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[6260000], rate=13414285.71/min [6270000], rate=13435714.29/min [6280000], rate=13457142.86/min [6290000], rate=13478571.43/min [6300000], rate=13500000.00/min [6310000], rate=13521428.57/min [6320000], rate=13542857.14/min [6330000], rate=13564285.71/min [6340000], rate=13585714.29/min [6350000], rate=13607142.86/min [6360000], rate=13628571.43/min [6370000], rate=13650000.00/min [6380000], rate=13671428.57/min [6390000], rate=13220689.66/min [6400000], rate=13241379.31/min [6410000], rate=13262068.97/min [6420000], rate=13282758.62/min [6430000], rate=13303448.28/min [6440000], rate=13324137.93/min [6450000], rate=13344827.59/min [6460000], rate=13365517.24/min [6470000], rate=13386206.90/min [6480000], rate=13406896.55/min [6490000], rate=13427586.21/min [6500000], rate=13448275.86/min [6510000], rate=13468965.52/min [6520000], rate=13489655.17/min [6530000], rate=13510344.83/min [6540000], rate=13531034.48/min [6550000], rate=13551724.14/min [6560000], rate=13572413.79/min [6570000], rate=13593103.45/min [6580000], rate=13613793.10/min [6590000], rate=13634482.76/min [6600000], rate=13655172.41/min [6610000], rate=13675862.07/min [6620000], rate=13696551.72/min [6630000], rate=13717241.38/min [6640000], rate=13737931.03/min 20:39:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-b567d0-R1_A23YTGFLT4_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. -aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns: identified 6517 cancer introns 20:39:07 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns.prelim 20:39:07 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 20:39:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns 20:39:07 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns 20:39:07 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 20:39:07 : INFO : -found 2180 cancer introns 20:39:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:39:08 : INFO : Creating the BED File. 20:39:14 : INFO : Saving Bed File as aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:39:14 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed 20:39:14 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 20:39:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-b567d0-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 20:57:16 : INFO : Execution Time = 18.04 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-b567d0-R1_A23YTGFLT4_1 20:57:16 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 20:57:16 : INFO : Running: samtools sort -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.bam 20:57:17 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.bam 20:57:17 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 20:57:17 : INFO : Running: samtools sort -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 73 files and 1 in-memory blocks... 21:15:04 : INFO : Execution Time = 17.79 minutes. CMD: samtools sort -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.bam 21:15:04 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok 21:15:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.bam 21:20:26 : INFO : Execution Time = 5.35 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.bam 21:20:26 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 21:20:26 : INFO : Running: samtools sort -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 21:21:19 : INFO : Execution Time = 0.89 minutes. CMD: samtools sort -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp 21:21:19 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 21:21:19 : INFO : Running: samtools index aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 21:21:25 : INFO : Execution Time = 0.10 minutes. CMD: samtools index aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 21:21:25 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 21:21:25 : INFO : Running: samtools index aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 21:21:25 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 21:21:25 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 21:21:25 : INFO : Running: create_report aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-b567d0-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-b567d0-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-b567d0-R1_A23YTGFLT4_1' 21:27:44 : INFO : Execution Time = 6.31 minutes. CMD: create_report aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-b567d0-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-b567d0-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-b567d0-R1_A23YTGFLT4_1' 21:27:44 : INFO : Running: touch /tmp/nxf.nVsfkjmRp4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok 21:27:44 : INFO : done.