Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/60cec82a57883ba7a92e8f29b228e6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/320c77402664fc25775a7c2675bb8d/rna_s1200_S21.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/320c77402664fc25775a7c2675bb8d/rna_s1200_S21.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/320c77402664fc25775a7c2675bb8d/rna_s1200_S21.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/60cec82a57883ba7a92e8f29b228e6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/613d27af2da60f89ec407c24b98028/rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)

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 
Done with chr chr1.
Done with chr chr2.
Done with chr chr6.
Done with chr chr7.
Done with chr chr8.
Done with chr chr9.
Done with chr chr12.
Done with chr chr17.
Done with chr chr20.
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.