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rate=14271428.57/min [10000000], rate=14285714.29/min [10010000], rate=14300000.00/min [10020000], rate=13981395.35/min [10030000], rate=13995348.84/min [10040000], rate=14009302.33/min [10050000], rate=14023255.81/min [10060000], rate=14037209.30/min [10070000], rate=14051162.79/min [10080000], rate=14065116.28/min [10090000], rate=14079069.77/min [10100000], rate=14093023.26/min [10110000], rate=14106976.74/min [10120000], rate=14120930.23/min [10130000], rate=14134883.72/min [10140000], rate=14148837.21/min [10150000], rate=14162790.70/min [10160000], rate=14176744.19/min [10170000], rate=14190697.67/min [10180000], rate=14204651.16/min [10190000], rate=14218604.65/min [10200000], rate=14232558.14/min [10210000], rate=14246511.63/min [10220000], rate=14260465.12/min [10230000], rate=14274418.60/min [10240000], rate=14288372.09/min [10250000], rate=14302325.58/min [10260000], rate=14316279.07/min [10270000], rate=14330232.56/min [10280000], rate=14018181.82/min [10290000], rate=14031818.18/min [10300000], rate=14045454.55/min [10310000], rate=14059090.91/min [10320000], rate=14072727.27/min [10330000], rate=14086363.64/min [10340000], rate=14100000.00/min [10350000], rate=14113636.36/min [10360000], rate=14127272.73/min [10370000], rate=14140909.09/min [10380000], rate=14154545.45/min [10390000], rate=14168181.82/min [10400000], rate=14181818.18/min [10410000], rate=14195454.55/min [10420000], rate=14209090.91/min [10430000], rate=14222727.27/min [10440000], rate=14236363.64/min [10450000], rate=14250000.00/min [10460000], rate=14263636.36/min [10470000], rate=14277272.73/min [10480000], rate=14290909.09/min [10490000], rate=14304545.45/min [10500000], rate=14318181.82/min [10510000], rate=14331818.18/min [10520000], rate=14026666.67/min [10530000], rate=14040000.00/min [10540000], rate=14053333.33/min [10550000], rate=14066666.67/min [10560000], rate=14080000.00/min [10570000], rate=14093333.33/min [10580000], rate=14106666.67/min [10590000], rate=14120000.00/min [10600000], rate=14133333.33/min [10610000], rate=14146666.67/min [10620000], rate=14160000.00/min [10630000], rate=14173333.33/min [10640000], rate=14186666.67/min 08:47:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00115_23H5VFLT4_s35.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00115_23H5VFLT4_s35.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_00115_23H5VFLT4_s35.introns: identified 3650 cancer introns 08:47:33 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00115_23H5VFLT4_s35.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00115_23H5VFLT4_s35.cancer.introns.prelim 08:47:33 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/prelim_introns.ok 08:47:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00115_23H5VFLT4_s35.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00115_23H5VFLT4_s35.cancer.introns 08:47:33 : 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_00115_23H5VFLT4_s35.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00115_23H5VFLT4_s35.cancer.introns 08:47:33 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/introns_filtered.ok 08:47:33 : INFO : -found 1684 cancer introns 08:47:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00115_23H5VFLT4_s35.introns --cancer_introns tih_rna_sample_00115_23H5VFLT4_s35.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00115_23H5VFLT4_s35.introns.for_IGV.bed 08:47:34 : INFO : Creating the BED File. 08:47:39 : INFO : Saving Bed File as tih_rna_sample_00115_23H5VFLT4_s35.introns.for_IGV.bed 08:47:40 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00115_23H5VFLT4_s35.introns --cancer_introns tih_rna_sample_00115_23H5VFLT4_s35.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00115_23H5VFLT4_s35.introns.for_IGV.bed 08:47:40 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/intron_igv_bed.ok 08:47:40 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00115_23H5VFLT4_s35.introns.for_IGV.bed --bam tih_rna_sample_00115_23H5VFLT4_s35.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00115_23H5VFLT4_s35 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00115_23H5VFLT4_s35.Aligned.sortedByCoord.out.bam.bai 09:03:09 : INFO : Execution Time = 15.49 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00115_23H5VFLT4_s35.introns.for_IGV.bed --bam tih_rna_sample_00115_23H5VFLT4_s35.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00115_23H5VFLT4_s35 09:03:09 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/reads_alignments_extracted.ok 09:03:09 : INFO : Running: samtools sort -o tih_rna_sample_00115_23H5VFLT4_s35.cancer_intron_reads.sorted.bam tih_rna_sample_00115_23H5VFLT4_s35.cancer_intron_reads.bam 09:03:09 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00115_23H5VFLT4_s35.cancer_intron_reads.sorted.bam tih_rna_sample_00115_23H5VFLT4_s35.cancer_intron_reads.bam 09:03:09 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/sort_cancer_intron_reads.ok 09:03:09 : INFO : Running: samtools sort -o tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.bam tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.bam [bam_sort_core] merging from 73 files and 1 in-memory blocks... 09:20:34 : INFO : Execution Time = 17.41 minutes. CMD: samtools sort -o tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.bam tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.bam 09:20:34 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/sort_gene_reads.ok 09:20:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.bam 09:28:37 : INFO : Execution Time = 8.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.bam 09:28:37 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam.tmp.ok 09:28:37 : INFO : Running: samtools sort -o tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 7 files and 1 in-memory blocks... 09:30:38 : INFO : Execution Time = 2.01 minutes. CMD: samtools sort -o tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam.tmp 09:30:38 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:30:38 : INFO : Running: samtools index tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam 09:30:50 : INFO : Execution Time = 0.20 minutes. CMD: samtools index tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam 09:30:50 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/tih_rna_sample_00115_23H5VFLT4_s35.gene_reads.sorted.sifted.bam.indexed.ok 09:30:51 : INFO : Running: samtools index tih_rna_sample_00115_23H5VFLT4_s35.cancer_intron_reads.sorted.bam 09:30:51 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00115_23H5VFLT4_s35.cancer_intron_reads.sorted.bam 09:30:51 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/tih_rna_sample_00115_23H5VFLT4_s35.cancer_intron_reads.sorted.bam.indexed.ok 09:30:51 : INFO : Running: create_report tih_rna_sample_00115_23H5VFLT4_s35.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00115_23H5VFLT4_s35.ctat-splicing.igv.html --track-config tih_rna_sample_00115_23H5VFLT4_s35.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00115_23H5VFLT4_s35' 09:37:17 : INFO : Execution Time = 6.44 minutes. CMD: create_report tih_rna_sample_00115_23H5VFLT4_s35.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00115_23H5VFLT4_s35.ctat-splicing.igv.html --track-config tih_rna_sample_00115_23H5VFLT4_s35.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00115_23H5VFLT4_s35' 09:37:17 : INFO : Running: touch /tmp/nxf.Ly0XttFChN/tih_rna_sample_00115_23H5VFLT4_s35.chckpts/igv_create_html.ok 09:37:17 : INFO : done.