08:06:44 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=14400000.00/min [250000], rate=15000000.00/min [260000], rate=15600000.00/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=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=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=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=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=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=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=13800000.00/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=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=13500000.00/min [1360000], rate=13600000.00/min [1370000], rate=13700000.00/min [1380000], rate=13800000.00/min [1390000], rate=13900000.00/min [1400000], rate=14000000.00/min [1410000], rate=14100000.00/min [1420000], rate=14200000.00/min [1430000], rate=14300000.00/min [1440000], rate=14400000.00/min [1450000], rate=14500000.00/min [1460000], rate=14600000.00/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=13114285.71/min [1540000], rate=13200000.00/min [1550000], rate=13285714.29/min [1560000], rate=13371428.57/min [1570000], rate=13457142.86/min [1580000], rate=13542857.14/min [1590000], rate=13628571.43/min [1600000], rate=13714285.71/min [1610000], rate=13800000.00/min [1620000], rate=13885714.29/min [1630000], rate=13971428.57/min [1640000], rate=14057142.86/min [1650000], rate=14142857.14/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=12900000.00/min [1730000], rate=12975000.00/min [1740000], rate=13050000.00/min [1750000], rate=13125000.00/min [1760000], rate=13200000.00/min [1770000], rate=13275000.00/min [1780000], rate=13350000.00/min [1790000], rate=13425000.00/min [1800000], rate=13500000.00/min [1810000], rate=13575000.00/min [1820000], rate=13650000.00/min [1830000], rate=13725000.00/min [1840000], rate=13800000.00/min [1850000], rate=13875000.00/min [1860000], rate=13950000.00/min [1870000], rate=14025000.00/min [1880000], rate=14100000.00/min [1890000], rate=14175000.00/min [1900000], rate=14250000.00/min [1910000], rate=14325000.00/min [1920000], rate=14400000.00/min [1930000], rate=12866666.67/min [1940000], rate=12933333.33/min [1950000], rate=13000000.00/min [1960000], rate=13066666.67/min [1970000], rate=13133333.33/min [1980000], rate=13200000.00/min [1990000], rate=13266666.67/min [2000000], rate=13333333.33/min [2010000], rate=13400000.00/min [2020000], rate=13466666.67/min [2030000], rate=13533333.33/min [2040000], rate=13600000.00/min [2050000], rate=13666666.67/min [2060000], rate=13733333.33/min [2070000], rate=13800000.00/min [2080000], rate=13866666.67/min [2090000], rate=13933333.33/min [2100000], rate=14000000.00/min [2110000], rate=14066666.67/min [2120000], rate=14133333.33/min [2130000], rate=14200000.00/min [2140000], rate=14266666.67/min [2150000], rate=14333333.33/min [2160000], rate=14400000.00/min [2170000], rate=14466666.67/min [2180000], rate=14533333.33/min [2190000], rate=14600000.00/min [2200000], rate=13200000.00/min [2210000], rate=13260000.00/min [2220000], rate=13320000.00/min [2230000], rate=13380000.00/min [2240000], rate=13440000.00/min [2250000], rate=13500000.00/min [2260000], rate=13560000.00/min [2270000], rate=13620000.00/min [2280000], rate=13680000.00/min [2290000], rate=13740000.00/min [2300000], rate=13800000.00/min [2310000], rate=13860000.00/min [2320000], rate=13920000.00/min [2330000], rate=13980000.00/min [2340000], rate=14040000.00/min [2350000], rate=14100000.00/min [2360000], rate=14160000.00/min [2370000], rate=14220000.00/min [2380000], rate=14280000.00/min [2390000], rate=14340000.00/min [2400000], rate=14400000.00/min [2410000], rate=14460000.00/min [2420000], rate=14520000.00/min [2430000], rate=14580000.00/min [2440000], rate=14640000.00/min [2450000], rate=14700000.00/min 08:07:01 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-64cace-R1_A23WJ53LT4_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-64cace-R1_A23WJ53LT4_1.introns: identified 4257 cancer introns 08:07:02 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer.introns.prelim 08:07:02 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/prelim_introns.ok 08:07:02 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer.introns 08:07:03 : 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-64cace-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer.introns 08:07:03 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/introns_filtered.ok 08:07:03 : INFO : -found 733 cancer introns 08:07:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns --cancer_introns aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns.for_IGV.bed 08:07:03 : INFO : Creating the BED File. 08:07:05 : INFO : Saving Bed File as aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns.for_IGV.bed 08:07:05 : INFO : Execution Time = 0.04 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns --cancer_introns aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns.for_IGV.bed 08:07:05 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/intron_igv_bed.ok 08:07:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns.for_IGV.bed --bam aih-tih-sc-64cace-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-64cace-R1_A23WJ53LT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-64cace-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai 08:10:29 : INFO : Execution Time = 3.40 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns.for_IGV.bed --bam aih-tih-sc-64cace-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-64cace-R1_A23WJ53LT4_1 08:10:29 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/reads_alignments_extracted.ok 08:10:29 : INFO : Running: samtools sort -o aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer_intron_reads.bam 08:10:29 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer_intron_reads.bam 08:10:29 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/sort_cancer_intron_reads.ok 08:10:29 : INFO : Running: samtools sort -o aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.bam aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.bam [bam_sort_core] merging from 15 files and 1 in-memory blocks... 08:14:26 : INFO : Execution Time = 3.94 minutes. CMD: samtools sort -o aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.bam aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.bam 08:14:26 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/sort_gene_reads.ok 08:14:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.bam 08:15:40 : INFO : Execution Time = 1.23 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.bam 08:15:40 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 08:15:40 : INFO : Running: samtools sort -o aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 1 files and 1 in-memory blocks... 08:16:03 : INFO : Execution Time = 0.38 minutes. CMD: samtools sort -o aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp 08:16:03 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:16:03 : INFO : Running: samtools index aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam 08:16:05 : INFO : Execution Time = 0.05 minutes. CMD: samtools index aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam 08:16:05 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-64cace-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 08:16:05 : INFO : Running: samtools index aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam 08:16:05 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam 08:16:05 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-64cace-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 08:16:06 : INFO : Running: create_report aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-64cace-R1_A23WJ53LT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-64cace-R1_A23WJ53LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-64cace-R1_A23WJ53LT4_1' 08:20:04 : INFO : Execution Time = 3.98 minutes. CMD: create_report aih-tih-sc-64cace-R1_A23WJ53LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-64cace-R1_A23WJ53LT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-64cace-R1_A23WJ53LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-64cace-R1_A23WJ53LT4_1' 08:20:04 : INFO : Running: touch /tmp/nxf.XDD1g8fnjE/aih-tih-sc-64cace-R1_A23WJ53LT4_1.chckpts/igv_create_html.ok 08:20:04 : INFO : done.