Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/3cd21f6907d732f6a81760cedfd06b/NTC_0001_0001_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
  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/cd/d6c5ad570b0c97ab6f2dd13076877c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/cbdab0b8019e7b3b3d7ba3897518d5/NTC_0001_0001_B23WHYVLT4_1.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/cbdab0b8019e7b3b3d7ba3897518d5/NTC_0001_0001_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/d6c5ad570b0c97ab6f2dd13076877c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/cbdab0b8019e7b3b3d7ba3897518d5/NTC_0001_0001_B23WHYVLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)

07:28:21 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
07:28:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file NTC_0001_0001_B23WHYVLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > NTC_0001_0001_B23WHYVLT4_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.
-NTC_0001_0001_B23WHYVLT4_1.introns: identified 1 cancer introns
07:28:25 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file NTC_0001_0001_B23WHYVLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > NTC_0001_0001_B23WHYVLT4_1.cancer.introns.prelim 
07:28:25 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/prelim_introns.ok
07:28:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates NTC_0001_0001_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5  > NTC_0001_0001_B23WHYVLT4_1.cancer.introns 
07:28:25 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates NTC_0001_0001_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5  > NTC_0001_0001_B23WHYVLT4_1.cancer.introns 
07:28:25 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/introns_filtered.ok
07:28:25 : INFO : -found 1 cancer introns
07:28:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns NTC_0001_0001_B23WHYVLT4_1.introns  --cancer_introns NTC_0001_0001_B23WHYVLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed NTC_0001_0001_B23WHYVLT4_1.introns.for_IGV.bed 
07:28:26 : INFO :  Creating the BED File.
07:28:26 : INFO : Saving Bed File as NTC_0001_0001_B23WHYVLT4_1.introns.for_IGV.bed
07:28:26 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns NTC_0001_0001_B23WHYVLT4_1.introns  --cancer_introns NTC_0001_0001_B23WHYVLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed NTC_0001_0001_B23WHYVLT4_1.introns.for_IGV.bed 
07:28:26 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/intron_igv_bed.ok
07:28:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed NTC_0001_0001_B23WHYVLT4_1.introns.for_IGV.bed  --bam NTC_0001_0001_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix NTC_0001_0001_B23WHYVLT4_1 
07:28:26 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed NTC_0001_0001_B23WHYVLT4_1.introns.for_IGV.bed  --bam NTC_0001_0001_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix NTC_0001_0001_B23WHYVLT4_1 
07:28:26 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/reads_alignments_extracted.ok
07:28:26 : INFO : Running: samtools sort -o NTC_0001_0001_B23WHYVLT4_1.cancer_intron_reads.sorted.bam NTC_0001_0001_B23WHYVLT4_1.cancer_intron_reads.bam
07:28:26 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o NTC_0001_0001_B23WHYVLT4_1.cancer_intron_reads.sorted.bam NTC_0001_0001_B23WHYVLT4_1.cancer_intron_reads.bam
07:28:26 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/sort_cancer_intron_reads.ok
07:28:26 : INFO : Running: samtools sort -o NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.bam NTC_0001_0001_B23WHYVLT4_1.gene_reads.bam
07:28:26 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.bam NTC_0001_0001_B23WHYVLT4_1.gene_reads.bam
07:28:26 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/sort_gene_reads.ok
07:28:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.bam 
Done with chr chr1.
07:28:26 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.bam 
07:28:26 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:28:26 : INFO : Running: samtools sort -o NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp
07:28:26 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp
07:28:26 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:28:26 : INFO : Running: samtools index NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam 
07:28:26 : INFO : Execution Time = 0.00 minutes. CMD: samtools index NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam 
07:28:26 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/NTC_0001_0001_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:28:26 : INFO : Running: samtools index NTC_0001_0001_B23WHYVLT4_1.cancer_intron_reads.sorted.bam 
07:28:26 : INFO : Execution Time = 0.00 minutes. CMD: samtools index NTC_0001_0001_B23WHYVLT4_1.cancer_intron_reads.sorted.bam 
07:28:26 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/NTC_0001_0001_B23WHYVLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:28:26 : INFO : Running: create_report NTC_0001_0001_B23WHYVLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output NTC_0001_0001_B23WHYVLT4_1.ctat-splicing.igv.html  --track-config NTC_0001_0001_B23WHYVLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: NTC_0001_0001_B23WHYVLT4_1' 
07:28:27 : INFO : Execution Time = 0.00 minutes. CMD: create_report NTC_0001_0001_B23WHYVLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output NTC_0001_0001_B23WHYVLT4_1.ctat-splicing.igv.html  --track-config NTC_0001_0001_B23WHYVLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: NTC_0001_0001_B23WHYVLT4_1' 
07:28:27 : INFO : Running: touch /tmp/nxf.owfOgiYs6H/NTC_0001_0001_B23WHYVLT4_1.chckpts/igv_create_html.ok
07:28:27 : INFO : done.