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.