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rate=10500000.00/min [8760000], rate=10512000.00/min [8770000], rate=10524000.00/min [8780000], rate=10536000.00/min [8790000], rate=10548000.00/min [8800000], rate=10560000.00/min [8810000], rate=10572000.00/min [8820000], rate=10584000.00/min [8830000], rate=10596000.00/min [8840000], rate=10608000.00/min [8850000], rate=10620000.00/min [8860000], rate=10632000.00/min [8870000], rate=10644000.00/min [8880000], rate=10447058.82/min [8890000], rate=10458823.53/min [8900000], rate=10470588.24/min [8910000], rate=10482352.94/min [8920000], rate=10494117.65/min [8930000], rate=10505882.35/min [8940000], rate=10517647.06/min [8950000], rate=10529411.76/min [8960000], rate=10541176.47/min [8970000], rate=10552941.18/min [8980000], rate=10564705.88/min [8990000], rate=10576470.59/min [9000000], rate=10588235.29/min [9010000], rate=10600000.00/min [9020000], rate=10611764.71/min [9030000], rate=10623529.41/min [9040000], rate=10635294.12/min [9050000], rate=10647058.82/min [9060000], rate=10658823.53/min [9070000], rate=10670588.24/min [9080000], rate=10682352.94/min [9090000], rate=10694117.65/min [9100000], rate=10705882.35/min [9110000], rate=10717647.06/min [9120000], rate=10729411.76/min [9130000], rate=10741176.47/min [9140000], rate=10752941.18/min [9150000], rate=10557692.31/min [9160000], rate=10569230.77/min [9170000], rate=10580769.23/min [9180000], rate=10592307.69/min [9190000], rate=10603846.15/min [9200000], rate=10615384.62/min [9210000], rate=10626923.08/min [9220000], rate=10638461.54/min [9230000], rate=10650000.00/min [9240000], rate=10661538.46/min [9250000], rate=10673076.92/min [9260000], rate=10684615.38/min [9270000], rate=10696153.85/min [9280000], rate=10707692.31/min [9290000], rate=10719230.77/min [9300000], rate=10730769.23/min [9310000], rate=10742307.69/min [9320000], rate=10753846.15/min [9330000], rate=10765384.62/min [9340000], rate=10776923.08/min [9350000], rate=10788461.54/min [9360000], rate=10800000.00/min [9370000], rate=10811538.46/min [9380000], rate=10823076.92/min [9390000], rate=10630188.68/min [9400000], rate=10641509.43/min [9410000], rate=10652830.19/min [9420000], rate=10664150.94/min [9430000], rate=10675471.70/min [9440000], rate=10686792.45/min [9450000], rate=10698113.21/min [9460000], rate=10709433.96/min [9470000], rate=10720754.72/min [9480000], rate=10732075.47/min [9490000], rate=10743396.23/min [9500000], rate=10754716.98/min [9510000], rate=10766037.74/min [9520000], rate=10777358.49/min [9530000], rate=10788679.25/min [9540000], rate=10800000.00/min [9550000], rate=10811320.75/min [9560000], rate=10822641.51/min [9570000], rate=10833962.26/min [9580000], rate=10845283.02/min [9590000], rate=10856603.77/min [9600000], rate=10867924.53/min [9610000], rate=10879245.28/min [9620000], rate=10890566.04/min [9630000], rate=10901886.79/min [9640000], rate=10913207.55/min [9650000], rate=10722222.22/min [9660000], rate=10733333.33/min [9670000], rate=10744444.44/min [9680000], rate=10755555.56/min [9690000], rate=10766666.67/min [9700000], rate=10777777.78/min [9710000], rate=10788888.89/min [9720000], rate=10800000.00/min [9730000], rate=10811111.11/min [9740000], rate=10822222.22/min [9750000], rate=10833333.33/min [9760000], rate=10844444.44/min [9770000], rate=10855555.56/min [9780000], rate=10866666.67/min [9790000], rate=10877777.78/min [9800000], rate=10888888.89/min [9810000], rate=10900000.00/min [9820000], rate=10911111.11/min [9830000], rate=10922222.22/min [9840000], rate=10933333.33/min [9850000], rate=10944444.44/min [9860000], rate=10955555.56/min [9870000], rate=10966666.67/min [9880000], rate=10977777.78/min [9890000], rate=10988888.89/min [9900000], rate=11000000.00/min [9910000], rate=10810909.09/min [9920000], rate=10821818.18/min [9930000], rate=10832727.27/min [9940000], rate=10843636.36/min [9950000], rate=10854545.45/min [9960000], rate=10865454.55/min [9970000], rate=10876363.64/min [9980000], rate=10887272.73/min [9990000], rate=10898181.82/min [10000000], rate=10909090.91/min [10010000], rate=10920000.00/min [10020000], rate=10930909.09/min [10030000], rate=10941818.18/min [10040000], rate=10952727.27/min [10050000], rate=10963636.36/min [10060000], rate=10974545.45/min 09:08:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00737_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00737_B23MVV7LT4_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. -tih_rna_sample_00737_B23MVV7LT4_1.introns: identified 7628 cancer introns 09:08:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00737_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns.prelim 09:08:57 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/prelim_introns.ok 09:08:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns 09:08:58 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns 09:08:58 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/introns_filtered.ok 09:08:58 : INFO : -found 3571 cancer introns 09:08:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00737_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed 09:08:58 : INFO : Creating the BED File. 09:09:11 : INFO : Saving Bed File as tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed 09:09:12 : INFO : Execution Time = 0.23 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00737_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00737_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed 09:09:12 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 09:09:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00737_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00737_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00737_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 09:36:39 : INFO : Execution Time = 27.45 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00737_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00737_B23MVV7LT4_1 09:36:39 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 09:36:39 : INFO : Running: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.bam 09:36:40 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.bam 09:36:40 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 09:36:40 : INFO : Running: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 116 files and 1 in-memory blocks... 10:03:19 : INFO : Execution Time = 26.65 minutes. CMD: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.bam 10:03:19 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 10:03:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.bam 10:13:27 : INFO : Execution Time = 10.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.bam 10:13:27 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:13:28 : INFO : Running: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:14:23 : INFO : Execution Time = 0.93 minutes. CMD: samtools sort -o tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 10:14:23 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:14:23 : INFO : Running: samtools index tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 10:14:30 : INFO : Execution Time = 0.11 minutes. CMD: samtools index tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 10:14:30 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/tih_rna_sample_00737_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:14:30 : INFO : Running: samtools index tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 10:14:30 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 10:14:30 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/tih_rna_sample_00737_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:14:30 : INFO : Running: create_report tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00737_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00737_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00737_B23MVV7LT4_1' 10:21:26 : INFO : Execution Time = 6.93 minutes. CMD: create_report tih_rna_sample_00737_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00737_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00737_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00737_B23MVV7LT4_1' 10:21:26 : INFO : Running: touch /tmp/nxf.cgx1ErY3go/tih_rna_sample_00737_B23MVV7LT4_1.chckpts/igv_create_html.ok 10:21:26 : INFO : done.