08:51:38 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10050000], rate=10050000.00/min 08:52:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file V4_0001_RNA_0005_23H5VFLT4_s25.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > V4_0001_RNA_0005_23H5VFLT4_s25.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.
-V4_0001_RNA_0005_23H5VFLT4_s25.introns: identified 5944 cancer introns
08:52:50 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file V4_0001_RNA_0005_23H5VFLT4_s25.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > V4_0001_RNA_0005_23H5VFLT4_s25.cancer.introns.prelim
08:52:50 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/prelim_introns.ok
08:52:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates V4_0001_RNA_0005_23H5VFLT4_s25.cancer.introns.prelim --min_total_reads 5 > V4_0001_RNA_0005_23H5VFLT4_s25.cancer.introns
08:52:51 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates V4_0001_RNA_0005_23H5VFLT4_s25.cancer.introns.prelim --min_total_reads 5 > V4_0001_RNA_0005_23H5VFLT4_s25.cancer.introns
08:52:51 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/introns_filtered.ok
08:52:51 : INFO : -found 3313 cancer introns
08:52:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns V4_0001_RNA_0005_23H5VFLT4_s25.introns --cancer_introns V4_0001_RNA_0005_23H5VFLT4_s25.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed V4_0001_RNA_0005_23H5VFLT4_s25.introns.for_IGV.bed
08:52:51 : INFO : Creating the BED File.
08:53:03 : INFO : Saving Bed File as V4_0001_RNA_0005_23H5VFLT4_s25.introns.for_IGV.bed
08:53:03 : INFO : Execution Time = 0.21 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns V4_0001_RNA_0005_23H5VFLT4_s25.introns --cancer_introns V4_0001_RNA_0005_23H5VFLT4_s25.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed V4_0001_RNA_0005_23H5VFLT4_s25.introns.for_IGV.bed
08:53:03 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/intron_igv_bed.ok
08:53:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed V4_0001_RNA_0005_23H5VFLT4_s25.introns.for_IGV.bed --bam V4_0001_RNA_0005_23H5VFLT4_s25.Aligned.sortedByCoord.out.bam --output_prefix V4_0001_RNA_0005_23H5VFLT4_s25
[W::hts_idx_load3] The index file is older than the data file: V4_0001_RNA_0005_23H5VFLT4_s25.Aligned.sortedByCoord.out.bam.bai
09:17:03 : INFO : Execution Time = 23.99 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed V4_0001_RNA_0005_23H5VFLT4_s25.introns.for_IGV.bed --bam V4_0001_RNA_0005_23H5VFLT4_s25.Aligned.sortedByCoord.out.bam --output_prefix V4_0001_RNA_0005_23H5VFLT4_s25
09:17:03 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/reads_alignments_extracted.ok
09:17:03 : INFO : Running: samtools sort -o V4_0001_RNA_0005_23H5VFLT4_s25.cancer_intron_reads.sorted.bam V4_0001_RNA_0005_23H5VFLT4_s25.cancer_intron_reads.bam
09:17:04 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o V4_0001_RNA_0005_23H5VFLT4_s25.cancer_intron_reads.sorted.bam V4_0001_RNA_0005_23H5VFLT4_s25.cancer_intron_reads.bam
09:17:04 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/sort_cancer_intron_reads.ok
09:17:04 : INFO : Running: samtools sort -o V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.bam V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.bam
[bam_sort_core] merging from 87 files and 1 in-memory blocks...
09:41:34 : INFO : Execution Time = 24.50 minutes. CMD: samtools sort -o V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.bam V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.bam
09:41:34 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/sort_gene_reads.ok
09:41:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam.tmp --keep_secondary V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.bam
09:49:59 : INFO : Execution Time = 8.42 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam.tmp --keep_secondary V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.bam
09:49:59 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam.tmp.ok
09:49:59 : INFO : Running: samtools sort -o V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 7 files and 1 in-memory blocks...
09:52:05 : INFO : Execution Time = 2.10 minutes. CMD: samtools sort -o V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam.tmp
09:52:05 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:52:05 : INFO : Running: samtools index V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam
09:52:18 : INFO : Execution Time = 0.22 minutes. CMD: samtools index V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam
09:52:18 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/V4_0001_RNA_0005_23H5VFLT4_s25.gene_reads.sorted.sifted.bam.indexed.ok
09:52:18 : INFO : Running: samtools index V4_0001_RNA_0005_23H5VFLT4_s25.cancer_intron_reads.sorted.bam
09:52:19 : INFO : Execution Time = 0.00 minutes. CMD: samtools index V4_0001_RNA_0005_23H5VFLT4_s25.cancer_intron_reads.sorted.bam
09:52:19 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/V4_0001_RNA_0005_23H5VFLT4_s25.cancer_intron_reads.sorted.bam.indexed.ok
09:52:19 : INFO : Running: create_report V4_0001_RNA_0005_23H5VFLT4_s25.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output V4_0001_RNA_0005_23H5VFLT4_s25.ctat-splicing.igv.html --track-config V4_0001_RNA_0005_23H5VFLT4_s25.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: V4_0001_RNA_0005_23H5VFLT4_s25'
09:57:18 : INFO : Execution Time = 4.99 minutes. CMD: create_report V4_0001_RNA_0005_23H5VFLT4_s25.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output V4_0001_RNA_0005_23H5VFLT4_s25.ctat-splicing.igv.html --track-config V4_0001_RNA_0005_23H5VFLT4_s25.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: V4_0001_RNA_0005_23H5VFLT4_s25'
09:57:18 : INFO : Running: touch /tmp/nxf.6iM8FpqWZn/V4_0001_RNA_0005_23H5VFLT4_s25.chckpts/igv_create_html.ok
09:57:18 : INFO : done.