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rate=11334375.00/min [12100000], rate=11343750.00/min [12110000], rate=11353125.00/min [12120000], rate=11362500.00/min [12130000], rate=11196923.08/min [12140000], rate=11206153.85/min [12150000], rate=11215384.62/min [12160000], rate=11224615.38/min [12170000], rate=11233846.15/min [12180000], rate=11243076.92/min [12190000], rate=11252307.69/min [12200000], rate=11261538.46/min [12210000], rate=11270769.23/min [12220000], rate=11280000.00/min [12230000], rate=11289230.77/min [12240000], rate=11298461.54/min [12250000], rate=11307692.31/min [12260000], rate=11316923.08/min [12270000], rate=11326153.85/min [12280000], rate=11335384.62/min [12290000], rate=11344615.38/min [12300000], rate=11353846.15/min [12310000], rate=11363076.92/min [12320000], rate=11372307.69/min [12330000], rate=11381538.46/min [12340000], rate=11390769.23/min [12350000], rate=11227272.73/min [12360000], rate=11236363.64/min [12370000], rate=11245454.55/min [12380000], rate=11254545.45/min [12390000], rate=11263636.36/min [12400000], rate=11272727.27/min [12410000], rate=11281818.18/min [12420000], rate=11290909.09/min [12430000], rate=11300000.00/min [12440000], rate=11309090.91/min [12450000], rate=11318181.82/min [12460000], rate=11327272.73/min [12470000], rate=11336363.64/min [12480000], rate=11345454.55/min [12490000], rate=11354545.45/min [12500000], rate=11363636.36/min [12510000], rate=11372727.27/min [12520000], rate=11381818.18/min [12530000], rate=11390909.09/min [12540000], rate=11400000.00/min [12550000], rate=11409090.91/min [12560000], rate=11247761.19/min [12570000], rate=11256716.42/min [12580000], rate=11265671.64/min [12590000], rate=11274626.87/min [12600000], rate=11283582.09/min [12610000], rate=11292537.31/min [12620000], rate=11301492.54/min [12630000], rate=11310447.76/min [12640000], rate=11319402.99/min [12650000], rate=11328358.21/min [12660000], rate=11337313.43/min [12670000], rate=11346268.66/min [12680000], rate=11355223.88/min [12690000], rate=11364179.10/min [12700000], rate=11373134.33/min [12710000], rate=11382089.55/min [12720000], rate=11391044.78/min [12730000], rate=11400000.00/min [12740000], rate=11408955.22/min [12750000], rate=11417910.45/min [12760000], rate=11426865.67/min [12770000], rate=11267647.06/min [12780000], rate=11276470.59/min [12790000], rate=11285294.12/min [12800000], rate=11294117.65/min [12810000], rate=11302941.18/min [12820000], rate=11311764.71/min [12830000], rate=11320588.24/min [12840000], rate=11329411.76/min [12850000], rate=11338235.29/min [12860000], rate=11347058.82/min [12870000], rate=11355882.35/min [12880000], rate=11364705.88/min [12890000], rate=11373529.41/min [12900000], rate=11382352.94/min [12910000], rate=11391176.47/min [12920000], rate=11400000.00/min [12930000], rate=11408823.53/min [12940000], rate=11417647.06/min [12950000], rate=11426470.59/min [12960000], rate=11435294.12/min [12970000], rate=11444117.65/min [12980000], rate=11452941.18/min [12990000], rate=11295652.17/min [13000000], rate=11304347.83/min [13010000], rate=11313043.48/min [13020000], rate=11321739.13/min [13030000], rate=11330434.78/min [13040000], rate=11339130.43/min [13050000], rate=11347826.09/min [13060000], rate=11356521.74/min [13070000], rate=11365217.39/min [13080000], rate=11373913.04/min [13090000], rate=11382608.70/min [13100000], rate=11391304.35/min [13110000], rate=11400000.00/min [13120000], rate=11408695.65/min [13130000], rate=11417391.30/min [13140000], rate=11426086.96/min [13150000], rate=11434782.61/min [13160000], rate=11443478.26/min [13170000], rate=11452173.91/min [13180000], rate=11460869.57/min [13190000], rate=11469565.22/min [13200000], rate=11478260.87/min [13210000], rate=11322857.14/min [13220000], rate=11331428.57/min [13230000], rate=11340000.00/min [13240000], rate=11348571.43/min 07:41:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_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. -1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 829 cancer introns 07:41:26 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim 07:41:26 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok 07:41:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 07:41:27 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 07:41:27 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok 07:41:27 : INFO : -found 112 cancer introns 07:41:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 07:41:27 : INFO : Creating the BED File. 07:41:28 : INFO : Saving Bed File as 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 07:41:28 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 07:41:28 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok 07:41:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1 [W::hts_idx_load3] The index file is older than the data file: 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai 07:42:14 : INFO : Execution Time = 0.76 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1 07:42:14 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok 07:42:14 : INFO : Running: samtools sort -o 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 07:42:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 07:42:14 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok 07:42:14 : INFO : Running: samtools sort -o 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam [bam_sort_core] merging from 2 files and 1 in-memory blocks... 07:43:04 : INFO : Execution Time = 0.84 minutes. CMD: samtools sort -o 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam 07:43:04 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok 07:43:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 07:43:23 : INFO : Execution Time = 0.30 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 07:43:23 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 07:43:23 : INFO : Running: samtools sort -o 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp 07:43:32 : INFO : Execution Time = 0.15 minutes. CMD: samtools sort -o 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp 07:43:32 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 07:43:32 : INFO : Running: samtools index 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 07:43:33 : INFO : Execution Time = 0.02 minutes. CMD: samtools index 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 07:43:33 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 07:43:33 : INFO : Running: samtools index 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 07:43:33 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 07:43:33 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 07:43:33 : INFO : Running: create_report 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1' 07:46:20 : INFO : Execution Time = 2.79 minutes. CMD: create_report 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1' 07:46:20 : INFO : Running: touch /tmp/nxf.HGPnQ2QO3O/1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok 07:46:20 : INFO : done.