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rate=16022727.27/min [11760000], rate=16036363.64/min [11770000], rate=16050000.00/min [11780000], rate=16063636.36/min [11790000], rate=16077272.73/min [11800000], rate=16090909.09/min [11810000], rate=16104545.45/min [11820000], rate=15760000.00/min [11830000], rate=15773333.33/min [11840000], rate=15786666.67/min [11850000], rate=15800000.00/min [11860000], rate=15813333.33/min [11870000], rate=15826666.67/min [11880000], rate=15840000.00/min [11890000], rate=15853333.33/min [11900000], rate=15866666.67/min [11910000], rate=15880000.00/min [11920000], rate=15893333.33/min [11930000], rate=15906666.67/min [11940000], rate=15920000.00/min [11950000], rate=15933333.33/min [11960000], rate=15946666.67/min [11970000], rate=15960000.00/min [11980000], rate=15973333.33/min [11990000], rate=15986666.67/min [12000000], rate=16000000.00/min [12010000], rate=16013333.33/min [12020000], rate=16026666.67/min [12030000], rate=16040000.00/min [12040000], rate=16053333.33/min [12050000], rate=16066666.67/min [12060000], rate=16080000.00/min [12070000], rate=16093333.33/min [12080000], rate=16106666.67/min [12090000], rate=16120000.00/min [12100000], rate=16133333.33/min [12110000], rate=15795652.17/min [12120000], rate=15808695.65/min [12130000], rate=15821739.13/min [12140000], rate=15834782.61/min [12150000], rate=15847826.09/min [12160000], rate=15860869.57/min [12170000], rate=15873913.04/min [12180000], rate=15886956.52/min [12190000], rate=15900000.00/min [12200000], rate=15913043.48/min [12210000], rate=15926086.96/min [12220000], rate=15939130.43/min [12230000], rate=15952173.91/min [12240000], rate=15965217.39/min [12250000], rate=15978260.87/min [12260000], rate=15991304.35/min [12270000], rate=16004347.83/min [12280000], rate=16017391.30/min [12290000], rate=16030434.78/min [12300000], rate=16043478.26/min [12310000], rate=16056521.74/min [12320000], rate=16069565.22/min [12330000], rate=16082608.70/min [12340000], rate=16095652.17/min [12350000], rate=16108695.65/min [12360000], rate=16121739.13/min [12370000], rate=16134782.61/min [12380000], rate=16147826.09/min [12390000], rate=16160869.57/min 09:13:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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. -1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns: identified 7370 cancer introns 09:13:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim 09:13:24 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/prelim_introns.ok 09:13:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns 09:13:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns 09:13:24 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/introns_filtered.ok 09:13:24 : INFO : -found 2514 cancer introns 09:13:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:13:24 : INFO : Creating the BED File. 09:13:30 : INFO : Saving Bed File as 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:13:30 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:13:30 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/intron_igv_bed.ok 09:13:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 [W::hts_idx_load3] The index file is older than the data file: 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai 09:37:30 : INFO : Execution Time = 23.99 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 09:37:30 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/reads_alignments_extracted.ok 09:37:30 : INFO : Running: samtools sort -o 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam 09:37:31 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam 09:37:31 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_cancer_intron_reads.ok 09:37:31 : INFO : Running: samtools sort -o 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam [bam_sort_core] merging from 106 files and 1 in-memory blocks... 10:04:32 : INFO : Execution Time = 27.01 minutes. CMD: samtools sort -o 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam 10:04:32 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_gene_reads.ok 10:04:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 10:11:32 : INFO : Execution Time = 7.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 10:11:32 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp.ok 10:11:32 : INFO : Running: samtools sort -o 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:12:23 : INFO : Execution Time = 0.85 minutes. CMD: samtools sort -o 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp 10:12:23 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:12:23 : INFO : Running: samtools index 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 10:12:28 : INFO : Execution Time = 0.09 minutes. CMD: samtools index 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 10:12:28 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.indexed.ok 10:12:28 : INFO : Running: samtools index 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 10:12:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 10:12:28 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam.indexed.ok 10:12:28 : INFO : Running: create_report 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2' 10:19:01 : INFO : Execution Time = 6.54 minutes. CMD: create_report 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2' 10:19:01 : INFO : Running: touch /tmp/nxf.MiZ8wRbqt3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/igv_create_html.ok 10:19:01 : INFO : done.