20:24:02 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=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=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=20700000.00/min [700000], rate=21000000.00/min [710000], rate=21300000.00/min [720000], rate=21600000.00/min [730000], rate=21900000.00/min [740000], rate=22200000.00/min [750000], rate=22500000.00/min [760000], rate=22800000.00/min [770000], rate=23100000.00/min [780000], rate=23400000.00/min [790000], rate=23700000.00/min [800000], rate=24000000.00/min [810000], rate=24300000.00/min [820000], rate=24600000.00/min [830000], rate=24900000.00/min [840000], rate=25200000.00/min [850000], rate=25500000.00/min [860000], rate=25800000.00/min [870000], rate=17400000.00/min [880000], rate=17600000.00/min [890000], rate=17800000.00/min [900000], rate=18000000.00/min [910000], rate=18200000.00/min [920000], rate=18400000.00/min [930000], rate=18600000.00/min [940000], rate=18800000.00/min [950000], rate=19000000.00/min [960000], rate=19200000.00/min [970000], rate=19400000.00/min [980000], rate=19600000.00/min [990000], rate=19800000.00/min [1000000], rate=20000000.00/min [1010000], rate=20200000.00/min [1020000], rate=20400000.00/min [1030000], rate=20600000.00/min [1040000], rate=20800000.00/min [1050000], rate=21000000.00/min [1060000], rate=21200000.00/min [1070000], rate=21400000.00/min [1080000], rate=21600000.00/min [1090000], rate=21800000.00/min [1100000], rate=22000000.00/min [1110000], rate=22200000.00/min [1120000], rate=22400000.00/min [1130000], rate=22600000.00/min [1140000], rate=22800000.00/min [1150000], rate=23000000.00/min [1160000], rate=23200000.00/min [1170000], rate=23400000.00/min [1180000], rate=23600000.00/min [1190000], rate=23800000.00/min [1200000], rate=24000000.00/min [1210000], rate=18150000.00/min [1220000], rate=18300000.00/min [1230000], rate=18450000.00/min [1240000], rate=18600000.00/min [1250000], rate=18750000.00/min [1260000], rate=18900000.00/min [1270000], rate=19050000.00/min [1280000], rate=19200000.00/min [1290000], rate=19350000.00/min [1300000], rate=19500000.00/min [1310000], rate=19650000.00/min [1320000], rate=19800000.00/min [1330000], rate=19950000.00/min [1340000], rate=20100000.00/min [1350000], rate=20250000.00/min [1360000], rate=20400000.00/min [1370000], rate=20550000.00/min [1380000], rate=20700000.00/min [1390000], rate=20850000.00/min [1400000], rate=21000000.00/min [1410000], rate=21150000.00/min [1420000], rate=21300000.00/min [1430000], rate=21450000.00/min [1440000], rate=21600000.00/min [1450000], rate=21750000.00/min [1460000], rate=21900000.00/min [1470000], rate=22050000.00/min [1480000], rate=22200000.00/min [1490000], rate=22350000.00/min [1500000], rate=22500000.00/min [1510000], rate=22650000.00/min [1520000], rate=22800000.00/min [1530000], rate=22950000.00/min [1540000], rate=23100000.00/min [1550000], rate=23250000.00/min [1560000], rate=23400000.00/min [1570000], rate=23550000.00/min [1580000], rate=18960000.00/min [1590000], rate=19080000.00/min [1600000], rate=19200000.00/min [1610000], rate=19320000.00/min [1620000], rate=19440000.00/min [1630000], rate=19560000.00/min [1640000], rate=19680000.00/min [1650000], rate=19800000.00/min [1660000], rate=19920000.00/min [1670000], rate=20040000.00/min [1680000], rate=20160000.00/min [1690000], rate=20280000.00/min [1700000], rate=20400000.00/min [1710000], rate=20520000.00/min [1720000], rate=20640000.00/min [1730000], rate=20760000.00/min [1740000], rate=20880000.00/min [1750000], rate=21000000.00/min [1760000], rate=21120000.00/min [1770000], rate=21240000.00/min [1780000], rate=21360000.00/min [1790000], rate=21480000.00/min [1800000], rate=21600000.00/min [1810000], rate=21720000.00/min [1820000], rate=21840000.00/min [1830000], rate=18300000.00/min [1840000], rate=18400000.00/min [1850000], rate=18500000.00/min [1860000], rate=18600000.00/min [1870000], rate=18700000.00/min [1880000], rate=18800000.00/min [1890000], rate=18900000.00/min [1900000], rate=19000000.00/min [1910000], rate=19100000.00/min [1920000], rate=19200000.00/min [1930000], rate=19300000.00/min [1940000], rate=19400000.00/min [1950000], rate=19500000.00/min [1960000], rate=19600000.00/min [1970000], rate=19700000.00/min [1980000], rate=19800000.00/min [1990000], rate=19900000.00/min [2000000], rate=20000000.00/min [2010000], rate=20100000.00/min [2020000], rate=20200000.00/min [2030000], rate=17400000.00/min [2040000], rate=17485714.29/min [2050000], rate=17571428.57/min [2060000], rate=17657142.86/min [2070000], rate=17742857.14/min [2080000], rate=17828571.43/min [2090000], rate=17914285.71/min [2100000], rate=18000000.00/min [2110000], rate=18085714.29/min [2120000], rate=18171428.57/min [2130000], rate=18257142.86/min [2140000], rate=18342857.14/min [2150000], rate=18428571.43/min [2160000], rate=18514285.71/min [2170000], rate=18600000.00/min [2180000], rate=18685714.29/min [2190000], rate=18771428.57/min [2200000], rate=18857142.86/min [2210000], rate=18942857.14/min [2220000], rate=16650000.00/min [2230000], rate=16725000.00/min [2240000], rate=16800000.00/min [2250000], rate=16875000.00/min [2260000], rate=16950000.00/min [2270000], rate=17025000.00/min [2280000], rate=17100000.00/min [2290000], rate=17175000.00/min [2300000], rate=17250000.00/min [2310000], rate=17325000.00/min [2320000], rate=17400000.00/min [2330000], rate=17475000.00/min [2340000], rate=17550000.00/min [2350000], rate=17625000.00/min [2360000], rate=17700000.00/min [2370000], rate=17775000.00/min [2380000], rate=17850000.00/min [2390000], rate=17925000.00/min [2400000], rate=18000000.00/min [2410000], rate=16066666.67/min [2420000], rate=16133333.33/min [2430000], rate=16200000.00/min [2440000], rate=16266666.67/min [2450000], rate=16333333.33/min [2460000], rate=16400000.00/min [2470000], rate=16466666.67/min [2480000], rate=16533333.33/min [2490000], rate=16600000.00/min [2500000], rate=16666666.67/min [2510000], rate=16733333.33/min [2520000], rate=16800000.00/min [2530000], rate=16866666.67/min [2540000], rate=16933333.33/min [2550000], rate=17000000.00/min [2560000], rate=17066666.67/min [2570000], rate=17133333.33/min [2580000], rate=17200000.00/min [2590000], rate=15540000.00/min [2600000], rate=15600000.00/min [2610000], rate=15660000.00/min [2620000], rate=15720000.00/min [2630000], rate=15780000.00/min [2640000], rate=15840000.00/min [2650000], rate=15900000.00/min [2660000], rate=15960000.00/min [2670000], rate=16020000.00/min [2680000], rate=16080000.00/min [2690000], rate=16140000.00/min [2700000], rate=16200000.00/min [2710000], rate=16260000.00/min [2720000], rate=16320000.00/min [2730000], rate=16380000.00/min [2740000], rate=16440000.00/min [2750000], rate=16500000.00/min [2760000], rate=16560000.00/min [2770000], rate=16620000.00/min [2780000], rate=16680000.00/min [2790000], rate=16740000.00/min [2800000], rate=16800000.00/min [2810000], rate=16860000.00/min [2820000], rate=16920000.00/min [2830000], rate=16980000.00/min [2840000], rate=17040000.00/min [2850000], rate=17100000.00/min [2860000], rate=17160000.00/min [2870000], rate=17220000.00/min [2880000], rate=17280000.00/min [2890000], rate=17340000.00/min [2900000], rate=17400000.00/min [2910000], rate=17460000.00/min [2920000], rate=15927272.73/min [2930000], rate=15981818.18/min [2940000], rate=16036363.64/min [2950000], rate=16090909.09/min [2960000], rate=16145454.55/min [2970000], rate=16200000.00/min [2980000], rate=16254545.45/min [2990000], rate=16309090.91/min [3000000], rate=16363636.36/min [3010000], rate=16418181.82/min [3020000], rate=16472727.27/min [3030000], rate=16527272.73/min [3040000], rate=16581818.18/min [3050000], rate=16636363.64/min [3060000], rate=16690909.09/min [3070000], rate=16745454.55/min [3080000], rate=16800000.00/min [3090000], rate=16854545.45/min [3100000], rate=16909090.91/min [3110000], rate=16963636.36/min [3120000], rate=17018181.82/min [3130000], rate=17072727.27/min [3140000], rate=15700000.00/min [3150000], rate=15750000.00/min [3160000], rate=15800000.00/min [3170000], rate=15850000.00/min [3180000], rate=15900000.00/min [3190000], rate=15950000.00/min [3200000], rate=16000000.00/min [3210000], rate=16050000.00/min [3220000], rate=16100000.00/min [3230000], rate=16150000.00/min [3240000], rate=16200000.00/min [3250000], rate=16250000.00/min [3260000], rate=16300000.00/min [3270000], rate=16350000.00/min [3280000], rate=16400000.00/min [3290000], rate=16450000.00/min [3300000], rate=16500000.00/min [3310000], rate=16550000.00/min [3320000], rate=16600000.00/min [3330000], rate=16650000.00/min [3340000], rate=16700000.00/min [3350000], rate=16750000.00/min [3360000], rate=15507692.31/min [3370000], rate=15553846.15/min [3380000], rate=15600000.00/min [3390000], rate=15646153.85/min [3400000], rate=15692307.69/min [3410000], rate=15738461.54/min [3420000], rate=15784615.38/min [3430000], rate=15830769.23/min [3440000], rate=15876923.08/min [3450000], rate=15923076.92/min [3460000], rate=15969230.77/min [3470000], rate=16015384.62/min [3480000], rate=16061538.46/min [3490000], rate=16107692.31/min [3500000], rate=16153846.15/min [3510000], rate=16200000.00/min [3520000], rate=16246153.85/min [3530000], rate=16292307.69/min [3540000], rate=16338461.54/min [3550000], rate=16384615.38/min [3560000], rate=16430769.23/min [3570000], rate=16476923.08/min [3580000], rate=16523076.92/min [3590000], rate=16569230.77/min [3600000], rate=16615384.62/min [3610000], rate=16661538.46/min [3620000], rate=16707692.31/min [3630000], rate=16753846.15/min [3640000], rate=16800000.00/min [3650000], rate=16846153.85/min [3660000], rate=16892307.69/min 20:24:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNB_FFPE_L02_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_L02_RNA_01_B23LG7FLT4_1.introns: identified 172 cancer introns 20:24:20 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns.prelim 20:24:20 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok 20:24:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns 20:24:21 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns 20:24:21 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok 20:24:21 : INFO : -found 112 cancer introns 20:24:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns --cancer_introns BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:24:21 : INFO : Creating the BED File. 20:24:22 : INFO : Saving Bed File as BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:24:22 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns --cancer_introns BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:24:22 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok 20:24:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1 [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai 20:25:14 : INFO : Execution Time = 0.86 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1 20:25:14 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok 20:25:14 : INFO : Running: samtools sort -o BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam 20:25:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam 20:25:14 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok 20:25:14 : INFO : Running: samtools sort -o BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.bam [bam_sort_core] merging from 3 files and 1 in-memory blocks... 20:26:08 : INFO : Execution Time = 0.90 minutes. CMD: samtools sort -o BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.bam 20:26:08 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok 20:26:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 20:26:20 : INFO : Execution Time = 0.21 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 20:26:20 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 20:26:20 : INFO : Running: samtools sort -o BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 20:26:22 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 20:26:22 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 20:26:22 : INFO : Running: samtools index BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 20:26:22 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 20:26:22 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 20:26:22 : INFO : Running: samtools index BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 20:26:22 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 20:26:22 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 20:26:22 : INFO : Running: create_report BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1' [W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi 20:26:35 : INFO : Execution Time = 0.22 minutes. CMD: create_report BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1' 20:26:35 : INFO : Running: touch /tmp/nxf.gpmBzQFY3Y/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok 20:26:35 : INFO : done.