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rate=27115384.62/min [11760000], rate=27138461.54/min [11770000], rate=27161538.46/min [11780000], rate=27184615.38/min [11790000], rate=27207692.31/min [11800000], rate=27230769.23/min [11810000], rate=27253846.15/min [11820000], rate=27276923.08/min [11830000], rate=27300000.00/min [11840000], rate=27323076.92/min [11850000], rate=27346153.85/min [11860000], rate=27369230.77/min [11870000], rate=27392307.69/min [11880000], rate=27415384.62/min [11890000], rate=27438461.54/min [11900000], rate=27461538.46/min [11910000], rate=27484615.38/min [11920000], rate=27507692.31/min [11930000], rate=27530769.23/min [11940000], rate=27553846.15/min [11950000], rate=27576923.08/min [11960000], rate=27600000.00/min [11970000], rate=27623076.92/min [11980000], rate=27646153.85/min [11990000], rate=27669230.77/min [12000000], rate=27692307.69/min [12010000], rate=27715384.62/min [12020000], rate=27738461.54/min [12030000], rate=27761538.46/min [12040000], rate=27784615.38/min [12050000], rate=27807692.31/min [12060000], rate=27830769.23/min [12070000], rate=27853846.15/min [12080000], rate=27876923.08/min [12090000], rate=27900000.00/min [12100000], rate=27923076.92/min [12110000], rate=26911111.11/min [12120000], rate=26933333.33/min [12130000], rate=26955555.56/min [12140000], rate=26977777.78/min [12150000], rate=27000000.00/min [12160000], rate=27022222.22/min [12170000], rate=27044444.44/min [12180000], rate=27066666.67/min [12190000], rate=27088888.89/min [12200000], rate=27111111.11/min [12210000], rate=27133333.33/min [12220000], rate=27155555.56/min [12230000], rate=27177777.78/min [12240000], rate=27200000.00/min [12250000], rate=27222222.22/min [12260000], rate=27244444.44/min [12270000], rate=27266666.67/min [12280000], rate=27288888.89/min 09:18:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-f27606-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-f27606-R1_A23YTGFLT4_1.introns: identified 3399 cancer introns 09:18:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer.introns.prelim 09:18:57 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 09:18:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer.introns 09:18:57 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer.introns 09:18:57 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 09:18:57 : INFO : -found 2163 cancer introns 09:18:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:18:58 : INFO : Creating the BED File. 09:19:02 : INFO : Saving Bed File as aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:19:02 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns.for_IGV.bed 09:19:02 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 09:19:02 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-f27606-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-f27606-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f27606-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 09:31:22 : INFO : Execution Time = 12.33 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-f27606-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-f27606-R1_A23YTGFLT4_1 09:31:22 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 09:31:22 : INFO : Running: samtools sort -o aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:31:22 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:31:22 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 09:31:22 : INFO : Running: samtools sort -o aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.bam [bam_sort_core] merging from 79 files and 1 in-memory blocks... 09:46:14 : INFO : Execution Time = 14.86 minutes. CMD: samtools sort -o aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.bam 09:46:14 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/sort_gene_reads.ok 09:46:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.bam 09:50:25 : INFO : Execution Time = 4.19 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.bam 09:50:25 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:50:25 : INFO : Running: samtools sort -o aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 2 files and 1 in-memory blocks... 09:50:56 : INFO : Execution Time = 0.52 minutes. CMD: samtools sort -o aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmp 09:50:56 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:50:56 : INFO : Running: samtools index aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 09:51:00 : INFO : Execution Time = 0.06 minutes. CMD: samtools index aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam 09:51:00 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-f27606-R1_A23YTGFLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:51:00 : INFO : Running: samtools index aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 09:51:00 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam 09:51:00 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/aih-tih-sc-f27606-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:51:00 : INFO : Running: create_report aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-f27606-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-f27606-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-f27606-R1_A23YTGFLT4_1' 09:53:40 : INFO : Execution Time = 2.66 minutes. CMD: create_report aih-tih-sc-f27606-R1_A23YTGFLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-f27606-R1_A23YTGFLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-f27606-R1_A23YTGFLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-f27606-R1_A23YTGFLT4_1' 09:53:40 : INFO : Running: touch /tmp/nxf.FBZpBo7PGz/aih-tih-sc-f27606-R1_A23YTGFLT4_1.chckpts/igv_create_html.ok 09:53:40 : INFO : done.