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rate=14353846.15/min [6230000], rate=14376923.08/min [6240000], rate=14400000.00/min [6250000], rate=14423076.92/min [6260000], rate=14446153.85/min [6270000], rate=14469230.77/min [6280000], rate=14492307.69/min [6290000], rate=14515384.62/min [6300000], rate=14538461.54/min [6310000], rate=14561538.46/min [6320000], rate=14584615.38/min [6330000], rate=14607692.31/min [6340000], rate=14630769.23/min [6350000], rate=14653846.15/min [6360000], rate=14676923.08/min [6370000], rate=14700000.00/min [6380000], rate=14723076.92/min [6390000], rate=14746153.85/min [6400000], rate=14769230.77/min [6410000], rate=14792307.69/min [6420000], rate=14815384.62/min [6430000], rate=14838461.54/min [6440000], rate=14861538.46/min [6450000], rate=14884615.38/min [6460000], rate=14355555.56/min [6470000], rate=14377777.78/min [6480000], rate=14400000.00/min [6490000], rate=14422222.22/min [6500000], rate=14444444.44/min [6510000], rate=14466666.67/min [6520000], rate=14488888.89/min [6530000], rate=14511111.11/min [6540000], rate=14533333.33/min [6550000], rate=14555555.56/min [6560000], rate=14577777.78/min [6570000], rate=14600000.00/min [6580000], rate=14622222.22/min [6590000], rate=14644444.44/min [6600000], rate=14666666.67/min [6610000], rate=14688888.89/min [6620000], rate=14711111.11/min [6630000], rate=14733333.33/min [6640000], rate=14755555.56/min [6650000], rate=14777777.78/min [6660000], rate=14800000.00/min [6670000], rate=14822222.22/min [6680000], rate=14844444.44/min [6690000], rate=14866666.67/min [6700000], rate=14888888.89/min [6710000], rate=14911111.11/min [6720000], rate=14933333.33/min [6730000], rate=14955555.56/min [6740000], rate=14977777.78/min [6750000], rate=15000000.00/min [6760000], rate=14485714.29/min [6770000], rate=14507142.86/min [6780000], rate=14528571.43/min [6790000], rate=14550000.00/min [6800000], rate=14571428.57/min [6810000], rate=14592857.14/min [6820000], rate=14614285.71/min [6830000], rate=14635714.29/min [6840000], rate=14657142.86/min [6850000], rate=14678571.43/min [6860000], rate=14700000.00/min [6870000], rate=14721428.57/min [6880000], rate=14742857.14/min [6890000], rate=14764285.71/min [6900000], rate=14785714.29/min [6910000], rate=14807142.86/min [6920000], rate=14828571.43/min [6930000], rate=14850000.00/min [6940000], rate=14871428.57/min [6950000], rate=14892857.14/min [6960000], rate=14914285.71/min [6970000], rate=14935714.29/min [6980000], rate=14957142.86/min [6990000], rate=14978571.43/min [7000000], rate=15000000.00/min [7010000], rate=15021428.57/min [7020000], rate=15042857.14/min [7030000], rate=14544827.59/min [7040000], rate=14565517.24/min [7050000], rate=14586206.90/min [7060000], rate=14606896.55/min [7070000], rate=14627586.21/min [7080000], rate=14648275.86/min [7090000], rate=14668965.52/min [7100000], rate=14689655.17/min [7110000], rate=14710344.83/min [7120000], rate=14731034.48/min [7130000], rate=14751724.14/min [7140000], rate=14772413.79/min [7150000], rate=14793103.45/min [7160000], rate=14813793.10/min [7170000], rate=14834482.76/min [7180000], rate=14855172.41/min [7190000], rate=14875862.07/min [7200000], rate=14896551.72/min [7210000], rate=14917241.38/min [7220000], rate=14937931.03/min [7230000], rate=14460000.00/min [7240000], rate=14480000.00/min [7250000], rate=14500000.00/min [7260000], rate=14520000.00/min [7270000], rate=14540000.00/min [7280000], rate=14560000.00/min [7290000], rate=14580000.00/min [7300000], rate=14600000.00/min [7310000], rate=14620000.00/min [7320000], rate=14640000.00/min [7330000], rate=14660000.00/min [7340000], rate=14680000.00/min [7350000], rate=14700000.00/min [7360000], rate=14720000.00/min [7370000], rate=14740000.00/min [7380000], rate=14760000.00/min [7390000], rate=14780000.00/min [7400000], rate=14800000.00/min [7410000], rate=14820000.00/min [7420000], rate=14361290.32/min [7430000], rate=14380645.16/min [7440000], rate=14400000.00/min [7450000], rate=14419354.84/min [7460000], rate=14438709.68/min [7470000], rate=14458064.52/min [7480000], rate=14477419.35/min [7490000], rate=14496774.19/min [7500000], rate=14516129.03/min [7510000], rate=14535483.87/min [7520000], rate=14554838.71/min [7530000], rate=14574193.55/min [7540000], rate=14593548.39/min [7550000], rate=14612903.23/min [7560000], rate=14632258.06/min [7570000], rate=14651612.90/min [7580000], rate=14670967.74/min [7590000], rate=14690322.58/min [7600000], rate=14709677.42/min [7610000], rate=14268750.00/min [7620000], rate=14287500.00/min [7630000], rate=14306250.00/min [7640000], rate=14325000.00/min [7650000], rate=14343750.00/min [7660000], rate=14362500.00/min [7670000], rate=14381250.00/min [7680000], rate=14400000.00/min [7690000], rate=14418750.00/min [7700000], rate=14437500.00/min [7710000], rate=14456250.00/min [7720000], rate=14475000.00/min [7730000], rate=14493750.00/min 09:02:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-45523c-R1_A23YTGFLT4_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-45523c-R1_A23YTGFLT4_1.introns: identified 4437 cancer introns 09:02:19 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer.introns.prelim 09:02:19 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 09:02:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer.introns 09:02:19 : 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-45523c-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer.introns 09:02:19 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 09:02:19 : INFO : -found 1800 cancer introns 09:02:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:02:20 : INFO : Creating the BED File. 09:02:25 : INFO : Saving Bed File as aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:02:25 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:02:25 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 09:02:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-45523c-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 09:20:28 : INFO : Execution Time = 18.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-45523c-R1_A23YTGFLT4_1 09:20:28 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 09:20:28 : INFO : Running: samtools sort -o aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:20:28 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:20:28 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 09:20:28 : INFO : Running: samtools sort -o aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 78 files and 1 in-memory blocks... 09:39:03 : INFO : Execution Time = 18.58 minutes. CMD: samtools sort -o aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.bam 09:39:03 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok 09:39:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.bam 09:44:28 : INFO : Execution Time = 5.41 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.bam 09:44:28 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:44:28 : INFO : Running: samtools sort -o aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:45:18 : INFO : Execution Time = 0.84 minutes. CMD: samtools sort -o aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp 09:45:18 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:45:18 : INFO : Running: samtools index aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 09:45:23 : INFO : Execution Time = 0.09 minutes. CMD: samtools index aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 09:45:23 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:45:23 : INFO : Running: samtools index aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 09:45:24 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 09:45:24 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-45523c-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:45:24 : INFO : Running: create_report aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-45523c-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-45523c-R1_A23YTGFLT4_1' 09:51:04 : INFO : Execution Time = 5.68 minutes. CMD: create_report aih-tih-sc-45523c-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-45523c-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-45523c-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-45523c-R1_A23YTGFLT4_1' 09:51:04 : INFO : Running: touch /tmp/nxf.BUSfIjHyMv/aih-tih-sc-45523c-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok 09:51:04 : INFO : done.