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rate=30371428.57/min [10640000], rate=30400000.00/min [10650000], rate=30428571.43/min [10660000], rate=30457142.86/min 09:22:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00673_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00673_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_00673_B23MVV7LT4_1.introns: identified 4735 cancer introns 09:22:07 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00673_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00673_B23MVV7LT4_1.cancer.introns.prelim 09:22:07 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/prelim_introns.ok 09:22:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00673_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00673_B23MVV7LT4_1.cancer.introns 09:22:07 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00673_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00673_B23MVV7LT4_1.cancer.introns 09:22:07 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/introns_filtered.ok 09:22:07 : INFO : -found 2361 cancer introns 09:22:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00673_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00673_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00673_B23MVV7LT4_1.introns.for_IGV.bed 09:22:07 : INFO : Creating the BED File. 09:22:10 : INFO : Saving Bed File as tih_rna_sample_00673_B23MVV7LT4_1.introns.for_IGV.bed 09:22:10 : INFO : Execution Time = 0.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00673_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00673_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00673_B23MVV7LT4_1.introns.for_IGV.bed 09:22:10 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 09:22:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00673_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00673_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00673_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00673_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 09:33:19 : INFO : Execution Time = 11.15 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00673_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00673_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00673_B23MVV7LT4_1 09:33:19 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 09:33:19 : INFO : Running: samtools sort -o tih_rna_sample_00673_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00673_B23MVV7LT4_1.cancer_intron_reads.bam 09:33:19 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o tih_rna_sample_00673_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00673_B23MVV7LT4_1.cancer_intron_reads.bam 09:33:19 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 09:33:19 : INFO : Running: samtools sort -o tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 99 files and 1 in-memory blocks... 09:46:23 : INFO : Execution Time = 13.06 minutes. CMD: samtools sort -o tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.bam 09:46:23 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 09:46:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.bam 09:51:03 : INFO : Execution Time = 4.66 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.bam 09:51:03 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:51:03 : INFO : Running: samtools sort -o tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:51:28 : INFO : Execution Time = 0.42 minutes. CMD: samtools sort -o tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 09:51:28 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:51:28 : INFO : Running: samtools index tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 09:51:31 : INFO : Execution Time = 0.05 minutes. CMD: samtools index tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 09:51:31 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/tih_rna_sample_00673_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:51:31 : INFO : Running: samtools index tih_rna_sample_00673_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 09:51:31 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00673_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 09:51:31 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/tih_rna_sample_00673_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:51:31 : INFO : Running: create_report tih_rna_sample_00673_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00673_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00673_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00673_B23MVV7LT4_1' 09:54:46 : INFO : Execution Time = 3.25 minutes. CMD: create_report tih_rna_sample_00673_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00673_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00673_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00673_B23MVV7LT4_1' 09:54:46 : INFO : Running: touch /tmp/nxf.NWtSkGa7Zi/tih_rna_sample_00673_B23MVV7LT4_1.chckpts/igv_create_html.ok 09:54:46 : INFO : done.