07:37:09 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=30000000.00/min [510000], rate=30600000.00/min [520000], rate=31200000.00/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=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=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=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=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=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=17880000.00/min [1500000], rate=18000000.00/min [1510000], rate=18120000.00/min [1520000], rate=18240000.00/min [1530000], rate=18360000.00/min [1540000], rate=18480000.00/min [1550000], rate=18600000.00/min [1560000], rate=18720000.00/min [1570000], rate=18840000.00/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=17000000.00/min [1710000], rate=17100000.00/min [1720000], rate=17200000.00/min [1730000], rate=17300000.00/min [1740000], rate=17400000.00/min [1750000], rate=17500000.00/min [1760000], rate=17600000.00/min [1770000], rate=17700000.00/min [1780000], rate=17800000.00/min [1790000], rate=17900000.00/min [1800000], rate=18000000.00/min [1810000], rate=18100000.00/min [1820000], rate=18200000.00/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=17057142.86/min [2000000], rate=17142857.14/min [2010000], rate=17228571.43/min [2020000], rate=17314285.71/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 07:37:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_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. -BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns: identified 360 cancer introns 07:37:21 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns.prelim 07:37:21 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/prelim_introns.ok 07:37:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns 07:37:22 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns 07:37:22 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/introns_filtered.ok 07:37:22 : INFO : -found 170 cancer introns 07:37:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns --cancer_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed 07:37:22 : INFO : Creating the BED File. 07:37:23 : INFO : Saving Bed File as BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed 07:37:23 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns --cancer_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed 07:37:23 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/intron_igv_bed.ok 07:37:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed --bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1 [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai 07:37:35 : INFO : Execution Time = 0.20 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed --bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1 07:37:35 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/reads_alignments_extracted.ok 07:37:35 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.bam 07:37:35 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.bam 07:37:35 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/sort_cancer_intron_reads.ok 07:37:35 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.bam 07:37:49 : INFO : Execution Time = 0.23 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.bam 07:37:49 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/sort_gene_reads.ok 07:37:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.bam 07:37:53 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.bam 07:37:53 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 07:37:53 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp 07:37:54 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp 07:37:54 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 07:37:54 : INFO : Running: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam 07:37:55 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam 07:37:55 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 07:37:55 : INFO : Running: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.sorted.bam 07:37:55 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.sorted.bam 07:37:55 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 07:37:55 : INFO : Running: create_report BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1' 07:38:14 : INFO : Execution Time = 0.32 minutes. CMD: create_report BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1' 07:38:14 : INFO : Running: touch /tmp/nxf.9SvOKBz7P6/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_1.chckpts/igv_create_html.ok 07:38:14 : INFO : done.