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/71/2f5b2cf073cb8f230c0f7088e20c9d/tih_rna_sample_00378_23H5VFLT4_s24.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/037f4b3dd23028fc91c946e2bae3bc/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/037f4b3dd23028fc91c946e2bae3bc/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/2f5b2cf073cb8f230c0f7088e20c9d/tih_rna_sample_00378_23H5VFLT4_s24.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/b657aacdc9a530eea958dc16e0ad23/tih_rna_sample_00378_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/2f5b2cf073cb8f230c0f7088e20c9d/tih_rna_sample_00378_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)
07:48:03 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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=9900000.00/min
[340000], rate=10200000.00/min
[350000], rate=10500000.00/min
[360000], rate=10800000.00/min
[370000], rate=11100000.00/min
[380000], rate=11400000.00/min
[390000], rate=11700000.00/min
[400000], rate=12000000.00/min
[410000], rate=12300000.00/min
[420000], rate=12600000.00/min
[430000], rate=12900000.00/min
[440000], rate=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=9800000.00/min
[500000], rate=10000000.00/min
[510000], rate=10200000.00/min
[520000], rate=10400000.00/min
[530000], rate=10600000.00/min
[540000], rate=10800000.00/min
[550000], rate=11000000.00/min
[560000], rate=11200000.00/min
[570000], rate=11400000.00/min
[580000], rate=11600000.00/min
[590000], rate=11800000.00/min
[600000], rate=12000000.00/min
[610000], rate=12200000.00/min
[620000], rate=12400000.00/min
[630000], rate=12600000.00/min
[640000], rate=12800000.00/min
[650000], rate=9750000.00/min
[660000], rate=9900000.00/min
[670000], rate=10050000.00/min
[680000], rate=10200000.00/min
[690000], rate=10350000.00/min
[700000], rate=10500000.00/min
[710000], rate=10650000.00/min
[720000], rate=10800000.00/min
[730000], rate=10950000.00/min
[740000], rate=11100000.00/min
[750000], rate=11250000.00/min
[760000], rate=11400000.00/min
[770000], rate=11550000.00/min
[780000], rate=11700000.00/min
[790000], rate=11850000.00/min
[800000], rate=12000000.00/min
[810000], rate=12150000.00/min
[820000], rate=12300000.00/min
[830000], rate=9960000.00/min
[840000], rate=10080000.00/min
[850000], rate=10200000.00/min
[860000], rate=10320000.00/min
[870000], rate=10440000.00/min
[880000], rate=10560000.00/min
[890000], rate=10680000.00/min
[900000], rate=10800000.00/min
[910000], rate=10920000.00/min
[920000], rate=11040000.00/min
[930000], rate=11160000.00/min
[940000], rate=11280000.00/min
[950000], rate=11400000.00/min
[960000], rate=11520000.00/min
[970000], rate=11640000.00/min
[980000], rate=11760000.00/min
[990000], rate=11880000.00/min
[1000000], rate=12000000.00/min
[1010000], rate=12120000.00/min
[1020000], rate=12240000.00/min
[1030000], rate=12360000.00/min
[1040000], rate=12480000.00/min
[1050000], rate=10500000.00/min
[1060000], rate=10600000.00/min
[1070000], rate=10700000.00/min
[1080000], rate=10800000.00/min
[1090000], rate=10900000.00/min
[1100000], rate=11000000.00/min
[1110000], rate=11100000.00/min
[1120000], rate=11200000.00/min
[1130000], rate=11300000.00/min
[1140000], rate=11400000.00/min
[1150000], rate=11500000.00/min
[1160000], rate=11600000.00/min
[1170000], rate=11700000.00/min
[1180000], rate=11800000.00/min
[1190000], rate=11900000.00/min
[1200000], rate=12000000.00/min
[1210000], rate=12100000.00/min
[1220000], rate=12200000.00/min
[1230000], rate=12300000.00/min
[1240000], rate=10628571.43/min
[1250000], rate=10714285.71/min
[1260000], rate=10800000.00/min
[1270000], rate=10885714.29/min
[1280000], rate=10971428.57/min
[1290000], rate=11057142.86/min
[1300000], rate=11142857.14/min
[1310000], rate=11228571.43/min
[1320000], rate=11314285.71/min
[1330000], rate=11400000.00/min
[1340000], rate=11485714.29/min
[1350000], rate=11571428.57/min
[1360000], rate=11657142.86/min
[1370000], rate=11742857.14/min
[1380000], rate=11828571.43/min
[1390000], rate=11914285.71/min
[1400000], rate=12000000.00/min
[1410000], rate=12085714.29/min
[1420000], rate=12171428.57/min
[1430000], rate=10725000.00/min
[1440000], rate=10800000.00/min
[1450000], rate=10875000.00/min
[1460000], rate=10950000.00/min
[1470000], rate=11025000.00/min
[1480000], rate=11100000.00/min
[1490000], rate=11175000.00/min
[1500000], rate=11250000.00/min
[1510000], rate=11325000.00/min
[1520000], rate=11400000.00/min
[1530000], rate=11475000.00/min
[1540000], rate=11550000.00/min
[1550000], rate=11625000.00/min
[1560000], rate=11700000.00/min
[1570000], rate=11775000.00/min
[1580000], rate=11850000.00/min
[1590000], rate=11925000.00/min
[1600000], rate=10666666.67/min
[1610000], rate=10733333.33/min
[1620000], rate=10800000.00/min
[1630000], rate=10866666.67/min
[1640000], rate=10933333.33/min
[1650000], rate=11000000.00/min
[1660000], rate=11066666.67/min
[1670000], rate=11133333.33/min
[1680000], rate=11200000.00/min
[1690000], rate=11266666.67/min
[1700000], rate=11333333.33/min
[1710000], rate=11400000.00/min
[1720000], rate=11466666.67/min
[1730000], rate=11533333.33/min
[1740000], rate=11600000.00/min
[1750000], rate=11666666.67/min
[1760000], rate=11733333.33/min
[1770000], rate=11800000.00/min
[1780000], rate=10680000.00/min
[1790000], rate=10740000.00/min
[1800000], rate=10800000.00/min
[1810000], rate=10860000.00/min
[1820000], rate=10920000.00/min
[1830000], rate=10980000.00/min
[1840000], rate=11040000.00/min
[1850000], rate=11100000.00/min
[1860000], rate=11160000.00/min
[1870000], rate=11220000.00/min
[1880000], rate=11280000.00/min
[1890000], rate=11340000.00/min
[1900000], rate=11400000.00/min
[1910000], rate=11460000.00/min
[1920000], rate=11520000.00/min
[1930000], rate=11580000.00/min
[1940000], rate=11640000.00/min
[1950000], rate=11700000.00/min
[1960000], rate=11760000.00/min
[1970000], rate=11820000.00/min
[1980000], rate=10800000.00/min
[1990000], rate=10854545.45/min
[2000000], rate=10909090.91/min
[2010000], rate=10963636.36/min
[2020000], rate=11018181.82/min
[2030000], rate=11072727.27/min
[2040000], rate=11127272.73/min
[2050000], rate=11181818.18/min
[2060000], rate=11236363.64/min
[2070000], rate=11290909.09/min
[2080000], rate=11345454.55/min
[2090000], rate=11400000.00/min
[2100000], rate=11454545.45/min
[2110000], rate=11509090.91/min
[2120000], rate=11563636.36/min
[2130000], rate=11618181.82/min
[2140000], rate=11672727.27/min
[2150000], rate=11727272.73/min
[2160000], rate=10800000.00/min
[2170000], rate=10850000.00/min
[2180000], rate=10900000.00/min
[2190000], rate=10950000.00/min
[2200000], rate=11000000.00/min
[2210000], rate=11050000.00/min
[2220000], rate=11100000.00/min
[2230000], rate=11150000.00/min
[2240000], rate=11200000.00/min
[2250000], rate=11250000.00/min
[2260000], rate=11300000.00/min
[2270000], rate=11350000.00/min
[2280000], rate=11400000.00/min
[2290000], rate=11450000.00/min
[2300000], rate=11500000.00/min
[2310000], rate=11550000.00/min
[2320000], rate=11600000.00/min
[2330000], rate=11650000.00/min
[2340000], rate=11700000.00/min
[2350000], rate=11750000.00/min
[2360000], rate=11800000.00/min
[2370000], rate=11850000.00/min
[2380000], rate=11900000.00/min
[2390000], rate=11950000.00/min
[2400000], rate=11076923.08/min
[2410000], rate=11123076.92/min
[2420000], rate=11169230.77/min
[2430000], rate=11215384.62/min
[2440000], rate=11261538.46/min
[2450000], rate=11307692.31/min
[2460000], rate=11353846.15/min
[2470000], rate=11400000.00/min
[2480000], rate=11446153.85/min
[2490000], rate=11492307.69/min
[2500000], rate=11538461.54/min
[2510000], rate=11584615.38/min
[2520000], rate=11630769.23/min
[2530000], rate=11676923.08/min
[2540000], rate=11723076.92/min
[2550000], rate=11769230.77/min
[2560000], rate=11815384.62/min
[2570000], rate=11861538.46/min
[2580000], rate=11907692.31/min
[2590000], rate=11953846.15/min
[2600000], rate=12000000.00/min
[2610000], rate=12046153.85/min
[2620000], rate=12092307.69/min
[2630000], rate=11271428.57/min
[2640000], rate=11314285.71/min
[2650000], rate=11357142.86/min
[2660000], rate=11400000.00/min
[2670000], rate=11442857.14/min
[2680000], rate=11485714.29/min
[2690000], rate=11528571.43/min
[2700000], rate=11571428.57/min
[2710000], rate=11614285.71/min
[2720000], rate=11657142.86/min
[2730000], rate=11700000.00/min
[2740000], rate=11742857.14/min
[2750000], rate=11785714.29/min
[2760000], rate=11828571.43/min
[2770000], rate=11871428.57/min
[2780000], rate=11914285.71/min
[2790000], rate=11957142.86/min
[2800000], rate=12000000.00/min
[2810000], rate=12042857.14/min
[2820000], rate=12085714.29/min
[2830000], rate=11320000.00/min
[2840000], rate=11360000.00/min
[2850000], rate=11400000.00/min
[2860000], rate=11440000.00/min
[2870000], rate=11480000.00/min
[2880000], rate=11520000.00/min
[2890000], rate=11560000.00/min
[2900000], rate=11600000.00/min
[2910000], rate=11640000.00/min
[2920000], rate=11680000.00/min
[2930000], rate=11720000.00/min
[2940000], rate=11760000.00/min
[2950000], rate=11800000.00/min
[2960000], rate=11840000.00/min
[2970000], rate=11880000.00/min
[2980000], rate=11920000.00/min
[2990000], rate=11960000.00/min
[3000000], rate=12000000.00/min
[3010000], rate=11287500.00/min
[3020000], rate=11325000.00/min
[3030000], rate=11362500.00/min
[3040000], rate=11400000.00/min
[3050000], rate=11437500.00/min
[3060000], rate=11475000.00/min
[3070000], rate=11512500.00/min
[3080000], rate=11550000.00/min
[3090000], rate=11587500.00/min
[3100000], rate=11625000.00/min
[3110000], rate=11662500.00/min
[3120000], rate=11700000.00/min
[3130000], rate=11737500.00/min
[3140000], rate=11775000.00/min
[3150000], rate=11812500.00/min
[3160000], rate=11850000.00/min
[3170000], rate=11188235.29/min
[3180000], rate=11223529.41/min
[3190000], rate=11258823.53/min
[3200000], rate=11294117.65/min
[3210000], rate=11329411.76/min
[3220000], rate=11364705.88/min
[3230000], rate=11400000.00/min
[3240000], rate=11435294.12/min
[3250000], rate=11470588.24/min
[3260000], rate=11505882.35/min
[3270000], rate=11541176.47/min
[3280000], rate=11576470.59/min
[3290000], rate=11611764.71/min
[3300000], rate=11647058.82/min
[3310000], rate=11682352.94/min
[3320000], rate=11717647.06/min
[3330000], rate=11752941.18/min
[3340000], rate=11788235.29/min
[3350000], rate=11823529.41/min
[3360000], rate=11858823.53/min
[3370000], rate=11233333.33/min
[3380000], rate=11266666.67/min
[3390000], rate=11300000.00/min
[3400000], rate=11333333.33/min
[3410000], rate=11366666.67/min
[3420000], rate=11400000.00/min
[3430000], rate=11433333.33/min
[3440000], rate=11466666.67/min
[3450000], rate=11500000.00/min
[3460000], rate=11533333.33/min
[3470000], rate=11566666.67/min
[3480000], rate=11600000.00/min
[3490000], rate=11633333.33/min
[3500000], rate=11666666.67/min
[3510000], rate=11700000.00/min
[3520000], rate=11733333.33/min
[3530000], rate=11766666.67/min
[3540000], rate=11800000.00/min
[3550000], rate=11833333.33/min
[3560000], rate=11866666.67/min
[3570000], rate=11273684.21/min
[3580000], rate=11305263.16/min
[3590000], rate=11336842.11/min
[3600000], rate=11368421.05/min
[3610000], rate=11400000.00/min
[3620000], rate=11431578.95/min
[3630000], rate=11463157.89/min
[3640000], rate=11494736.84/min
[3650000], rate=11526315.79/min
[3660000], rate=11557894.74/min
[3670000], rate=11589473.68/min
[3680000], rate=11621052.63/min
[3690000], rate=11652631.58/min
[3700000], rate=11684210.53/min
[3710000], rate=11715789.47/min
[3720000], rate=11747368.42/min
[3730000], rate=11778947.37/min
[3740000], rate=11810526.32/min
[3750000], rate=11842105.26/min
[3760000], rate=11873684.21/min
[3770000], rate=11905263.16/min
[3780000], rate=11936842.11/min
[3790000], rate=11968421.05/min
[3800000], rate=12000000.00/min
[3810000], rate=11430000.00/min
[3820000], rate=11460000.00/min
[3830000], rate=11490000.00/min
[3840000], rate=11520000.00/min
[3850000], rate=11550000.00/min
[3860000], rate=11580000.00/min
[3870000], rate=11610000.00/min
[3880000], rate=11640000.00/min
[3890000], rate=11670000.00/min
[3900000], rate=11700000.00/min
[3910000], rate=11730000.00/min
[3920000], rate=11760000.00/min
[3930000], rate=11790000.00/min
[3940000], rate=11820000.00/min
[3950000], rate=11850000.00/min
[3960000], rate=11880000.00/min
[3970000], rate=11910000.00/min
[3980000], rate=11940000.00/min
[3990000], rate=11970000.00/min
[4000000], rate=11428571.43/min
[4010000], rate=11457142.86/min
[4020000], rate=11485714.29/min
[4030000], rate=11514285.71/min
[4040000], rate=11542857.14/min
[4050000], rate=11571428.57/min
[4060000], rate=11600000.00/min
[4070000], rate=11628571.43/min
[4080000], rate=11657142.86/min
[4090000], rate=11685714.29/min
[4100000], rate=11714285.71/min
[4110000], rate=11742857.14/min
[4120000], rate=11771428.57/min
[4130000], rate=11800000.00/min
[4140000], rate=11828571.43/min
[4150000], rate=11857142.86/min
[4160000], rate=11345454.55/min
[4170000], rate=11372727.27/min
[4180000], rate=11400000.00/min
[4190000], rate=11427272.73/min
[4200000], rate=11454545.45/min
[4210000], rate=11481818.18/min
[4220000], rate=11509090.91/min
[4230000], rate=11536363.64/min
[4240000], rate=11563636.36/min
[4250000], rate=11590909.09/min
[4260000], rate=11618181.82/min
[4270000], rate=11645454.55/min
[4280000], rate=11672727.27/min
[4290000], rate=11700000.00/min
[4300000], rate=11727272.73/min
[4310000], rate=11754545.45/min
[4320000], rate=11781818.18/min
[4330000], rate=11809090.91/min
[4340000], rate=11836363.64/min
[4350000], rate=11863636.36/min
[4360000], rate=11890909.09/min
[4370000], rate=11400000.00/min
[4380000], rate=11426086.96/min
[4390000], rate=11452173.91/min
[4400000], rate=11478260.87/min
[4410000], rate=11504347.83/min
[4420000], rate=11530434.78/min
[4430000], rate=11556521.74/min
[4440000], rate=11582608.70/min
[4450000], rate=11608695.65/min
[4460000], rate=11634782.61/min
[4470000], rate=11660869.57/min
[4480000], rate=11686956.52/min
[4490000], rate=11713043.48/min
[4500000], rate=11739130.43/min
[4510000], rate=11765217.39/min
[4520000], rate=11791304.35/min
[4530000], rate=11817391.30/min
[4540000], rate=11843478.26/min
[4550000], rate=11869565.22/min
[4560000], rate=11895652.17/min
[4570000], rate=11425000.00/min
[4580000], rate=11450000.00/min
[4590000], rate=11475000.00/min
[4600000], rate=11500000.00/min
[4610000], rate=11525000.00/min
[4620000], rate=11550000.00/min
[4630000], rate=11575000.00/min
[4640000], rate=11600000.00/min
[4650000], rate=11625000.00/min
[4660000], rate=11650000.00/min
[4670000], rate=11675000.00/min
[4680000], rate=11700000.00/min
[4690000], rate=11725000.00/min
[4700000], rate=11750000.00/min
[4710000], rate=11775000.00/min
[4720000], rate=11800000.00/min
[4730000], rate=11825000.00/min
[4740000], rate=11850000.00/min
[4750000], rate=11875000.00/min
[4760000], rate=11424000.00/min
[4770000], rate=11448000.00/min
[4780000], rate=11472000.00/min
[4790000], rate=11496000.00/min
[4800000], rate=11520000.00/min
[4810000], rate=11544000.00/min
[4820000], rate=11568000.00/min
[4830000], rate=11592000.00/min
[4840000], rate=11616000.00/min
[4850000], rate=11640000.00/min
[4860000], rate=11664000.00/min
[4870000], rate=11688000.00/min
[4880000], rate=11712000.00/min
[4890000], rate=11736000.00/min
[4900000], rate=11760000.00/min
[4910000], rate=11784000.00/min
[4920000], rate=11808000.00/min
[4930000], rate=11376923.08/min
[4940000], rate=11400000.00/min
[4950000], rate=11423076.92/min
[4960000], rate=11446153.85/min
[4970000], rate=11469230.77/min
[4980000], rate=11492307.69/min
[4990000], rate=11515384.62/min
[5000000], rate=11538461.54/min
[5010000], rate=11561538.46/min
[5020000], rate=11584615.38/min
[5030000], rate=11607692.31/min
[5040000], rate=11630769.23/min
[5050000], rate=11653846.15/min
[5060000], rate=11676923.08/min
[5070000], rate=11700000.00/min
[5080000], rate=11723076.92/min
[5090000], rate=11746153.85/min
[5100000], rate=11769230.77/min
[5110000], rate=11792307.69/min
[5120000], rate=11815384.62/min
[5130000], rate=11400000.00/min
[5140000], rate=11422222.22/min
[5150000], rate=11444444.44/min
[5160000], rate=11466666.67/min
[5170000], rate=11488888.89/min
[5180000], rate=11511111.11/min
[5190000], rate=11533333.33/min
[5200000], rate=11555555.56/min
[5210000], rate=11577777.78/min
[5220000], rate=11600000.00/min
[5230000], rate=11622222.22/min
[5240000], rate=11644444.44/min
[5250000], rate=11666666.67/min
[5260000], rate=11688888.89/min
[5270000], rate=11711111.11/min
[5280000], rate=11733333.33/min
[5290000], rate=11755555.56/min
[5300000], rate=11777777.78/min
[5310000], rate=11800000.00/min
[5320000], rate=11400000.00/min
[5330000], rate=11421428.57/min
[5340000], rate=11442857.14/min
[5350000], rate=11464285.71/min
[5360000], rate=11485714.29/min
[5370000], rate=11507142.86/min
[5380000], rate=11528571.43/min
[5390000], rate=11550000.00/min
[5400000], rate=11571428.57/min
[5410000], rate=11592857.14/min
[5420000], rate=11614285.71/min
[5430000], rate=11635714.29/min
[5440000], rate=11657142.86/min
[5450000], rate=11678571.43/min
[5460000], rate=11700000.00/min
[5470000], rate=11721428.57/min
[5480000], rate=11742857.14/min
[5490000], rate=11764285.71/min
[5500000], rate=11785714.29/min
[5510000], rate=11807142.86/min
[5520000], rate=11828571.43/min
[5530000], rate=11441379.31/min
[5540000], rate=11462068.97/min
[5550000], rate=11482758.62/min
[5560000], rate=11503448.28/min
[5570000], rate=11524137.93/min
[5580000], rate=11544827.59/min
[5590000], rate=11565517.24/min
[5600000], rate=11586206.90/min
[5610000], rate=11606896.55/min
[5620000], rate=11627586.21/min
[5630000], rate=11648275.86/min
[5640000], rate=11668965.52/min
[5650000], rate=11689655.17/min
[5660000], rate=11710344.83/min
[5670000], rate=11731034.48/min
[5680000], rate=11751724.14/min
[5690000], rate=11772413.79/min
[5700000], rate=11793103.45/min
[5710000], rate=11420000.00/min
[5720000], rate=11440000.00/min
[5730000], rate=11460000.00/min
[5740000], rate=11480000.00/min
[5750000], rate=11500000.00/min
[5760000], rate=11520000.00/min
[5770000], rate=11540000.00/min
[5780000], rate=11560000.00/min
[5790000], rate=11580000.00/min
[5800000], rate=11600000.00/min
[5810000], rate=11620000.00/min
[5820000], rate=11640000.00/min
[5830000], rate=11660000.00/min
[5840000], rate=11680000.00/min
[5850000], rate=11700000.00/min
[5860000], rate=11720000.00/min
[5870000], rate=11740000.00/min
[5880000], rate=11760000.00/min
[5890000], rate=11780000.00/min
[5900000], rate=11800000.00/min
[5910000], rate=11820000.00/min
[5920000], rate=11840000.00/min
[5930000], rate=11860000.00/min
[5940000], rate=11880000.00/min
[5950000], rate=11900000.00/min
[5960000], rate=11920000.00/min
[5970000], rate=11554838.71/min
[5980000], rate=11574193.55/min
[5990000], rate=11593548.39/min
[6000000], rate=11612903.23/min
[6010000], rate=11632258.06/min
[6020000], rate=11651612.90/min
[6030000], rate=11670967.74/min
[6040000], rate=11690322.58/min
[6050000], rate=11709677.42/min
[6060000], rate=11729032.26/min
[6070000], rate=11748387.10/min
[6080000], rate=11767741.94/min
[6090000], rate=11787096.77/min
[6100000], rate=11806451.61/min
[6110000], rate=11825806.45/min
[6120000], rate=11845161.29/min
[6130000], rate=11864516.13/min
[6140000], rate=11883870.97/min
[6150000], rate=11903225.81/min
[6160000], rate=11922580.65/min
[6170000], rate=11941935.48/min
[6180000], rate=11961290.32/min
[6190000], rate=11980645.16/min
[6200000], rate=12000000.00/min
[6210000], rate=12019354.84/min
[6220000], rate=11662500.00/min
[6230000], rate=11681250.00/min
[6240000], rate=11700000.00/min
[6250000], rate=11718750.00/min
[6260000], rate=11737500.00/min
[6270000], rate=11756250.00/min
[6280000], rate=11775000.00/min
[6290000], rate=11793750.00/min
[6300000], rate=11812500.00/min
[6310000], rate=11831250.00/min
[6320000], rate=11850000.00/min
[6330000], rate=11868750.00/min
[6340000], rate=11887500.00/min
[6350000], rate=11906250.00/min
[6360000], rate=11925000.00/min
[6370000], rate=11943750.00/min
[6380000], rate=11962500.00/min
[6390000], rate=11981250.00/min
[6400000], rate=12000000.00/min
[6410000], rate=12018750.00/min
[6420000], rate=12037500.00/min
[6430000], rate=12056250.00/min
[6440000], rate=12075000.00/min
[6450000], rate=11727272.73/min
[6460000], rate=11745454.55/min
[6470000], rate=11763636.36/min
[6480000], rate=11781818.18/min
[6490000], rate=11800000.00/min
[6500000], rate=11818181.82/min
[6510000], rate=11836363.64/min
[6520000], rate=11854545.45/min
[6530000], rate=11872727.27/min
[6540000], rate=11890909.09/min
[6550000], rate=11909090.91/min
[6560000], rate=11927272.73/min
[6570000], rate=11945454.55/min
[6580000], rate=11963636.36/min
[6590000], rate=11981818.18/min
[6600000], rate=12000000.00/min
[6610000], rate=12018181.82/min
[6620000], rate=12036363.64/min
[6630000], rate=12054545.45/min
[6640000], rate=12072727.27/min
[6650000], rate=12090909.09/min
[6660000], rate=11752941.18/min
[6670000], rate=11770588.24/min
[6680000], rate=11788235.29/min
[6690000], rate=11805882.35/min
[6700000], rate=11823529.41/min
[6710000], rate=11841176.47/min
[6720000], rate=11858823.53/min
[6730000], rate=11876470.59/min
[6740000], rate=11894117.65/min
[6750000], rate=11911764.71/min
[6760000], rate=11929411.76/min
[6770000], rate=11947058.82/min
[6780000], rate=11964705.88/min
[6790000], rate=11982352.94/min
[6800000], rate=12000000.00/min
[6810000], rate=12017647.06/min
[6820000], rate=12035294.12/min
[6830000], rate=12052941.18/min
[6840000], rate=12070588.24/min
[6850000], rate=12088235.29/min
[6860000], rate=12105882.35/min
[6870000], rate=12123529.41/min
[6880000], rate=12141176.47/min
[6890000], rate=11811428.57/min
[6900000], rate=11828571.43/min
[6910000], rate=11845714.29/min
[6920000], rate=11862857.14/min
[6930000], rate=11880000.00/min
[6940000], rate=11897142.86/min
[6950000], rate=11914285.71/min
[6960000], rate=11931428.57/min
[6970000], rate=11948571.43/min
[6980000], rate=11965714.29/min
[6990000], rate=11982857.14/min
[7000000], rate=12000000.00/min
[7010000], rate=12017142.86/min
[7020000], rate=12034285.71/min
[7030000], rate=12051428.57/min
[7040000], rate=12068571.43/min
[7050000], rate=12085714.29/min
[7060000], rate=12102857.14/min
[7070000], rate=12120000.00/min
[7080000], rate=12137142.86/min
[7090000], rate=12154285.71/min
[7100000], rate=12171428.57/min
[7110000], rate=12188571.43/min
[7120000], rate=12205714.29/min
[7130000], rate=11883333.33/min
[7140000], rate=11900000.00/min
[7150000], rate=11916666.67/min
[7160000], rate=11933333.33/min
[7170000], rate=11950000.00/min
[7180000], rate=11966666.67/min
[7190000], rate=11983333.33/min
[7200000], rate=12000000.00/min
[7210000], rate=12016666.67/min
[7220000], rate=12033333.33/min
[7230000], rate=12050000.00/min
[7240000], rate=12066666.67/min
[7250000], rate=12083333.33/min
[7260000], rate=12100000.00/min
[7270000], rate=12116666.67/min
[7280000], rate=12133333.33/min
[7290000], rate=12150000.00/min
[7300000], rate=12166666.67/min
[7310000], rate=12183333.33/min
[7320000], rate=11870270.27/min
[7330000], rate=11886486.49/min
[7340000], rate=11902702.70/min
[7350000], rate=11918918.92/min
[7360000], rate=11935135.14/min
[7370000], rate=11951351.35/min
[7380000], rate=11967567.57/min
[7390000], rate=11983783.78/min
[7400000], rate=12000000.00/min
[7410000], rate=12016216.22/min
[7420000], rate=12032432.43/min
[7430000], rate=12048648.65/min
[7440000], rate=12064864.86/min
[7450000], rate=12081081.08/min
[7460000], rate=12097297.30/min
[7470000], rate=12113513.51/min
[7480000], rate=12129729.73/min
[7490000], rate=12145945.95/min
[7500000], rate=12162162.16/min
[7510000], rate=12178378.38/min
[7520000], rate=12194594.59/min
[7530000], rate=12210810.81/min
[7540000], rate=12227027.03/min
[7550000], rate=11921052.63/min
[7560000], rate=11936842.11/min
[7570000], rate=11952631.58/min
[7580000], rate=11968421.05/min
[7590000], rate=11984210.53/min
[7600000], rate=12000000.00/min
[7610000], rate=12015789.47/min
[7620000], rate=12031578.95/min
[7630000], rate=12047368.42/min
[7640000], rate=12063157.89/min
[7650000], rate=12078947.37/min
[7660000], rate=12094736.84/min
[7670000], rate=12110526.32/min
[7680000], rate=12126315.79/min
[7690000], rate=12142105.26/min
[7700000], rate=12157894.74/min
[7710000], rate=12173684.21/min
[7720000], rate=12189473.68/min
[7730000], rate=12205263.16/min
[7740000], rate=12221052.63/min
[7750000], rate=12236842.11/min
[7760000], rate=11938461.54/min
[7770000], rate=11953846.15/min
[7780000], rate=11969230.77/min
[7790000], rate=11984615.38/min
[7800000], rate=12000000.00/min
[7810000], rate=12015384.62/min
[7820000], rate=12030769.23/min
[7830000], rate=12046153.85/min
[7840000], rate=12061538.46/min
[7850000], rate=12076923.08/min
[7860000], rate=12092307.69/min
[7870000], rate=12107692.31/min
[7880000], rate=12123076.92/min
[7890000], rate=12138461.54/min
[7900000], rate=12153846.15/min
[7910000], rate=12169230.77/min
[7920000], rate=12184615.38/min
[7930000], rate=11895000.00/min
[7940000], rate=11910000.00/min
[7950000], rate=11925000.00/min
[7960000], rate=11940000.00/min
[7970000], rate=11955000.00/min
[7980000], rate=11970000.00/min
[7990000], rate=11985000.00/min
[8000000], rate=12000000.00/min
[8010000], rate=12015000.00/min
[8020000], rate=12030000.00/min
[8030000], rate=12045000.00/min
[8040000], rate=12060000.00/min
[8050000], rate=12075000.00/min
[8060000], rate=12090000.00/min
[8070000], rate=12105000.00/min
[8080000], rate=12120000.00/min
[8090000], rate=12135000.00/min
[8100000], rate=12150000.00/min
[8110000], rate=12165000.00/min
[8120000], rate=12180000.00/min
[8130000], rate=11897560.98/min
[8140000], rate=11912195.12/min
[8150000], rate=11926829.27/min
[8160000], rate=11941463.41/min
[8170000], rate=11956097.56/min
[8180000], rate=11970731.71/min
[8190000], rate=11985365.85/min
[8200000], rate=12000000.00/min
[8210000], rate=12014634.15/min
[8220000], rate=12029268.29/min
[8230000], rate=12043902.44/min
[8240000], rate=12058536.59/min
[8250000], rate=12073170.73/min
[8260000], rate=12087804.88/min
[8270000], rate=12102439.02/min
[8280000], rate=12117073.17/min
[8290000], rate=12131707.32/min
[8300000], rate=12146341.46/min
[8310000], rate=12160975.61/min
[8320000], rate=12175609.76/min
[8330000], rate=12190243.90/min
[8340000], rate=12204878.05/min
[8350000], rate=12219512.20/min
[8360000], rate=12234146.34/min
[8370000], rate=12248780.49/min
[8380000], rate=12263414.63/min
[8390000], rate=12278048.78/min
[8400000], rate=12292682.93/min
[8410000], rate=12014285.71/min
[8420000], rate=12028571.43/min
[8430000], rate=12042857.14/min
[8440000], rate=12057142.86/min
[8450000], rate=12071428.57/min
[8460000], rate=12085714.29/min
[8470000], rate=12100000.00/min
[8480000], rate=12114285.71/min
[8490000], rate=12128571.43/min
[8500000], rate=12142857.14/min
[8510000], rate=12157142.86/min
[8520000], rate=12171428.57/min
[8530000], rate=12185714.29/min
[8540000], rate=12200000.00/min
[8550000], rate=12214285.71/min
[8560000], rate=12228571.43/min
[8570000], rate=12242857.14/min
[8580000], rate=12257142.86/min
[8590000], rate=12271428.57/min
[8600000], rate=12285714.29/min
[8610000], rate=12300000.00/min
[8620000], rate=12314285.71/min
[8630000], rate=12328571.43/min
[8640000], rate=12342857.14/min 07:48:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00378_23H5VFLT4_s24.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00378_23H5VFLT4_s24.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_00378_23H5VFLT4_s24.introns: identified 4801 cancer introns
07:48:59 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00378_23H5VFLT4_s24.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns.prelim
07:48:59 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/prelim_introns.ok
07:48:59 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns
07:49:00 : 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_00378_23H5VFLT4_s24.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns
07:49:00 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/introns_filtered.ok
07:49:00 : INFO : -found 1540 cancer introns
07:49:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00378_23H5VFLT4_s24.introns --cancer_introns tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed
07:49:00 : INFO : Creating the BED File.
07:49:06 : INFO : Saving Bed File as tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed
07:49:06 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00378_23H5VFLT4_s24.introns --cancer_introns tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed
07:49:06 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/intron_igv_bed.ok
07:49:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed --bam tih_rna_sample_00378_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00378_23H5VFLT4_s24
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00378_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
08:00:34 : INFO : Execution Time = 11.45 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed --bam tih_rna_sample_00378_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00378_23H5VFLT4_s24
08:00:34 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/reads_alignments_extracted.ok
08:00:34 : INFO : Running: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.sorted.bam tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.bam
08:00:34 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.sorted.bam tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.bam
08:00:34 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/sort_cancer_intron_reads.ok
08:00:34 : INFO : Running: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.bam tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.bam
[bam_sort_core] merging from 40 files and 1 in-memory blocks...
08:12:06 : INFO : Execution Time = 11.54 minutes. CMD: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.bam tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.bam
08:12:06 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/sort_gene_reads.ok
08:12:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00378_23H5VFLT4_s24.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.
08:16:32 : INFO : Execution Time = 4.43 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.bam
08:16:32 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp.ok
08:16:32 : INFO : Running: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
08:18:19 : INFO : Execution Time = 1.77 minutes. CMD: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp
08:18:19 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmpsorted.ok
08:18:19 : INFO : Running: samtools index tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam
08:18:30 : INFO : Execution Time = 0.19 minutes. CMD: samtools index tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam
08:18:30 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.indexed.ok
08:18:30 : INFO : Running: samtools index tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.sorted.bam
08:18:30 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.sorted.bam
08:18:30 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.sorted.bam.indexed.ok
08:18:30 : INFO : Running: create_report tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00378_23H5VFLT4_s24.ctat-splicing.igv.html --track-config tih_rna_sample_00378_23H5VFLT4_s24.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00378_23H5VFLT4_s24'
08:25:13 : INFO : Execution Time = 6.71 minutes. CMD: create_report tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00378_23H5VFLT4_s24.ctat-splicing.igv.html --track-config tih_rna_sample_00378_23H5VFLT4_s24.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00378_23H5VFLT4_s24'
08:25:13 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/igv_create_html.ok
08:25:13 : INFO : done.