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/0d/69b7317f280f1edaeb2ee4aaa39abf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/ebb454649b9ac609ab407d41fec8e2/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/ebb454649b9ac609ab407d41fec8e2/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/31c39c8f066eda72f7e73d301df784/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/69b7317f280f1edaeb2ee4aaa39abf/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/ebb454649b9ac609ab407d41fec8e2/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)

07:40:11 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

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[3930000], rate=29475000.00/min 07:40:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > BreastNB_FFPE_L01_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.
-BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns: identified 178 cancer introns
07:40:23 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim 
07:40:23 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok
07:40:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5  > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns 
07:40:24 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5  > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns 
07:40:24 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok
07:40:24 : INFO : -found 119 cancer introns
07:40:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns  --cancer_introns BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 
07:40:24 : INFO :  Creating the BED File.
07:40:24 : INFO : Saving Bed File as BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:40:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns  --cancer_introns BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed 
07:40:24 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
07:40:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  --bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1 
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
07:40:39 : INFO : Execution Time = 0.24 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  --bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1 
07:40:39 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
07:40:39 : INFO : Running: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
07:40:39 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
07:40:39 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
07:40:39 : INFO : Running: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.bam
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
07:40:57 : INFO : Execution Time = 0.30 minutes. CMD: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.bam
07:40:57 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
07:40:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  BreastNB_FFPE_L01_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 chr13.
Done with chr chr14.
Done with chr chr15.
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Done with chr chr18.
Done with chr chr19.
Done with chr chr20.
Done with chr chr22.
07:41:02 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam 
07:41:02 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:41:02 : INFO : Running: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
07:41:03 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
07:41:03 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:41:03 : INFO : Running: samtools index BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 
07:41:03 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 
07:41:03 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:41:03 : INFO : Running: samtools index BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 
07:41:03 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 
07:41:03 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:41:03 : INFO : Running: create_report BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html  --track-config BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1' 
07:41:16 : INFO : Execution Time = 0.20 minutes. CMD: create_report BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html  --track-config BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1' 
07:41:16 : INFO : Running: touch /tmp/nxf.5OYamzHcay/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok
07:41:16 : INFO : done.