08:50:40 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10540000], rate=19163636.36/min 08:51:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 786-O_FFPE_RNA_0001_B23LG7FLT4_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.
-786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns: identified 7589 cancer introns
08:51:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim
08:51:24 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/prelim_introns.ok
08:51:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns
08:51:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns
08:51:24 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/introns_filtered.ok
08:51:24 : INFO : -found 3573 cancer introns
08:51:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns --cancer_introns 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
08:51:24 : INFO : Creating the BED File.
08:51:31 : INFO : Saving Bed File as 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
08:51:31 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns --cancer_introns 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
08:51:31 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
08:51:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed --bam 786-O_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_1
[W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
09:16:43 : INFO : Execution Time = 25.20 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed --bam 786-O_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_1
09:16:43 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
09:16:43 : INFO : Running: samtools sort -o 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.bam
09:16:44 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.bam
09:16:44 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
09:16:44 : INFO : Running: samtools sort -o 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.bam
[bam_sort_core] merging from 123 files and 1 in-memory blocks...
09:45:11 : INFO : Execution Time = 28.45 minutes. CMD: samtools sort -o 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.bam
09:45:11 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
09:45:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam
09:54:38 : INFO : Execution Time = 9.44 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam
09:54:38 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
09:54:38 : INFO : Running: samtools sort -o 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 7 files and 1 in-memory blocks...
09:56:33 : INFO : Execution Time = 1.93 minutes. CMD: samtools sort -o 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
09:56:33 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:56:33 : INFO : Running: samtools index 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
09:56:45 : INFO : Execution Time = 0.19 minutes. CMD: samtools index 786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
09:56:45 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
09:56:45 : INFO : Running: samtools index 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
09:56:45 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
09:56:45 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/786-O_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
09:56:45 : INFO : Running: create_report 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 786-O_FFPE_RNA_0001_B23LG7FLT4_1.ctat-splicing.igv.html --track-config 786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 786-O_FFPE_RNA_0001_B23LG7FLT4_1'
10:04:30 : INFO : Execution Time = 7.75 minutes. CMD: create_report 786-O_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 786-O_FFPE_RNA_0001_B23LG7FLT4_1.ctat-splicing.igv.html --track-config 786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 786-O_FFPE_RNA_0001_B23LG7FLT4_1'
10:04:30 : INFO : Running: touch /tmp/nxf.7E4bV6PNN7/786-O_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/igv_create_html.ok
10:04:30 : INFO : done.