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[8840000], rate=12936585.37/min [8850000], rate=12642857.14/min [8860000], rate=12657142.86/min [8870000], rate=12671428.57/min [8880000], rate=12685714.29/min [8890000], rate=12700000.00/min [8900000], rate=12714285.71/min [8910000], rate=12728571.43/min [8920000], rate=12742857.14/min [8930000], rate=12757142.86/min [8940000], rate=12771428.57/min [8950000], rate=12785714.29/min [8960000], rate=12800000.00/min [8970000], rate=12814285.71/min [8980000], rate=12828571.43/min [8990000], rate=12842857.14/min [9000000], rate=12857142.86/min [9010000], rate=12871428.57/min [9020000], rate=12885714.29/min [9030000], rate=12900000.00/min [9040000], rate=12914285.71/min [9050000], rate=12928571.43/min [9060000], rate=12942857.14/min [9070000], rate=12957142.86/min [9080000], rate=12971428.57/min [9090000], rate=12985714.29/min [9100000], rate=13000000.00/min [9110000], rate=13014285.71/min [9120000], rate=13028571.43/min [9130000], rate=13042857.14/min [9140000], rate=12753488.37/min [9150000], rate=12767441.86/min [9160000], rate=12781395.35/min [9170000], rate=12795348.84/min [9180000], rate=12809302.33/min [9190000], rate=12823255.81/min [9200000], rate=12837209.30/min [9210000], rate=12851162.79/min [9220000], rate=12865116.28/min [9230000], rate=12879069.77/min [9240000], rate=12893023.26/min [9250000], rate=12906976.74/min [9260000], rate=12920930.23/min [9270000], rate=12934883.72/min [9280000], rate=12948837.21/min [9290000], rate=12962790.70/min [9300000], rate=12976744.19/min [9310000], rate=12990697.67/min [9320000], rate=13004651.16/min [9330000], rate=13018604.65/min [9340000], rate=13032558.14/min [9350000], rate=13046511.63/min [9360000], rate=13060465.12/min [9370000], rate=13074418.60/min [9380000], rate=13088372.09/min [9390000], rate=13102325.58/min [9400000], rate=13116279.07/min [9410000], rate=13130232.56/min [9420000], rate=13144186.05/min [9430000], rate=13158139.53/min [9440000], rate=12872727.27/min [9450000], rate=12886363.64/min [9460000], rate=12900000.00/min [9470000], rate=12913636.36/min [9480000], rate=12927272.73/min [9490000], rate=12940909.09/min [9500000], rate=12954545.45/min [9510000], rate=12968181.82/min [9520000], rate=12981818.18/min [9530000], rate=12995454.55/min [9540000], rate=13009090.91/min [9550000], rate=13022727.27/min [9560000], rate=13036363.64/min [9570000], rate=13050000.00/min [9580000], rate=13063636.36/min [9590000], rate=13077272.73/min [9600000], rate=13090909.09/min [9610000], rate=13104545.45/min [9620000], rate=13118181.82/min [9630000], rate=13131818.18/min [9640000], rate=13145454.55/min [9650000], rate=13159090.91/min [9660000], rate=13172727.27/min [9670000], rate=13186363.64/min [9680000], rate=13200000.00/min [9690000], rate=13213636.36/min [9700000], rate=13227272.73/min [9710000], rate=13240909.09/min [9720000], rate=13254545.45/min [9730000], rate=12973333.33/min [9740000], rate=12986666.67/min [9750000], rate=13000000.00/min [9760000], rate=13013333.33/min [9770000], rate=13026666.67/min [9780000], rate=13040000.00/min [9790000], rate=13053333.33/min [9800000], rate=13066666.67/min [9810000], rate=13080000.00/min [9820000], rate=13093333.33/min [9830000], rate=13106666.67/min [9840000], rate=13120000.00/min [9850000], rate=13133333.33/min [9860000], rate=13146666.67/min [9870000], rate=13160000.00/min [9880000], rate=13173333.33/min [9890000], rate=13186666.67/min [9900000], rate=13200000.00/min [9910000], rate=13213333.33/min [9920000], rate=13226666.67/min [9930000], rate=13240000.00/min [9940000], rate=13253333.33/min [9950000], rate=13266666.67/min [9960000], rate=13280000.00/min [9970000], rate=13293333.33/min [9980000], rate=13306666.67/min [9990000], rate=13320000.00/min [10000000], rate=13333333.33/min [10010000], rate=13346666.67/min 09:27:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bQZ-T1-TRNA-1_A23MVY2LT4_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. -659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns: identified 7461 cancer introns 09:27:14 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns.prelim 09:27:14 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/prelim_introns.ok 09:27:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns 09:27:15 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns 09:27:15 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/introns_filtered.ok 09:27:15 : INFO : -found 3562 cancer introns 09:27:15 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns --cancer_introns 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed 09:27:15 : INFO : Creating the BED File. 09:27:23 : INFO : Saving Bed File as 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed 09:27:23 : INFO : Execution Time = 0.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns --cancer_introns 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed 09:27:23 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/intron_igv_bed.ok 09:27:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed --bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bQZ-T1-TRNA-1_A23MVY2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai 09:51:21 : INFO : Execution Time = 23.96 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed --bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bQZ-T1-TRNA-1_A23MVY2LT4_1 09:51:21 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/reads_alignments_extracted.ok 09:51:21 : INFO : Running: samtools sort -o 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.sorted.bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.bam 09:51:22 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.sorted.bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.bam 09:51:22 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/sort_cancer_intron_reads.ok 09:51:22 : INFO : Running: samtools sort -o 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.bam [bam_sort_core] merging from 110 files and 1 in-memory blocks... 10:16:46 : INFO : Execution Time = 25.41 minutes. CMD: samtools sort -o 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.bam 10:16:46 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/sort_gene_reads.ok 10:16:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.bam 10:24:51 : INFO : Execution Time = 8.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.bam 10:24:51 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:24:51 : INFO : Running: samtools sort -o 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:25:47 : INFO : Execution Time = 0.94 minutes. CMD: samtools sort -o 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmp 10:25:47 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:25:47 : INFO : Running: samtools index 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam 10:25:54 : INFO : Execution Time = 0.11 minutes. CMD: samtools index 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam 10:25:54 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:25:54 : INFO : Running: samtools index 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.sorted.bam 10:25:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.sorted.bam 10:25:54 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:25:54 : INFO : Running: create_report 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.ctat-splicing.igv.html --track-config 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1' 10:32:23 : INFO : Execution Time = 6.49 minutes. CMD: create_report 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.ctat-splicing.igv.html --track-config 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1' 10:32:23 : INFO : Running: touch /tmp/nxf.aXwIhbiEWR/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.chckpts/igv_create_html.ok 10:32:23 : INFO : done.