Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/72436ebb9ac2c7d604654cd976f2b9/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.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/cb/8c2e919eb2e47b1c24dc5ddb3863d8/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/213021ca5713ac56d4b9a80efc19d1/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/72436ebb9ac2c7d604654cd976f2b9/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/72436ebb9ac2c7d604654cd976f2b9/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/213021ca5713ac56d4b9a80efc19d1/.command.run
==> STAGING COMPLETE (7 inputs)
09:11:36 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[50000], rate=3000000.00/min
[60000], rate=3600000.00/min
[70000], rate=4200000.00/min
[80000], rate=4800000.00/min
[90000], rate=5400000.00/min
[100000], rate=6000000.00/min
[110000], rate=6600000.00/min
[120000], rate=7200000.00/min
[130000], rate=7800000.00/min
[140000], rate=8400000.00/min
[150000], rate=9000000.00/min
[160000], rate=9600000.00/min
[170000], rate=10200000.00/min
[180000], rate=10800000.00/min
[190000], rate=11400000.00/min
[200000], rate=12000000.00/min
[210000], rate=12600000.00/min
[220000], rate=13200000.00/min
[230000], rate=13800000.00/min
[240000], rate=14400000.00/min
[250000], rate=15000000.00/min
[260000], rate=15600000.00/min
[270000], rate=16200000.00/min
[280000], rate=16800000.00/min
[290000], rate=17400000.00/min
[300000], rate=18000000.00/min
[310000], rate=18600000.00/min
[320000], rate=19200000.00/min
[330000], rate=19800000.00/min
[340000], rate=20400000.00/min
[350000], rate=21000000.00/min
[360000], rate=21600000.00/min
[370000], rate=22200000.00/min
[380000], rate=22800000.00/min
[390000], rate=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=17400000.00/min
[590000], rate=17700000.00/min
[600000], rate=18000000.00/min
[610000], rate=18300000.00/min
[620000], rate=18600000.00/min
[630000], rate=18900000.00/min
[640000], rate=19200000.00/min
[650000], rate=19500000.00/min
[660000], rate=19800000.00/min
[670000], rate=20100000.00/min
[680000], rate=20400000.00/min
[690000], rate=20700000.00/min
[700000], rate=21000000.00/min
[710000], rate=21300000.00/min
[720000], rate=21600000.00/min
[730000], rate=21900000.00/min
[740000], rate=22200000.00/min
[750000], rate=22500000.00/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=22000000.00/min
[1110000], rate=22200000.00/min
[1120000], rate=22400000.00/min
[1130000], rate=22600000.00/min
[1140000], rate=22800000.00/min
[1150000], rate=23000000.00/min
[1160000], rate=23200000.00/min
[1170000], rate=23400000.00/min
[1180000], rate=23600000.00/min
[1190000], rate=23800000.00/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=31400000.00/min
[1580000], rate=31600000.00/min
[1590000], rate=31800000.00/min
[1600000], rate=32000000.00/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=29700000.00/min
[1990000], rate=29850000.00/min
[2000000], rate=30000000.00/min
[2010000], rate=30150000.00/min
[2020000], rate=30300000.00/min
[2030000], rate=30450000.00/min
[2040000], rate=30600000.00/min
[2050000], rate=30750000.00/min
[2060000], rate=30900000.00/min
[2070000], rate=31050000.00/min
[2080000], rate=31200000.00/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=28560000.00/min
[2390000], rate=28680000.00/min
[2400000], rate=28800000.00/min
[2410000], rate=28920000.00/min
[2420000], rate=29040000.00/min
[2430000], rate=29160000.00/min
[2440000], rate=29280000.00/min
[2450000], rate=29400000.00/min
[2460000], rate=29520000.00/min
[2470000], rate=29640000.00/min
[2480000], rate=29760000.00/min
[2490000], rate=29880000.00/min
[2500000], rate=30000000.00/min
[2510000], rate=30120000.00/min
[2520000], rate=30240000.00/min
[2530000], rate=30360000.00/min
[2540000], rate=30480000.00/min
[2550000], rate=30600000.00/min
[2560000], rate=30720000.00/min
[2570000], rate=30840000.00/min
[2580000], rate=30960000.00/min
[2590000], rate=31080000.00/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=27400000.00/min
[2750000], rate=27500000.00/min
[2760000], rate=27600000.00/min
[2770000], rate=27700000.00/min
[2780000], rate=27800000.00/min
[2790000], rate=27900000.00/min
[2800000], rate=28000000.00/min
[2810000], rate=28100000.00/min
[2820000], rate=28200000.00/min
[2830000], rate=28300000.00/min
[2840000], rate=28400000.00/min
[2850000], rate=28500000.00/min
[2860000], rate=28600000.00/min
[2870000], rate=28700000.00/min
[2880000], rate=28800000.00/min
[2890000], rate=28900000.00/min
[2900000], rate=29000000.00/min
[2910000], rate=29100000.00/min
[2920000], rate=29200000.00/min
[2930000], rate=29300000.00/min
[2940000], rate=29400000.00/min
[2950000], rate=29500000.00/min
[2960000], rate=29600000.00/min
[2970000], rate=29700000.00/min
[2980000], rate=29800000.00/min
[2990000], rate=29900000.00/min
[3000000], rate=30000000.00/min
[3010000], rate=30100000.00/min
[3020000], rate=30200000.00/min
[3030000], rate=30300000.00/min
[3040000], rate=30400000.00/min
[3050000], rate=30500000.00/min
[3060000], rate=30600000.00/min
[3070000], rate=30700000.00/min
[3080000], rate=30800000.00/min
[3090000], rate=30900000.00/min
[3100000], rate=31000000.00/min
[3110000], rate=31100000.00/min
[3120000], rate=31200000.00/min
[3130000], rate=26828571.43/min
[3140000], rate=26914285.71/min
[3150000], rate=27000000.00/min
[3160000], rate=27085714.29/min
[3170000], rate=27171428.57/min
[3180000], rate=27257142.86/min
[3190000], rate=27342857.14/min
[3200000], rate=27428571.43/min
[3210000], rate=27514285.71/min
[3220000], rate=27600000.00/min
[3230000], rate=27685714.29/min
[3240000], rate=27771428.57/min
[3250000], rate=27857142.86/min
[3260000], rate=27942857.14/min
[3270000], rate=28028571.43/min
[3280000], rate=28114285.71/min
[3290000], rate=28200000.00/min
[3300000], rate=28285714.29/min
[3310000], rate=28371428.57/min
[3320000], rate=28457142.86/min
[3330000], rate=28542857.14/min
[3340000], rate=28628571.43/min
[3350000], rate=28714285.71/min
[3360000], rate=28800000.00/min
[3370000], rate=28885714.29/min
[3380000], rate=28971428.57/min
[3390000], rate=29057142.86/min
[3400000], rate=29142857.14/min
[3410000], rate=29228571.43/min
[3420000], rate=29314285.71/min
[3430000], rate=29400000.00/min
[3440000], rate=29485714.29/min
[3450000], rate=29571428.57/min
[3460000], rate=29657142.86/min
[3470000], rate=29742857.14/min
[3480000], rate=29828571.43/min
[3490000], rate=29914285.71/min
[3500000], rate=30000000.00/min
[3510000], rate=30085714.29/min
[3520000], rate=30171428.57/min
[3530000], rate=30257142.86/min
[3540000], rate=30342857.14/min
[3550000], rate=30428571.43/min
[3560000], rate=30514285.71/min
[3570000], rate=30600000.00/min
[3580000], rate=30685714.29/min
[3590000], rate=30771428.57/min
[3600000], rate=30857142.86/min
[3610000], rate=30942857.14/min
[3620000], rate=31028571.43/min
[3630000], rate=31114285.71/min
[3640000], rate=31200000.00/min
[3650000], rate=31285714.29/min
[3660000], rate=27450000.00/min
[3670000], rate=27525000.00/min
[3680000], rate=27600000.00/min
[3690000], rate=27675000.00/min
[3700000], rate=27750000.00/min
[3710000], rate=27825000.00/min
[3720000], rate=27900000.00/min
[3730000], rate=27975000.00/min
[3740000], rate=28050000.00/min
[3750000], rate=28125000.00/min
[3760000], rate=28200000.00/min
[3770000], rate=28275000.00/min
[3780000], rate=28350000.00/min
[3790000], rate=28425000.00/min
[3800000], rate=28500000.00/min
[3810000], rate=28575000.00/min
[3820000], rate=28650000.00/min
[3830000], rate=28725000.00/min
[3840000], rate=28800000.00/min
[3850000], rate=28875000.00/min
[3860000], rate=28950000.00/min
[3870000], rate=29025000.00/min
[3880000], rate=29100000.00/min
[3890000], rate=29175000.00/min
[3900000], rate=29250000.00/min
[3910000], rate=29325000.00/min
[3920000], rate=29400000.00/min
[3930000], rate=29475000.00/min
[3940000], rate=29550000.00/min
[3950000], rate=29625000.00/min
[3960000], rate=29700000.00/min
[3970000], rate=29775000.00/min
[3980000], rate=29850000.00/min
[3990000], rate=29925000.00/min
[4000000], rate=30000000.00/min
[4010000], rate=30075000.00/min
[4020000], rate=30150000.00/min
[4030000], rate=30225000.00/min
[4040000], rate=30300000.00/min
[4050000], rate=30375000.00/min
[4060000], rate=30450000.00/min
[4070000], rate=30525000.00/min
[4080000], rate=30600000.00/min
[4090000], rate=30675000.00/min
[4100000], rate=30750000.00/min
[4110000], rate=30825000.00/min
[4120000], rate=30900000.00/min
[4130000], rate=30975000.00/min
[4140000], rate=27600000.00/min
[4150000], rate=27666666.67/min
[4160000], rate=27733333.33/min
[4170000], rate=27800000.00/min
[4180000], rate=27866666.67/min
[4190000], rate=27933333.33/min
[4200000], rate=28000000.00/min
[4210000], rate=28066666.67/min
[4220000], rate=28133333.33/min
[4230000], rate=28200000.00/min
[4240000], rate=28266666.67/min
[4250000], rate=28333333.33/min
[4260000], rate=28400000.00/min
[4270000], rate=28466666.67/min
[4280000], rate=28533333.33/min
[4290000], rate=28600000.00/min
[4300000], rate=28666666.67/min
[4310000], rate=28733333.33/min
[4320000], rate=28800000.00/min
[4330000], rate=28866666.67/min
[4340000], rate=28933333.33/min
[4350000], rate=29000000.00/min
[4360000], rate=29066666.67/min
[4370000], rate=29133333.33/min
[4380000], rate=29200000.00/min
[4390000], rate=29266666.67/min
[4400000], rate=29333333.33/min
[4410000], rate=29400000.00/min
[4420000], rate=29466666.67/min
[4430000], rate=29533333.33/min
[4440000], rate=29600000.00/min
[4450000], rate=29666666.67/min
[4460000], rate=29733333.33/min
[4470000], rate=29800000.00/min
[4480000], rate=29866666.67/min
[4490000], rate=29933333.33/min
[4500000], rate=30000000.00/min
[4510000], rate=30066666.67/min
[4520000], rate=30133333.33/min
[4530000], rate=30200000.00/min
[4540000], rate=30266666.67/min
[4550000], rate=30333333.33/min
[4560000], rate=30400000.00/min
[4570000], rate=30466666.67/min
[4580000], rate=30533333.33/min
[4590000], rate=30600000.00/min
[4600000], rate=30666666.67/min
[4610000], rate=30733333.33/min
[4620000], rate=30800000.00/min
[4630000], rate=30866666.67/min
[4640000], rate=30933333.33/min
[4650000], rate=31000000.00/min
[4660000], rate=31066666.67/min
[4670000], rate=28020000.00/min
[4680000], rate=28080000.00/min
[4690000], rate=28140000.00/min
[4700000], rate=28200000.00/min
[4710000], rate=28260000.00/min
[4720000], rate=28320000.00/min
[4730000], rate=28380000.00/min
[4740000], rate=28440000.00/min
[4750000], rate=28500000.00/min
[4760000], rate=28560000.00/min
[4770000], rate=28620000.00/min
[4780000], rate=28680000.00/min
[4790000], rate=28740000.00/min
[4800000], rate=28800000.00/min
[4810000], rate=28860000.00/min
[4820000], rate=28920000.00/min
[4830000], rate=28980000.00/min
[4840000], rate=29040000.00/min
[4850000], rate=29100000.00/min
[4860000], rate=29160000.00/min
[4870000], rate=29220000.00/min
[4880000], rate=29280000.00/min
[4890000], rate=29340000.00/min
[4900000], rate=29400000.00/min
[4910000], rate=29460000.00/min
[4920000], rate=29520000.00/min
[4930000], rate=29580000.00/min
[4940000], rate=29640000.00/min
[4950000], rate=29700000.00/min
[4960000], rate=29760000.00/min
[4970000], rate=29820000.00/min
[4980000], rate=29880000.00/min
[4990000], rate=29940000.00/min
[5000000], rate=30000000.00/min
[5010000], rate=30060000.00/min
[5020000], rate=30120000.00/min
[5030000], rate=30180000.00/min
[5040000], rate=30240000.00/min
[5050000], rate=30300000.00/min
[5060000], rate=30360000.00/min
[5070000], rate=30420000.00/min
[5080000], rate=30480000.00/min
[5090000], rate=30540000.00/min
[5100000], rate=30600000.00/min
[5110000], rate=30660000.00/min
[5120000], rate=30720000.00/min
[5130000], rate=30780000.00/min
[5140000], rate=30840000.00/min
[5150000], rate=30900000.00/min
[5160000], rate=30960000.00/min
[5170000], rate=31020000.00/min
[5180000], rate=31080000.00/min
[5190000], rate=28309090.91/min
[5200000], rate=28363636.36/min
[5210000], rate=28418181.82/min
[5220000], rate=28472727.27/min
[5230000], rate=28527272.73/min
[5240000], rate=28581818.18/min
[5250000], rate=28636363.64/min
[5260000], rate=28690909.09/min
[5270000], rate=28745454.55/min
[5280000], rate=28800000.00/min
[5290000], rate=28854545.45/min
[5300000], rate=28909090.91/min
[5310000], rate=28963636.36/min
[5320000], rate=29018181.82/min
[5330000], rate=29072727.27/min
[5340000], rate=29127272.73/min
[5350000], rate=29181818.18/min
[5360000], rate=29236363.64/min
[5370000], rate=29290909.09/min
[5380000], rate=29345454.55/min
[5390000], rate=29400000.00/min
[5400000], rate=29454545.45/min
[5410000], rate=29509090.91/min
[5420000], rate=29563636.36/min
[5430000], rate=29618181.82/min
[5440000], rate=29672727.27/min
[5450000], rate=29727272.73/min
[5460000], rate=29781818.18/min
[5470000], rate=29836363.64/min
[5480000], rate=29890909.09/min
[5490000], rate=29945454.55/min
[5500000], rate=30000000.00/min
[5510000], rate=30054545.45/min
[5520000], rate=30109090.91/min
[5530000], rate=30163636.36/min
[5540000], rate=30218181.82/min
[5550000], rate=30272727.27/min
[5560000], rate=30327272.73/min
[5570000], rate=30381818.18/min
[5580000], rate=30436363.64/min
[5590000], rate=30490909.09/min
[5600000], rate=30545454.55/min
[5610000], rate=30600000.00/min
[5620000], rate=30654545.45/min
[5630000], rate=30709090.91/min
[5640000], rate=30763636.36/min
[5650000], rate=30818181.82/min
[5660000], rate=30872727.27/min
[5670000], rate=30927272.73/min
[5680000], rate=28400000.00/min
[5690000], rate=28450000.00/min
[5700000], rate=28500000.00/min
[5710000], rate=28550000.00/min
[5720000], rate=28600000.00/min
[5730000], rate=28650000.00/min
[5740000], rate=28700000.00/min
[5750000], rate=28750000.00/min
[5760000], rate=28800000.00/min
[5770000], rate=28850000.00/min
[5780000], rate=28900000.00/min
[5790000], rate=28950000.00/min
[5800000], rate=29000000.00/min
[5810000], rate=29050000.00/min
[5820000], rate=29100000.00/min
[5830000], rate=29150000.00/min
[5840000], rate=29200000.00/min
[5850000], rate=29250000.00/min
[5860000], rate=29300000.00/min
[5870000], rate=29350000.00/min
[5880000], rate=29400000.00/min
[5890000], rate=29450000.00/min
[5900000], rate=29500000.00/min
[5910000], rate=29550000.00/min
[5920000], rate=29600000.00/min
[5930000], rate=29650000.00/min
[5940000], rate=29700000.00/min
[5950000], rate=29750000.00/min
[5960000], rate=29800000.00/min
[5970000], rate=29850000.00/min
[5980000], rate=29900000.00/min
[5990000], rate=29950000.00/min
[6000000], rate=30000000.00/min
[6010000], rate=30050000.00/min
[6020000], rate=30100000.00/min
[6030000], rate=27830769.23/min
[6040000], rate=27876923.08/min
[6050000], rate=27923076.92/min
[6060000], rate=27969230.77/min
[6070000], rate=28015384.62/min
[6080000], rate=28061538.46/min
[6090000], rate=28107692.31/min
[6100000], rate=28153846.15/min
[6110000], rate=28200000.00/min
[6120000], rate=28246153.85/min
[6130000], rate=28292307.69/min
[6140000], rate=28338461.54/min
[6150000], rate=28384615.38/min
[6160000], rate=28430769.23/min
[6170000], rate=28476923.08/min
[6180000], rate=28523076.92/min
[6190000], rate=28569230.77/min
[6200000], rate=28615384.62/min
[6210000], rate=28661538.46/min
[6220000], rate=28707692.31/min
[6230000], rate=28753846.15/min
[6240000], rate=28800000.00/min
[6250000], rate=28846153.85/min
[6260000], rate=28892307.69/min
[6270000], rate=28938461.54/min
[6280000], rate=28984615.38/min
[6290000], rate=29030769.23/min
[6300000], rate=29076923.08/min
[6310000], rate=29123076.92/min
[6320000], rate=29169230.77/min
[6330000], rate=29215384.62/min
[6340000], rate=29261538.46/min
[6350000], rate=29307692.31/min
[6360000], rate=29353846.15/min
[6370000], rate=29400000.00/min
[6380000], rate=29446153.85/min
[6390000], rate=29492307.69/min
[6400000], rate=29538461.54/min
[6410000], rate=29584615.38/min
[6420000], rate=29630769.23/min
[6430000], rate=29676923.08/min
[6440000], rate=29723076.92/min
[6450000], rate=29769230.77/min
[6460000], rate=27685714.29/min
[6470000], rate=27728571.43/min
[6480000], rate=27771428.57/min
[6490000], rate=27814285.71/min
[6500000], rate=27857142.86/min
[6510000], rate=27900000.00/min
[6520000], rate=27942857.14/min
[6530000], rate=27985714.29/min
[6540000], rate=28028571.43/min
[6550000], rate=28071428.57/min
[6560000], rate=28114285.71/min
[6570000], rate=28157142.86/min
[6580000], rate=28200000.00/min
[6590000], rate=28242857.14/min
[6600000], rate=28285714.29/min
[6610000], rate=28328571.43/min
[6620000], rate=28371428.57/min
[6630000], rate=28414285.71/min
[6640000], rate=28457142.86/min
[6650000], rate=28500000.00/min
[6660000], rate=28542857.14/min
[6670000], rate=28585714.29/min
[6680000], rate=28628571.43/min
[6690000], rate=28671428.57/min
[6700000], rate=28714285.71/min
[6710000], rate=28757142.86/min
[6720000], rate=28800000.00/min
[6730000], rate=28842857.14/min
[6740000], rate=28885714.29/min
[6750000], rate=28928571.43/min
[6760000], rate=28971428.57/min
[6770000], rate=29014285.71/min
[6780000], rate=29057142.86/min
[6790000], rate=29100000.00/min
[6800000], rate=29142857.14/min
[6810000], rate=29185714.29/min
[6820000], rate=29228571.43/min
[6830000], rate=29271428.57/min
[6840000], rate=29314285.71/min
[6850000], rate=29357142.86/min
[6860000], rate=29400000.00/min
[6870000], rate=29442857.14/min
[6880000], rate=29485714.29/min
[6890000], rate=29528571.43/min
[6900000], rate=29571428.57/min
[6910000], rate=29614285.71/min
[6920000], rate=29657142.86/min
[6930000], rate=29700000.00/min
[6940000], rate=29742857.14/min
[6950000], rate=29785714.29/min
[6960000], rate=29828571.43/min
[6970000], rate=29871428.57/min
[6980000], rate=29914285.71/min
[6990000], rate=29957142.86/min
[7000000], rate=30000000.00/min
[7010000], rate=30042857.14/min
[7020000], rate=30085714.29/min
[7030000], rate=30128571.43/min
[7040000], rate=30171428.57/min
[7050000], rate=28200000.00/min
[7060000], rate=28240000.00/min
[7070000], rate=28280000.00/min
[7080000], rate=28320000.00/min
[7090000], rate=28360000.00/min
[7100000], rate=28400000.00/min
[7110000], rate=28440000.00/min
[7120000], rate=28480000.00/min
[7130000], rate=28520000.00/min
[7140000], rate=28560000.00/min
[7150000], rate=28600000.00/min
[7160000], rate=28640000.00/min
[7170000], rate=28680000.00/min
[7180000], rate=28720000.00/min
[7190000], rate=28760000.00/min
[7200000], rate=28800000.00/min
[7210000], rate=28840000.00/min
[7220000], rate=28880000.00/min
[7230000], rate=28920000.00/min
[7240000], rate=28960000.00/min
[7250000], rate=29000000.00/min
[7260000], rate=29040000.00/min
[7270000], rate=29080000.00/min
[7280000], rate=29120000.00/min
[7290000], rate=29160000.00/min
[7300000], rate=29200000.00/min
[7310000], rate=29240000.00/min
[7320000], rate=29280000.00/min
[7330000], rate=29320000.00/min
[7340000], rate=29360000.00/min
[7350000], rate=29400000.00/min
[7360000], rate=29440000.00/min
[7370000], rate=29480000.00/min
[7380000], rate=29520000.00/min
[7390000], rate=29560000.00/min
[7400000], rate=29600000.00/min
[7410000], rate=29640000.00/min
[7420000], rate=29680000.00/min
[7430000], rate=29720000.00/min
[7440000], rate=29760000.00/min
[7450000], rate=29800000.00/min
[7460000], rate=29840000.00/min
[7470000], rate=29880000.00/min
[7480000], rate=29920000.00/min
[7490000], rate=29960000.00/min
[7500000], rate=30000000.00/min
[7510000], rate=28162500.00/min
[7520000], rate=28200000.00/min
[7530000], rate=28237500.00/min
[7540000], rate=28275000.00/min
[7550000], rate=28312500.00/min
[7560000], rate=28350000.00/min
[7570000], rate=28387500.00/min
[7580000], rate=28425000.00/min
[7590000], rate=28462500.00/min
[7600000], rate=28500000.00/min
[7610000], rate=28537500.00/min
[7620000], rate=28575000.00/min
[7630000], rate=28612500.00/min
[7640000], rate=28650000.00/min
[7650000], rate=28687500.00/min
[7660000], rate=28725000.00/min
[7670000], rate=28762500.00/min
[7680000], rate=28800000.00/min
[7690000], rate=28837500.00/min
[7700000], rate=28875000.00/min
[7710000], rate=28912500.00/min
[7720000], rate=28950000.00/min
[7730000], rate=28987500.00/min
[7740000], rate=29025000.00/min
[7750000], rate=29062500.00/min
[7760000], rate=29100000.00/min
[7770000], rate=29137500.00/min
[7780000], rate=29175000.00/min
[7790000], rate=29212500.00/min
[7800000], rate=29250000.00/min
[7810000], rate=29287500.00/min
[7820000], rate=29325000.00/min
[7830000], rate=29362500.00/min
[7840000], rate=29400000.00/min
[7850000], rate=29437500.00/min
[7860000], rate=29475000.00/min
[7870000], rate=29512500.00/min
[7880000], rate=29550000.00/min
[7890000], rate=29587500.00/min
[7900000], rate=29625000.00/min
[7910000], rate=29662500.00/min
[7920000], rate=29700000.00/min
[7930000], rate=29737500.00/min
[7940000], rate=29775000.00/min
[7950000], rate=29812500.00/min
[7960000], rate=29850000.00/min
[7970000], rate=29887500.00/min
[7980000], rate=29925000.00/min
[7990000], rate=29962500.00/min
[8000000], rate=30000000.00/min
[8010000], rate=30037500.00/min
[8020000], rate=30075000.00/min
[8030000], rate=28341176.47/min
[8040000], rate=28376470.59/min
[8050000], rate=28411764.71/min
[8060000], rate=28447058.82/min
[8070000], rate=28482352.94/min
[8080000], rate=28517647.06/min
[8090000], rate=28552941.18/min
[8100000], rate=28588235.29/min
[8110000], rate=28623529.41/min
[8120000], rate=28658823.53/min
[8130000], rate=28694117.65/min
[8140000], rate=28729411.76/min
[8150000], rate=28764705.88/min
[8160000], rate=28800000.00/min
[8170000], rate=28835294.12/min
[8180000], rate=28870588.24/min
[8190000], rate=28905882.35/min
[8200000], rate=28941176.47/min
[8210000], rate=28976470.59/min
[8220000], rate=29011764.71/min
[8230000], rate=29047058.82/min
[8240000], rate=29082352.94/min
[8250000], rate=29117647.06/min
[8260000], rate=29152941.18/min
[8270000], rate=29188235.29/min
[8280000], rate=29223529.41/min
[8290000], rate=29258823.53/min
[8300000], rate=29294117.65/min
[8310000], rate=29329411.76/min
[8320000], rate=29364705.88/min
[8330000], rate=29400000.00/min
[8340000], rate=29435294.12/min
[8350000], rate=29470588.24/min
[8360000], rate=29505882.35/min
[8370000], rate=29541176.47/min
[8380000], rate=29576470.59/min
[8390000], rate=29611764.71/min
[8400000], rate=29647058.82/min
[8410000], rate=29682352.94/min
[8420000], rate=29717647.06/min
[8430000], rate=29752941.18/min
[8440000], rate=29788235.29/min
[8450000], rate=29823529.41/min
[8460000], rate=29858823.53/min
[8470000], rate=29894117.65/min
[8480000], rate=29929411.76/min
[8490000], rate=29964705.88/min
[8500000], rate=30000000.00/min
[8510000], rate=30035294.12/min
[8520000], rate=30070588.24/min
[8530000], rate=30105882.35/min
[8540000], rate=28466666.67/min
[8550000], rate=28500000.00/min
[8560000], rate=28533333.33/min
[8570000], rate=28566666.67/min
[8580000], rate=28600000.00/min
[8590000], rate=28633333.33/min
[8600000], rate=28666666.67/min
[8610000], rate=28700000.00/min
[8620000], rate=28733333.33/min
[8630000], rate=28766666.67/min
[8640000], rate=28800000.00/min
[8650000], rate=28833333.33/min
[8660000], rate=28866666.67/min
[8670000], rate=28900000.00/min
[8680000], rate=28933333.33/min
[8690000], rate=28966666.67/min
[8700000], rate=29000000.00/min
[8710000], rate=29033333.33/min
[8720000], rate=29066666.67/min
[8730000], rate=29100000.00/min
[8740000], rate=29133333.33/min
[8750000], rate=29166666.67/min
[8760000], rate=29200000.00/min
[8770000], rate=29233333.33/min
[8780000], rate=29266666.67/min
[8790000], rate=29300000.00/min
[8800000], rate=29333333.33/min
[8810000], rate=29366666.67/min
[8820000], rate=29400000.00/min
[8830000], rate=29433333.33/min
[8840000], rate=29466666.67/min
[8850000], rate=29500000.00/min
[8860000], rate=29533333.33/min
[8870000], rate=29566666.67/min
[8880000], rate=29600000.00/min
[8890000], rate=29633333.33/min
[8900000], rate=29666666.67/min
[8910000], rate=29700000.00/min
[8920000], rate=29733333.33/min
[8930000], rate=29766666.67/min
[8940000], rate=29800000.00/min
[8950000], rate=29833333.33/min
[8960000], rate=29866666.67/min
[8970000], rate=29900000.00/min
[8980000], rate=29933333.33/min
[8990000], rate=29966666.67/min
[9000000], rate=30000000.00/min
[9010000], rate=30033333.33/min
[9020000], rate=30066666.67/min
[9030000], rate=30100000.00/min
[9040000], rate=30133333.33/min
[9050000], rate=30166666.67/min
[9060000], rate=30200000.00/min
[9070000], rate=28642105.26/min
[9080000], rate=28673684.21/min
[9090000], rate=28705263.16/min
[9100000], rate=28736842.11/min
[9110000], rate=28768421.05/min
[9120000], rate=28800000.00/min
[9130000], rate=28831578.95/min
[9140000], rate=28863157.89/min
[9150000], rate=28894736.84/min
[9160000], rate=28926315.79/min
[9170000], rate=28957894.74/min
[9180000], rate=28989473.68/min
[9190000], rate=29021052.63/min
[9200000], rate=29052631.58/min
[9210000], rate=29084210.53/min
[9220000], rate=29115789.47/min
[9230000], rate=29147368.42/min
[9240000], rate=29178947.37/min
[9250000], rate=29210526.32/min
[9260000], rate=29242105.26/min
[9270000], rate=29273684.21/min
[9280000], rate=29305263.16/min
[9290000], rate=29336842.11/min
[9300000], rate=29368421.05/min
[9310000], rate=29400000.00/min
[9320000], rate=29431578.95/min
[9330000], rate=29463157.89/min
[9340000], rate=29494736.84/min
[9350000], rate=29526315.79/min
[9360000], rate=29557894.74/min
[9370000], rate=29589473.68/min
[9380000], rate=29621052.63/min
[9390000], rate=29652631.58/min
[9400000], rate=29684210.53/min
[9410000], rate=29715789.47/min
[9420000], rate=29747368.42/min
[9430000], rate=29778947.37/min
[9440000], rate=29810526.32/min
[9450000], rate=29842105.26/min
[9460000], rate=29873684.21/min
[9470000], rate=29905263.16/min
[9480000], rate=29936842.11/min
[9490000], rate=29968421.05/min
[9500000], rate=30000000.00/min
[9510000], rate=30031578.95/min
[9520000], rate=30063157.89/min
[9530000], rate=30094736.84/min
[9540000], rate=30126315.79/min
[9550000], rate=30157894.74/min
[9560000], rate=30189473.68/min
[9570000], rate=30221052.63/min
[9580000], rate=30252631.58/min
[9590000], rate=30284210.53/min
[9600000], rate=30315789.47/min
[9610000], rate=30347368.42/min
[9620000], rate=28860000.00/min
[9630000], rate=28890000.00/min
[9640000], rate=28920000.00/min
[9650000], rate=28950000.00/min
[9660000], rate=28980000.00/min
[9670000], rate=29010000.00/min
[9680000], rate=29040000.00/min
[9690000], rate=29070000.00/min
[9700000], rate=29100000.00/min
[9710000], rate=29130000.00/min
[9720000], rate=29160000.00/min
[9730000], rate=29190000.00/min
[9740000], rate=29220000.00/min
[9750000], rate=29250000.00/min
[9760000], rate=29280000.00/min
[9770000], rate=29310000.00/min
[9780000], rate=29340000.00/min
[9790000], rate=29370000.00/min
[9800000], rate=29400000.00/min
[9810000], rate=29430000.00/min
[9820000], rate=29460000.00/min
[9830000], rate=29490000.00/min
[9840000], rate=29520000.00/min
[9850000], rate=29550000.00/min
[9860000], rate=29580000.00/min
[9870000], rate=29610000.00/min
[9880000], rate=29640000.00/min
[9890000], rate=29670000.00/min
[9900000], rate=29700000.00/min
[9910000], rate=29730000.00/min
[9920000], rate=29760000.00/min
[9930000], rate=29790000.00/min
[9940000], rate=29820000.00/min
[9950000], rate=29850000.00/min
[9960000], rate=29880000.00/min
[9970000], rate=29910000.00/min
[9980000], rate=29940000.00/min
[9990000], rate=29970000.00/min
[10000000], rate=30000000.00/min
[10010000], rate=30030000.00/min
[10020000], rate=30060000.00/min
[10030000], rate=30090000.00/min
[10040000], rate=30120000.00/min
[10050000], rate=30150000.00/min
[10060000], rate=30180000.00/min
[10070000], rate=30210000.00/min
[10080000], rate=30240000.00/min
[10090000], rate=30270000.00/min
[10100000], rate=30300000.00/min
[10110000], rate=30330000.00/min
[10120000], rate=30360000.00/min
[10130000], rate=30390000.00/min
[10140000], rate=28971428.57/min
[10150000], rate=29000000.00/min
[10160000], rate=29028571.43/min
[10170000], rate=29057142.86/min
[10180000], rate=29085714.29/min
[10190000], rate=29114285.71/min
[10200000], rate=29142857.14/min
[10210000], rate=29171428.57/min
[10220000], rate=29200000.00/min 09:12:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3376ed-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3376ed-R1_B23WHYVLT4_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.
-aih-tih-sc-3376ed-R1_B23WHYVLT4_1.introns: identified 7646 cancer introns
09:12:03 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3376ed-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer.introns.prelim
09:12:03 : INFO : Running: touch /tmp/nxf.WY5AB1kHbJ/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok
09:12:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer.introns
09:12:03 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer.introns
09:12:03 : INFO : Running: touch /tmp/nxf.WY5AB1kHbJ/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok
09:12:03 : INFO : -found 4026 cancer introns
09:12:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3376ed-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3376ed-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:12:04 : INFO : Creating the BED File.
09:12:08 : INFO : Saving Bed File as aih-tih-sc-3376ed-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:12:08 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3376ed-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3376ed-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:12:08 : INFO : Running: touch /tmp/nxf.WY5AB1kHbJ/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok
09:12:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3376ed-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-3376ed-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3376ed-R1_B23WHYVLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
09:28:51 : INFO : Execution Time = 16.72 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3376ed-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-3376ed-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3376ed-R1_B23WHYVLT4_1
09:28:51 : INFO : Running: touch /tmp/nxf.WY5AB1kHbJ/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.chckpts/reads_alignments_extracted.ok
09:28:51 : INFO : Running: samtools sort -o aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer_intron_reads.bam
09:28:52 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3376ed-R1_B23WHYVLT4_1.cancer_intron_reads.bam
09:28:52 : INFO : Running: touch /tmp/nxf.WY5AB1kHbJ/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.chckpts/sort_cancer_intron_reads.ok
09:28:52 : INFO : Running: samtools sort -o aih-tih-sc-3376ed-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-3376ed-R1_B23WHYVLT4_1.gene_reads.bam
[bam_sort_core] merging from 142 files and 1 in-memory blocks...