19:33:05 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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=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=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=10800000.00/min
[550000], rate=11000000.00/min
[560000], rate=11200000.00/min
[570000], rate=11400000.00/min
[580000], rate=11600000.00/min
[590000], rate=11800000.00/min
[600000], rate=12000000.00/min
[610000], rate=12200000.00/min
[620000], rate=12400000.00/min
[630000], rate=12600000.00/min
[640000], rate=12800000.00/min
[650000], rate=13000000.00/min
[660000], rate=13200000.00/min
[670000], rate=13400000.00/min
[680000], rate=13600000.00/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=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=12900000.00/min
[870000], rate=13050000.00/min
[880000], rate=13200000.00/min
[890000], rate=13350000.00/min
[900000], rate=13500000.00/min
[910000], rate=13650000.00/min
[920000], rate=13800000.00/min
[930000], rate=13950000.00/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=12720000.00/min
[1070000], rate=12840000.00/min
[1080000], rate=12960000.00/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=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=12800000.00/min
[1290000], rate=12900000.00/min
[1300000], rate=13000000.00/min
[1310000], rate=13100000.00/min
[1320000], rate=13200000.00/min
[1330000], rate=13300000.00/min
[1340000], rate=13400000.00/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=12857142.86/min
[1510000], rate=12942857.14/min
[1520000], rate=13028571.43/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=12825000.00/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=11460000.00/min
[1920000], rate=11520000.00/min
[1930000], rate=11580000.00/min
[1940000], rate=11640000.00/min
[1950000], rate=11700000.00/min
[1960000], rate=11760000.00/min
[1970000], rate=11820000.00/min
[1980000], rate=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=11563636.36/min
[2130000], rate=11618181.82/min
[2140000], rate=11672727.27/min
[2150000], rate=11727272.73/min
[2160000], rate=11781818.18/min
[2170000], rate=11836363.64/min
[2180000], rate=11890909.09/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=11350000.00/min
[2280000], rate=11400000.00/min
[2290000], rate=11450000.00/min
[2300000], rate=11500000.00/min
[2310000], rate=11550000.00/min
[2320000], rate=11600000.00/min
[2330000], rate=11650000.00/min
[2340000], rate=11700000.00/min
[2350000], rate=11750000.00/min
[2360000], rate=11800000.00/min
[2370000], rate=11850000.00/min
[2380000], rate=11900000.00/min
[2390000], rate=11950000.00/min
[2400000], rate=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=11307692.31/min
[2460000], rate=11353846.15/min
[2470000], rate=11400000.00/min
[2480000], rate=11446153.85/min
[2490000], rate=11492307.69/min
[2500000], rate=11538461.54/min
[2510000], rate=11584615.38/min
[2520000], rate=11630769.23/min
[2530000], rate=11676923.08/min
[2540000], rate=11723076.92/min
[2550000], rate=11769230.77/min
[2560000], rate=11815384.62/min
[2570000], rate=11861538.46/min
[2580000], rate=11907692.31/min
[2590000], rate=11953846.15/min
[2600000], rate=12000000.00/min
[2610000], rate=12046153.85/min
[2620000], rate=12092307.69/min
[2630000], rate=12138461.54/min
[2640000], rate=12184615.38/min
[2650000], rate=12230769.23/min
[2660000], rate=11400000.00/min
[2670000], rate=11442857.14/min
[2680000], rate=11485714.29/min
[2690000], rate=11528571.43/min
[2700000], rate=11571428.57/min
[2710000], rate=11614285.71/min
[2720000], rate=11657142.86/min
[2730000], rate=11700000.00/min
[2740000], rate=11742857.14/min
[2750000], rate=11785714.29/min
[2760000], rate=11828571.43/min
[2770000], rate=11871428.57/min
[2780000], rate=11914285.71/min
[2790000], rate=11957142.86/min
[2800000], rate=12000000.00/min
[2810000], rate=12042857.14/min
[2820000], rate=12085714.29/min
[2830000], rate=12128571.43/min
[2840000], rate=12171428.57/min
[2850000], rate=12214285.71/min
[2860000], rate=12257142.86/min
[2870000], rate=12300000.00/min
[2880000], rate=12342857.14/min
[2890000], rate=12385714.29/min
[2900000], rate=11600000.00/min
[2910000], rate=11640000.00/min
[2920000], rate=11680000.00/min
[2930000], rate=11720000.00/min
[2940000], rate=11760000.00/min
[2950000], rate=11800000.00/min
[2960000], rate=11840000.00/min
[2970000], rate=11880000.00/min
[2980000], rate=11920000.00/min
[2990000], rate=11960000.00/min
[3000000], rate=12000000.00/min
[3010000], rate=12040000.00/min
[3020000], rate=12080000.00/min
[3030000], rate=12120000.00/min
[3040000], rate=12160000.00/min
[3050000], rate=12200000.00/min
[3060000], rate=12240000.00/min
[3070000], rate=12280000.00/min
[3080000], rate=12320000.00/min
[3090000], rate=11587500.00/min
[3100000], rate=11625000.00/min
[3110000], rate=11662500.00/min
[3120000], rate=11700000.00/min
[3130000], rate=11737500.00/min
[3140000], rate=11775000.00/min
[3150000], rate=11812500.00/min
[3160000], rate=11850000.00/min
[3170000], rate=11887500.00/min
[3180000], rate=11925000.00/min
[3190000], rate=11962500.00/min
[3200000], rate=12000000.00/min
[3210000], rate=12037500.00/min
[3220000], rate=12075000.00/min
[3230000], rate=12112500.00/min
[3240000], rate=12150000.00/min
[3250000], rate=12187500.00/min
[3260000], rate=12225000.00/min
[3270000], rate=11541176.47/min
[3280000], rate=11576470.59/min
[3290000], rate=11611764.71/min
[3300000], rate=11647058.82/min
[3310000], rate=11682352.94/min
[3320000], rate=11717647.06/min
[3330000], rate=11752941.18/min
[3340000], rate=11788235.29/min
[3350000], rate=11823529.41/min
[3360000], rate=11858823.53/min
[3370000], rate=11894117.65/min
[3380000], rate=11929411.76/min
[3390000], rate=11964705.88/min
[3400000], rate=12000000.00/min
[3410000], rate=12035294.12/min
[3420000], rate=12070588.24/min
[3430000], rate=12105882.35/min
[3440000], rate=12141176.47/min
[3450000], rate=12176470.59/min
[3460000], rate=12211764.71/min
[3470000], rate=12247058.82/min
[3480000], rate=12282352.94/min
[3490000], rate=12317647.06/min
[3500000], rate=12352941.18/min
[3510000], rate=12388235.29/min
[3520000], rate=12423529.41/min
[3530000], rate=12458823.53/min
[3540000], rate=11800000.00/min
[3550000], rate=11833333.33/min
[3560000], rate=11866666.67/min
[3570000], rate=11900000.00/min
[3580000], rate=11933333.33/min
[3590000], rate=11966666.67/min
[3600000], rate=12000000.00/min
[3610000], rate=12033333.33/min
[3620000], rate=12066666.67/min
[3630000], rate=12100000.00/min
[3640000], rate=12133333.33/min
[3650000], rate=12166666.67/min
[3660000], rate=12200000.00/min
[3670000], rate=12233333.33/min
[3680000], rate=12266666.67/min
[3690000], rate=12300000.00/min
[3700000], rate=12333333.33/min
[3710000], rate=12366666.67/min
[3720000], rate=12400000.00/min
[3730000], rate=12433333.33/min
[3740000], rate=12466666.67/min
[3750000], rate=12500000.00/min
[3760000], rate=12533333.33/min
[3770000], rate=12566666.67/min
[3780000], rate=12600000.00/min
[3790000], rate=12633333.33/min
[3800000], rate=12000000.00/min
[3810000], rate=12031578.95/min
[3820000], rate=12063157.89/min
[3830000], rate=12094736.84/min
[3840000], rate=12126315.79/min
[3850000], rate=12157894.74/min
[3860000], rate=12189473.68/min 19:33:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3b436b-R1_A23YTGFLT4_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-3b436b-R1_A23YTGFLT4_1.introns: identified 6792 cancer introns
19:33:32 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer.introns.prelim
19:33:32 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok
19:33:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer.introns
19:33:33 : 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-3b436b-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer.introns
19:33:33 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok
19:33:33 : INFO : -found 1897 cancer introns
19:33:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns.for_IGV.bed
19:33:33 : INFO : Creating the BED File.
19:33:38 : INFO : Saving Bed File as aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns.for_IGV.bed
19:33:38 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns.for_IGV.bed
19:33:38 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok
19:33:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3b436b-R1_A23YTGFLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
19:42:50 : INFO : Execution Time = 9.20 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3b436b-R1_A23YTGFLT4_1
19:42:50 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok
19:42:50 : INFO : Running: samtools sort -o aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer_intron_reads.bam
19:42:50 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer_intron_reads.bam
19:42:50 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok
19:42:50 : INFO : Running: samtools sort -o aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.bam
[bam_sort_core] merging from 40 files and 1 in-memory blocks...
19:52:53 : INFO : Execution Time = 10.04 minutes. CMD: samtools sort -o aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.bam
19:52:53 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok
19:52:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.bam
19:56:38 : INFO : Execution Time = 3.75 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.bam
19:56:38 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
19:56:38 : INFO : Running: samtools sort -o aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
19:57:23 : INFO : Execution Time = 0.76 minutes. CMD: samtools sort -o aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp
19:57:23 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
19:57:23 : INFO : Running: samtools index aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam
19:57:28 : INFO : Execution Time = 0.08 minutes. CMD: samtools index aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam
19:57:28 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
19:57:28 : INFO : Running: samtools index aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam
19:57:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam
19:57:28 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
19:57:28 : INFO : Running: create_report aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-3b436b-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-3b436b-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-3b436b-R1_A23YTGFLT4_1'
20:03:12 : INFO : Execution Time = 5.73 minutes. CMD: create_report aih-tih-sc-3b436b-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-3b436b-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-3b436b-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-3b436b-R1_A23YTGFLT4_1'
20:03:12 : INFO : Running: touch /tmp/nxf.N7LSVMAxgQ/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok
20:03:12 : INFO : done.