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rate=20438709.68/min [10570000], rate=20458064.52/min [10580000], rate=20477419.35/min [10590000], rate=20496774.19/min [10600000], rate=20516129.03/min [10610000], rate=20535483.87/min [10620000], rate=20554838.71/min [10630000], rate=20574193.55/min [10640000], rate=20593548.39/min [10650000], rate=20612903.23/min [10660000], rate=20632258.06/min [10670000], rate=20651612.90/min [10680000], rate=20670967.74/min [10690000], rate=20690322.58/min [10700000], rate=20709677.42/min [10710000], rate=20729032.26/min [10720000], rate=20748387.10/min [10730000], rate=20767741.94/min [10740000], rate=20787096.77/min [10750000], rate=20806451.61/min [10760000], rate=20825806.45/min [10770000], rate=20845161.29/min [10780000], rate=20864516.13/min [10790000], rate=20883870.97/min [10800000], rate=20903225.81/min [10810000], rate=20922580.65/min [10820000], rate=20941935.48/min [10830000], rate=20961290.32/min [10840000], rate=20980645.16/min [10850000], rate=20343750.00/min [10860000], rate=20362500.00/min [10870000], rate=20381250.00/min [10880000], rate=20400000.00/min [10890000], rate=20418750.00/min [10900000], rate=20437500.00/min [10910000], rate=20456250.00/min [10920000], rate=20475000.00/min [10930000], rate=20493750.00/min [10940000], rate=20512500.00/min [10950000], rate=20531250.00/min [10960000], rate=20550000.00/min [10970000], rate=20568750.00/min [10980000], rate=20587500.00/min [10990000], rate=20606250.00/min 09:01:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > KG1_FFPE_01_RNA_0003_B23LG7FLT4_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. -KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns: identified 6740 cancer introns 09:01:37 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer.introns.prelim 09:01:37 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/prelim_introns.ok 09:01:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer.introns 09:01:37 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer.introns 09:01:37 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/introns_filtered.ok 09:01:38 : INFO : -found 3203 cancer introns 09:01:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns --cancer_introns KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns.for_IGV.bed 09:01:38 : INFO : Creating the BED File. 09:01:43 : INFO : Saving Bed File as KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns.for_IGV.bed 09:01:43 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns --cancer_introns KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns.for_IGV.bed 09:01:43 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/intron_igv_bed.ok 09:01:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns.for_IGV.bed --bam KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix KG1_FFPE_01_RNA_0003_B23LG7FLT4_1 [W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai 09:23:43 : INFO : Execution Time = 21.99 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns.for_IGV.bed --bam KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix KG1_FFPE_01_RNA_0003_B23LG7FLT4_1 09:23:43 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok 09:23:43 : INFO : Running: samtools sort -o KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer_intron_reads.sorted.bam KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer_intron_reads.bam 09:23:44 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer_intron_reads.sorted.bam KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer_intron_reads.bam 09:23:44 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok 09:23:44 : INFO : Running: samtools sort -o KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.bam KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.bam [bam_sort_core] merging from 122 files and 1 in-memory blocks... 09:49:31 : INFO : Execution Time = 25.79 minutes. CMD: samtools sort -o KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.bam KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.bam 09:49:31 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/sort_gene_reads.ok 09:49:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.bam 09:58:53 : INFO : Execution Time = 9.38 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.bam 09:58:53 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:58:54 : INFO : Running: samtools sort -o KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 8 files and 1 in-memory blocks... 10:00:49 : INFO : Execution Time = 1.93 minutes. CMD: samtools sort -o KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp 10:00:49 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:00:49 : INFO : Running: samtools index KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 10:01:02 : INFO : Execution Time = 0.21 minutes. CMD: samtools index KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 10:01:02 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 10:01:02 : INFO : Running: samtools index KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 10:01:02 : INFO : Execution Time = 0.00 minutes. CMD: samtools index KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 10:01:02 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 10:01:02 : INFO : Running: create_report KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.ctat-splicing.igv.html --track-config KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: KG1_FFPE_01_RNA_0003_B23LG7FLT4_1' [W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi 10:08:01 : INFO : Execution Time = 6.98 minutes. CMD: create_report KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.ctat-splicing.igv.html --track-config KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: KG1_FFPE_01_RNA_0003_B23LG7FLT4_1' 10:08:01 : INFO : Running: touch /tmp/nxf.7ue8ylbBba/KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.chckpts/igv_create_html.ok 10:08:01 : INFO : done.