07:57:12 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[8490000], rate=28300000.00/min 07:57:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.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.
-SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns: identified 248 cancer introns
07:57:35 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer.introns.prelim
07:57:35 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/prelim_introns.ok
07:57:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer.introns
07:57:35 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer.introns
07:57:35 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/introns_filtered.ok
07:57:35 : INFO : -found 162 cancer introns
07:57:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns --cancer_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed
07:57:35 : INFO : Creating the BED File.
07:57:36 : INFO : Saving Bed File as SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed
07:57:36 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns --cancer_introns SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed
07:57:36 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/intron_igv_bed.ok
07:57:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed --bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2
[W::hts_idx_load3] The index file is older than the data file: SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
08:00:22 : INFO : Execution Time = 2.77 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed --bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2
08:00:22 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok
08:00:22 : INFO : Running: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer_intron_reads.bam
08:00:22 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer_intron_reads.bam
08:00:22 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok
08:00:22 : INFO : Running: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.bam
[bam_sort_core] merging from 15 files and 1 in-memory blocks...
08:04:58 : INFO : Execution Time = 4.59 minutes. CMD: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.bam
08:04:58 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/sort_gene_reads.ok
08:04:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam
08:05:56 : INFO : Execution Time = 0.97 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.bam
08:05:56 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
08:05:56 : INFO : Running: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp
08:05:59 : INFO : Execution Time = 0.04 minutes. CMD: samtools sort -o SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp
08:05:59 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
08:05:59 : INFO : Running: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam
08:05:59 : INFO : Execution Time = 0.01 minutes. CMD: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam
08:05:59 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
08:05:59 : INFO : Running: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam
08:05:59 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam
08:05:59 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
08:05:59 : INFO : Running: create_report SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.ctat-splicing.igv.html --track-config SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
08:06:19 : INFO : Execution Time = 0.33 minutes. CMD: create_report SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.ctat-splicing.igv.html --track-config SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2'
08:06:19 : INFO : Running: touch /tmp/nxf.4avfjpP6kU/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.chckpts/igv_create_html.ok
08:06:19 : INFO : done.