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/a2/5a8966bec5d146d12802b7b8467a55/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/ba6e601cda803c9e1be0a06f487572/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/5a8966bec5d146d12802b7b8467a55/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/ba6e601cda803c9e1be0a06f487572/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/1fe52a363a5178c4ba1cdfc8e4a78f/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/5a8966bec5d146d12802b7b8467a55/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)
07:31:25 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[3150000], rate=21000000.00/min 07:31:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNP_FFPE_L03_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.
-BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns: identified 110 cancer introns
07:31:41 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns.prelim
07:31:41 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok
07:31:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns
07:31:41 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns
07:31:41 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok
07:31:41 : INFO : -found 81 cancer introns
07:31:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --cancer_introns BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:31:42 : INFO : Creating the BED File.
07:31:42 : INFO : Saving Bed File as BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:31:42 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns --cancer_introns BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
07:31:42 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
07:31:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
07:32:31 : INFO : Execution Time = 0.81 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1
07:32:31 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
07:32:31 : INFO : Running: samtools sort -o BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
07:32:31 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
07:32:31 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
07:32:31 : INFO : Running: samtools sort -o BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.bam
[bam_sort_core] merging from 4 files and 1 in-memory blocks...
07:33:34 : INFO : Execution Time = 1.05 minutes. CMD: samtools sort -o BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.bam
07:33:34 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
07:33:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNP_FFPE_L03_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.
Done with chr chr16.
Done with chr chr17.
Done with chr chr18.
Done with chr chr19.
Done with chr chr20.
Done with chr chr21.
07:33:44 : INFO : Execution Time = 0.16 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam
07:33:44 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:33:44 : INFO : Running: samtools sort -o BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
07:33:45 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
07:33:45 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:33:45 : INFO : Running: samtools index BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
07:33:45 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
07:33:45 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:33:45 : INFO : Running: samtools index BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
07:33:45 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
07:33:45 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:33:45 : INFO : Running: create_report BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1'
07:33:53 : INFO : Execution Time = 0.14 minutes. CMD: create_report BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1'
07:33:53 : INFO : Running: touch /tmp/nxf.awXffl4axk/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok
07:33:53 : INFO : done.