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[6360000], rate=10902857.14/min [6370000], rate=10920000.00/min [6380000], rate=10937142.86/min [6390000], rate=10954285.71/min [6400000], rate=10971428.57/min [6410000], rate=10988571.43/min [6420000], rate=11005714.29/min [6430000], rate=11022857.14/min [6440000], rate=11040000.00/min [6450000], rate=11057142.86/min [6460000], rate=11074285.71/min [6470000], rate=11091428.57/min [6480000], rate=11108571.43/min [6490000], rate=11125714.29/min [6500000], rate=11142857.14/min [6510000], rate=11160000.00/min [6520000], rate=11177142.86/min [6530000], rate=11194285.71/min [6540000], rate=11211428.57/min [6550000], rate=11228571.43/min [6560000], rate=11245714.29/min [6570000], rate=11262857.14/min [6580000], rate=11280000.00/min [6590000], rate=11297142.86/min [6600000], rate=11314285.71/min [6610000], rate=11331428.57/min [6620000], rate=11033333.33/min [6630000], rate=11050000.00/min [6640000], rate=11066666.67/min [6650000], rate=11083333.33/min [6660000], rate=11100000.00/min [6670000], rate=11116666.67/min [6680000], rate=11133333.33/min [6690000], rate=11150000.00/min [6700000], rate=11166666.67/min [6710000], rate=11183333.33/min [6720000], rate=11200000.00/min [6730000], rate=11216666.67/min [6740000], rate=11233333.33/min [6750000], rate=11250000.00/min [6760000], rate=11266666.67/min [6770000], rate=11283333.33/min [6780000], rate=11300000.00/min [6790000], rate=11316666.67/min [6800000], rate=11333333.33/min [6810000], rate=11350000.00/min [6820000], rate=11366666.67/min [6830000], rate=11383333.33/min [6840000], rate=11400000.00/min [6850000], rate=11416666.67/min [6860000], rate=11433333.33/min [6870000], rate=11450000.00/min [6880000], rate=11156756.76/min [6890000], rate=11172972.97/min [6900000], rate=11189189.19/min [6910000], rate=11205405.41/min [6920000], rate=11221621.62/min [6930000], rate=11237837.84/min [6940000], rate=11254054.05/min [6950000], rate=11270270.27/min [6960000], rate=11286486.49/min [6970000], rate=11302702.70/min [6980000], rate=11318918.92/min [6990000], rate=11335135.14/min [7000000], rate=11351351.35/min [7010000], rate=11367567.57/min [7020000], rate=11383783.78/min [7030000], rate=11400000.00/min [7040000], rate=11416216.22/min [7050000], rate=11432432.43/min 09:22:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3e4d53-R1_A23WJ53LT4_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. -aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns: identified 7502 cancer introns 09:22:46 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer.introns.prelim 09:22:46 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/prelim_introns.ok 09:22:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer.introns 09:22:47 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer.introns 09:22:47 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/introns_filtered.ok 09:22:47 : INFO : -found 3228 cancer introns 09:22:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns --cancer_introns aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns.for_IGV.bed 09:22:47 : INFO : Creating the BED File. 09:22:54 : INFO : Saving Bed File as aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns.for_IGV.bed 09:22:54 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns --cancer_introns aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns.for_IGV.bed 09:22:54 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/intron_igv_bed.ok 09:22:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns.for_IGV.bed --bam aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3e4d53-R1_A23WJ53LT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai 09:46:17 : INFO : Execution Time = 23.38 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns.for_IGV.bed --bam aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3e4d53-R1_A23WJ53LT4_1 09:46:17 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/reads_alignments_extracted.ok 09:46:17 : INFO : Running: samtools sort -o aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer_intron_reads.bam 09:46:17 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer_intron_reads.bam 09:46:17 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/sort_cancer_intron_reads.ok 09:46:17 : INFO : Running: samtools sort -o aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.bam aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.bam [bam_sort_core] merging from 107 files and 1 in-memory blocks... 10:11:46 : INFO : Execution Time = 25.48 minutes. CMD: samtools sort -o aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.bam aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.bam 10:11:46 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/sort_gene_reads.ok 10:11:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.bam 10:18:45 : INFO : Execution Time = 6.98 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.bam 10:18:45 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 10:18:45 : INFO : Running: samtools sort -o aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:19:39 : INFO : Execution Time = 0.90 minutes. CMD: samtools sort -o aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmp 10:19:39 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:19:39 : INFO : Running: samtools index aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam 10:19:45 : INFO : Execution Time = 0.10 minutes. CMD: samtools index aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam 10:19:45 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:19:45 : INFO : Running: samtools index aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam 10:19:45 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam 10:19:45 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:19:45 : INFO : Running: create_report aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-3e4d53-R1_A23WJ53LT4_1' 10:26:11 : INFO : Execution Time = 6.44 minutes. CMD: create_report aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-3e4d53-R1_A23WJ53LT4_1' 10:26:11 : INFO : Running: touch /tmp/nxf.bShWLIgkDn/aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.chckpts/igv_create_html.ok 10:26:11 : INFO : done.