07:47:18 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[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=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=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=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=17200000.00/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=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=17400000.00/min
[1170000], rate=17550000.00/min
[1180000], rate=17700000.00/min
[1190000], rate=17850000.00/min
[1200000], rate=18000000.00/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=17400000.00/min
[1460000], rate=17520000.00/min
[1470000], rate=17640000.00/min
[1480000], rate=17760000.00/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=16800000.00/min
[1690000], rate=16900000.00/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=14475000.00/min
[1940000], rate=14550000.00/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=14666666.67/min
[2210000], rate=14733333.33/min
[2220000], rate=14800000.00/min
[2230000], rate=14866666.67/min
[2240000], rate=14933333.33/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=14580000.00/min
[2440000], rate=14640000.00/min
[2450000], rate=14700000.00/min
[2460000], rate=14760000.00/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=15840000.00/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
[2720000], rate=14836363.64/min
[2730000], rate=14890909.09/min
[2740000], rate=14945454.55/min
[2750000], rate=15000000.00/min
[2760000], rate=15054545.45/min
[2770000], rate=15109090.91/min
[2780000], rate=15163636.36/min
[2790000], rate=15218181.82/min
[2800000], rate=15272727.27/min
[2810000], rate=15327272.73/min
[2820000], rate=15381818.18/min
[2830000], rate=15436363.64/min
[2840000], rate=15490909.09/min
[2850000], rate=15545454.55/min
[2860000], rate=15600000.00/min
[2870000], rate=15654545.45/min
[2880000], rate=15709090.91/min
[2890000], rate=15763636.36/min
[2900000], rate=15818181.82/min
[2910000], rate=14550000.00/min
[2920000], rate=14600000.00/min
[2930000], rate=14650000.00/min
[2940000], rate=14700000.00/min
[2950000], rate=14750000.00/min
[2960000], rate=14800000.00/min
[2970000], rate=14850000.00/min
[2980000], rate=14900000.00/min 07:47:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file dna_s755.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > dna_s755.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.
-dna_s755.introns: identified 16 cancer introns
07:47:35 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file dna_s755.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > dna_s755.cancer.introns.prelim
07:47:35 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/prelim_introns.ok
07:47:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates dna_s755.cancer.introns.prelim --min_total_reads 5 > dna_s755.cancer.introns
07:47:36 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates dna_s755.cancer.introns.prelim --min_total_reads 5 > dna_s755.cancer.introns
07:47:36 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/introns_filtered.ok
07:47:36 : INFO : -found 4 cancer introns
07:47:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns dna_s755.introns --cancer_introns dna_s755.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed dna_s755.introns.for_IGV.bed
07:47:36 : INFO : Creating the BED File.
07:47:36 : INFO : Saving Bed File as dna_s755.introns.for_IGV.bed
07:47:36 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns dna_s755.introns --cancer_introns dna_s755.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed dna_s755.introns.for_IGV.bed
07:47:36 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/intron_igv_bed.ok
07:47:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed dna_s755.introns.for_IGV.bed --bam dna_s755.Aligned.sortedByCoord.out.bam --output_prefix dna_s755
[W::hts_idx_load3] The index file is older than the data file: dna_s755.Aligned.sortedByCoord.out.bam.bai
07:47:37 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed dna_s755.introns.for_IGV.bed --bam dna_s755.Aligned.sortedByCoord.out.bam --output_prefix dna_s755
07:47:37 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/reads_alignments_extracted.ok
07:47:37 : INFO : Running: samtools sort -o dna_s755.cancer_intron_reads.sorted.bam dna_s755.cancer_intron_reads.bam
07:47:37 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o dna_s755.cancer_intron_reads.sorted.bam dna_s755.cancer_intron_reads.bam
07:47:37 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/sort_cancer_intron_reads.ok
07:47:37 : INFO : Running: samtools sort -o dna_s755.gene_reads.sorted.bam dna_s755.gene_reads.bam
07:47:38 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o dna_s755.gene_reads.sorted.bam dna_s755.gene_reads.bam
07:47:38 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/sort_gene_reads.ok
07:47:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o dna_s755.gene_reads.sorted.sifted.bam.tmp --keep_secondary dna_s755.gene_reads.sorted.bam
07:47:38 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o dna_s755.gene_reads.sorted.sifted.bam.tmp --keep_secondary dna_s755.gene_reads.sorted.bam
07:47:38 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/dna_s755.gene_reads.sorted.sifted.bam.tmp.ok
07:47:38 : INFO : Running: samtools sort -o dna_s755.gene_reads.sorted.sifted.bam dna_s755.gene_reads.sorted.sifted.bam.tmp
07:47:38 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o dna_s755.gene_reads.sorted.sifted.bam dna_s755.gene_reads.sorted.sifted.bam.tmp
07:47:38 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/dna_s755.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:47:38 : INFO : Running: samtools index dna_s755.gene_reads.sorted.sifted.bam
07:47:38 : INFO : Execution Time = 0.00 minutes. CMD: samtools index dna_s755.gene_reads.sorted.sifted.bam
07:47:38 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/dna_s755.gene_reads.sorted.sifted.bam.indexed.ok
07:47:38 : INFO : Running: samtools index dna_s755.cancer_intron_reads.sorted.bam
07:47:38 : INFO : Execution Time = 0.00 minutes. CMD: samtools index dna_s755.cancer_intron_reads.sorted.bam
07:47:38 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/dna_s755.cancer_intron_reads.sorted.bam.indexed.ok
07:47:38 : INFO : Running: create_report dna_s755.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output dna_s755.ctat-splicing.igv.html --track-config dna_s755.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: dna_s755'
07:47:39 : INFO : Execution Time = 0.02 minutes. CMD: create_report dna_s755.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output dna_s755.ctat-splicing.igv.html --track-config dna_s755.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: dna_s755'
07:47:39 : INFO : Running: touch /tmp/nxf.3ynxplPf0g/dna_s755.chckpts/igv_create_html.ok
07:47:39 : INFO : done.