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rate=25000000.00/min [11260000], rate=25022222.22/min [11270000], rate=25044444.44/min [11280000], rate=25066666.67/min [11290000], rate=25088888.89/min [11300000], rate=25111111.11/min [11310000], rate=25133333.33/min [11320000], rate=25155555.56/min [11330000], rate=25177777.78/min [11340000], rate=25200000.00/min [11350000], rate=25222222.22/min [11360000], rate=25244444.44/min [11370000], rate=25266666.67/min [11380000], rate=25288888.89/min [11390000], rate=25311111.11/min [11400000], rate=25333333.33/min [11410000], rate=25355555.56/min [11420000], rate=25377777.78/min [11430000], rate=25400000.00/min [11440000], rate=25422222.22/min [11450000], rate=25444444.44/min [11460000], rate=25466666.67/min [11470000], rate=25488888.89/min [11480000], rate=25511111.11/min [11490000], rate=25533333.33/min [11500000], rate=25555555.56/min [11510000], rate=25577777.78/min [11520000], rate=25600000.00/min [11530000], rate=24707142.86/min [11540000], rate=24728571.43/min [11550000], rate=24750000.00/min [11560000], rate=24771428.57/min [11570000], rate=24792857.14/min [11580000], rate=24814285.71/min [11590000], rate=24835714.29/min [11600000], rate=24857142.86/min [11610000], rate=24878571.43/min [11620000], rate=24900000.00/min [11630000], rate=24921428.57/min [11640000], rate=24942857.14/min [11650000], rate=24964285.71/min [11660000], rate=24985714.29/min [11670000], rate=25007142.86/min 09:15:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.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. -1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns: identified 4343 cancer introns 09:15:42 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim 09:15:42 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/prelim_introns.ok 09:15:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns 09:15:42 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns 09:15:42 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/introns_filtered.ok 09:15:42 : INFO : -found 1474 cancer introns 09:15:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:15:42 : INFO : Creating the BED File. 09:15:45 : INFO : Saving Bed File as 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:15:45 : INFO : Execution Time = 0.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed 09:15:45 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/intron_igv_bed.ok 09:15:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2 [W::hts_idx_load3] The index file is older than the data file: 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai 09:27:26 : INFO : Execution Time = 11.67 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2 09:27:26 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/reads_alignments_extracted.ok 09:27:26 : INFO : Running: samtools sort -o 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam 09:27:26 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam 09:27:26 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_cancer_intron_reads.ok 09:27:26 : INFO : Running: samtools sort -o 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam [bam_sort_core] merging from 71 files and 1 in-memory blocks... 09:41:49 : INFO : Execution Time = 14.37 minutes. CMD: samtools sort -o 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam 09:41:49 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_gene_reads.ok 09:41:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 09:45:46 : INFO : Execution Time = 3.96 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 09:45:46 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp.ok 09:45:46 : INFO : Running: samtools sort -o 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 2 files and 1 in-memory blocks... 09:46:15 : INFO : Execution Time = 0.48 minutes. CMD: samtools sort -o 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp 09:46:15 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:46:15 : INFO : Running: samtools index 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 09:46:18 : INFO : Execution Time = 0.05 minutes. CMD: samtools index 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 09:46:18 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.indexed.ok 09:46:18 : INFO : Running: samtools index 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 09:46:18 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 09:46:18 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam.indexed.ok 09:46:18 : INFO : Running: create_report 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2' 09:50:38 : INFO : Execution Time = 4.33 minutes. CMD: create_report 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2' 09:50:38 : INFO : Running: touch /tmp/nxf.YzHLqvjIu3/1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/igv_create_html.ok 09:50:38 : INFO : done.