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rate=11937931.03/min [11550000], rate=11948275.86/min [11560000], rate=11958620.69/min [11570000], rate=11968965.52/min [11580000], rate=11979310.34/min [11590000], rate=11989655.17/min [11600000], rate=12000000.00/min [11610000], rate=11806779.66/min [11620000], rate=11816949.15/min [11630000], rate=11827118.64/min [11640000], rate=11837288.14/min [11650000], rate=11847457.63/min [11660000], rate=11857627.12/min [11670000], rate=11867796.61/min [11680000], rate=11877966.10/min [11690000], rate=11888135.59/min [11700000], rate=11898305.08/min [11710000], rate=11908474.58/min [11720000], rate=11918644.07/min [11730000], rate=11928813.56/min [11740000], rate=11938983.05/min [11750000], rate=11949152.54/min [11760000], rate=11959322.03/min [11770000], rate=11969491.53/min [11780000], rate=11979661.02/min [11790000], rate=11989830.51/min [11800000], rate=12000000.00/min [11810000], rate=12010169.49/min [11820000], rate=12020338.98/min [11830000], rate=12030508.47/min [11840000], rate=12040677.97/min [11850000], rate=12050847.46/min [11860000], rate=12061016.95/min [11870000], rate=12071186.44/min [11880000], rate=12081355.93/min [11890000], rate=12091525.42/min [11900000], rate=11900000.00/min [11910000], rate=11910000.00/min [11920000], rate=11920000.00/min [11930000], rate=11930000.00/min [11940000], rate=11940000.00/min [11950000], rate=11950000.00/min [11960000], rate=11960000.00/min [11970000], rate=11970000.00/min [11980000], rate=11980000.00/min [11990000], rate=11990000.00/min [12000000], rate=12000000.00/min [12010000], rate=12010000.00/min [12020000], rate=12020000.00/min [12030000], rate=12030000.00/min [12040000], rate=12040000.00/min [12050000], rate=12050000.00/min [12060000], rate=12060000.00/min [12070000], rate=12070000.00/min [12080000], rate=12080000.00/min [12090000], rate=12090000.00/min [12100000], rate=12100000.00/min [12110000], rate=12110000.00/min [12120000], rate=12120000.00/min [12130000], rate=12130000.00/min [12140000], rate=12140000.00/min [12150000], rate=12150000.00/min [12160000], rate=12160000.00/min [12170000], rate=12170000.00/min [12180000], rate=11980327.87/min [12190000], rate=11990163.93/min [12200000], rate=12000000.00/min [12210000], rate=12009836.07/min [12220000], rate=12019672.13/min [12230000], rate=12029508.20/min [12240000], rate=12039344.26/min [12250000], rate=12049180.33/min [12260000], rate=12059016.39/min [12270000], rate=12068852.46/min [12280000], rate=12078688.52/min [12290000], rate=12088524.59/min [12300000], rate=12098360.66/min [12310000], rate=12108196.72/min [12320000], rate=12118032.79/min [12330000], rate=12127868.85/min [12340000], rate=12137704.92/min [12350000], rate=12147540.98/min [12360000], rate=12157377.05/min [12370000], rate=12167213.11/min [12380000], rate=12177049.18/min [12390000], rate=12186885.25/min [12400000], rate=12196721.31/min [12410000], rate=12206557.38/min [12420000], rate=12216393.44/min [12430000], rate=12226229.51/min [12440000], rate=12236065.57/min [12450000], rate=12245901.64/min [12460000], rate=12255737.70/min [12470000], rate=12265573.77/min [12480000], rate=12275409.84/min [12490000], rate=12087096.77/min [12500000], rate=12096774.19/min [12510000], rate=12106451.61/min [12520000], rate=12116129.03/min [12530000], rate=12125806.45/min [12540000], rate=12135483.87/min [12550000], rate=12145161.29/min [12560000], rate=12154838.71/min [12570000], rate=12164516.13/min [12580000], rate=12174193.55/min [12590000], rate=12183870.97/min [12600000], rate=12193548.39/min [12610000], rate=12203225.81/min [12620000], rate=12212903.23/min [12630000], rate=12222580.65/min [12640000], rate=12232258.06/min [12650000], rate=12241935.48/min [12660000], rate=12251612.90/min [12670000], rate=12261290.32/min [12680000], rate=12270967.74/min [12690000], rate=12280645.16/min [12700000], rate=12290322.58/min [12710000], rate=12300000.00/min [12720000], rate=12114285.71/min [12730000], rate=12123809.52/min [12740000], rate=12133333.33/min [12750000], rate=12142857.14/min [12760000], rate=12152380.95/min [12770000], rate=12161904.76/min [12780000], rate=12171428.57/min [12790000], rate=12180952.38/min [12800000], rate=12190476.19/min [12810000], rate=12200000.00/min [12820000], rate=12209523.81/min [12830000], rate=12219047.62/min [12840000], rate=12228571.43/min [12850000], rate=12238095.24/min [12860000], rate=12247619.05/min [12870000], rate=12257142.86/min [12880000], rate=12266666.67/min [12890000], rate=12276190.48/min [12900000], rate=12285714.29/min [12910000], rate=12295238.10/min [12920000], rate=12304761.90/min [12930000], rate=12314285.71/min [12940000], rate=12323809.52/min [12950000], rate=12333333.33/min [12960000], rate=12342857.14/min [12970000], rate=12352380.95/min [12980000], rate=12361904.76/min [12990000], rate=12371428.57/min [13000000], rate=12380952.38/min [13010000], rate=12390476.19/min [13020000], rate=12400000.00/min [13030000], rate=12215625.00/min [13040000], rate=12225000.00/min [13050000], rate=12234375.00/min [13060000], rate=12243750.00/min [13070000], rate=12253125.00/min [13080000], rate=12262500.00/min [13090000], rate=12271875.00/min [13100000], rate=12281250.00/min [13110000], rate=12290625.00/min [13120000], rate=12300000.00/min [13130000], rate=12309375.00/min [13140000], rate=12318750.00/min [13150000], rate=12328125.00/min [13160000], rate=12337500.00/min [13170000], rate=12346875.00/min [13180000], rate=12356250.00/min [13190000], rate=12365625.00/min [13200000], rate=12375000.00/min [13210000], rate=12384375.00/min [13220000], rate=12393750.00/min [13230000], rate=12403125.00/min [13240000], rate=12412500.00/min [13250000], rate=12421875.00/min [13260000], rate=12431250.00/min [13270000], rate=12440625.00/min [13280000], rate=12450000.00/min [13290000], rate=12459375.00/min [13300000], rate=12468750.00/min [13310000], rate=12478125.00/min [13320000], rate=12295384.62/min [13330000], rate=12304615.38/min [13340000], rate=12313846.15/min [13350000], rate=12323076.92/min [13360000], rate=12332307.69/min [13370000], rate=12341538.46/min [13380000], rate=12350769.23/min [13390000], rate=12360000.00/min [13400000], rate=12369230.77/min [13410000], rate=12378461.54/min [13420000], rate=12387692.31/min [13430000], rate=12396923.08/min [13440000], rate=12406153.85/min [13450000], rate=12415384.62/min [13460000], rate=12424615.38/min [13470000], rate=12433846.15/min [13480000], rate=12443076.92/min [13490000], rate=12452307.69/min [13500000], rate=12461538.46/min [13510000], rate=12470769.23/min [13520000], rate=12480000.00/min [13530000], rate=12489230.77/min [13540000], rate=12498461.54/min [13550000], rate=12507692.31/min [13560000], rate=12516923.08/min [13570000], rate=12526153.85/min [13580000], rate=12535384.62/min [13590000], rate=12544615.38/min [13600000], rate=12553846.15/min [13610000], rate=12563076.92/min [13620000], rate=12572307.69/min [13630000], rate=12581538.46/min [13640000], rate=12400000.00/min [13650000], rate=12409090.91/min [13660000], rate=12418181.82/min 09:08:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_GXL_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_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns: identified 3557 cancer introns 09:08:50 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim 09:08:50 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/prelim_introns.ok 09:08:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns 09:08:51 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns 09:08:51 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/introns_filtered.ok 09:08:51 : INFO : -found 1622 cancer introns 09:08:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:08:51 : INFO : Creating the BED File. 09:08:57 : INFO : Saving Bed File as 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:08:58 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:08:58 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/intron_igv_bed.ok 09:08:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2 [W::hts_idx_load3] The index file is older than the data file: 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai 09:25:43 : INFO : Execution Time = 16.76 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2 09:25:43 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/reads_alignments_extracted.ok 09:25:43 : INFO : Running: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam 09:25:43 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam 09:25:43 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_cancer_intron_reads.ok 09:25:43 : INFO : Running: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam [bam_sort_core] merging from 68 files and 1 in-memory blocks... 09:42:06 : INFO : Execution Time = 16.38 minutes. CMD: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam 09:42:06 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_gene_reads.ok 09:42:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 09:48:13 : INFO : Execution Time = 6.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 09:48:13 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp.ok 09:48:13 : INFO : Running: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 2 files and 1 in-memory blocks... 09:48:49 : INFO : Execution Time = 0.61 minutes. CMD: samtools sort -o 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp 09:48:49 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:48:49 : INFO : Running: samtools index 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 09:48:53 : INFO : Execution Time = 0.07 minutes. CMD: samtools index 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 09:48:53 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.indexed.ok 09:48:53 : INFO : Running: samtools index 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 09:48:53 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 09:48:53 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam.indexed.ok 09:48:53 : INFO : Running: create_report 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_GXL_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 09:54:02 : INFO : Execution Time = 5.15 minutes. CMD: create_report 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2' 09:54:02 : INFO : Running: touch /tmp/nxf.8CucsSjEGe/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/igv_create_html.ok 09:54:02 : INFO : done.