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rate=14516666.67/min [8720000], rate=14533333.33/min [8730000], rate=14550000.00/min [8740000], rate=14566666.67/min [8750000], rate=14583333.33/min [8760000], rate=14600000.00/min [8770000], rate=14616666.67/min [8780000], rate=14633333.33/min [8790000], rate=14650000.00/min [8800000], rate=14666666.67/min [8810000], rate=14683333.33/min [8820000], rate=14700000.00/min [8830000], rate=14716666.67/min [8840000], rate=14733333.33/min [8850000], rate=14750000.00/min [8860000], rate=14766666.67/min [8870000], rate=14783333.33/min [8880000], rate=14800000.00/min [8890000], rate=14816666.67/min [8900000], rate=14833333.33/min [8910000], rate=14850000.00/min [8920000], rate=14866666.67/min [8930000], rate=14883333.33/min [8940000], rate=14900000.00/min [8950000], rate=14513513.51/min [8960000], rate=14529729.73/min [8970000], rate=14545945.95/min [8980000], rate=14562162.16/min [8990000], rate=14578378.38/min [9000000], rate=14594594.59/min [9010000], rate=14610810.81/min [9020000], rate=14627027.03/min [9030000], rate=14643243.24/min [9040000], rate=14659459.46/min [9050000], rate=14675675.68/min [9060000], rate=14691891.89/min [9070000], rate=14708108.11/min [9080000], rate=14724324.32/min [9090000], rate=14740540.54/min [9100000], rate=14756756.76/min [9110000], rate=14772972.97/min [9120000], rate=14789189.19/min [9130000], rate=14805405.41/min [9140000], rate=14821621.62/min [9150000], rate=14837837.84/min [9160000], rate=14854054.05/min [9170000], rate=14870270.27/min [9180000], rate=14886486.49/min [9190000], rate=14902702.70/min [9200000], rate=14918918.92/min [9210000], rate=14542105.26/min [9220000], rate=14557894.74/min [9230000], rate=14573684.21/min [9240000], rate=14589473.68/min [9250000], rate=14605263.16/min [9260000], rate=14621052.63/min [9270000], rate=14636842.11/min [9280000], rate=14652631.58/min [9290000], rate=14668421.05/min [9300000], rate=14684210.53/min [9310000], rate=14700000.00/min [9320000], rate=14715789.47/min [9330000], rate=14731578.95/min [9340000], rate=14747368.42/min [9350000], rate=14763157.89/min [9360000], rate=14778947.37/min [9370000], rate=14794736.84/min [9380000], rate=14810526.32/min [9390000], rate=14826315.79/min [9400000], rate=14842105.26/min [9410000], rate=14857894.74/min [9420000], rate=14873684.21/min [9430000], rate=14889473.68/min [9440000], rate=14905263.16/min [9450000], rate=14921052.63/min [9460000], rate=14553846.15/min [9470000], rate=14569230.77/min [9480000], rate=14584615.38/min [9490000], rate=14600000.00/min [9500000], rate=14615384.62/min [9510000], rate=14630769.23/min [9520000], rate=14646153.85/min [9530000], rate=14661538.46/min [9540000], rate=14676923.08/min [9550000], rate=14692307.69/min [9560000], rate=14707692.31/min [9570000], rate=14723076.92/min [9580000], rate=14738461.54/min [9590000], rate=14753846.15/min [9600000], rate=14769230.77/min [9610000], rate=14784615.38/min [9620000], rate=14800000.00/min [9630000], rate=14815384.62/min [9640000], rate=14830769.23/min [9650000], rate=14846153.85/min [9660000], rate=14861538.46/min [9670000], rate=14876923.08/min [9680000], rate=14892307.69/min [9690000], rate=14907692.31/min [9700000], rate=14923076.92/min [9710000], rate=14938461.54/min [9720000], rate=14953846.15/min [9730000], rate=14595000.00/min [9740000], rate=14610000.00/min [9750000], rate=14625000.00/min [9760000], rate=14640000.00/min [9770000], rate=14655000.00/min [9780000], rate=14670000.00/min [9790000], rate=14685000.00/min [9800000], rate=14700000.00/min [9810000], rate=14715000.00/min [9820000], rate=14730000.00/min [9830000], rate=14745000.00/min [9840000], rate=14760000.00/min [9850000], rate=14775000.00/min [9860000], rate=14790000.00/min [9870000], rate=14805000.00/min [9880000], rate=14820000.00/min [9890000], rate=14835000.00/min [9900000], rate=14850000.00/min [9910000], rate=14865000.00/min [9920000], rate=14880000.00/min [9930000], rate=14895000.00/min [9940000], rate=14910000.00/min [9950000], rate=14925000.00/min 09:28:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00665_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00665_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_00665_B23MVV7LT4_1.introns: identified 8698 cancer introns 09:28:47 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00665_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00665_B23MVV7LT4_1.cancer.introns.prelim 09:28:47 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/prelim_introns.ok 09:28:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00665_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00665_B23MVV7LT4_1.cancer.introns 09:28:47 : 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_00665_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00665_B23MVV7LT4_1.cancer.introns 09:28:47 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/introns_filtered.ok 09:28:47 : INFO : -found 3885 cancer introns 09:28:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00665_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00665_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00665_B23MVV7LT4_1.introns.for_IGV.bed 09:28:47 : INFO : Creating the BED File. 09:28:56 : INFO : Saving Bed File as tih_rna_sample_00665_B23MVV7LT4_1.introns.for_IGV.bed 09:28:56 : INFO : Execution Time = 0.15 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00665_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00665_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00665_B23MVV7LT4_1.introns.for_IGV.bed 09:28:56 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 09:28:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00665_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00665_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00665_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00665_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 09:55:59 : INFO : Execution Time = 27.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00665_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00665_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00665_B23MVV7LT4_1 09:55:59 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 09:55:59 : INFO : Running: samtools sort -o tih_rna_sample_00665_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00665_B23MVV7LT4_1.cancer_intron_reads.bam 09:56:00 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o tih_rna_sample_00665_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00665_B23MVV7LT4_1.cancer_intron_reads.bam 09:56:00 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 09:56:00 : INFO : Running: samtools sort -o tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 127 files and 1 in-memory blocks... 10:25:35 : INFO : Execution Time = 29.59 minutes. CMD: samtools sort -o tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.bam 10:25:35 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 10:25:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.bam 10:34:25 : INFO : Execution Time = 8.82 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.bam 10:34:25 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:34:25 : INFO : Running: samtools sort -o tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:35:19 : INFO : Execution Time = 0.91 minutes. CMD: samtools sort -o tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 10:35:19 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:35:19 : INFO : Running: samtools index tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 10:35:26 : INFO : Execution Time = 0.11 minutes. CMD: samtools index tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 10:35:26 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/tih_rna_sample_00665_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:35:26 : INFO : Running: samtools index tih_rna_sample_00665_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 10:35:26 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00665_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 10:35:26 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/tih_rna_sample_00665_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:35:26 : INFO : Running: create_report tih_rna_sample_00665_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00665_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00665_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00665_B23MVV7LT4_1' 10:42:49 : INFO : Execution Time = 7.39 minutes. CMD: create_report tih_rna_sample_00665_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00665_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00665_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00665_B23MVV7LT4_1' 10:42:49 : INFO : Running: touch /tmp/nxf.GL7W7evw4M/tih_rna_sample_00665_B23MVV7LT4_1.chckpts/igv_create_html.ok 10:42:49 : INFO : done.