07:40:11 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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=34800000.00/min
[590000], rate=35400000.00/min
[600000], rate=36000000.00/min
[610000], rate=36600000.00/min
[620000], rate=37200000.00/min
[630000], rate=37800000.00/min
[640000], rate=38400000.00/min
[650000], rate=39000000.00/min
[660000], rate=39600000.00/min
[670000], rate=40200000.00/min
[680000], rate=40800000.00/min
[690000], rate=41400000.00/min
[700000], rate=42000000.00/min
[710000], rate=42600000.00/min
[720000], rate=43200000.00/min
[730000], rate=43800000.00/min
[740000], rate=44400000.00/min
[750000], rate=45000000.00/min
[760000], rate=45600000.00/min
[770000], rate=46200000.00/min
[780000], rate=46800000.00/min
[790000], rate=47400000.00/min
[800000], rate=48000000.00/min
[810000], rate=48600000.00/min
[820000], rate=49200000.00/min
[830000], rate=49800000.00/min
[840000], rate=50400000.00/min
[850000], rate=51000000.00/min
[860000], rate=51600000.00/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=33000000.00/min
[1110000], rate=33300000.00/min
[1120000], rate=33600000.00/min
[1130000], rate=33900000.00/min
[1140000], rate=34200000.00/min
[1150000], rate=34500000.00/min
[1160000], rate=34800000.00/min
[1170000], rate=35100000.00/min
[1180000], rate=35400000.00/min
[1190000], rate=35700000.00/min
[1200000], rate=36000000.00/min
[1210000], rate=36300000.00/min
[1220000], rate=36600000.00/min
[1230000], rate=36900000.00/min
[1240000], rate=37200000.00/min
[1250000], rate=37500000.00/min
[1260000], rate=37800000.00/min
[1270000], rate=38100000.00/min
[1280000], rate=38400000.00/min
[1290000], rate=38700000.00/min
[1300000], rate=39000000.00/min
[1310000], rate=39300000.00/min
[1320000], rate=39600000.00/min
[1330000], rate=39900000.00/min
[1340000], rate=40200000.00/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=32200000.00/min
[1620000], rate=32400000.00/min
[1630000], rate=32600000.00/min
[1640000], rate=32800000.00/min
[1650000], rate=33000000.00/min
[1660000], rate=33200000.00/min
[1670000], rate=33400000.00/min
[1680000], rate=33600000.00/min
[1690000], rate=33800000.00/min
[1700000], rate=34000000.00/min
[1710000], rate=34200000.00/min
[1720000], rate=34400000.00/min
[1730000], rate=34600000.00/min
[1740000], rate=34800000.00/min
[1750000], rate=35000000.00/min
[1760000], rate=35200000.00/min
[1770000], rate=35400000.00/min
[1780000], rate=35600000.00/min
[1790000], rate=35800000.00/min
[1800000], rate=36000000.00/min
[1810000], rate=36200000.00/min
[1820000], rate=36400000.00/min
[1830000], rate=36600000.00/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=31350000.00/min
[2100000], rate=31500000.00/min
[2110000], rate=31650000.00/min
[2120000], rate=31800000.00/min
[2130000], rate=31950000.00/min
[2140000], rate=32100000.00/min
[2150000], rate=32250000.00/min
[2160000], rate=32400000.00/min
[2170000], rate=32550000.00/min
[2180000], rate=32700000.00/min
[2190000], rate=32850000.00/min
[2200000], rate=33000000.00/min
[2210000], rate=33150000.00/min
[2220000], rate=33300000.00/min
[2230000], rate=33450000.00/min
[2240000], rate=33600000.00/min
[2250000], rate=33750000.00/min
[2260000], rate=33900000.00/min
[2270000], rate=34050000.00/min
[2280000], rate=34200000.00/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=31200000.00/min
[2610000], rate=31320000.00/min
[2620000], rate=31440000.00/min
[2630000], rate=31560000.00/min
[2640000], rate=31680000.00/min
[2650000], rate=31800000.00/min
[2660000], rate=31920000.00/min
[2670000], rate=32040000.00/min
[2680000], rate=32160000.00/min
[2690000], rate=32280000.00/min
[2700000], rate=32400000.00/min
[2710000], rate=32520000.00/min
[2720000], rate=32640000.00/min
[2730000], rate=32760000.00/min
[2740000], rate=32880000.00/min
[2750000], rate=33000000.00/min
[2760000], rate=33120000.00/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=31300000.00/min
[3140000], rate=31400000.00/min
[3150000], rate=31500000.00/min
[3160000], rate=31600000.00/min
[3170000], rate=31700000.00/min
[3180000], rate=31800000.00/min
[3190000], rate=31900000.00/min
[3200000], rate=32000000.00/min
[3210000], rate=32100000.00/min
[3220000], rate=32200000.00/min
[3230000], rate=32300000.00/min
[3240000], rate=32400000.00/min
[3250000], rate=32500000.00/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=31371428.57/min
[3670000], rate=31457142.86/min
[3680000], rate=31542857.14/min
[3690000], rate=31628571.43/min
[3700000], rate=31714285.71/min
[3710000], rate=31800000.00/min
[3720000], rate=31885714.29/min
[3730000], rate=31971428.57/min
[3740000], rate=32057142.86/min
[3750000], rate=32142857.14/min
[3760000], rate=32228571.43/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 07:40:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_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.
-BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns: identified 178 cancer introns
07:40:23 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim
07:40:23 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok
07:40:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns
07:40:24 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns
07:40:24 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok
07:40:24 : INFO : -found 119 cancer introns
07:40:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns --cancer_introns BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:40:24 : INFO : Creating the BED File.
07:40:24 : INFO : Saving Bed File as BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:40:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns --cancer_introns BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:40:24 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
07:40:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
07:40:39 : INFO : Execution Time = 0.24 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1
07:40:39 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
07:40:39 : INFO : Running: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
07:40:39 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
07:40:39 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
07:40:39 : INFO : Running: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.bam
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
07:40:57 : INFO : Execution Time = 0.30 minutes. CMD: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.bam
07:40:57 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
07:40:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam
07:41:02 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam
07:41:02 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:41:02 : INFO : Running: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
07:41:03 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
07:41:03 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:41:03 : INFO : Running: samtools index BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
07:41:03 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
07:41:03 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:41:03 : INFO : Running: samtools index BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
07:41:03 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
07:41:03 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:41:03 : INFO : Running: create_report BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1'
07:41:16 : INFO : Execution Time = 0.20 minutes. CMD: create_report BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1'
07:41:16 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok
07:41:16 : INFO : done.