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rate=15117391.30/min [11600000], rate=15130434.78/min [11610000], rate=15143478.26/min [11620000], rate=15156521.74/min [11630000], rate=15169565.22/min [11640000], rate=15182608.70/min [11650000], rate=15195652.17/min [11660000], rate=15208695.65/min [11670000], rate=15221739.13/min [11680000], rate=15234782.61/min [11690000], rate=15247826.09/min [11700000], rate=15260869.57/min [11710000], rate=15273913.04/min [11720000], rate=15286956.52/min [11730000], rate=15300000.00/min [11740000], rate=15313043.48/min [11750000], rate=15326086.96/min [11760000], rate=15339130.43/min [11770000], rate=15352173.91/min [11780000], rate=15365217.39/min [11790000], rate=15378260.87/min [11800000], rate=15391304.35/min [11810000], rate=15404347.83/min [11820000], rate=15417391.30/min [11830000], rate=15430434.78/min [11840000], rate=15443478.26/min [11850000], rate=15456521.74/min [11860000], rate=15140425.53/min [11870000], rate=15153191.49/min [11880000], rate=15165957.45/min [11890000], rate=15178723.40/min [11900000], rate=15191489.36/min [11910000], rate=15204255.32/min [11920000], rate=15217021.28/min [11930000], rate=15229787.23/min [11940000], rate=15242553.19/min [11950000], rate=15255319.15/min [11960000], rate=15268085.11/min [11970000], rate=15280851.06/min [11980000], rate=15293617.02/min [11990000], rate=15306382.98/min [12000000], rate=15319148.94/min [12010000], rate=15331914.89/min [12020000], rate=15344680.85/min [12030000], rate=15357446.81/min [12040000], rate=15370212.77/min [12050000], rate=15382978.72/min [12060000], rate=15395744.68/min [12070000], rate=15408510.64/min [12080000], rate=15421276.60/min [12090000], rate=15434042.55/min [12100000], rate=15446808.51/min [12110000], rate=15459574.47/min [12120000], rate=15472340.43/min [12130000], rate=15485106.38/min [12140000], rate=15497872.34/min [12150000], rate=15510638.30/min [12160000], rate=15200000.00/min [12170000], rate=15212500.00/min [12180000], rate=15225000.00/min [12190000], rate=15237500.00/min [12200000], rate=15250000.00/min [12210000], rate=15262500.00/min [12220000], rate=15275000.00/min [12230000], rate=15287500.00/min [12240000], rate=15300000.00/min [12250000], rate=15312500.00/min [12260000], rate=15325000.00/min [12270000], rate=15337500.00/min [12280000], rate=15350000.00/min [12290000], rate=15362500.00/min [12300000], rate=15375000.00/min [12310000], rate=15387500.00/min [12320000], rate=15400000.00/min [12330000], rate=15412500.00/min [12340000], rate=15425000.00/min [12350000], rate=15437500.00/min [12360000], rate=15450000.00/min [12370000], rate=15462500.00/min [12380000], rate=15475000.00/min [12390000], rate=15487500.00/min [12400000], rate=15500000.00/min [12410000], rate=15512500.00/min [12420000], rate=15525000.00/min [12430000], rate=15537500.00/min [12440000], rate=15550000.00/min [12450000], rate=15562500.00/min [12460000], rate=15575000.00/min [12470000], rate=15269387.76/min [12480000], rate=15281632.65/min [12490000], rate=15293877.55/min [12500000], rate=15306122.45/min [12510000], rate=15318367.35/min [12520000], rate=15330612.24/min [12530000], rate=15342857.14/min [12540000], rate=15355102.04/min [12550000], rate=15367346.94/min [12560000], rate=15379591.84/min [12570000], rate=15391836.73/min [12580000], rate=15404081.63/min [12590000], rate=15416326.53/min [12600000], rate=15428571.43/min [12610000], rate=15440816.33/min [12620000], rate=15453061.22/min 09:04:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_Q7O_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_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns: identified 5452 cancer introns 09:04:11 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim 09:04:11 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/prelim_introns.ok 09:04:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns 09:04:12 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns 09:04:12 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/introns_filtered.ok 09:04:12 : INFO : -found 1748 cancer introns 09:04:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:04:12 : INFO : Creating the BED File. 09:04:16 : INFO : Saving Bed File as 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:04:16 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:04:16 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/intron_igv_bed.ok 09:04:16 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2 [W::hts_idx_load3] The index file is older than the data file: 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai 09:21:36 : INFO : Execution Time = 17.33 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2 09:21:36 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/reads_alignments_extracted.ok 09:21:36 : INFO : Running: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam 09:21:37 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam 09:21:37 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_cancer_intron_reads.ok 09:21:37 : INFO : Running: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam [bam_sort_core] merging from 78 files and 1 in-memory blocks... 09:41:08 : INFO : Execution Time = 19.51 minutes. CMD: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam 09:41:08 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_gene_reads.ok 09:41:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 09:46:28 : INFO : Execution Time = 5.34 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 09:46:28 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp.ok 09:46:28 : INFO : Running: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 2 files and 1 in-memory blocks... 09:47:08 : INFO : Execution Time = 0.66 minutes. CMD: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp 09:47:08 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:47:08 : INFO : Running: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 09:47:13 : INFO : Execution Time = 0.07 minutes. CMD: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 09:47:13 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.indexed.ok 09:47:13 : INFO : Running: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 09:47:13 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 09:47:13 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam.indexed.ok 09:47:13 : INFO : Running: create_report 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2' [W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi 09:52:52 : INFO : Execution Time = 5.66 minutes. CMD: create_report 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2' 09:52:52 : INFO : Running: touch /tmp/nxf.aGnZQSGpAy/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/igv_create_html.ok 09:52:52 : INFO : done.