07:45:31 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[1000000], rate=30000000.00/min
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[1160000], rate=23200000.00/min
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[1340000], rate=20100000.00/min
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[1670000], rate=20040000.00/min
[1680000], rate=20160000.00/min
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[1860000], rate=18600000.00/min
[1870000], rate=18700000.00/min
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[1940000], rate=19400000.00/min
[1950000], rate=19500000.00/min
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[1980000], rate=19800000.00/min
[1990000], rate=19900000.00/min
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[2020000], rate=20200000.00/min
[2030000], rate=20300000.00/min
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[2050000], rate=20500000.00/min
[2060000], rate=20600000.00/min
[2070000], rate=20700000.00/min
[2080000], rate=20800000.00/min
[2090000], rate=20900000.00/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
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[2200000], rate=18857142.86/min
[2210000], rate=18942857.14/min
[2220000], rate=19028571.43/min
[2230000], rate=19114285.71/min
[2240000], rate=19200000.00/min
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[2260000], rate=19371428.57/min
[2270000], rate=19457142.86/min
[2280000], rate=19542857.14/min
[2290000], rate=19628571.43/min
[2300000], rate=19714285.71/min
[2310000], rate=19800000.00/min
[2320000], rate=19885714.29/min
[2330000], rate=19971428.57/min
[2340000], rate=20057142.86/min
[2350000], rate=20142857.14/min
[2360000], rate=20228571.43/min
[2370000], rate=20314285.71/min
[2380000], rate=20400000.00/min
[2390000], rate=20485714.29/min
[2400000], rate=18000000.00/min
[2410000], rate=18075000.00/min
[2420000], rate=18150000.00/min
[2430000], rate=18225000.00/min
[2440000], rate=18300000.00/min
[2450000], rate=18375000.00/min
[2460000], rate=18450000.00/min
[2470000], rate=18525000.00/min
[2480000], rate=18600000.00/min
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[2500000], rate=18750000.00/min
[2510000], rate=18825000.00/min
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[2540000], rate=19050000.00/min
[2550000], rate=19125000.00/min
[2560000], rate=19200000.00/min 07:45:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file dna_s764.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > dna_s764.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_s764.introns: identified 14 cancer introns
07:45:43 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file dna_s764.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > dna_s764.cancer.introns.prelim
07:45:43 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/prelim_introns.ok
07:45:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates dna_s764.cancer.introns.prelim --min_total_reads 5 > dna_s764.cancer.introns
07:45:43 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates dna_s764.cancer.introns.prelim --min_total_reads 5 > dna_s764.cancer.introns
07:45:43 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/introns_filtered.ok
07:45:43 : INFO : -found 3 cancer introns
07:45:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns dna_s764.introns --cancer_introns dna_s764.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed dna_s764.introns.for_IGV.bed
07:45:44 : INFO : Creating the BED File.
07:45:44 : INFO : Saving Bed File as dna_s764.introns.for_IGV.bed
07:45:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns dna_s764.introns --cancer_introns dna_s764.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed dna_s764.introns.for_IGV.bed
07:45:44 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/intron_igv_bed.ok
07:45:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed dna_s764.introns.for_IGV.bed --bam dna_s764.Aligned.sortedByCoord.out.bam --output_prefix dna_s764
[W::hts_idx_load3] The index file is older than the data file: dna_s764.Aligned.sortedByCoord.out.bam.bai
07:45:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed dna_s764.introns.for_IGV.bed --bam dna_s764.Aligned.sortedByCoord.out.bam --output_prefix dna_s764
07:45:44 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/reads_alignments_extracted.ok
07:45:44 : INFO : Running: samtools sort -o dna_s764.cancer_intron_reads.sorted.bam dna_s764.cancer_intron_reads.bam
07:45:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o dna_s764.cancer_intron_reads.sorted.bam dna_s764.cancer_intron_reads.bam
07:45:44 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/sort_cancer_intron_reads.ok
07:45:44 : INFO : Running: samtools sort -o dna_s764.gene_reads.sorted.bam dna_s764.gene_reads.bam
07:45:45 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o dna_s764.gene_reads.sorted.bam dna_s764.gene_reads.bam
07:45:45 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/sort_gene_reads.ok
07:45:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o dna_s764.gene_reads.sorted.sifted.bam.tmp --keep_secondary dna_s764.gene_reads.sorted.bam
07:45:45 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o dna_s764.gene_reads.sorted.sifted.bam.tmp --keep_secondary dna_s764.gene_reads.sorted.bam
07:45:45 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/dna_s764.gene_reads.sorted.sifted.bam.tmp.ok
07:45:45 : INFO : Running: samtools sort -o dna_s764.gene_reads.sorted.sifted.bam dna_s764.gene_reads.sorted.sifted.bam.tmp
07:45:45 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o dna_s764.gene_reads.sorted.sifted.bam dna_s764.gene_reads.sorted.sifted.bam.tmp
07:45:45 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/dna_s764.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:45:45 : INFO : Running: samtools index dna_s764.gene_reads.sorted.sifted.bam
07:45:45 : INFO : Execution Time = 0.00 minutes. CMD: samtools index dna_s764.gene_reads.sorted.sifted.bam
07:45:45 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/dna_s764.gene_reads.sorted.sifted.bam.indexed.ok
07:45:45 : INFO : Running: samtools index dna_s764.cancer_intron_reads.sorted.bam
07:45:45 : INFO : Execution Time = 0.00 minutes. CMD: samtools index dna_s764.cancer_intron_reads.sorted.bam
07:45:45 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/dna_s764.cancer_intron_reads.sorted.bam.indexed.ok
07:45:45 : INFO : Running: create_report dna_s764.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output dna_s764.ctat-splicing.igv.html --track-config dna_s764.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: dna_s764'
07:45:46 : INFO : Execution Time = 0.01 minutes. CMD: create_report dna_s764.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output dna_s764.ctat-splicing.igv.html --track-config dna_s764.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: dna_s764'
07:45:46 : INFO : Running: touch /tmp/nxf.aSwV4Y6yDY/dna_s764.chckpts/igv_create_html.ok
07:45:46 : INFO : done.