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rate=17940000.00/min [5990000], rate=17970000.00/min [6000000], rate=18000000.00/min [6010000], rate=18030000.00/min [6020000], rate=18060000.00/min [6030000], rate=18090000.00/min [6040000], rate=18120000.00/min [6050000], rate=18150000.00/min [6060000], rate=18180000.00/min [6070000], rate=18210000.00/min [6080000], rate=18240000.00/min [6090000], rate=18270000.00/min [6100000], rate=18300000.00/min [6110000], rate=18330000.00/min [6120000], rate=18360000.00/min [6130000], rate=18390000.00/min [6140000], rate=18420000.00/min 08:46:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00742_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00742_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_00742_B23MVV7LT4_1.introns: identified 5039 cancer introns 08:46:23 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00742_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00742_B23MVV7LT4_1.cancer.introns.prelim 08:46:23 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/prelim_introns.ok 08:46:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00742_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00742_B23MVV7LT4_1.cancer.introns 08:46:23 : 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_00742_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00742_B23MVV7LT4_1.cancer.introns 08:46:23 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/introns_filtered.ok 08:46:23 : INFO : -found 1340 cancer introns 08:46:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00742_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00742_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00742_B23MVV7LT4_1.introns.for_IGV.bed 08:46:23 : INFO : Creating the BED File. 08:46:26 : INFO : Saving Bed File as tih_rna_sample_00742_B23MVV7LT4_1.introns.for_IGV.bed 08:46:26 : INFO : Execution Time = 0.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00742_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00742_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00742_B23MVV7LT4_1.introns.for_IGV.bed 08:46:26 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 08:46:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00742_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00742_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00742_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00742_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 08:53:46 : INFO : Execution Time = 7.33 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00742_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00742_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00742_B23MVV7LT4_1 08:53:46 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 08:53:46 : INFO : Running: samtools sort -o tih_rna_sample_00742_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00742_B23MVV7LT4_1.cancer_intron_reads.bam 08:53:46 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o tih_rna_sample_00742_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00742_B23MVV7LT4_1.cancer_intron_reads.bam 08:53:46 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 08:53:46 : INFO : Running: samtools sort -o tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 41 files and 1 in-memory blocks... 09:02:33 : INFO : Execution Time = 8.78 minutes. CMD: samtools sort -o tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.bam 09:02:33 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 09:02:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.bam 09:04:54 : INFO : Execution Time = 2.35 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.bam 09:04:54 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:04:54 : INFO : Running: samtools sort -o tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 2 files and 1 in-memory blocks... 09:05:24 : INFO : Execution Time = 0.49 minutes. CMD: samtools sort -o tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 09:05:24 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:05:24 : INFO : Running: samtools index tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 09:05:27 : INFO : Execution Time = 0.05 minutes. CMD: samtools index tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 09:05:27 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/tih_rna_sample_00742_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:05:27 : INFO : Running: samtools index tih_rna_sample_00742_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 09:05:27 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00742_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 09:05:27 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/tih_rna_sample_00742_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:05:27 : INFO : Running: create_report tih_rna_sample_00742_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00742_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00742_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00742_B23MVV7LT4_1' 09:09:54 : INFO : Execution Time = 4.45 minutes. CMD: create_report tih_rna_sample_00742_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00742_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00742_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00742_B23MVV7LT4_1' 09:09:54 : INFO : Running: touch /tmp/nxf.BjmTB3AP3W/tih_rna_sample_00742_B23MVV7LT4_1.chckpts/igv_create_html.ok 09:09:54 : INFO : done.