00:14:11 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[2800000], rate=7636363.64/min 00:14:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00096_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00096_B23WHTKLT4_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.
-tih_rna_sample_00096_B23WHTKLT4_2.introns: identified 4913 cancer introns
00:14:45 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00096_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00096_B23WHTKLT4_2.cancer.introns.prelim
00:14:45 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/prelim_introns.ok
00:14:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00096_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00096_B23WHTKLT4_2.cancer.introns
00:14:46 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00096_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00096_B23WHTKLT4_2.cancer.introns
00:14:46 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/introns_filtered.ok
00:14:46 : INFO : -found 1242 cancer introns
00:14:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00096_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00096_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00096_B23WHTKLT4_2.introns.for_IGV.bed
00:14:46 : INFO : Creating the BED File.
00:14:52 : INFO : Saving Bed File as tih_rna_sample_00096_B23WHTKLT4_2.introns.for_IGV.bed
00:14:52 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00096_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00096_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00096_B23WHTKLT4_2.introns.for_IGV.bed
00:14:52 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/intron_igv_bed.ok
00:14:52 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00096_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00096_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00096_B23WHTKLT4_2
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00096_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam.bai
00:19:42 : INFO : Execution Time = 4.83 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00096_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00096_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00096_B23WHTKLT4_2
00:19:42 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/reads_alignments_extracted.ok
00:19:42 : INFO : Running: samtools sort -o tih_rna_sample_00096_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00096_B23WHTKLT4_2.cancer_intron_reads.bam
00:19:42 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00096_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00096_B23WHTKLT4_2.cancer_intron_reads.bam
00:19:42 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/sort_cancer_intron_reads.ok
00:19:42 : INFO : Running: samtools sort -o tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.bam
[bam_sort_core] merging from 16 files and 1 in-memory blocks...
00:25:18 : INFO : Execution Time = 5.59 minutes. CMD: samtools sort -o tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.bam
00:25:18 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/sort_gene_reads.ok
00:25:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.bam
00:27:01 : INFO : Execution Time = 1.71 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.bam
00:27:01 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
00:27:01 : INFO : Running: samtools sort -o tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
00:27:25 : INFO : Execution Time = 0.40 minutes. CMD: samtools sort -o tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp
00:27:25 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
00:27:25 : INFO : Running: samtools index tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam
00:27:28 : INFO : Execution Time = 0.04 minutes. CMD: samtools index tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam
00:27:28 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/tih_rna_sample_00096_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
00:27:28 : INFO : Running: samtools index tih_rna_sample_00096_B23WHTKLT4_2.cancer_intron_reads.sorted.bam
00:27:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00096_B23WHTKLT4_2.cancer_intron_reads.sorted.bam
00:27:28 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/tih_rna_sample_00096_B23WHTKLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
00:27:28 : INFO : Running: create_report tih_rna_sample_00096_B23WHTKLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00096_B23WHTKLT4_2.ctat-splicing.igv.html --track-config tih_rna_sample_00096_B23WHTKLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00096_B23WHTKLT4_2'
00:29:32 : INFO : Execution Time = 2.07 minutes. CMD: create_report tih_rna_sample_00096_B23WHTKLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00096_B23WHTKLT4_2.ctat-splicing.igv.html --track-config tih_rna_sample_00096_B23WHTKLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00096_B23WHTKLT4_2'
00:29:32 : INFO : Running: touch /tmp/nxf.rfxGmi59Gt/tih_rna_sample_00096_B23WHTKLT4_2.chckpts/igv_create_html.ok
00:29:32 : INFO : done.