09:17:57 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[9500000], rate=17812500.00/min 09:18:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bGW-T1-TRNA-1_B23WHTKLT4_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.
-659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns: identified 5141 cancer introns
09:18:37 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim
09:18:37 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/prelim_introns.ok
09:18:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
09:18:37 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
09:18:37 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/introns_filtered.ok
09:18:37 : INFO : -found 3038 cancer introns
09:18:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
09:18:38 : INFO : Creating the BED File.
09:18:44 : INFO : Saving Bed File as 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
09:18:44 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
09:18:44 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/intron_igv_bed.ok
09:18:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_bGW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
09:41:49 : INFO : Execution Time = 23.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_bGW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1
09:41:49 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok
09:41:49 : INFO : Running: samtools sort -o 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
09:41:50 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
09:41:50 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok
09:41:50 : INFO : Running: samtools sort -o 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
[bam_sort_core] merging from 109 files and 1 in-memory blocks...
10:07:12 : INFO : Execution Time = 25.36 minutes. CMD: samtools sort -o 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
10:07:12 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_gene_reads.ok
10:07:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
10:15:15 : INFO : Execution Time = 8.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
10:15:15 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
10:15:15 : INFO : Running: samtools sort -o 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
10:16:03 : INFO : Execution Time = 0.79 minutes. CMD: samtools sort -o 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
10:16:03 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:16:03 : INFO : Running: samtools index 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
10:16:08 : INFO : Execution Time = 0.09 minutes. CMD: samtools index 659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
10:16:08 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
10:16:08 : INFO : Running: samtools index 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
10:16:08 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
10:16:08 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bGW-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
10:16:08 : INFO : Running: create_report 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bGW-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bGW-T1-TRNA-1_B23WHTKLT4_1'
10:22:06 : INFO : Execution Time = 5.96 minutes. CMD: create_report 659_bGW-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bGW-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bGW-T1-TRNA-1_B23WHTKLT4_1'
10:22:06 : INFO : Running: touch /tmp/nxf.QK9ExAJvhW/659_bGW-T1-TRNA-1_B23WHTKLT4_1.chckpts/igv_create_html.ok
10:22:06 : INFO : done.