08:03:44 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [180000], rate=10800000.00/min [190000], rate=11400000.00/min [200000], rate=12000000.00/min [210000], rate=12600000.00/min [220000], rate=13200000.00/min [230000], rate=13800000.00/min [240000], rate=14400000.00/min [250000], rate=15000000.00/min [260000], rate=15600000.00/min [270000], rate=16200000.00/min [280000], rate=16800000.00/min [290000], rate=17400000.00/min [300000], rate=18000000.00/min [310000], rate=18600000.00/min [320000], rate=19200000.00/min [330000], rate=19800000.00/min [340000], rate=20400000.00/min [350000], rate=21000000.00/min [360000], rate=21600000.00/min [370000], rate=22200000.00/min [380000], rate=22800000.00/min [390000], rate=23400000.00/min [400000], rate=24000000.00/min [410000], rate=24600000.00/min [420000], rate=25200000.00/min [430000], rate=12900000.00/min [440000], rate=13200000.00/min [450000], rate=13500000.00/min [460000], 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[4510000], rate=15033333.33/min [4520000], rate=15066666.67/min [4530000], rate=15100000.00/min [4540000], rate=15133333.33/min [4550000], rate=14368421.05/min [4560000], rate=14400000.00/min [4570000], rate=14431578.95/min [4580000], rate=14463157.89/min [4590000], rate=14494736.84/min [4600000], rate=14526315.79/min [4610000], rate=14557894.74/min [4620000], rate=14589473.68/min [4630000], rate=14621052.63/min [4640000], rate=14652631.58/min [4650000], rate=14684210.53/min [4660000], rate=14715789.47/min [4670000], rate=14747368.42/min [4680000], rate=14778947.37/min [4690000], rate=14810526.32/min [4700000], rate=14842105.26/min [4710000], rate=14873684.21/min [4720000], rate=14905263.16/min [4730000], rate=14936842.11/min [4740000], rate=14968421.05/min [4750000], rate=15000000.00/min [4760000], rate=15031578.95/min [4770000], rate=15063157.89/min [4780000], rate=15094736.84/min [4790000], rate=15126315.79/min [4800000], rate=15157894.74/min [4810000], rate=15189473.68/min [4820000], rate=15221052.63/min [4830000], rate=15252631.58/min [4840000], rate=15284210.53/min [4850000], rate=14550000.00/min [4860000], rate=14580000.00/min [4870000], rate=14610000.00/min [4880000], rate=14640000.00/min [4890000], rate=14670000.00/min [4900000], rate=14700000.00/min [4910000], rate=14730000.00/min [4920000], rate=14760000.00/min [4930000], rate=14790000.00/min [4940000], rate=14820000.00/min [4950000], rate=14850000.00/min [4960000], rate=14880000.00/min [4970000], rate=14910000.00/min [4980000], rate=14940000.00/min [4990000], rate=14970000.00/min [5000000], rate=15000000.00/min [5010000], rate=15030000.00/min [5020000], rate=15060000.00/min [5030000], rate=15090000.00/min [5040000], rate=15120000.00/min [5050000], rate=15150000.00/min [5060000], rate=15180000.00/min [5070000], rate=15210000.00/min [5080000], rate=15240000.00/min [5090000], rate=15270000.00/min [5100000], rate=15300000.00/min [5110000], rate=15330000.00/min [5120000], rate=15360000.00/min [5130000], rate=14657142.86/min [5140000], rate=14685714.29/min [5150000], rate=14714285.71/min 08:04:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-2f84cc-R1_B23WHYVLT4_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-2f84cc-R1_B23WHYVLT4_1.introns: identified 2781 cancer introns 08:04:14 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns.prelim 08:04:14 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok 08:04:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns 08:04:14 : 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-2f84cc-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns 08:04:14 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok 08:04:14 : INFO : -found 844 cancer introns 08:04:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed 08:04:15 : INFO : Creating the BED File. 08:04:18 : INFO : Saving Bed File as aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed 08:04:18 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed 08:04:18 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok 08:04:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-2f84cc-R1_B23WHYVLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai 08:11:05 : INFO : Execution Time = 6.78 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-2f84cc-R1_B23WHYVLT4_1 08:11:05 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/reads_alignments_extracted.ok 08:11:05 : INFO : Running: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.bam 08:11:06 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.bam 08:11:06 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/sort_cancer_intron_reads.ok 08:11:06 : INFO : Running: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.bam [bam_sort_core] merging from 28 files and 1 in-memory blocks... 08:17:56 : INFO : Execution Time = 6.83 minutes. CMD: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.bam 08:17:56 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/sort_gene_reads.ok 08:17:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.bam 08:19:49 : INFO : Execution Time = 1.90 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.bam 08:19:49 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 08:19:49 : INFO : Running: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 1 files and 1 in-memory blocks... 08:20:15 : INFO : Execution Time = 0.43 minutes. CMD: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp 08:20:15 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:20:15 : INFO : Running: samtools index aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam 08:20:18 : INFO : Execution Time = 0.05 minutes. CMD: samtools index aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam 08:20:18 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 08:20:19 : INFO : Running: samtools index aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam 08:20:19 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam 08:20:19 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 08:20:19 : INFO : Running: create_report aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-2f84cc-R1_B23WHYVLT4_1' 08:24:22 : INFO : Execution Time = 4.05 minutes. CMD: create_report aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-2f84cc-R1_B23WHYVLT4_1' 08:24:22 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/igv_create_html.ok 08:24:22 : INFO : done.