20:22:08 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
20:22:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > 659_Kh-T1-TRNA-1_B23MHV2LT4_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.
-659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns: identified 81 cancer introns
20:22:12 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 
20:22:12 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok
20:22:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5  > 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 
20:22:12 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5  > 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 
20:22:12 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok
20:22:12 : INFO : -found 42 cancer introns
20:22:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns  --cancer_introns 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 
20:22:12 : INFO :  Creating the BED File.
20:22:12 : INFO : Saving Bed File as 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
20:22:12 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns  --cancer_introns 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 
20:22:12 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok
20:22:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed  --bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam  --output_prefix 659_Kh-T1-TRNA-1_B23MHV2LT4_1 
[W::hts_idx_load3] The index file is older than the data file: 659_Kh-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
20:22:13 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed  --bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam  --output_prefix 659_Kh-T1-TRNA-1_B23MHV2LT4_1 
20:22:13 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok
20:22:13 : INFO : Running: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam
20:22:13 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam
20:22:13 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok
20:22:13 : INFO : Running: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam
20:22:13 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam
20:22:13 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_gene_reads.ok
20:22:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 
20:22:14 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 
20:22:14 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok
20:22:14 : INFO : Running: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp
20:22:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp
20:22:14 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
20:22:14 : INFO : Running: samtools index 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 
20:22:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 
20:22:14 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok
20:22:14 : INFO : Running: samtools index 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 
20:22:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 
20:22:14 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok
20:22:14 : INFO : Running: create_report 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output 659_Kh-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html  --track-config 659_Kh-T1-TRNA-1_B23MHV2LT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: 659_Kh-T1-TRNA-1_B23MHV2LT4_1' 
20:22:20 : INFO : Execution Time = 0.10 minutes. CMD: create_report 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output 659_Kh-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html  --track-config 659_Kh-T1-TRNA-1_B23MHV2LT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: 659_Kh-T1-TRNA-1_B23MHV2LT4_1' 
20:22:20 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/igv_create_html.ok
20:22:20 : INFO : done.