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[8310000], rate=12160975.61/min [8320000], rate=12175609.76/min [8330000], rate=12190243.90/min [8340000], rate=12204878.05/min [8350000], rate=12219512.20/min [8360000], rate=12234146.34/min [8370000], rate=12248780.49/min [8380000], rate=12263414.63/min [8390000], rate=12278048.78/min [8400000], rate=12000000.00/min [8410000], rate=12014285.71/min [8420000], rate=12028571.43/min [8430000], rate=12042857.14/min [8440000], rate=12057142.86/min [8450000], rate=12071428.57/min [8460000], rate=12085714.29/min [8470000], rate=12100000.00/min [8480000], rate=12114285.71/min [8490000], rate=12128571.43/min [8500000], rate=12142857.14/min [8510000], rate=12157142.86/min [8520000], rate=12171428.57/min [8530000], rate=11902325.58/min [8540000], rate=11916279.07/min [8550000], rate=11930232.56/min [8560000], rate=11944186.05/min [8570000], rate=11958139.53/min [8580000], rate=11972093.02/min [8590000], rate=11986046.51/min [8600000], rate=12000000.00/min [8610000], rate=12013953.49/min [8620000], rate=12027906.98/min [8630000], rate=12041860.47/min [8640000], rate=12055813.95/min [8650000], rate=12069767.44/min [8660000], rate=12083720.93/min [8670000], rate=12097674.42/min [8680000], rate=12111627.91/min [8690000], rate=12125581.40/min [8700000], rate=12139534.88/min [8710000], rate=12153488.37/min [8720000], rate=12167441.86/min [8730000], rate=12181395.35/min [8740000], rate=12195348.84/min [8750000], rate=12209302.33/min [8760000], rate=11945454.55/min [8770000], rate=11959090.91/min [8780000], rate=11972727.27/min [8790000], rate=11986363.64/min [8800000], rate=12000000.00/min [8810000], rate=12013636.36/min [8820000], rate=12027272.73/min [8830000], rate=12040909.09/min [8840000], rate=12054545.45/min [8850000], rate=12068181.82/min [8860000], rate=12081818.18/min [8870000], rate=12095454.55/min [8880000], rate=12109090.91/min [8890000], rate=12122727.27/min [8900000], rate=12136363.64/min [8910000], rate=12150000.00/min [8920000], rate=12163636.36/min [8930000], rate=12177272.73/min [8940000], rate=12190909.09/min [8950000], rate=12204545.45/min [8960000], rate=12218181.82/min [8970000], rate=12231818.18/min [8980000], rate=12245454.55/min [8990000], rate=12259090.91/min [9000000], rate=12272727.27/min [9010000], rate=12286363.64/min [9020000], rate=12300000.00/min [9030000], rate=12313636.36/min [9040000], rate=12327272.73/min [9050000], rate=12066666.67/min [9060000], rate=12080000.00/min [9070000], rate=12093333.33/min [9080000], rate=12106666.67/min [9090000], rate=12120000.00/min [9100000], rate=12133333.33/min [9110000], rate=12146666.67/min [9120000], rate=12160000.00/min [9130000], rate=12173333.33/min [9140000], rate=12186666.67/min [9150000], rate=12200000.00/min [9160000], rate=12213333.33/min [9170000], rate=12226666.67/min [9180000], rate=12240000.00/min [9190000], rate=12253333.33/min [9200000], rate=12266666.67/min [9210000], rate=12280000.00/min [9220000], rate=12293333.33/min [9230000], rate=12306666.67/min [9240000], rate=12320000.00/min [9250000], rate=12333333.33/min [9260000], rate=12346666.67/min [9270000], rate=12360000.00/min [9280000], rate=12373333.33/min [9290000], rate=12386666.67/min [9300000], rate=12400000.00/min [9310000], rate=12413333.33/min [9320000], rate=12426666.67/min [9330000], rate=12440000.00/min [9340000], rate=12453333.33/min [9350000], rate=12466666.67/min [9360000], rate=12208695.65/min [9370000], rate=12221739.13/min [9380000], rate=12234782.61/min [9390000], rate=12247826.09/min [9400000], rate=12260869.57/min [9410000], rate=12273913.04/min [9420000], rate=12286956.52/min [9430000], rate=12300000.00/min [9440000], rate=12313043.48/min [9450000], rate=12326086.96/min [9460000], rate=12339130.43/min [9470000], rate=12352173.91/min [9480000], rate=12365217.39/min [9490000], rate=12378260.87/min [9500000], rate=12391304.35/min [9510000], rate=12404347.83/min [9520000], rate=12417391.30/min [9530000], rate=12430434.78/min [9540000], rate=12443478.26/min [9550000], rate=12456521.74/min [9560000], rate=12469565.22/min [9570000], rate=12482608.70/min [9580000], rate=12495652.17/min [9590000], rate=12508695.65/min [9600000], rate=12521739.13/min 08:55:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_cWx-T1-TRNA-1_B23MHV2LT4_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_cWx-T1-TRNA-1_B23MHV2LT4_1.introns: identified 7847 cancer introns 08:55:35 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 08:55:35 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 08:55:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:55:36 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:55:36 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 08:55:36 : INFO : -found 3395 cancer introns 08:55:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:55:36 : INFO : Creating the BED File. 08:55:47 : INFO : Saving Bed File as 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:55:47 : INFO : Execution Time = 0.19 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:55:47 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 08:55:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_cWx-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_cWx-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_cWx-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 09:27:04 : INFO : Execution Time = 31.28 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_cWx-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_cWx-T1-TRNA-1_B23MHV2LT4_1 09:27:04 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 09:27:04 : INFO : Running: samtools sort -o 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:27:05 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:27:05 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 09:27:05 : INFO : Running: samtools sort -o 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam [bam_sort_core] merging from 125 files and 1 in-memory blocks... 09:58:50 : INFO : Execution Time = 31.75 minutes. CMD: samtools sort -o 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam 09:58:50 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_gene_reads.ok 09:58:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 10:07:20 : INFO : Execution Time = 8.49 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 10:07:20 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:07:20 : INFO : Running: samtools sort -o 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:08:18 : INFO : Execution Time = 0.97 minutes. CMD: samtools sort -o 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp 10:08:18 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:08:18 : INFO : Running: samtools index 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 10:08:25 : INFO : Execution Time = 0.11 minutes. CMD: samtools index 659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 10:08:25 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_cWx-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:08:25 : INFO : Running: samtools index 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 10:08:25 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 10:08:25 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_cWx-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:08:25 : INFO : Running: create_report 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_cWx-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_cWx-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_cWx-T1-TRNA-1_B23MHV2LT4_1' 10:15:12 : INFO : Execution Time = 6.78 minutes. CMD: create_report 659_cWx-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_cWx-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_cWx-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_cWx-T1-TRNA-1_B23MHV2LT4_1' 10:15:12 : INFO : Running: touch /tmp/nxf.m5XSzhKlVV/659_cWx-T1-TRNA-1_B23MHV2LT4_1.chckpts/igv_create_html.ok 10:15:12 : INFO : done.