rate=24750000.00/min
[4960000], rate=24800000.00/min
[4970000], rate=24850000.00/min
[4980000], rate=24900000.00/min
[4990000], rate=23030769.23/min
[5000000], rate=23076923.08/min
[5010000], rate=23123076.92/min
[5020000], rate=23169230.77/min
[5030000], rate=23215384.62/min
[5040000], rate=23261538.46/min
[5050000], rate=23307692.31/min
[5060000], rate=23353846.15/min
[5070000], rate=23400000.00/min
[5080000], rate=23446153.85/min
[5090000], rate=23492307.69/min
[5100000], rate=23538461.54/min
[5110000], rate=23584615.38/min
[5120000], rate=23630769.23/min
[5130000], rate=23676923.08/min
[5140000], rate=23723076.92/min
[5150000], rate=23769230.77/min
[5160000], rate=23815384.62/min
[5170000], rate=23861538.46/min
[5180000], rate=23907692.31/min
[5190000], rate=23953846.15/min
[5200000], rate=24000000.00/min
[5210000], rate=24046153.85/min
[5220000], rate=24092307.69/min
[5230000], rate=24138461.54/min
[5240000], rate=24184615.38/min
[5250000], rate=24230769.23/min
[5260000], rate=24276923.08/min
[5270000], rate=24323076.92/min
[5280000], rate=24369230.77/min
[5290000], rate=24415384.62/min
[5300000], rate=24461538.46/min
[5310000], rate=24507692.31/min
[5320000], rate=24553846.15/min
[5330000], rate=24600000.00/min
[5340000], rate=24646153.85/min
[5350000], rate=24692307.69/min
[5360000], rate=24738461.54/min
[5370000], rate=24784615.38/min
[5380000], rate=24830769.23/min
[5390000], rate=24876923.08/min
[5400000], rate=23142857.14/min
[5410000], rate=23185714.29/min
[5420000], rate=23228571.43/min
[5430000], rate=23271428.57/min
[5440000], rate=23314285.71/min
[5450000], rate=23357142.86/min
[5460000], rate=23400000.00/min
[5470000], rate=23442857.14/min
[5480000], rate=23485714.29/min
[5490000], rate=23528571.43/min
[5500000], rate=23571428.57/min
[5510000], rate=23614285.71/min
[5520000], rate=23657142.86/min
[5530000], rate=23700000.00/min
[5540000], rate=23742857.14/min
[5550000], rate=23785714.29/min
[5560000], rate=23828571.43/min
[5570000], rate=23871428.57/min
[5580000], rate=23914285.71/min
[5590000], rate=23957142.86/min
[5600000], rate=24000000.00/min
[5610000], rate=24042857.14/min
[5620000], rate=24085714.29/min
[5630000], rate=24128571.43/min
[5640000], rate=24171428.57/min
[5650000], rate=24214285.71/min
[5660000], rate=24257142.86/min
[5670000], rate=24300000.00/min
[5680000], rate=24342857.14/min
[5690000], rate=24385714.29/min
[5700000], rate=24428571.43/min
[5710000], rate=24471428.57/min
[5720000], rate=24514285.71/min
[5730000], rate=24557142.86/min
[5740000], rate=24600000.00/min
[5750000], rate=24642857.14/min
[5760000], rate=24685714.29/min
[5770000], rate=24728571.43/min
[5780000], rate=24771428.57/min
[5790000], rate=24814285.71/min
[5800000], rate=23200000.00/min
[5810000], rate=23240000.00/min
[5820000], rate=23280000.00/min
[5830000], rate=23320000.00/min
[5840000], rate=23360000.00/min
[5850000], rate=23400000.00/min
[5860000], rate=23440000.00/min
[5870000], rate=23480000.00/min
[5880000], rate=23520000.00/min
[5890000], rate=23560000.00/min
[5900000], rate=23600000.00/min
[5910000], rate=23640000.00/min
[5920000], rate=23680000.00/min
[5930000], rate=23720000.00/min
[5940000], rate=23760000.00/min
[5950000], rate=23800000.00/min
[5960000], rate=23840000.00/min
[5970000], rate=23880000.00/min
[5980000], rate=23920000.00/min
[5990000], rate=23960000.00/min
[6000000], rate=24000000.00/min
[6010000], rate=24040000.00/min
[6020000], rate=24080000.00/min
[6030000], rate=24120000.00/min
[6040000], rate=24160000.00/min
[6050000], rate=24200000.00/min
[6060000], rate=24240000.00/min
[6070000], rate=24280000.00/min
[6080000], rate=24320000.00/min
[6090000], rate=24360000.00/min
[6100000], rate=24400000.00/min
[6110000], rate=24440000.00/min
[6120000], rate=24480000.00/min
[6130000], rate=24520000.00/min
[6140000], rate=24560000.00/min
[6150000], rate=24600000.00/min
[6160000], rate=24640000.00/min
[6170000], rate=24680000.00/min
[6180000], rate=24720000.00/min
[6190000], rate=24760000.00/min
[6200000], rate=24800000.00/min
[6210000], rate=24840000.00/min
[6220000], rate=24880000.00/min
[6230000], rate=23362500.00/min
[6240000], rate=23400000.00/min
[6250000], rate=23437500.00/min
[6260000], rate=23475000.00/min
[6270000], rate=23512500.00/min
[6280000], rate=23550000.00/min
[6290000], rate=23587500.00/min
[6300000], rate=23625000.00/min
[6310000], rate=23662500.00/min
[6320000], rate=23700000.00/min
[6330000], rate=23737500.00/min
[6340000], rate=23775000.00/min
[6350000], rate=23812500.00/min
[6360000], rate=23850000.00/min
[6370000], rate=23887500.00/min
[6380000], rate=23925000.00/min
[6390000], rate=23962500.00/min
[6400000], rate=24000000.00/min
[6410000], rate=24037500.00/min
[6420000], rate=24075000.00/min
[6430000], rate=24112500.00/min
[6440000], rate=24150000.00/min
[6450000], rate=24187500.00/min
[6460000], rate=24225000.00/min
[6470000], rate=24262500.00/min
[6480000], rate=24300000.00/min
[6490000], rate=24337500.00/min
[6500000], rate=24375000.00/min
[6510000], rate=24412500.00/min
[6520000], rate=24450000.00/min
[6530000], rate=24487500.00/min
[6540000], rate=24525000.00/min
[6550000], rate=24562500.00/min
[6560000], rate=24600000.00/min
[6570000], rate=24637500.00/min
[6580000], rate=24675000.00/min
[6590000], rate=24712500.00/min
[6600000], rate=24750000.00/min
[6610000], rate=24787500.00/min
[6620000], rate=24825000.00/min
[6630000], rate=24862500.00/min
[6640000], rate=24900000.00/min
[6650000], rate=24937500.00/min
[6660000], rate=24975000.00/min
[6670000], rate=25012500.00/min
[6680000], rate=25050000.00/min
[6690000], rate=23611764.71/min
[6700000], rate=23647058.82/min
[6710000], rate=23682352.94/min
[6720000], rate=23717647.06/min
[6730000], rate=23752941.18/min
[6740000], rate=23788235.29/min
[6750000], rate=23823529.41/min
[6760000], rate=23858823.53/min
[6770000], rate=23894117.65/min
[6780000], rate=23929411.76/min
[6790000], rate=23964705.88/min
[6800000], rate=24000000.00/min
[6810000], rate=24035294.12/min
[6820000], rate=24070588.24/min
[6830000], rate=24105882.35/min
[6840000], rate=24141176.47/min
[6850000], rate=24176470.59/min
[6860000], rate=24211764.71/min
[6870000], rate=24247058.82/min
[6880000], rate=24282352.94/min
[6890000], rate=24317647.06/min
[6900000], rate=24352941.18/min
[6910000], rate=24388235.29/min
[6920000], rate=24423529.41/min
[6930000], rate=24458823.53/min
[6940000], rate=24494117.65/min
[6950000], rate=24529411.76/min
[6960000], rate=24564705.88/min
[6970000], rate=24600000.00/min
[6980000], rate=24635294.12/min
[6990000], rate=24670588.24/min
[7000000], rate=24705882.35/min
[7010000], rate=24741176.47/min
[7020000], rate=24776470.59/min
[7030000], rate=24811764.71/min 08:26:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.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.
-BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns: identified 2221 cancer introns
08:26:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer.introns.prelim
08:26:24 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/prelim_introns.ok
08:26:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer.introns
08:26:25 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer.introns
08:26:25 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/introns_filtered.ok
08:26:25 : INFO : -found 1262 cancer introns
08:26:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns --cancer_introns BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns.for_IGV.bed
08:26:25 : INFO : Creating the BED File.
08:26:27 : INFO : Saving Bed File as BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns.for_IGV.bed
08:26:27 : INFO : Execution Time = 0.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns --cancer_introns BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns.for_IGV.bed
08:26:27 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/intron_igv_bed.ok
08:26:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns.for_IGV.bed --bam BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
08:31:21 : INFO : Execution Time = 4.90 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns.for_IGV.bed --bam BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3
08:31:21 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/reads_alignments_extracted.ok
08:31:21 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer_intron_reads.bam
08:31:21 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer_intron_reads.bam
08:31:21 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/sort_cancer_intron_reads.ok
08:31:22 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.bam BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.bam
[bam_sort_core] merging from 30 files and 1 in-memory blocks...
08:37:31 : INFO : Execution Time = 6.16 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.bam BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.bam
08:37:31 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/sort_gene_reads.ok
08:37:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.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.
08:39:42 : INFO : Execution Time = 2.18 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.bam
08:39:42 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmp.ok
08:39:42 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
08:39:56 : INFO : Execution Time = 0.23 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmp
08:39:56 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmpsorted.ok
08:39:56 : INFO : Running: samtools index BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam
08:39:58 : INFO : Execution Time = 0.03 minutes. CMD: samtools index BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam
08:39:58 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.indexed.ok
08:39:58 : INFO : Running: samtools index BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer_intron_reads.sorted.bam
08:39:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer_intron_reads.sorted.bam
08:39:58 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.cancer_intron_reads.sorted.bam.indexed.ok
08:39:58 : INFO : Running: create_report BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3'
08:41:29 : INFO : Execution Time = 1.51 minutes. CMD: create_report BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3'
08:41:29 : INFO : Running: touch /tmp/nxf.MeIYKtgtML/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.chckpts/igv_create_html.ok
08:41:29 : INFO : done.