08:44:16 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

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[22420000], rate=28621276.60/min 08:45:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > OvarianN_FFPE_L04_RNA_01_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.
-OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns: identified 1205 cancer introns
08:45:09 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns.prelim 
08:45:09 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok
08:45:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5  > OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns 
08:45:10 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5  > OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns 
08:45:10 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok
08:45:10 : INFO : -found 893 cancer introns
08:45:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns  --cancer_introns OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 
08:45:10 : INFO :  Creating the BED File.
08:45:12 : INFO : Saving Bed File as OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
08:45:12 : INFO : Execution Time = 0.04 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns  --cancer_introns OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 
08:45:12 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
08:45:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  --bam OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1 
[W::hts_idx_load3] The index file is older than the data file: OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
08:49:57 : INFO : Execution Time = 4.75 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  --bam OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1 
08:49:57 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
08:49:57 : INFO : Running: samtools sort -o OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
08:49:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
08:49:58 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
08:49:58 : INFO : Running: samtools sort -o OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.bam
[bam_sort_core] merging from 33 files and 1 in-memory blocks...
08:55:46 : INFO : Execution Time = 5.81 minutes. CMD: samtools sort -o OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.bam
08:55:46 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
08:55:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 
08:58:10 : INFO : Execution Time = 2.40 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 
08:58:10 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
08:58:10 : INFO : Running: samtools sort -o OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
08:58:28 : INFO : Execution Time = 0.30 minutes. CMD: samtools sort -o OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
08:58:28 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
08:58:28 : INFO : Running: samtools index OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 
08:58:30 : INFO : Execution Time = 0.04 minutes. CMD: samtools index OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 
08:58:30 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
08:58:30 : INFO : Running: samtools index OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 
08:58:30 : INFO : Execution Time = 0.00 minutes. CMD: samtools index OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 
08:58:30 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
08:58:30 : INFO : Running: create_report OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html  --track-config OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1' 
09:00:02 : INFO : Execution Time = 1.53 minutes. CMD: create_report OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html  --track-config OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1' 
09:00:02 : INFO : Running: touch /tmp/nxf.BYqmF8am6C/OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok
09:00:02 : INFO : done.