20:12:29 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
[210000], rate=12600000.00/min
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[630000], rate=18900000.00/min
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[1180000], rate=17700000.00/min
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[1200000], rate=18000000.00/min
[1210000], rate=18150000.00/min
[1220000], rate=18300000.00/min
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[1710000], rate=17100000.00/min
[1720000], rate=17200000.00/min
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[1740000], rate=17400000.00/min
[1750000], rate=17500000.00/min
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[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
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[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=16457142.86/min
[1930000], rate=16542857.14/min
[1940000], rate=16628571.43/min
[1950000], rate=16714285.71/min
[1960000], rate=16800000.00/min
[1970000], rate=16885714.29/min
[1980000], rate=16971428.57/min
[1990000], rate=17057142.86/min
[2000000], rate=17142857.14/min
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[2030000], rate=17400000.00/min
[2040000], rate=17485714.29/min
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[2060000], rate=17657142.86/min
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[2080000], rate=17828571.43/min
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[2100000], rate=18000000.00/min
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[2120000], rate=18171428.57/min
[2130000], rate=18257142.86/min 20:12:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 22Rv1_FFPE_RNA_0001_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.
-22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns: identified 218 cancer introns
20:12:43 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim
20:12:43 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/prelim_introns.ok
20:12:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns
20:12:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns
20:12:44 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/introns_filtered.ok
20:12:44 : INFO : -found 83 cancer introns
20:12:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns --cancer_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
20:12:44 : INFO : Creating the BED File.
20:12:44 : INFO : Saving Bed File as 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
20:12:45 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns --cancer_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
20:12:45 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
20:12:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed --bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
20:12:50 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed --bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1
20:12:50 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
20:12:50 : INFO : Running: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.bam
20:12:50 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.bam
20:12:50 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
20:12:50 : INFO : Running: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.bam
20:12:56 : INFO : Execution Time = 0.09 minutes. CMD: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.bam
20:12:56 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
20:12:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam
20:12:58 : INFO : Execution Time = 0.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam
20:12:58 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
20:12:58 : INFO : Running: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
20:12:59 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
20:12:59 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
20:12:59 : INFO : Running: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
20:12:59 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
20:12:59 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
20:12:59 : INFO : Running: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
20:12:59 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
20:12:59 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
20:12:59 : INFO : Running: create_report 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.ctat-splicing.igv.html --track-config 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1'
20:13:10 : INFO : Execution Time = 0.19 minutes. CMD: create_report 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.ctat-splicing.igv.html --track-config 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1'
20:13:10 : INFO : Running: touch /tmp/nxf.uQAfHf8ON2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/igv_create_html.ok
20:13:10 : INFO : done.