07:47:20 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [30000], rate=1800000.00/min [40000], rate=2400000.00/min [50000], rate=3000000.00/min [60000], rate=3600000.00/min [70000], rate=4200000.00/min [80000], rate=4800000.00/min [90000], rate=5400000.00/min [100000], rate=6000000.00/min [110000], rate=6600000.00/min [120000], rate=7200000.00/min [130000], rate=7800000.00/min [140000], rate=8400000.00/min [150000], rate=9000000.00/min [160000], rate=9600000.00/min [170000], rate=10200000.00/min [180000], rate=10800000.00/min [190000], rate=11400000.00/min [200000], rate=12000000.00/min [210000], rate=12600000.00/min [220000], rate=13200000.00/min [230000], rate=13800000.00/min [240000], rate=14400000.00/min [250000], rate=7500000.00/min [260000], rate=7800000.00/min [270000], rate=8100000.00/min [280000], rate=8400000.00/min [290000], rate=8700000.00/min [300000], rate=9000000.00/min [310000], rate=9300000.00/min [320000], rate=9600000.00/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=9600000.00/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=9480000.00/min [800000], rate=9600000.00/min [810000], rate=9720000.00/min [820000], rate=9840000.00/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=9500000.00/min [960000], rate=9600000.00/min [970000], rate=9700000.00/min [980000], rate=9800000.00/min [990000], rate=9900000.00/min [1000000], rate=10000000.00/min [1010000], rate=10100000.00/min [1020000], rate=10200000.00/min [1030000], rate=10300000.00/min [1040000], rate=10400000.00/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=9428571.43/min [1110000], rate=9514285.71/min [1120000], rate=9600000.00/min [1130000], rate=9685714.29/min [1140000], rate=9771428.57/min [1150000], rate=9857142.86/min [1160000], rate=9942857.14/min [1170000], rate=10028571.43/min [1180000], rate=10114285.71/min [1190000], rate=10200000.00/min [1200000], rate=10285714.29/min [1210000], rate=10371428.57/min [1220000], rate=10457142.86/min [1230000], rate=10542857.14/min [1240000], rate=10628571.43/min [1250000], rate=9375000.00/min [1260000], rate=9450000.00/min [1270000], rate=9525000.00/min [1280000], rate=9600000.00/min [1290000], rate=9675000.00/min [1300000], rate=9750000.00/min [1310000], rate=9825000.00/min [1320000], rate=9900000.00/min [1330000], rate=9975000.00/min [1340000], rate=10050000.00/min [1350000], rate=10125000.00/min [1360000], rate=10200000.00/min [1370000], rate=10275000.00/min [1380000], rate=10350000.00/min [1390000], rate=9266666.67/min [1400000], rate=9333333.33/min [1410000], rate=9400000.00/min [1420000], rate=9466666.67/min [1430000], rate=9533333.33/min [1440000], rate=9600000.00/min [1450000], rate=9666666.67/min [1460000], rate=9733333.33/min [1470000], rate=9800000.00/min [1480000], rate=9866666.67/min [1490000], rate=9933333.33/min [1500000], rate=10000000.00/min [1510000], rate=10066666.67/min [1520000], rate=10133333.33/min [1530000], rate=10200000.00/min [1540000], rate=9240000.00/min [1550000], rate=9300000.00/min [1560000], rate=9360000.00/min [1570000], rate=9420000.00/min [1580000], rate=9480000.00/min [1590000], rate=9540000.00/min [1600000], rate=9600000.00/min [1610000], rate=9660000.00/min [1620000], rate=9720000.00/min [1630000], rate=9780000.00/min [1640000], rate=9840000.00/min [1650000], rate=9900000.00/min [1660000], rate=9960000.00/min [1670000], rate=10020000.00/min [1680000], rate=10080000.00/min [1690000], rate=10140000.00/min [1700000], rate=10200000.00/min [1710000], rate=9327272.73/min [1720000], rate=9381818.18/min [1730000], rate=9436363.64/min [1740000], rate=9490909.09/min [1750000], rate=9545454.55/min [1760000], rate=9600000.00/min [1770000], rate=9654545.45/min [1780000], rate=9709090.91/min [1790000], rate=9763636.36/min [1800000], rate=9818181.82/min [1810000], rate=9872727.27/min [1820000], rate=9927272.73/min [1830000], rate=9981818.18/min [1840000], rate=10036363.64/min [1850000], rate=10090909.09/min [1860000], rate=10145454.55/min [1870000], rate=10200000.00/min [1880000], rate=10254545.45/min [1890000], rate=10309090.91/min [1900000], rate=10363636.36/min [1910000], rate=10418181.82/min [1920000], rate=10472727.27/min [1930000], rate=9650000.00/min [1940000], rate=9700000.00/min [1950000], rate=9750000.00/min [1960000], rate=9800000.00/min [1970000], rate=9850000.00/min [1980000], rate=9900000.00/min [1990000], rate=9950000.00/min [2000000], rate=10000000.00/min [2010000], rate=10050000.00/min [2020000], rate=10100000.00/min [2030000], rate=10150000.00/min [2040000], rate=10200000.00/min [2050000], rate=10250000.00/min [2060000], rate=10300000.00/min [2070000], rate=10350000.00/min [2080000], rate=10400000.00/min [2090000], rate=10450000.00/min [2100000], rate=10500000.00/min [2110000], rate=10550000.00/min [2120000], rate=10600000.00/min [2130000], rate=10650000.00/min [2140000], rate=10700000.00/min [2150000], rate=10750000.00/min [2160000], rate=10800000.00/min [2170000], rate=10850000.00/min [2180000], rate=10061538.46/min [2190000], rate=10107692.31/min [2200000], rate=10153846.15/min [2210000], rate=10200000.00/min [2220000], rate=10246153.85/min [2230000], rate=10292307.69/min [2240000], rate=10338461.54/min [2250000], rate=10384615.38/min [2260000], rate=10430769.23/min [2270000], rate=10476923.08/min [2280000], rate=10523076.92/min [2290000], rate=10569230.77/min [2300000], rate=10615384.62/min [2310000], rate=10661538.46/min [2320000], rate=10707692.31/min [2330000], rate=10753846.15/min [2340000], rate=10800000.00/min [2350000], rate=10846153.85/min [2360000], rate=10114285.71/min [2370000], rate=10157142.86/min [2380000], rate=10200000.00/min [2390000], rate=10242857.14/min [2400000], rate=10285714.29/min [2410000], rate=10328571.43/min [2420000], rate=10371428.57/min [2430000], rate=10414285.71/min [2440000], rate=10457142.86/min [2450000], rate=10500000.00/min [2460000], rate=10542857.14/min [2470000], rate=10585714.29/min [2480000], rate=10628571.43/min [2490000], rate=9960000.00/min [2500000], rate=10000000.00/min [2510000], rate=10040000.00/min [2520000], rate=10080000.00/min [2530000], rate=10120000.00/min [2540000], rate=10160000.00/min [2550000], rate=10200000.00/min [2560000], rate=10240000.00/min [2570000], rate=10280000.00/min [2580000], rate=10320000.00/min [2590000], rate=10360000.00/min [2600000], rate=10400000.00/min [2610000], rate=10440000.00/min [2620000], rate=10480000.00/min [2630000], rate=9862500.00/min [2640000], rate=9900000.00/min [2650000], rate=9937500.00/min [2660000], rate=9975000.00/min [2670000], rate=10012500.00/min [2680000], rate=10050000.00/min [2690000], rate=10087500.00/min [2700000], rate=10125000.00/min [2710000], rate=10162500.00/min [2720000], rate=10200000.00/min [2730000], rate=10237500.00/min [2740000], rate=10275000.00/min [2750000], rate=9705882.35/min [2760000], rate=9741176.47/min [2770000], rate=9776470.59/min [2780000], rate=9811764.71/min [2790000], rate=9847058.82/min [2800000], rate=9882352.94/min [2810000], rate=9917647.06/min [2820000], rate=9952941.18/min [2830000], rate=9988235.29/min [2840000], rate=10023529.41/min [2850000], rate=10058823.53/min [2860000], rate=10094117.65/min [2870000], rate=10129411.76/min [2880000], rate=10164705.88/min [2890000], rate=10200000.00/min [2900000], rate=9666666.67/min [2910000], rate=9700000.00/min [2920000], rate=9733333.33/min [2930000], rate=9766666.67/min [2940000], rate=9800000.00/min [2950000], rate=9833333.33/min [2960000], rate=9866666.67/min [2970000], rate=9900000.00/min [2980000], rate=9933333.33/min [2990000], rate=9966666.67/min [3000000], rate=10000000.00/min [3010000], rate=10033333.33/min [3020000], rate=10066666.67/min [3030000], rate=9568421.05/min [3040000], rate=9600000.00/min [3050000], rate=9631578.95/min [3060000], rate=9663157.89/min [3070000], rate=9694736.84/min [3080000], rate=9726315.79/min [3090000], rate=9757894.74/min [3100000], rate=9789473.68/min [3110000], rate=9821052.63/min [3120000], rate=9852631.58/min [3130000], rate=9884210.53/min [3140000], rate=9915789.47/min [3150000], rate=9947368.42/min [3160000], rate=9978947.37/min [3170000], rate=10010526.32/min [3180000], rate=9540000.00/min [3190000], rate=9570000.00/min [3200000], rate=9600000.00/min [3210000], rate=9630000.00/min [3220000], rate=9660000.00/min [3230000], rate=9690000.00/min [3240000], rate=9720000.00/min [3250000], rate=9750000.00/min [3260000], rate=9780000.00/min [3270000], rate=9810000.00/min [3280000], rate=9840000.00/min [3290000], rate=9870000.00/min [3300000], rate=9900000.00/min [3310000], rate=9930000.00/min [3320000], rate=9960000.00/min [3330000], rate=9514285.71/min [3340000], rate=9542857.14/min [3350000], rate=9571428.57/min [3360000], rate=9600000.00/min [3370000], rate=9628571.43/min [3380000], rate=9657142.86/min [3390000], rate=9685714.29/min [3400000], rate=9714285.71/min [3410000], rate=9742857.14/min [3420000], rate=9771428.57/min [3430000], rate=9800000.00/min [3440000], rate=9828571.43/min [3450000], rate=9857142.86/min [3460000], rate=9885714.29/min [3470000], rate=9914285.71/min [3480000], rate=9942857.14/min [3490000], rate=9971428.57/min [3500000], rate=10000000.00/min [3510000], rate=10028571.43/min [3520000], rate=10057142.86/min [3530000], rate=9627272.73/min [3540000], rate=9654545.45/min [3550000], rate=9681818.18/min [3560000], rate=9709090.91/min [3570000], rate=9736363.64/min [3580000], rate=9763636.36/min [3590000], rate=9790909.09/min [3600000], rate=9818181.82/min [3610000], rate=9845454.55/min [3620000], rate=9872727.27/min [3630000], rate=9900000.00/min [3640000], rate=9927272.73/min [3650000], rate=9954545.45/min [3660000], rate=9981818.18/min [3670000], rate=10009090.91/min [3680000], rate=10036363.64/min [3690000], rate=10063636.36/min [3700000], rate=10090909.09/min [3710000], rate=10118181.82/min [3720000], rate=10145454.55/min [3730000], rate=10172727.27/min [3740000], rate=10200000.00/min [3750000], rate=10227272.73/min [3760000], rate=10254545.45/min [3770000], rate=10281818.18/min [3780000], rate=10309090.91/min [3790000], rate=9886956.52/min [3800000], rate=9913043.48/min [3810000], rate=9939130.43/min [3820000], rate=9965217.39/min [3830000], rate=9991304.35/min [3840000], rate=10017391.30/min [3850000], rate=10043478.26/min [3860000], rate=10069565.22/min [3870000], rate=10095652.17/min [3880000], rate=10121739.13/min [3890000], rate=10147826.09/min [3900000], rate=10173913.04/min [3910000], rate=10200000.00/min [3920000], rate=10226086.96/min [3930000], rate=10252173.91/min [3940000], rate=10278260.87/min [3950000], rate=10304347.83/min [3960000], rate=10330434.78/min [3970000], rate=10356521.74/min [3980000], rate=10382608.70/min [3990000], rate=10408695.65/min [4000000], rate=10434782.61/min [4010000], rate=10460869.57/min [4020000], rate=10486956.52/min [4030000], rate=10513043.48/min [4040000], rate=10100000.00/min [4050000], rate=10125000.00/min [4060000], rate=10150000.00/min [4070000], rate=10175000.00/min [4080000], rate=10200000.00/min [4090000], rate=10225000.00/min [4100000], rate=10250000.00/min [4110000], rate=10275000.00/min [4120000], rate=10300000.00/min [4130000], rate=10325000.00/min [4140000], rate=10350000.00/min [4150000], rate=10375000.00/min [4160000], rate=10400000.00/min [4170000], rate=10425000.00/min [4180000], rate=10450000.00/min [4190000], rate=10475000.00/min [4200000], rate=10500000.00/min [4210000], rate=10525000.00/min [4220000], rate=10550000.00/min [4230000], rate=10152000.00/min [4240000], rate=10176000.00/min [4250000], rate=10200000.00/min [4260000], rate=10224000.00/min [4270000], rate=10248000.00/min [4280000], rate=10272000.00/min [4290000], rate=10296000.00/min [4300000], rate=10320000.00/min [4310000], rate=10344000.00/min [4320000], rate=10368000.00/min 07:47:52 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns.prelim Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18. -BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns: identified 1349 cancer introns 07:47:53 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns.prelim 07:47:53 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/prelim_introns.ok 07:47:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns 07:47:53 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns 07:47:53 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/introns_filtered.ok 07:47:53 : INFO : -found 865 cancer introns 07:47:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns --cancer_introns BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed 07:47:54 : INFO : Creating the BED File. 07:47:57 : INFO : Saving Bed File as BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed 07:47:58 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns --cancer_introns BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed 07:47:58 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/intron_igv_bed.ok 07:47:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed --bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2 [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai 07:51:41 : INFO : Execution Time = 3.72 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed --bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2 07:51:41 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/reads_alignments_extracted.ok 07:51:41 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.bam 07:51:41 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.bam 07:51:41 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/sort_cancer_intron_reads.ok 07:51:41 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.bam [bam_sort_core] merging from 12 files and 1 in-memory blocks... 07:55:46 : INFO : Execution Time = 4.09 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.bam 07:55:46 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/sort_gene_reads.ok 07:55:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.bam 07:56:53 : INFO : Execution Time = 1.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.bam 07:56:53 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmp.ok 07:56:53 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmp 07:57:05 : INFO : Execution Time = 0.21 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmp 07:57:05 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 07:57:05 : INFO : Running: samtools index BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam 07:57:07 : INFO : Execution Time = 0.03 minutes. CMD: samtools index BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam 07:57:07 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.indexed.ok 07:57:07 : INFO : Running: samtools index BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.sorted.bam 07:57:07 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.sorted.bam 07:57:07 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.sorted.bam.indexed.ok 07:57:07 : INFO : Running: create_report BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2' 07:58:36 : INFO : Execution Time = 1.49 minutes. CMD: create_report BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2' 07:58:36 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/igv_create_html.ok 07:58:36 : INFO : done.