14:49:30 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
14:49:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1200_S21.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > rna_s1200_S21.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.
-rna_s1200_S21.introns: identified 1141 cancer introns
14:49:34 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1200_S21.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > rna_s1200_S21.cancer.introns.prelim 
14:49:34 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/prelim_introns.ok
14:49:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1200_S21.cancer.introns.prelim --min_total_reads 5  > rna_s1200_S21.cancer.introns 
14:49:34 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1200_S21.cancer.introns.prelim --min_total_reads 5  > rna_s1200_S21.cancer.introns 
14:49:34 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/introns_filtered.ok
14:49:34 : INFO : -found 17 cancer introns
14:49:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1200_S21.introns  --cancer_introns rna_s1200_S21.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed rna_s1200_S21.introns.for_IGV.bed 
14:49:34 : INFO :  Creating the BED File.
14:49:34 : INFO : Saving Bed File as rna_s1200_S21.introns.for_IGV.bed
14:49:35 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1200_S21.introns  --cancer_introns rna_s1200_S21.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed rna_s1200_S21.introns.for_IGV.bed 
14:49:35 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/intron_igv_bed.ok
14:49:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1200_S21.introns.for_IGV.bed  --bam rna_s1200_S21.Aligned.sortedByCoord.out.bam  --output_prefix rna_s1200_S21 
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
14:49:35 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1200_S21.introns.for_IGV.bed  --bam rna_s1200_S21.Aligned.sortedByCoord.out.bam  --output_prefix rna_s1200_S21 
14:49:35 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/reads_alignments_extracted.ok
14:49:35 : INFO : Running: samtools sort -o rna_s1200_S21.cancer_intron_reads.sorted.bam rna_s1200_S21.cancer_intron_reads.bam
14:49:35 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1200_S21.cancer_intron_reads.sorted.bam rna_s1200_S21.cancer_intron_reads.bam
14:49:35 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/sort_cancer_intron_reads.ok
14:49:35 : INFO : Running: samtools sort -o rna_s1200_S21.gene_reads.sorted.bam rna_s1200_S21.gene_reads.bam
14:49:35 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o rna_s1200_S21.gene_reads.sorted.bam rna_s1200_S21.gene_reads.bam
14:49:35 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/sort_gene_reads.ok
14:49:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  rna_s1200_S21.gene_reads.sorted.bam 
14:49:36 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  rna_s1200_S21.gene_reads.sorted.bam 
14:49:36 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp.ok
14:49:36 : INFO : Running: samtools sort -o rna_s1200_S21.gene_reads.sorted.sifted.bam rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp
14:49:36 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1200_S21.gene_reads.sorted.sifted.bam rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp
14:49:36 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.tmpsorted.ok
14:49:36 : INFO : Running: samtools index rna_s1200_S21.gene_reads.sorted.sifted.bam 
14:49:36 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1200_S21.gene_reads.sorted.sifted.bam 
14:49:36 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.indexed.ok
14:49:36 : INFO : Running: samtools index rna_s1200_S21.cancer_intron_reads.sorted.bam 
14:49:36 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1200_S21.cancer_intron_reads.sorted.bam 
14:49:36 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/rna_s1200_S21.cancer_intron_reads.sorted.bam.indexed.ok
14:49:36 : INFO : Running: create_report rna_s1200_S21.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output rna_s1200_S21.ctat-splicing.igv.html  --track-config rna_s1200_S21.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: rna_s1200_S21' 
14:49:38 : INFO : Execution Time = 0.03 minutes. CMD: create_report rna_s1200_S21.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output rna_s1200_S21.ctat-splicing.igv.html  --track-config rna_s1200_S21.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: rna_s1200_S21' 
14:49:38 : INFO : Running: touch /tmp/nxf.6sA2qQT2vf/rna_s1200_S21.chckpts/igv_create_html.ok
14:49:38 : INFO : done.