20:56:00 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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=9300000.00/min [320000], rate=9600000.00/min [330000], rate=9900000.00/min [340000], rate=10200000.00/min [350000], rate=10500000.00/min 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[4720000], rate=18880000.00/min [4730000], rate=18920000.00/min [4740000], rate=18960000.00/min [4750000], rate=19000000.00/min [4760000], rate=19040000.00/min [4770000], rate=19080000.00/min [4780000], rate=19120000.00/min [4790000], rate=19160000.00/min [4800000], rate=18000000.00/min [4810000], rate=18037500.00/min [4820000], rate=18075000.00/min [4830000], rate=18112500.00/min [4840000], rate=18150000.00/min [4850000], rate=18187500.00/min [4860000], rate=18225000.00/min [4870000], rate=18262500.00/min [4880000], rate=18300000.00/min [4890000], rate=18337500.00/min [4900000], rate=18375000.00/min [4910000], rate=18412500.00/min [4920000], rate=18450000.00/min [4930000], rate=18487500.00/min [4940000], rate=18525000.00/min [4950000], rate=18562500.00/min [4960000], rate=18600000.00/min [4970000], rate=18637500.00/min [4980000], rate=18675000.00/min [4990000], rate=18712500.00/min [5000000], rate=18750000.00/min [5010000], rate=18787500.00/min [5020000], rate=18825000.00/min [5030000], rate=18862500.00/min [5040000], rate=18900000.00/min [5050000], rate=17823529.41/min [5060000], rate=17858823.53/min [5070000], rate=17894117.65/min [5080000], rate=17929411.76/min [5090000], rate=17964705.88/min [5100000], rate=18000000.00/min [5110000], rate=18035294.12/min [5120000], rate=18070588.24/min [5130000], rate=18105882.35/min [5140000], rate=18141176.47/min [5150000], rate=18176470.59/min [5160000], rate=18211764.71/min [5170000], rate=18247058.82/min [5180000], rate=18282352.94/min [5190000], rate=18317647.06/min [5200000], rate=18352941.18/min [5210000], rate=18388235.29/min [5220000], rate=18423529.41/min [5230000], rate=18458823.53/min [5240000], rate=18494117.65/min [5250000], rate=18529411.76/min [5260000], rate=18564705.88/min [5270000], rate=18600000.00/min 20:56:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNB_FFPE_L03_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_L03_RNA_01_B23LG7FLT4_1.introns: identified 229 cancer introns 20:56:24 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns.prelim 20:56:24 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok 20:56:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns 20:56:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns 20:56:24 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok 20:56:24 : INFO : -found 156 cancer introns 20:56:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --cancer_introns BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:56:25 : INFO : Creating the BED File. 20:56:25 : INFO : Saving Bed File as BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:56:25 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --cancer_introns BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 20:56:25 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok 20:56:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1 [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai 20:56:47 : INFO : Execution Time = 0.37 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1 20:56:47 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok 20:56:48 : INFO : Running: samtools sort -o BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam 20:56:48 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam 20:56:48 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok 20:56:48 : INFO : Running: samtools sort -o BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.bam [bam_sort_core] merging from 1 files and 1 in-memory blocks... 20:57:11 : INFO : Execution Time = 0.39 minutes. CMD: samtools sort -o BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.bam 20:57:11 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok 20:57:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 20:57:18 : INFO : Execution Time = 0.13 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 20:57:18 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 20:57:18 : INFO : Running: samtools sort -o BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 20:57:21 : INFO : Execution Time = 0.05 minutes. CMD: samtools sort -o BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 20:57:21 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 20:57:21 : INFO : Running: samtools index BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 20:57:22 : INFO : Execution Time = 0.01 minutes. CMD: samtools index BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 20:57:22 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 20:57:22 : INFO : Running: samtools index BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 20:57:22 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 20:57:22 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 20:57:22 : INFO : Running: create_report BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1' 20:57:48 : INFO : Execution Time = 0.44 minutes. CMD: create_report BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1' 20:57:48 : INFO : Running: touch /tmp/nxf.kgHCBHLpHG/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok 20:57:48 : INFO : done.