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/c9/4517672559aea659b87a387d69f1f2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/12c82fb491644561d8884bf33db2a8/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/12c82fb491644561d8884bf33db2a8/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/8bde3efa82b1e8f1eb40464e3330e4/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/12c82fb491644561d8884bf33db2a8/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/4517672559aea659b87a387d69f1f2/.command.run
==> STAGING COMPLETE (7 inputs)

20:18:15 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

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[3250000], rate=19500000.00/min 20:18:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > OvarianNP_FFPE_L05_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.
-OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns: identified 77 cancer introns
20:18:30 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer.introns.prelim 
20:18:30 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok
20:18:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5  > OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer.introns 
20:18:31 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5  > OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer.introns 
20:18:31 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok
20:18:31 : INFO : -found 42 cancer introns
20:18:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns  --cancer_introns OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 
20:18:31 : INFO :  Creating the BED File.
20:18:32 : INFO : Saving Bed File as OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
20:18:32 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns  --cancer_introns OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 
20:18:32 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
20:18:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  --bam OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1 
[W::hts_idx_load3] The index file is older than the data file: OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
20:18:35 : INFO : Execution Time = 0.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  --bam OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1 
20:18:35 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
20:18:35 : INFO : Running: samtools sort -o OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
20:18:35 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
20:18:35 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
20:18:35 : INFO : Running: samtools sort -o OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.bam
20:18:39 : INFO : Execution Time = 0.05 minutes. CMD: samtools sort -o OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.bam
20:18:39 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
20:18:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 
Done with chr chr1.
Done with chr chr2.
Done with chr chr3.
Done with chr chr4.
Done with chr chr5.
Done with chr chr6.
Done with chr chr7.
Done with chr chr8.
Done with chr chr9.
Done with chr chr10.
Done with chr chr11.
Done with chr chr12.
Done with chr chr14.
Done with chr chr15.
Done with chr chr16.
Done with chr chr17.
Done with chr chr19.
Done with chr chr21.
Done with chr chr22.
20:18:40 : INFO : Execution Time = 0.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 
20:18:40 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
20:18:40 : INFO : Running: samtools sort -o OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
20:18:41 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
20:18:41 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
20:18:41 : INFO : Running: samtools index OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 
20:18:41 : INFO : Execution Time = 0.00 minutes. CMD: samtools index OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 
20:18:41 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
20:18:41 : INFO : Running: samtools index OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 
20:18:41 : INFO : Execution Time = 0.00 minutes. CMD: samtools index OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 
20:18:41 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
20:18:41 : INFO : Running: create_report OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html  --track-config OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1' 
20:18:48 : INFO : Execution Time = 0.11 minutes. CMD: create_report OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html  --track-config OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1' 
20:18:48 : INFO : Running: touch /tmp/nxf.c6a6AFbiAs/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok
20:18:48 : INFO : done.