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rate=18616216.22/min [11490000], rate=18632432.43/min [11500000], rate=18648648.65/min [11510000], rate=18664864.86/min [11520000], rate=18681081.08/min [11530000], rate=18697297.30/min [11540000], rate=18713513.51/min [11550000], rate=18729729.73/min [11560000], rate=18745945.95/min [11570000], rate=18762162.16/min [11580000], rate=18778378.38/min [11590000], rate=18794594.59/min [11600000], rate=18810810.81/min [11610000], rate=18827027.03/min [11620000], rate=18843243.24/min [11630000], rate=18859459.46/min [11640000], rate=18875675.68/min [11650000], rate=18891891.89/min [11660000], rate=18908108.11/min [11670000], rate=18924324.32/min [11680000], rate=18940540.54/min [11690000], rate=18457894.74/min [11700000], rate=18473684.21/min [11710000], rate=18489473.68/min [11720000], rate=18505263.16/min [11730000], rate=18521052.63/min [11740000], rate=18536842.11/min [11750000], rate=18552631.58/min [11760000], rate=18568421.05/min [11770000], rate=18584210.53/min [11780000], rate=18600000.00/min [11790000], rate=18615789.47/min [11800000], rate=18631578.95/min [11810000], rate=18647368.42/min [11820000], rate=18663157.89/min [11830000], rate=18678947.37/min [11840000], rate=18694736.84/min [11850000], rate=18710526.32/min [11860000], rate=18726315.79/min [11870000], rate=18742105.26/min [11880000], rate=18757894.74/min [11890000], rate=18773684.21/min [11900000], rate=18789473.68/min [11910000], rate=18805263.16/min [11920000], rate=18821052.63/min [11930000], rate=18836842.11/min [11940000], rate=18852631.58/min [11950000], rate=18868421.05/min [11960000], rate=18884210.53/min [11970000], rate=18900000.00/min [11980000], rate=18915789.47/min [11990000], rate=18931578.95/min [12000000], rate=18947368.42/min [12010000], rate=18963157.89/min [12020000], rate=18492307.69/min [12030000], rate=18507692.31/min [12040000], rate=18523076.92/min [12050000], rate=18538461.54/min [12060000], rate=18553846.15/min [12070000], rate=18569230.77/min [12080000], rate=18584615.38/min [12090000], rate=18600000.00/min [12100000], rate=18615384.62/min [12110000], rate=18630769.23/min [12120000], rate=18646153.85/min [12130000], rate=18661538.46/min [12140000], rate=18676923.08/min [12150000], rate=18692307.69/min [12160000], rate=18707692.31/min [12170000], rate=18723076.92/min [12180000], rate=18738461.54/min [12190000], rate=18753846.15/min [12200000], rate=18769230.77/min [12210000], rate=18784615.38/min [12220000], rate=18800000.00/min [12230000], rate=18815384.62/min [12240000], rate=18830769.23/min [12250000], rate=18846153.85/min [12260000], rate=18861538.46/min [12270000], rate=18876923.08/min [12280000], rate=18892307.69/min [12290000], rate=18907692.31/min [12300000], rate=18923076.92/min [12310000], rate=18938461.54/min [12320000], rate=18953846.15/min [12330000], rate=18969230.77/min [12340000], rate=18984615.38/min [12350000], rate=19000000.00/min [12360000], rate=18540000.00/min [12370000], rate=18555000.00/min [12380000], rate=18570000.00/min [12390000], rate=18585000.00/min [12400000], rate=18600000.00/min [12410000], rate=18615000.00/min [12420000], rate=18630000.00/min [12430000], rate=18645000.00/min [12440000], rate=18660000.00/min [12450000], rate=18675000.00/min [12460000], rate=18690000.00/min [12470000], rate=18705000.00/min [12480000], rate=18720000.00/min [12490000], rate=18735000.00/min [12500000], rate=18750000.00/min [12510000], rate=18765000.00/min [12520000], rate=18780000.00/min [12530000], rate=18795000.00/min [12540000], rate=18810000.00/min [12550000], rate=18825000.00/min 09:10:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00090_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00090_B23WHTKLT4_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. -tih_rna_sample_00090_B23WHTKLT4_2.introns: identified 4079 cancer introns 09:10:50 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00090_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns.prelim 09:10:50 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/prelim_introns.ok 09:10:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns 09:10:50 : 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_00090_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns 09:10:50 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/introns_filtered.ok 09:10:50 : INFO : -found 2574 cancer introns 09:10:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00090_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed 09:10:50 : INFO : Creating the BED File. 09:10:56 : INFO : Saving Bed File as tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed 09:10:57 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00090_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed 09:10:57 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/intron_igv_bed.ok 09:10:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00090_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00090_B23WHTKLT4_2 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00090_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam.bai 09:29:51 : INFO : Execution Time = 18.90 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00090_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00090_B23WHTKLT4_2 09:29:51 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/reads_alignments_extracted.ok 09:29:51 : INFO : Running: samtools sort -o tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.bam 09:29:51 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.bam 09:29:51 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/sort_cancer_intron_reads.ok 09:29:51 : INFO : Running: samtools sort -o tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.bam [bam_sort_core] merging from 89 files and 1 in-memory blocks... 09:50:59 : INFO : Execution Time = 21.13 minutes. CMD: samtools sort -o tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.bam 09:50:59 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/sort_gene_reads.ok 09:50:59 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.bam 09:57:21 : INFO : Execution Time = 6.36 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.bam 09:57:21 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp.ok 09:57:21 : INFO : Running: samtools sort -o tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 2 files and 1 in-memory blocks... 09:57:55 : INFO : Execution Time = 0.57 minutes. CMD: samtools sort -o tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp 09:57:55 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:57:55 : INFO : Running: samtools index tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam 09:57:58 : INFO : Execution Time = 0.06 minutes. CMD: samtools index tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam 09:57:58 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.indexed.ok 09:57:58 : INFO : Running: samtools index tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.sorted.bam 09:57:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.sorted.bam 09:57:58 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.sorted.bam.indexed.ok 09:57:58 : INFO : Running: create_report tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00090_B23WHTKLT4_2.ctat-splicing.igv.html --track-config tih_rna_sample_00090_B23WHTKLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00090_B23WHTKLT4_2' 10:00:54 : INFO : Execution Time = 2.92 minutes. CMD: create_report tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00090_B23WHTKLT4_2.ctat-splicing.igv.html --track-config tih_rna_sample_00090_B23WHTKLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00090_B23WHTKLT4_2' 10:00:54 : INFO : Running: touch /tmp/nxf.OyD7lOP670/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/igv_create_html.ok 10:00:54 : INFO : done.