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rate=15346666.67/min [11520000], rate=15360000.00/min [11530000], rate=15373333.33/min [11540000], rate=15386666.67/min [11550000], rate=15400000.00/min [11560000], rate=15078260.87/min [11570000], rate=15091304.35/min [11580000], rate=15104347.83/min [11590000], rate=15117391.30/min [11600000], rate=15130434.78/min [11610000], rate=15143478.26/min [11620000], rate=15156521.74/min [11630000], rate=15169565.22/min [11640000], rate=15182608.70/min [11650000], rate=15195652.17/min [11660000], rate=15208695.65/min [11670000], rate=15221739.13/min [11680000], rate=15234782.61/min [11690000], rate=15247826.09/min [11700000], rate=15260869.57/min [11710000], rate=15273913.04/min [11720000], rate=15286956.52/min [11730000], rate=15300000.00/min [11740000], rate=15313043.48/min [11750000], rate=15326086.96/min [11760000], rate=15339130.43/min [11770000], rate=15352173.91/min [11780000], rate=15365217.39/min [11790000], rate=15378260.87/min [11800000], rate=15391304.35/min [11810000], rate=15404347.83/min [11820000], rate=15417391.30/min [11830000], rate=15102127.66/min [11840000], rate=15114893.62/min [11850000], rate=15127659.57/min [11860000], rate=15140425.53/min [11870000], rate=15153191.49/min [11880000], rate=15165957.45/min [11890000], rate=15178723.40/min [11900000], rate=15191489.36/min [11910000], rate=15204255.32/min [11920000], rate=15217021.28/min [11930000], rate=15229787.23/min [11940000], rate=15242553.19/min [11950000], rate=15255319.15/min [11960000], rate=15268085.11/min [11970000], rate=15280851.06/min [11980000], rate=15293617.02/min [11990000], rate=15306382.98/min [12000000], rate=15319148.94/min [12010000], rate=15331914.89/min [12020000], rate=15344680.85/min [12030000], rate=15357446.81/min [12040000], rate=15370212.77/min [12050000], rate=15382978.72/min [12060000], rate=15395744.68/min [12070000], rate=15408510.64/min [12080000], rate=15421276.60/min [12090000], rate=15112500.00/min [12100000], rate=15125000.00/min [12110000], rate=15137500.00/min [12120000], rate=15150000.00/min [12130000], rate=15162500.00/min [12140000], rate=15175000.00/min [12150000], rate=15187500.00/min [12160000], rate=15200000.00/min [12170000], rate=15212500.00/min [12180000], rate=15225000.00/min [12190000], rate=15237500.00/min [12200000], rate=15250000.00/min [12210000], rate=15262500.00/min [12220000], rate=15275000.00/min [12230000], rate=15287500.00/min [12240000], rate=15300000.00/min [12250000], rate=15312500.00/min [12260000], rate=15325000.00/min [12270000], rate=15337500.00/min [12280000], rate=15350000.00/min [12290000], rate=15362500.00/min [12300000], rate=15375000.00/min [12310000], rate=15387500.00/min [12320000], rate=15400000.00/min [12330000], rate=15412500.00/min [12340000], rate=15425000.00/min [12350000], rate=15437500.00/min [12360000], rate=15134693.88/min [12370000], rate=15146938.78/min [12380000], rate=15159183.67/min [12390000], rate=15171428.57/min 08:04:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00104_23H5VFLT4_s20.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00104_23H5VFLT4_s20.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. -tih_rna_sample_00104_23H5VFLT4_s20.introns: identified 2457 cancer introns 08:04:54 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00104_23H5VFLT4_s20.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00104_23H5VFLT4_s20.cancer.introns.prelim 08:04:54 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/prelim_introns.ok 08:04:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00104_23H5VFLT4_s20.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00104_23H5VFLT4_s20.cancer.introns 08:04:54 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00104_23H5VFLT4_s20.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00104_23H5VFLT4_s20.cancer.introns 08:04:54 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/introns_filtered.ok 08:04:54 : INFO : -found 1460 cancer introns 08:04:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00104_23H5VFLT4_s20.introns --cancer_introns tih_rna_sample_00104_23H5VFLT4_s20.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00104_23H5VFLT4_s20.introns.for_IGV.bed 08:04:54 : INFO : Creating the BED File. 08:04:58 : INFO : Saving Bed File as tih_rna_sample_00104_23H5VFLT4_s20.introns.for_IGV.bed 08:04:58 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00104_23H5VFLT4_s20.introns --cancer_introns tih_rna_sample_00104_23H5VFLT4_s20.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00104_23H5VFLT4_s20.introns.for_IGV.bed 08:04:58 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/intron_igv_bed.ok 08:04:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00104_23H5VFLT4_s20.introns.for_IGV.bed --bam tih_rna_sample_00104_23H5VFLT4_s20.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00104_23H5VFLT4_s20 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00104_23H5VFLT4_s20.Aligned.sortedByCoord.out.bam.bai 08:13:04 : INFO : Execution Time = 8.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00104_23H5VFLT4_s20.introns.for_IGV.bed --bam tih_rna_sample_00104_23H5VFLT4_s20.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00104_23H5VFLT4_s20 08:13:04 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/reads_alignments_extracted.ok 08:13:05 : INFO : Running: samtools sort -o tih_rna_sample_00104_23H5VFLT4_s20.cancer_intron_reads.sorted.bam tih_rna_sample_00104_23H5VFLT4_s20.cancer_intron_reads.bam 08:13:05 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00104_23H5VFLT4_s20.cancer_intron_reads.sorted.bam tih_rna_sample_00104_23H5VFLT4_s20.cancer_intron_reads.bam 08:13:05 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/sort_cancer_intron_reads.ok 08:13:05 : INFO : Running: samtools sort -o tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.bam tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.bam [bam_sort_core] merging from 37 files and 1 in-memory blocks... 08:21:11 : INFO : Execution Time = 8.10 minutes. CMD: samtools sort -o tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.bam tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.bam 08:21:11 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/sort_gene_reads.ok 08:21:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.bam 08:25:20 : INFO : Execution Time = 4.15 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.bam 08:25:20 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam.tmp.ok 08:25:20 : INFO : Running: samtools sort -o tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 08:26:10 : INFO : Execution Time = 0.83 minutes. CMD: samtools sort -o tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam.tmp 08:26:10 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:26:10 : INFO : Running: samtools index tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam 08:26:15 : INFO : Execution Time = 0.09 minutes. CMD: samtools index tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam 08:26:15 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/tih_rna_sample_00104_23H5VFLT4_s20.gene_reads.sorted.sifted.bam.indexed.ok 08:26:15 : INFO : Running: samtools index tih_rna_sample_00104_23H5VFLT4_s20.cancer_intron_reads.sorted.bam 08:26:15 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00104_23H5VFLT4_s20.cancer_intron_reads.sorted.bam 08:26:15 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/tih_rna_sample_00104_23H5VFLT4_s20.cancer_intron_reads.sorted.bam.indexed.ok 08:26:15 : INFO : Running: create_report tih_rna_sample_00104_23H5VFLT4_s20.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00104_23H5VFLT4_s20.ctat-splicing.igv.html --track-config tih_rna_sample_00104_23H5VFLT4_s20.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00104_23H5VFLT4_s20' 08:28:35 : INFO : Execution Time = 2.33 minutes. CMD: create_report tih_rna_sample_00104_23H5VFLT4_s20.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00104_23H5VFLT4_s20.ctat-splicing.igv.html --track-config tih_rna_sample_00104_23H5VFLT4_s20.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00104_23H5VFLT4_s20' 08:28:35 : INFO : Running: touch /tmp/nxf.etoomKgeA3/tih_rna_sample_00104_23H5VFLT4_s20.chckpts/igv_create_html.ok 08:28:35 : INFO : done.