00:34:59 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[4730000], rate=23650000.00/min 00:35:16 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bld_02_100_25ng.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_bld_02_100_25ng.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_bld_02_100_25ng.introns: identified 2889 cancer introns
00:35:16 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bld_02_100_25ng.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_bld_02_100_25ng.cancer.introns.prelim
00:35:16 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/prelim_introns.ok
00:35:16 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bld_02_100_25ng.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_bld_02_100_25ng.cancer.introns
00:35:17 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bld_02_100_25ng.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_bld_02_100_25ng.cancer.introns
00:35:17 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/introns_filtered.ok
00:35:17 : INFO : -found 771 cancer introns
00:35:17 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bld_02_100_25ng.introns --cancer_introns BVT_FFPE_TRNA_bld_02_100_25ng.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_bld_02_100_25ng.introns.for_IGV.bed
00:35:17 : INFO : Creating the BED File.
00:35:19 : INFO : Saving Bed File as BVT_FFPE_TRNA_bld_02_100_25ng.introns.for_IGV.bed
00:35:19 : INFO : Execution Time = 0.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bld_02_100_25ng.introns --cancer_introns BVT_FFPE_TRNA_bld_02_100_25ng.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_bld_02_100_25ng.introns.for_IGV.bed
00:35:19 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/intron_igv_bed.ok
00:35:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bld_02_100_25ng.introns.for_IGV.bed --bam BVT_FFPE_TRNA_bld_02_100_25ng.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_bld_02_100_25ng
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_100_25ng.Aligned.sortedByCoord.out.bam.bai
00:37:14 : INFO : Execution Time = 1.91 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bld_02_100_25ng.introns.for_IGV.bed --bam BVT_FFPE_TRNA_bld_02_100_25ng.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_bld_02_100_25ng
00:37:14 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/reads_alignments_extracted.ok
00:37:14 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bld_02_100_25ng.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bld_02_100_25ng.cancer_intron_reads.bam
00:37:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bld_02_100_25ng.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bld_02_100_25ng.cancer_intron_reads.bam
00:37:14 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/sort_cancer_intron_reads.ok
00:37:14 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.bam BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.bam
[bam_sort_core] merging from 11 files and 1 in-memory blocks...
00:39:34 : INFO : Execution Time = 2.34 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.bam BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.bam
00:39:34 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/sort_gene_reads.ok
00:39:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.bam
00:40:09 : INFO : Execution Time = 0.58 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.bam
00:40:09 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam.tmp.ok
00:40:09 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam.tmp
00:40:17 : INFO : Execution Time = 0.13 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam.tmp
00:40:17 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam.tmpsorted.ok
00:40:17 : INFO : Running: samtools index BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam
00:40:18 : INFO : Execution Time = 0.02 minutes. CMD: samtools index BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam
00:40:18 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/BVT_FFPE_TRNA_bld_02_100_25ng.gene_reads.sorted.sifted.bam.indexed.ok
00:40:18 : INFO : Running: samtools index BVT_FFPE_TRNA_bld_02_100_25ng.cancer_intron_reads.sorted.bam
00:40:18 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BVT_FFPE_TRNA_bld_02_100_25ng.cancer_intron_reads.sorted.bam
00:40:18 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/BVT_FFPE_TRNA_bld_02_100_25ng.cancer_intron_reads.sorted.bam.indexed.ok
00:40:18 : INFO : Running: create_report BVT_FFPE_TRNA_bld_02_100_25ng.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_bld_02_100_25ng.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_bld_02_100_25ng.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_bld_02_100_25ng'
00:41:14 : INFO : Execution Time = 0.94 minutes. CMD: create_report BVT_FFPE_TRNA_bld_02_100_25ng.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_bld_02_100_25ng.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_bld_02_100_25ng.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_bld_02_100_25ng'
00:41:14 : INFO : Running: touch /tmp/nxf.EuQGadwahX/BVT_FFPE_TRNA_bld_02_100_25ng.chckpts/igv_create_html.ok
00:41:14 : INFO : done.