07:31:02 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [20000], rate=1200000.00/min [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=7200000.00/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=8600000.00/min [440000], rate=8800000.00/min [450000], rate=9000000.00/min [460000], rate=9200000.00/min [470000], rate=9400000.00/min [480000], rate=9600000.00/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=9450000.00/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=11850000.00/min [800000], rate=12000000.00/min [810000], rate=12150000.00/min [820000], rate=12300000.00/min [830000], rate=12450000.00/min [840000], rate=12600000.00/min [850000], rate=12750000.00/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=12600000.00/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=12400000.00/min [1250000], rate=12500000.00/min [1260000], rate=12600000.00/min [1270000], rate=12700000.00/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=12257142.86/min [1440000], rate=12342857.14/min [1450000], rate=12428571.43/min [1460000], rate=12514285.71/min [1470000], rate=12600000.00/min [1480000], rate=12685714.29/min [1490000], rate=12771428.57/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=12000000.00/min [1610000], rate=12075000.00/min [1620000], rate=12150000.00/min [1630000], rate=12225000.00/min [1640000], rate=12300000.00/min [1650000], rate=12375000.00/min [1660000], rate=12450000.00/min [1670000], rate=12525000.00/min [1680000], rate=12600000.00/min [1690000], rate=12675000.00/min [1700000], rate=12750000.00/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=11866666.67/min [1790000], rate=11933333.33/min [1800000], rate=12000000.00/min [1810000], rate=12066666.67/min [1820000], rate=12133333.33/min [1830000], rate=12200000.00/min [1840000], rate=12266666.67/min [1850000], rate=12333333.33/min [1860000], rate=12400000.00/min [1870000], rate=12466666.67/min [1880000], rate=12533333.33/min [1890000], rate=12600000.00/min [1900000], rate=12666666.67/min [1910000], rate=12733333.33/min [1920000], rate=12800000.00/min [1930000], rate=12866666.67/min [1940000], rate=12933333.33/min [1950000], rate=13000000.00/min [1960000], rate=11760000.00/min [1970000], rate=11820000.00/min [1980000], rate=11880000.00/min [1990000], rate=11940000.00/min [2000000], rate=12000000.00/min [2010000], rate=12060000.00/min [2020000], rate=12120000.00/min [2030000], rate=12180000.00/min [2040000], rate=12240000.00/min [2050000], rate=12300000.00/min [2060000], rate=12360000.00/min [2070000], rate=12420000.00/min [2080000], rate=12480000.00/min [2090000], rate=12540000.00/min [2100000], rate=12600000.00/min [2110000], rate=12660000.00/min [2120000], rate=12720000.00/min [2130000], rate=12780000.00/min [2140000], rate=12840000.00/min [2150000], rate=12900000.00/min [2160000], rate=12960000.00/min [2170000], rate=13020000.00/min [2180000], rate=13080000.00/min [2190000], rate=11945454.55/min [2200000], rate=12000000.00/min [2210000], rate=12054545.45/min [2220000], rate=12109090.91/min [2230000], rate=12163636.36/min [2240000], rate=12218181.82/min [2250000], rate=12272727.27/min [2260000], rate=12327272.73/min [2270000], rate=12381818.18/min [2280000], rate=12436363.64/min [2290000], rate=12490909.09/min [2300000], rate=12545454.55/min [2310000], rate=12600000.00/min [2320000], rate=12654545.45/min [2330000], rate=12709090.91/min [2340000], rate=12763636.36/min [2350000], rate=12818181.82/min [2360000], rate=12872727.27/min [2370000], rate=12927272.73/min [2380000], rate=12981818.18/min [2390000], rate=13036363.64/min [2400000], rate=12000000.00/min [2410000], rate=12050000.00/min [2420000], rate=12100000.00/min [2430000], rate=12150000.00/min [2440000], rate=12200000.00/min [2450000], rate=12250000.00/min [2460000], rate=12300000.00/min [2470000], rate=12350000.00/min [2480000], rate=12400000.00/min [2490000], rate=12450000.00/min [2500000], rate=12500000.00/min [2510000], rate=12550000.00/min [2520000], rate=12600000.00/min [2530000], rate=12650000.00/min [2540000], rate=12700000.00/min [2550000], rate=12750000.00/min [2560000], rate=12800000.00/min [2570000], rate=12850000.00/min [2580000], rate=12900000.00/min [2590000], rate=12950000.00/min [2600000], rate=12000000.00/min [2610000], rate=12046153.85/min [2620000], rate=12092307.69/min [2630000], rate=12138461.54/min [2640000], rate=12184615.38/min [2650000], rate=12230769.23/min [2660000], rate=12276923.08/min [2670000], rate=12323076.92/min [2680000], rate=12369230.77/min [2690000], rate=12415384.62/min [2700000], rate=12461538.46/min [2710000], rate=12507692.31/min [2720000], rate=12553846.15/min [2730000], rate=12600000.00/min [2740000], rate=12646153.85/min [2750000], rate=12692307.69/min [2760000], rate=12738461.54/min [2770000], rate=12784615.38/min [2780000], rate=12830769.23/min [2790000], rate=12876923.08/min [2800000], rate=12923076.92/min [2810000], rate=12969230.77/min [2820000], rate=13015384.62/min [2830000], rate=13061538.46/min [2840000], rate=13107692.31/min [2850000], rate=13153846.15/min [2860000], rate=13200000.00/min [2870000], rate=12300000.00/min [2880000], rate=12342857.14/min [2890000], rate=12385714.29/min [2900000], rate=12428571.43/min [2910000], rate=12471428.57/min [2920000], rate=12514285.71/min [2930000], rate=12557142.86/min [2940000], rate=12600000.00/min [2950000], rate=12642857.14/min [2960000], rate=12685714.29/min [2970000], rate=12728571.43/min [2980000], rate=12771428.57/min [2990000], rate=12814285.71/min [3000000], rate=12857142.86/min [3010000], rate=12900000.00/min [3020000], rate=12942857.14/min [3030000], rate=12985714.29/min [3040000], rate=13028571.43/min [3050000], rate=13071428.57/min [3060000], rate=13114285.71/min [3070000], rate=13157142.86/min [3080000], rate=13200000.00/min [3090000], rate=13242857.14/min [3100000], rate=12400000.00/min [3110000], rate=12440000.00/min [3120000], rate=12480000.00/min [3130000], rate=12520000.00/min [3140000], rate=12560000.00/min [3150000], rate=12600000.00/min [3160000], rate=12640000.00/min [3170000], rate=12680000.00/min [3180000], rate=12720000.00/min [3190000], rate=12760000.00/min [3200000], rate=12800000.00/min [3210000], rate=12840000.00/min [3220000], rate=12880000.00/min [3230000], rate=12920000.00/min [3240000], rate=12960000.00/min [3250000], rate=13000000.00/min [3260000], rate=13040000.00/min [3270000], rate=13080000.00/min [3280000], rate=13120000.00/min [3290000], rate=13160000.00/min [3300000], rate=13200000.00/min [3310000], rate=13240000.00/min [3320000], rate=13280000.00/min [3330000], rate=12487500.00/min [3340000], rate=12525000.00/min [3350000], rate=12562500.00/min [3360000], rate=12600000.00/min [3370000], rate=12637500.00/min [3380000], rate=12675000.00/min [3390000], rate=12712500.00/min [3400000], rate=12750000.00/min [3410000], rate=12787500.00/min [3420000], rate=12825000.00/min [3430000], rate=12862500.00/min [3440000], rate=12900000.00/min [3450000], rate=12937500.00/min [3460000], rate=12975000.00/min [3470000], rate=13012500.00/min [3480000], rate=13050000.00/min [3490000], rate=13087500.00/min [3500000], rate=13125000.00/min [3510000], rate=13162500.00/min [3520000], rate=13200000.00/min [3530000], rate=13237500.00/min [3540000], rate=13275000.00/min [3550000], rate=12529411.76/min [3560000], rate=12564705.88/min [3570000], rate=12600000.00/min [3580000], rate=12635294.12/min [3590000], rate=12670588.24/min [3600000], rate=12705882.35/min [3610000], rate=12741176.47/min [3620000], rate=12776470.59/min [3630000], rate=12811764.71/min [3640000], rate=12847058.82/min [3650000], rate=12882352.94/min [3660000], rate=12917647.06/min [3670000], rate=12952941.18/min [3680000], rate=12988235.29/min [3690000], rate=13023529.41/min [3700000], rate=13058823.53/min [3710000], rate=13094117.65/min [3720000], rate=13129411.76/min [3730000], rate=13164705.88/min [3740000], rate=13200000.00/min [3750000], rate=13235294.12/min [3760000], rate=13270588.24/min [3770000], rate=12566666.67/min [3780000], rate=12600000.00/min [3790000], rate=12633333.33/min [3800000], rate=12666666.67/min [3810000], rate=12700000.00/min [3820000], rate=12733333.33/min [3830000], rate=12766666.67/min [3840000], rate=12800000.00/min [3850000], rate=12833333.33/min [3860000], rate=12866666.67/min [3870000], rate=12900000.00/min [3880000], rate=12933333.33/min [3890000], rate=12966666.67/min [3900000], rate=13000000.00/min [3910000], rate=13033333.33/min [3920000], rate=13066666.67/min [3930000], rate=13100000.00/min [3940000], rate=13133333.33/min [3950000], rate=13166666.67/min [3960000], rate=13200000.00/min [3970000], rate=13233333.33/min [3980000], rate=13266666.67/min 07:31:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00105_23H5VFLT4_s21.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00105_23H5VFLT4_s21.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_00105_23H5VFLT4_s21.introns: identified 810 cancer introns 07:31:28 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00105_23H5VFLT4_s21.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00105_23H5VFLT4_s21.cancer.introns.prelim 07:31:28 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/prelim_introns.ok 07:31:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00105_23H5VFLT4_s21.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00105_23H5VFLT4_s21.cancer.introns 07:31:28 : 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_00105_23H5VFLT4_s21.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00105_23H5VFLT4_s21.cancer.introns 07:31:28 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/introns_filtered.ok 07:31:28 : INFO : -found 349 cancer introns 07:31:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00105_23H5VFLT4_s21.introns --cancer_introns tih_rna_sample_00105_23H5VFLT4_s21.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00105_23H5VFLT4_s21.introns.for_IGV.bed 07:31:29 : INFO : Creating the BED File. 07:31:30 : INFO : Saving Bed File as tih_rna_sample_00105_23H5VFLT4_s21.introns.for_IGV.bed 07:31:31 : INFO : Execution Time = 0.04 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00105_23H5VFLT4_s21.introns --cancer_introns tih_rna_sample_00105_23H5VFLT4_s21.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00105_23H5VFLT4_s21.introns.for_IGV.bed 07:31:31 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/intron_igv_bed.ok 07:31:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00105_23H5VFLT4_s21.introns.for_IGV.bed --bam tih_rna_sample_00105_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00105_23H5VFLT4_s21 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00105_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam.bai 07:32:22 : INFO : Execution Time = 0.86 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00105_23H5VFLT4_s21.introns.for_IGV.bed --bam tih_rna_sample_00105_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00105_23H5VFLT4_s21 07:32:22 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/reads_alignments_extracted.ok 07:32:22 : INFO : Running: samtools sort -o tih_rna_sample_00105_23H5VFLT4_s21.cancer_intron_reads.sorted.bam tih_rna_sample_00105_23H5VFLT4_s21.cancer_intron_reads.bam 07:32:22 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o tih_rna_sample_00105_23H5VFLT4_s21.cancer_intron_reads.sorted.bam tih_rna_sample_00105_23H5VFLT4_s21.cancer_intron_reads.bam 07:32:22 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/sort_cancer_intron_reads.ok 07:32:22 : INFO : Running: samtools sort -o tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.bam tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.bam [bam_sort_core] merging from 2 files and 1 in-memory blocks... 07:33:22 : INFO : Execution Time = 0.99 minutes. CMD: samtools sort -o tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.bam tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.bam 07:33:22 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/sort_gene_reads.ok 07:33:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.bam 07:33:47 : INFO : Execution Time = 0.42 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.bam 07:33:47 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam.tmp.ok 07:33:47 : INFO : Running: samtools sort -o tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam.tmp 07:33:59 : INFO : Execution Time = 0.20 minutes. CMD: samtools sort -o tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam.tmp 07:33:59 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam.tmpsorted.ok 07:33:59 : INFO : Running: samtools index tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam 07:34:01 : INFO : Execution Time = 0.03 minutes. CMD: samtools index tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam 07:34:01 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/tih_rna_sample_00105_23H5VFLT4_s21.gene_reads.sorted.sifted.bam.indexed.ok 07:34:01 : INFO : Running: samtools index tih_rna_sample_00105_23H5VFLT4_s21.cancer_intron_reads.sorted.bam 07:34:01 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00105_23H5VFLT4_s21.cancer_intron_reads.sorted.bam 07:34:01 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/tih_rna_sample_00105_23H5VFLT4_s21.cancer_intron_reads.sorted.bam.indexed.ok 07:34:01 : INFO : Running: create_report tih_rna_sample_00105_23H5VFLT4_s21.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00105_23H5VFLT4_s21.ctat-splicing.igv.html --track-config tih_rna_sample_00105_23H5VFLT4_s21.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00105_23H5VFLT4_s21' 07:34:46 : INFO : Execution Time = 0.75 minutes. CMD: create_report tih_rna_sample_00105_23H5VFLT4_s21.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00105_23H5VFLT4_s21.ctat-splicing.igv.html --track-config tih_rna_sample_00105_23H5VFLT4_s21.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00105_23H5VFLT4_s21' 07:34:46 : INFO : Running: touch /tmp/nxf.FGso0mHBGS/tih_rna_sample_00105_23H5VFLT4_s21.chckpts/igv_create_html.ok 07:34:46 : INFO : done.