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Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.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. -SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns: identified 7732 cancer introns 08:56:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim 08:56:44 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/prelim_introns.ok 08:56:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns 08:56:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns 08:56:44 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/introns_filtered.ok 08:56:44 : INFO : -found 3460 cancer introns 08:56:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns --cancer_introns SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed 08:56:45 : INFO : Creating the BED File. 08:56:56 : INFO : Saving Bed File as SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed 08:56:57 : INFO : Execution Time = 0.21 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns --cancer_introns SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed 08:56:57 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/intron_igv_bed.ok 08:56:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2 [W::hts_idx_load3] The index file is older than the data file: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai 09:30:56 : INFO : Execution Time = 33.99 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2 09:30:56 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok 09:30:56 : INFO : Running: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam 09:30:57 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam 09:30:57 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok 09:30:57 : INFO : Running: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.bam [bam_sort_core] merging from 139 files and 1 in-memory blocks... 10:05:42 : INFO : Execution Time = 34.76 minutes. CMD: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.bam 10:05:42 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/sort_gene_reads.ok 10:05:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam 10:16:15 : INFO : Execution Time = 10.54 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam 10:16:15 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp.ok 10:16:15 : INFO : Running: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 7 files and 1 in-memory blocks... 10:18:15 : INFO : Execution Time = 2.01 minutes. CMD: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp 10:18:15 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:18:15 : INFO : Running: samtools index SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 10:18:28 : INFO : Execution Time = 0.21 minutes. CMD: samtools index SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam 10:18:28 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.indexed.ok 10:18:28 : INFO : Running: samtools index SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 10:18:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam 10:18:28 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam.indexed.ok 10:18:28 : INFO : Running: create_report SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.ctat-splicing.igv.html --track-config SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2' 10:26:19 : INFO : Execution Time = 7.86 minutes. CMD: create_report SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.ctat-splicing.igv.html --track-config SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2' 10:26:19 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/igv_create_html.ok 10:26:19 : INFO : done.