07:39:43 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[2550000], rate=10200000.00/min 07:40:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.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_crv_02_A23WKFTLT4_3.introns: identified 397 cancer introns
07:40:05 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer.introns.prelim
07:40:05 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/prelim_introns.ok
07:40:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer.introns
07:40:06 : 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_crv_02_A23WKFTLT4_3.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer.introns
07:40:06 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/introns_filtered.ok
07:40:06 : INFO : -found 231 cancer introns
07:40:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns --cancer_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns.for_IGV.bed
07:40:06 : INFO : Creating the BED File.
07:40:08 : INFO : Saving Bed File as BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns.for_IGV.bed
07:40:08 : INFO : Execution Time = 0.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns --cancer_introns BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns.for_IGV.bed
07:40:08 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/intron_igv_bed.ok
07:40:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns.for_IGV.bed --bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
07:42:00 : INFO : Execution Time = 1.88 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns.for_IGV.bed --bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3
07:42:00 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/reads_alignments_extracted.ok
07:42:00 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer_intron_reads.bam
07:42:01 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer_intron_reads.bam
07:42:01 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/sort_cancer_intron_reads.ok
07:42:01 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.bam
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
07:44:03 : INFO : Execution Time = 2.04 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.bam
07:44:03 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/sort_gene_reads.ok
07:44:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.bam
07:44:32 : INFO : Execution Time = 0.48 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmp --keep_secondary BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.bam
07:44:32 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmp.ok
07:44:32 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmp
07:44:35 : INFO : Execution Time = 0.05 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmp
07:44:35 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:44:35 : INFO : Running: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam
07:44:35 : INFO : Execution Time = 0.01 minutes. CMD: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam
07:44:35 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.gene_reads.sorted.sifted.bam.indexed.ok
07:44:35 : INFO : Running: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer_intron_reads.sorted.bam
07:44:35 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer_intron_reads.sorted.bam
07:44:35 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.cancer_intron_reads.sorted.bam.indexed.ok
07:44:35 : INFO : Running: create_report BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
07:44:58 : INFO : Execution Time = 0.37 minutes. CMD: create_report BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.ctat-splicing.igv.html --track-config BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3'
07:44:58 : INFO : Running: touch /tmp/nxf.HwtJSlTsXh/BVT_FFPE_TRNA_crv_02_A23WKFTLT4_3.chckpts/igv_create_html.ok
07:44:58 : INFO : done.