08:03:29 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=13800000.00/min [470000], rate=14100000.00/min [480000], rate=14400000.00/min [490000], rate=14700000.00/min [500000], rate=15000000.00/min [510000], rate=15300000.00/min [520000], rate=15600000.00/min [530000], rate=15900000.00/min [540000], rate=16200000.00/min [550000], rate=16500000.00/min [560000], rate=16800000.00/min [570000], rate=17100000.00/min [580000], rate=17400000.00/min [590000], rate=17700000.00/min [600000], rate=18000000.00/min [610000], rate=18300000.00/min [620000], rate=18600000.00/min [630000], rate=18900000.00/min [640000], rate=19200000.00/min [650000], rate=19500000.00/min [660000], rate=19800000.00/min [670000], rate=20100000.00/min [680000], rate=20400000.00/min [690000], rate=13800000.00/min [700000], rate=14000000.00/min [710000], rate=14200000.00/min [720000], rate=14400000.00/min [730000], rate=14600000.00/min [740000], rate=14800000.00/min [750000], rate=15000000.00/min [760000], rate=15200000.00/min [770000], rate=15400000.00/min [780000], rate=15600000.00/min [790000], rate=15800000.00/min [800000], rate=16000000.00/min [810000], rate=16200000.00/min [820000], rate=16400000.00/min [830000], rate=16600000.00/min [840000], rate=16800000.00/min [850000], rate=17000000.00/min [860000], rate=17200000.00/min [870000], rate=17400000.00/min [880000], rate=17600000.00/min [890000], rate=17800000.00/min [900000], rate=13500000.00/min [910000], rate=13650000.00/min [920000], rate=13800000.00/min [930000], rate=13950000.00/min [940000], rate=14100000.00/min [950000], rate=14250000.00/min [960000], rate=14400000.00/min [970000], rate=14550000.00/min [980000], rate=14700000.00/min [990000], rate=14850000.00/min [1000000], rate=15000000.00/min [1010000], rate=15150000.00/min [1020000], rate=15300000.00/min [1030000], rate=15450000.00/min [1040000], rate=15600000.00/min [1050000], rate=15750000.00/min [1060000], rate=15900000.00/min [1070000], rate=16050000.00/min [1080000], rate=16200000.00/min [1090000], rate=13080000.00/min [1100000], rate=13200000.00/min [1110000], rate=13320000.00/min [1120000], rate=13440000.00/min [1130000], rate=13560000.00/min [1140000], rate=13680000.00/min [1150000], rate=13800000.00/min [1160000], rate=13920000.00/min [1170000], rate=14040000.00/min [1180000], rate=14160000.00/min [1190000], rate=14280000.00/min [1200000], rate=14400000.00/min [1210000], rate=14520000.00/min [1220000], rate=14640000.00/min [1230000], rate=14760000.00/min [1240000], rate=14880000.00/min [1250000], rate=15000000.00/min [1260000], rate=15120000.00/min [1270000], rate=15240000.00/min [1280000], rate=15360000.00/min [1290000], rate=15480000.00/min [1300000], rate=15600000.00/min [1310000], rate=13100000.00/min [1320000], rate=13200000.00/min [1330000], rate=13300000.00/min [1340000], rate=13400000.00/min [1350000], rate=13500000.00/min [1360000], rate=13600000.00/min [1370000], rate=13700000.00/min [1380000], rate=13800000.00/min [1390000], rate=13900000.00/min [1400000], rate=14000000.00/min [1410000], rate=14100000.00/min [1420000], rate=14200000.00/min [1430000], rate=14300000.00/min [1440000], rate=14400000.00/min [1450000], rate=14500000.00/min [1460000], rate=14600000.00/min [1470000], rate=14700000.00/min [1480000], rate=14800000.00/min [1490000], rate=14900000.00/min [1500000], rate=15000000.00/min [1510000], rate=15100000.00/min [1520000], rate=15200000.00/min [1530000], rate=15300000.00/min [1540000], rate=13200000.00/min [1550000], rate=13285714.29/min [1560000], rate=13371428.57/min [1570000], rate=13457142.86/min [1580000], rate=13542857.14/min [1590000], rate=13628571.43/min [1600000], rate=13714285.71/min [1610000], rate=13800000.00/min [1620000], rate=13885714.29/min [1630000], rate=13971428.57/min [1640000], rate=14057142.86/min [1650000], rate=14142857.14/min [1660000], rate=14228571.43/min [1670000], rate=14314285.71/min [1680000], rate=14400000.00/min [1690000], rate=14485714.29/min [1700000], rate=14571428.57/min [1710000], rate=14657142.86/min [1720000], rate=14742857.14/min [1730000], rate=14828571.43/min [1740000], rate=14914285.71/min [1750000], rate=15000000.00/min [1760000], rate=15085714.29/min [1770000], rate=13275000.00/min [1780000], rate=13350000.00/min [1790000], rate=13425000.00/min [1800000], rate=13500000.00/min [1810000], rate=13575000.00/min [1820000], rate=13650000.00/min [1830000], rate=13725000.00/min [1840000], rate=13800000.00/min [1850000], rate=13875000.00/min [1860000], rate=13950000.00/min [1870000], rate=14025000.00/min [1880000], rate=14100000.00/min [1890000], rate=14175000.00/min [1900000], rate=14250000.00/min [1910000], rate=14325000.00/min [1920000], rate=14400000.00/min [1930000], rate=14475000.00/min [1940000], rate=14550000.00/min [1950000], rate=14625000.00/min [1960000], rate=14700000.00/min [1970000], rate=14775000.00/min [1980000], rate=14850000.00/min [1990000], rate=14925000.00/min [2000000], rate=15000000.00/min [2010000], rate=15075000.00/min [2020000], rate=13466666.67/min [2030000], rate=13533333.33/min [2040000], rate=13600000.00/min [2050000], rate=13666666.67/min [2060000], rate=13733333.33/min [2070000], rate=13800000.00/min [2080000], rate=13866666.67/min [2090000], rate=13933333.33/min [2100000], rate=14000000.00/min [2110000], rate=14066666.67/min [2120000], rate=14133333.33/min [2130000], rate=14200000.00/min [2140000], rate=14266666.67/min [2150000], rate=14333333.33/min [2160000], rate=14400000.00/min [2170000], rate=14466666.67/min [2180000], rate=14533333.33/min [2190000], rate=14600000.00/min [2200000], rate=14666666.67/min [2210000], rate=14733333.33/min [2220000], rate=14800000.00/min [2230000], rate=13380000.00/min [2240000], rate=13440000.00/min [2250000], rate=13500000.00/min [2260000], rate=13560000.00/min [2270000], rate=13620000.00/min [2280000], rate=13680000.00/min [2290000], rate=13740000.00/min [2300000], rate=13800000.00/min [2310000], rate=13860000.00/min [2320000], rate=13920000.00/min [2330000], rate=13980000.00/min [2340000], rate=14040000.00/min [2350000], rate=14100000.00/min [2360000], rate=14160000.00/min [2370000], rate=14220000.00/min [2380000], rate=14280000.00/min [2390000], rate=14340000.00/min [2400000], rate=14400000.00/min [2410000], rate=14460000.00/min [2420000], rate=14520000.00/min [2430000], rate=14580000.00/min [2440000], rate=14640000.00/min [2450000], rate=14700000.00/min [2460000], rate=14760000.00/min [2470000], rate=13472727.27/min [2480000], rate=13527272.73/min [2490000], rate=13581818.18/min [2500000], rate=13636363.64/min [2510000], rate=13690909.09/min [2520000], rate=13745454.55/min [2530000], rate=13800000.00/min [2540000], rate=13854545.45/min [2550000], rate=13909090.91/min [2560000], rate=13963636.36/min [2570000], rate=14018181.82/min [2580000], rate=14072727.27/min [2590000], rate=14127272.73/min [2600000], rate=14181818.18/min [2610000], rate=14236363.64/min [2620000], rate=14290909.09/min [2630000], rate=14345454.55/min [2640000], rate=14400000.00/min [2650000], rate=14454545.45/min [2660000], rate=14509090.91/min [2670000], rate=14563636.36/min [2680000], rate=14618181.82/min [2690000], rate=14672727.27/min [2700000], rate=14727272.73/min [2710000], rate=13550000.00/min [2720000], rate=13600000.00/min [2730000], rate=13650000.00/min [2740000], rate=13700000.00/min [2750000], rate=13750000.00/min [2760000], rate=13800000.00/min [2770000], rate=13850000.00/min [2780000], rate=13900000.00/min [2790000], rate=13950000.00/min [2800000], rate=14000000.00/min [2810000], rate=14050000.00/min [2820000], rate=14100000.00/min [2830000], rate=14150000.00/min [2840000], rate=14200000.00/min [2850000], rate=14250000.00/min [2860000], rate=14300000.00/min [2870000], rate=14350000.00/min [2880000], rate=14400000.00/min [2890000], rate=14450000.00/min [2900000], rate=13384615.38/min [2910000], rate=13430769.23/min [2920000], rate=13476923.08/min [2930000], rate=13523076.92/min [2940000], rate=13569230.77/min [2950000], rate=13615384.62/min [2960000], rate=13661538.46/min [2970000], rate=13707692.31/min [2980000], rate=13753846.15/min [2990000], rate=13800000.00/min [3000000], rate=13846153.85/min [3010000], rate=13892307.69/min [3020000], rate=13938461.54/min [3030000], rate=13984615.38/min [3040000], rate=14030769.23/min [3050000], rate=14076923.08/min [3060000], rate=13114285.71/min [3070000], rate=13157142.86/min [3080000], rate=13200000.00/min [3090000], rate=13242857.14/min [3100000], rate=13285714.29/min [3110000], rate=13328571.43/min [3120000], rate=13371428.57/min [3130000], rate=13414285.71/min [3140000], rate=13457142.86/min [3150000], rate=13500000.00/min [3160000], rate=13542857.14/min [3170000], rate=13585714.29/min [3180000], rate=13628571.43/min [3190000], rate=13671428.57/min [3200000], rate=13714285.71/min [3210000], rate=13757142.86/min [3220000], rate=13800000.00/min [3230000], rate=13842857.14/min [3240000], rate=13885714.29/min [3250000], rate=13928571.43/min [3260000], rate=13971428.57/min [3270000], rate=14014285.71/min [3280000], rate=14057142.86/min [3290000], rate=14100000.00/min [3300000], rate=14142857.14/min [3310000], rate=14185714.29/min [3320000], rate=13280000.00/min [3330000], rate=13320000.00/min [3340000], rate=13360000.00/min [3350000], rate=13400000.00/min [3360000], rate=13440000.00/min [3370000], rate=13480000.00/min [3380000], rate=13520000.00/min [3390000], rate=13560000.00/min [3400000], rate=13600000.00/min [3410000], rate=13640000.00/min [3420000], rate=13680000.00/min [3430000], rate=13720000.00/min [3440000], rate=13760000.00/min [3450000], rate=13800000.00/min [3460000], rate=13840000.00/min [3470000], rate=13880000.00/min [3480000], rate=13920000.00/min [3490000], rate=13960000.00/min [3500000], rate=14000000.00/min [3510000], rate=14040000.00/min [3520000], rate=14080000.00/min [3530000], rate=14120000.00/min [3540000], rate=14160000.00/min [3550000], rate=14200000.00/min [3560000], rate=13350000.00/min [3570000], rate=13387500.00/min [3580000], rate=13425000.00/min [3590000], rate=13462500.00/min [3600000], rate=13500000.00/min [3610000], rate=13537500.00/min [3620000], rate=13575000.00/min [3630000], rate=13612500.00/min [3640000], rate=13650000.00/min [3650000], rate=13687500.00/min [3660000], rate=13725000.00/min [3670000], rate=13762500.00/min [3680000], rate=13800000.00/min [3690000], rate=13837500.00/min [3700000], rate=13875000.00/min [3710000], rate=13912500.00/min [3720000], rate=13950000.00/min [3730000], rate=13987500.00/min [3740000], rate=14025000.00/min [3750000], rate=14062500.00/min [3760000], rate=14100000.00/min [3770000], rate=14137500.00/min [3780000], rate=14175000.00/min [3790000], rate=14212500.00/min [3800000], rate=13411764.71/min [3810000], rate=13447058.82/min [3820000], rate=13482352.94/min [3830000], rate=13517647.06/min [3840000], rate=13552941.18/min [3850000], rate=13588235.29/min [3860000], rate=13623529.41/min [3870000], rate=13658823.53/min [3880000], rate=13694117.65/min [3890000], rate=13729411.76/min [3900000], rate=13764705.88/min [3910000], rate=13800000.00/min [3920000], rate=13835294.12/min [3930000], rate=13870588.24/min [3940000], rate=13905882.35/min [3950000], rate=13941176.47/min [3960000], rate=13976470.59/min [3970000], rate=14011764.71/min [3980000], rate=14047058.82/min [3990000], rate=14082352.94/min [4000000], rate=14117647.06/min [4010000], rate=14152941.18/min [4020000], rate=14188235.29/min [4030000], rate=14223529.41/min [4040000], rate=13466666.67/min [4050000], rate=13500000.00/min [4060000], rate=13533333.33/min [4070000], rate=13566666.67/min [4080000], rate=13600000.00/min [4090000], rate=13633333.33/min [4100000], rate=13666666.67/min [4110000], rate=13700000.00/min [4120000], rate=13733333.33/min [4130000], rate=13766666.67/min [4140000], rate=13800000.00/min [4150000], rate=13833333.33/min [4160000], rate=13866666.67/min [4170000], rate=13900000.00/min [4180000], rate=13933333.33/min [4190000], rate=13966666.67/min [4200000], rate=14000000.00/min [4210000], rate=14033333.33/min [4220000], rate=14066666.67/min [4230000], rate=14100000.00/min [4240000], rate=14133333.33/min [4250000], rate=14166666.67/min [4260000], rate=14200000.00/min [4270000], rate=13484210.53/min [4280000], rate=13515789.47/min [4290000], rate=13547368.42/min [4300000], rate=13578947.37/min [4310000], rate=13610526.32/min [4320000], rate=13642105.26/min [4330000], rate=13673684.21/min [4340000], rate=13705263.16/min [4350000], rate=13736842.11/min [4360000], rate=13768421.05/min [4370000], rate=13800000.00/min [4380000], rate=13831578.95/min [4390000], rate=13863157.89/min [4400000], rate=13894736.84/min [4410000], rate=13926315.79/min [4420000], rate=13957894.74/min [4430000], rate=13989473.68/min [4440000], rate=14021052.63/min [4450000], rate=14052631.58/min [4460000], rate=13380000.00/min [4470000], rate=13410000.00/min [4480000], rate=13440000.00/min [4490000], rate=13470000.00/min [4500000], rate=13500000.00/min [4510000], rate=13530000.00/min [4520000], rate=13560000.00/min [4530000], rate=13590000.00/min [4540000], rate=13620000.00/min [4550000], rate=13650000.00/min [4560000], rate=13680000.00/min [4570000], rate=13710000.00/min [4580000], rate=13740000.00/min [4590000], rate=13770000.00/min [4600000], rate=13800000.00/min [4610000], rate=13830000.00/min [4620000], rate=13860000.00/min [4630000], rate=13890000.00/min [4640000], rate=13920000.00/min [4650000], rate=13950000.00/min [4660000], rate=13980000.00/min [4670000], rate=14010000.00/min [4680000], rate=14040000.00/min [4690000], rate=13400000.00/min [4700000], rate=13428571.43/min [4710000], rate=13457142.86/min [4720000], rate=13485714.29/min [4730000], rate=13514285.71/min [4740000], rate=13542857.14/min [4750000], rate=13571428.57/min [4760000], rate=13600000.00/min [4770000], rate=13628571.43/min [4780000], rate=13657142.86/min [4790000], rate=13685714.29/min [4800000], rate=13714285.71/min 08:03:59 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-60f9b9-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-60f9b9-R1_B23WHYVLT4_1.introns: identified 3726 cancer introns 08:03:59 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer.introns.prelim 08:03:59 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok 08:03:59 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer.introns 08:04:00 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer.introns 08:04:00 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok 08:04:00 : INFO : -found 1107 cancer introns 08:04:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns.for_IGV.bed 08:04:00 : INFO : Creating the BED File. 08:04:04 : INFO : Saving Bed File as aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns.for_IGV.bed 08:04:04 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns.for_IGV.bed 08:04:04 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok 08:04:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-60f9b9-R1_B23WHYVLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai 08:11:36 : INFO : Execution Time = 7.53 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-60f9b9-R1_B23WHYVLT4_1 08:11:36 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/reads_alignments_extracted.ok 08:11:36 : INFO : Running: samtools sort -o aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer_intron_reads.bam 08:11:36 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer_intron_reads.bam 08:11:36 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/sort_cancer_intron_reads.ok 08:11:36 : INFO : Running: samtools sort -o aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.bam [bam_sort_core] merging from 35 files and 1 in-memory blocks... 08:18:56 : INFO : Execution Time = 7.32 minutes. CMD: samtools sort -o aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.bam 08:18:56 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/sort_gene_reads.ok 08:18:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.bam 08:21:50 : INFO : Execution Time = 2.91 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.bam 08:21:50 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 08:21:50 : INFO : Running: samtools sort -o aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 1 files and 1 in-memory blocks... 08:22:13 : INFO : Execution Time = 0.39 minutes. CMD: samtools sort -o aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp 08:22:13 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:22:13 : INFO : Running: samtools index aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam 08:22:16 : INFO : Execution Time = 0.05 minutes. CMD: samtools index aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam 08:22:16 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 08:22:16 : INFO : Running: samtools index aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam 08:22:16 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam 08:22:16 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 08:22:16 : INFO : Running: create_report aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1' 08:26:29 : INFO : Execution Time = 4.21 minutes. CMD: create_report aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1' 08:26:29 : INFO : Running: touch /tmp/nxf.l4ExSkQqU9/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.chckpts/igv_create_html.ok 08:26:29 : INFO : done.