07:47:52 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=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=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=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=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=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=15000000.00/min [760000], rate=15200000.00/min [770000], rate=15400000.00/min [780000], rate=15600000.00/min [790000], rate=15800000.00/min [800000], rate=16000000.00/min [810000], rate=16200000.00/min [820000], rate=16400000.00/min [830000], rate=16600000.00/min [840000], rate=16800000.00/min [850000], rate=17000000.00/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=14100000.00/min [950000], rate=14250000.00/min [960000], rate=14400000.00/min [970000], rate=14550000.00/min [980000], rate=14700000.00/min [990000], rate=14850000.00/min [1000000], rate=15000000.00/min [1010000], rate=15150000.00/min [1020000], rate=15300000.00/min [1030000], rate=15450000.00/min [1040000], rate=15600000.00/min [1050000], rate=15750000.00/min [1060000], rate=15900000.00/min [1070000], rate=16050000.00/min [1080000], rate=16200000.00/min [1090000], rate=16350000.00/min [1100000], rate=16500000.00/min [1110000], rate=16650000.00/min [1120000], rate=16800000.00/min [1130000], rate=16950000.00/min [1140000], rate=17100000.00/min [1150000], rate=17250000.00/min [1160000], rate=13920000.00/min [1170000], rate=14040000.00/min [1180000], rate=14160000.00/min [1190000], rate=14280000.00/min [1200000], rate=14400000.00/min [1210000], rate=14520000.00/min [1220000], rate=14640000.00/min [1230000], rate=14760000.00/min [1240000], rate=14880000.00/min [1250000], rate=15000000.00/min [1260000], rate=15120000.00/min [1270000], rate=15240000.00/min [1280000], rate=15360000.00/min [1290000], rate=15480000.00/min [1300000], rate=15600000.00/min [1310000], rate=15720000.00/min [1320000], rate=15840000.00/min [1330000], rate=15960000.00/min [1340000], rate=16080000.00/min [1350000], rate=16200000.00/min [1360000], rate=16320000.00/min [1370000], rate=16440000.00/min [1380000], rate=16560000.00/min [1390000], rate=16680000.00/min [1400000], rate=16800000.00/min [1410000], rate=16920000.00/min [1420000], rate=17040000.00/min [1430000], rate=17160000.00/min [1440000], rate=17280000.00/min [1450000], rate=14500000.00/min [1460000], rate=14600000.00/min [1470000], rate=14700000.00/min [1480000], rate=14800000.00/min [1490000], rate=14900000.00/min [1500000], rate=15000000.00/min [1510000], rate=15100000.00/min [1520000], rate=15200000.00/min [1530000], rate=15300000.00/min [1540000], rate=15400000.00/min [1550000], rate=15500000.00/min [1560000], rate=15600000.00/min [1570000], rate=15700000.00/min [1580000], rate=15800000.00/min [1590000], rate=15900000.00/min [1600000], rate=16000000.00/min [1610000], rate=16100000.00/min [1620000], rate=16200000.00/min [1630000], rate=16300000.00/min [1640000], rate=16400000.00/min [1650000], rate=16500000.00/min [1660000], rate=16600000.00/min [1670000], rate=16700000.00/min [1680000], rate=14400000.00/min [1690000], rate=14485714.29/min [1700000], rate=14571428.57/min [1710000], rate=14657142.86/min [1720000], rate=14742857.14/min [1730000], rate=14828571.43/min [1740000], rate=14914285.71/min [1750000], rate=15000000.00/min [1760000], rate=15085714.29/min [1770000], rate=15171428.57/min [1780000], rate=15257142.86/min [1790000], rate=15342857.14/min [1800000], rate=15428571.43/min [1810000], rate=15514285.71/min [1820000], rate=15600000.00/min [1830000], rate=15685714.29/min [1840000], rate=15771428.57/min [1850000], rate=15857142.86/min [1860000], rate=15942857.14/min [1870000], rate=16028571.43/min [1880000], rate=16114285.71/min [1890000], rate=16200000.00/min [1900000], rate=16285714.29/min [1910000], rate=16371428.57/min [1920000], rate=16457142.86/min [1930000], rate=16542857.14/min [1940000], rate=16628571.43/min [1950000], rate=14625000.00/min [1960000], rate=14700000.00/min [1970000], rate=14775000.00/min [1980000], rate=14850000.00/min [1990000], rate=14925000.00/min [2000000], rate=15000000.00/min [2010000], rate=15075000.00/min [2020000], rate=15150000.00/min [2030000], rate=15225000.00/min [2040000], rate=15300000.00/min [2050000], rate=15375000.00/min [2060000], rate=15450000.00/min [2070000], rate=15525000.00/min [2080000], rate=15600000.00/min [2090000], rate=15675000.00/min [2100000], rate=15750000.00/min [2110000], rate=15825000.00/min [2120000], rate=15900000.00/min [2130000], rate=15975000.00/min [2140000], rate=16050000.00/min [2150000], rate=16125000.00/min [2160000], rate=16200000.00/min [2170000], rate=16275000.00/min [2180000], rate=16350000.00/min [2190000], rate=16425000.00/min [2200000], rate=16500000.00/min [2210000], rate=16575000.00/min [2220000], rate=16650000.00/min [2230000], rate=16725000.00/min [2240000], rate=16800000.00/min [2250000], rate=15000000.00/min [2260000], rate=15066666.67/min [2270000], rate=15133333.33/min [2280000], rate=15200000.00/min [2290000], rate=15266666.67/min [2300000], rate=15333333.33/min [2310000], rate=15400000.00/min [2320000], rate=15466666.67/min [2330000], rate=15533333.33/min [2340000], rate=15600000.00/min [2350000], rate=15666666.67/min [2360000], rate=15733333.33/min [2370000], rate=15800000.00/min [2380000], rate=15866666.67/min [2390000], rate=15933333.33/min [2400000], rate=16000000.00/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=14820000.00/min [2480000], rate=14880000.00/min [2490000], rate=14940000.00/min [2500000], rate=15000000.00/min [2510000], rate=15060000.00/min [2520000], rate=15120000.00/min [2530000], rate=15180000.00/min [2540000], rate=15240000.00/min [2550000], rate=15300000.00/min [2560000], rate=15360000.00/min [2570000], rate=15420000.00/min [2580000], rate=15480000.00/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=14400000.00/min [2650000], rate=14454545.45/min [2660000], rate=14509090.91/min [2670000], rate=14563636.36/min [2680000], rate=14618181.82/min [2690000], rate=14672727.27/min [2700000], rate=14727272.73/min [2710000], rate=14781818.18/min 07:48:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bCu-T1-TRNA-1_B23WHTKLT4_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. -659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns: identified 441 cancer introns 07:48:10 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim 07:48:10 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/prelim_introns.ok 07:48:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns 07:48:10 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns 07:48:10 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/introns_filtered.ok 07:48:10 : INFO : -found 330 cancer introns 07:48:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed 07:48:11 : INFO : Creating the BED File. 07:48:13 : INFO : Saving Bed File as 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed 07:48:14 : INFO : Execution Time = 0.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed 07:48:14 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/intron_igv_bed.ok 07:48:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bCu-T1-TRNA-1_B23WHTKLT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai 07:49:49 : INFO : Execution Time = 1.59 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bCu-T1-TRNA-1_B23WHTKLT4_1 07:49:49 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok 07:49:49 : INFO : Running: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam 07:49:49 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam 07:49:49 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok 07:49:49 : INFO : Running: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam [bam_sort_core] merging from 4 files and 1 in-memory blocks... 07:51:26 : INFO : Execution Time = 1.61 minutes. CMD: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam 07:51:26 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_gene_reads.ok 07:51:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 07:51:49 : INFO : Execution Time = 0.38 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 07:51:49 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 07:51:49 : INFO : Running: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp 07:51:54 : INFO : Execution Time = 0.08 minutes. CMD: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp 07:51:54 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 07:51:54 : INFO : Running: samtools index 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 07:51:55 : INFO : Execution Time = 0.01 minutes. CMD: samtools index 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 07:51:55 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 07:51:55 : INFO : Running: samtools index 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 07:51:55 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 07:51:55 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 07:51:55 : INFO : Running: create_report 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bCu-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_bCu-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bCu-T1-TRNA-1_B23WHTKLT4_1' 07:52:37 : INFO : Execution Time = 0.70 minutes. CMD: create_report 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bCu-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_bCu-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bCu-T1-TRNA-1_B23WHTKLT4_1' 07:52:37 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/igv_create_html.ok 07:52:37 : INFO : done.