09:26:28 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10600000], rate=13531914.89/min
[10610000], rate=13544680.85/min 09:27:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_bst_05_A23WKFTLT4_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.
-BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns: identified 6248 cancer introns
09:27:26 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer.introns.prelim
09:27:26 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/prelim_introns.ok
09:27:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer.introns
09:27:26 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer.introns
09:27:26 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/introns_filtered.ok
09:27:26 : INFO : -found 2271 cancer introns
09:27:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns --cancer_introns BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns.for_IGV.bed
09:27:27 : INFO : Creating the BED File.
09:27:32 : INFO : Saving Bed File as BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns.for_IGV.bed
09:27:32 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns --cancer_introns BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns.for_IGV.bed
09:27:32 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/intron_igv_bed.ok
09:27:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns.for_IGV.bed --bam BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
09:46:34 : INFO : Execution Time = 19.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns.for_IGV.bed --bam BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1
09:46:34 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/reads_alignments_extracted.ok
09:46:34 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer_intron_reads.bam
09:46:34 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer_intron_reads.bam
09:46:34 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/sort_cancer_intron_reads.ok
09:46:34 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.bam BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.bam
[bam_sort_core] merging from 89 files and 1 in-memory blocks...
10:07:42 : INFO : Execution Time = 21.13 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.bam BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.bam
10:07:42 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/sort_gene_reads.ok
10:07:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.bam
10:14:03 : INFO : Execution Time = 6.35 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.bam
10:14:03 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
10:14:03 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
10:14:53 : INFO : Execution Time = 0.84 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmp
10:14:53 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:14:53 : INFO : Running: samtools index BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam
10:14:59 : INFO : Execution Time = 0.09 minutes. CMD: samtools index BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam
10:14:59 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
10:14:59 : INFO : Running: samtools index BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer_intron_reads.sorted.bam
10:14:59 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer_intron_reads.sorted.bam
10:14:59 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
10:14:59 : INFO : Running: create_report BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
10:21:04 : INFO : Execution Time = 6.08 minutes. CMD: create_report BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1'
10:21:04 : INFO : Running: touch /tmp/nxf.y9ZqMHJsPb/BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.chckpts/igv_create_html.ok
10:21:04 : INFO : done.