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rate=21562500.00/min [11510000], rate=21581250.00/min [11520000], rate=21600000.00/min [11530000], rate=21618750.00/min [11540000], rate=20981818.18/min [11550000], rate=21000000.00/min [11560000], rate=21018181.82/min [11570000], rate=21036363.64/min [11580000], rate=21054545.45/min [11590000], rate=21072727.27/min [11600000], rate=21090909.09/min [11610000], rate=21109090.91/min [11620000], rate=21127272.73/min [11630000], rate=21145454.55/min [11640000], rate=21163636.36/min [11650000], rate=21181818.18/min [11660000], rate=21200000.00/min [11670000], rate=21218181.82/min [11680000], rate=21236363.64/min [11690000], rate=21254545.45/min [11700000], rate=21272727.27/min [11710000], rate=21290909.09/min [11720000], rate=21309090.91/min [11730000], rate=21327272.73/min [11740000], rate=21345454.55/min [11750000], rate=21363636.36/min [11760000], rate=21381818.18/min [11770000], rate=21400000.00/min [11780000], rate=21418181.82/min [11790000], rate=21436363.64/min [11800000], rate=21454545.45/min [11810000], rate=21472727.27/min [11820000], rate=21490909.09/min [11830000], rate=21509090.91/min [11840000], rate=21527272.73/min [11850000], rate=21545454.55/min [11860000], rate=20929411.76/min [11870000], rate=20947058.82/min [11880000], rate=20964705.88/min [11890000], rate=20982352.94/min [11900000], rate=21000000.00/min [11910000], rate=21017647.06/min [11920000], rate=21035294.12/min [11930000], rate=21052941.18/min [11940000], rate=21070588.24/min 09:09:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00654_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00654_B23MVV7LT4_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. -tih_rna_sample_00654_B23MVV7LT4_1.introns: identified 7116 cancer introns 09:09:32 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00654_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00654_B23MVV7LT4_1.cancer.introns.prelim 09:09:32 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/prelim_introns.ok 09:09:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00654_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00654_B23MVV7LT4_1.cancer.introns 09:09:33 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00654_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00654_B23MVV7LT4_1.cancer.introns 09:09:33 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/introns_filtered.ok 09:09:33 : INFO : -found 2932 cancer introns 09:09:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00654_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00654_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00654_B23MVV7LT4_1.introns.for_IGV.bed 09:09:33 : INFO : Creating the BED File. 09:09:38 : INFO : Saving Bed File as tih_rna_sample_00654_B23MVV7LT4_1.introns.for_IGV.bed 09:09:38 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00654_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00654_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00654_B23MVV7LT4_1.introns.for_IGV.bed 09:09:38 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 09:09:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00654_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00654_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00654_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00654_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 09:25:34 : INFO : Execution Time = 15.93 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00654_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00654_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00654_B23MVV7LT4_1 09:25:34 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 09:25:34 : INFO : Running: samtools sort -o tih_rna_sample_00654_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00654_B23MVV7LT4_1.cancer_intron_reads.bam 09:25:35 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00654_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00654_B23MVV7LT4_1.cancer_intron_reads.bam 09:25:35 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 09:25:35 : INFO : Running: samtools sort -o tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 100 files and 1 in-memory blocks... 09:44:28 : INFO : Execution Time = 18.88 minutes. CMD: samtools sort -o tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.bam 09:44:28 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 09:44:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.bam 09:50:36 : INFO : Execution Time = 6.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.bam 09:50:36 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:50:36 : INFO : Running: samtools sort -o tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:51:16 : INFO : Execution Time = 0.67 minutes. CMD: samtools sort -o tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp 09:51:16 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:51:16 : INFO : Running: samtools index tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 09:51:21 : INFO : Execution Time = 0.08 minutes. CMD: samtools index tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam 09:51:21 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/tih_rna_sample_00654_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:51:21 : INFO : Running: samtools index tih_rna_sample_00654_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 09:51:21 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00654_B23MVV7LT4_1.cancer_intron_reads.sorted.bam 09:51:21 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/tih_rna_sample_00654_B23MVV7LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:51:21 : INFO : Running: create_report tih_rna_sample_00654_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00654_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00654_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00654_B23MVV7LT4_1' [W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi 09:57:17 : INFO : Execution Time = 5.92 minutes. CMD: create_report tih_rna_sample_00654_B23MVV7LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00654_B23MVV7LT4_1.ctat-splicing.igv.html --track-config tih_rna_sample_00654_B23MVV7LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00654_B23MVV7LT4_1' 09:57:17 : INFO : Running: touch /tmp/nxf.DnPG7ZCThz/tih_rna_sample_00654_B23MVV7LT4_1.chckpts/igv_create_html.ok 09:57:17 : INFO : done.