09:07:48 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10060000], rate=10974545.45/min 09:08:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00737_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00737_B23MVV7LT4_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.
-tih_rna_sample_00737_B23MVV7LT4_1.introns: identified 7628 cancer introns
09:08:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00737_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns.prelim
09:08:57 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/prelim_introns.ok
09:08:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns
09:08:58 : 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_00737_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns
09:08:58 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/introns_filtered.ok
09:08:58 : INFO : -found 3571 cancer introns
09:08:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00737_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed
09:08:58 : INFO : Creating the BED File.
09:09:11 : INFO : Saving Bed File as tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed
09:09:12 : INFO : Execution Time = 0.23 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00737_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed
09:09:12 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/intron_igv_bed.ok
09:09:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00737_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00737_B23MVV7LT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00737_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
09:36:39 : INFO : Execution Time = 27.45 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00737_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00737_B23MVV7LT4_1
09:36:39 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok
09:36:39 : INFO : Running: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.bam
09:36:40 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.bam
09:36:40 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok
09:36:40 : INFO : Running: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.bam
[bam_sort_core] merging from 116 files and 1 in-memory blocks...
10:03:19 : INFO : Execution Time = 26.65 minutes. CMD: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.bam
10:03:19 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/sort_gene_reads.ok
10:03:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.bam
10:13:27 : INFO : Execution Time = 10.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.bam
10:13:27 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok
10:13:28 : INFO : Running: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
10:14:23 : INFO : Execution Time = 0.93 minutes. CMD: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp
10:14:23 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:14:23 : INFO : Running: samtools index tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam
10:14:30 : INFO : Execution Time = 0.11 minutes. CMD: samtools index tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam
10:14:30 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok
10:14:30 : INFO : Running: samtools index tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.sorted.bam
10:14:30 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.sorted.bam
10:14:30 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok
10:14:30 : INFO : Running: create_report tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00737_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00737_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00737_B23MVV7LT4_1'
10:21:26 : INFO : Execution Time = 6.93 minutes. CMD: create_report tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00737_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00737_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00737_B23MVV7LT4_1'
10:21:26 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/igv_create_html.ok
10:21:26 : INFO : done.