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/545a6d7388e356edd34476fd79f770/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/51c0141100d6d6ed2e74a9046977be/dna_s770.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/51c0141100d6d6ed2e74a9046977be/dna_s770.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/545a6d7388e356edd34476fd79f770/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/51c0141100d6d6ed2e74a9046977be/dna_s770.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/0d4879ae77d4487bdabe0354f91be2/dna_s770.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)
07:59:23 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[4670000], rate=16482352.94/min 07:59:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file dna_s770.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > dna_s770.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.
-dna_s770.introns: identified 18 cancer introns
07:59:46 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file dna_s770.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > dna_s770.cancer.introns.prelim
07:59:46 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/prelim_introns.ok
07:59:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates dna_s770.cancer.introns.prelim --min_total_reads 5 > dna_s770.cancer.introns
07:59:46 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates dna_s770.cancer.introns.prelim --min_total_reads 5 > dna_s770.cancer.introns
07:59:46 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/introns_filtered.ok
07:59:46 : INFO : -found 4 cancer introns
07:59:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns dna_s770.introns --cancer_introns dna_s770.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed dna_s770.introns.for_IGV.bed
07:59:47 : INFO : Creating the BED File.
07:59:47 : INFO : Saving Bed File as dna_s770.introns.for_IGV.bed
07:59:47 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns dna_s770.introns --cancer_introns dna_s770.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed dna_s770.introns.for_IGV.bed
07:59:47 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/intron_igv_bed.ok
07:59:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed dna_s770.introns.for_IGV.bed --bam dna_s770.Aligned.sortedByCoord.out.bam --output_prefix dna_s770
[W::hts_idx_load3] The index file is older than the data file: dna_s770.Aligned.sortedByCoord.out.bam.bai
07:59:48 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed dna_s770.introns.for_IGV.bed --bam dna_s770.Aligned.sortedByCoord.out.bam --output_prefix dna_s770
07:59:48 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/reads_alignments_extracted.ok
07:59:48 : INFO : Running: samtools sort -o dna_s770.cancer_intron_reads.sorted.bam dna_s770.cancer_intron_reads.bam
07:59:48 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o dna_s770.cancer_intron_reads.sorted.bam dna_s770.cancer_intron_reads.bam
07:59:48 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/sort_cancer_intron_reads.ok
07:59:48 : INFO : Running: samtools sort -o dna_s770.gene_reads.sorted.bam dna_s770.gene_reads.bam
07:59:49 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o dna_s770.gene_reads.sorted.bam dna_s770.gene_reads.bam
07:59:49 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/sort_gene_reads.ok
07:59:49 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o dna_s770.gene_reads.sorted.sifted.bam.tmp --keep_secondary dna_s770.gene_reads.sorted.bam
Done with chr chr1.
Done with chr chr4.
Done with chr chr11.
Done with chr chr12.
07:59:49 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o dna_s770.gene_reads.sorted.sifted.bam.tmp --keep_secondary dna_s770.gene_reads.sorted.bam
07:59:49 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/dna_s770.gene_reads.sorted.sifted.bam.tmp.ok
07:59:49 : INFO : Running: samtools sort -o dna_s770.gene_reads.sorted.sifted.bam dna_s770.gene_reads.sorted.sifted.bam.tmp
07:59:49 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o dna_s770.gene_reads.sorted.sifted.bam dna_s770.gene_reads.sorted.sifted.bam.tmp
07:59:49 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/dna_s770.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:59:49 : INFO : Running: samtools index dna_s770.gene_reads.sorted.sifted.bam
07:59:49 : INFO : Execution Time = 0.00 minutes. CMD: samtools index dna_s770.gene_reads.sorted.sifted.bam
07:59:49 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/dna_s770.gene_reads.sorted.sifted.bam.indexed.ok
07:59:49 : INFO : Running: samtools index dna_s770.cancer_intron_reads.sorted.bam
07:59:49 : INFO : Execution Time = 0.00 minutes. CMD: samtools index dna_s770.cancer_intron_reads.sorted.bam
07:59:49 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/dna_s770.cancer_intron_reads.sorted.bam.indexed.ok
07:59:49 : INFO : Running: create_report dna_s770.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output dna_s770.ctat-splicing.igv.html --track-config dna_s770.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: dna_s770'
07:59:50 : INFO : Execution Time = 0.01 minutes. CMD: create_report dna_s770.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output dna_s770.ctat-splicing.igv.html --track-config dna_s770.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: dna_s770'
07:59:50 : INFO : Running: touch /tmp/nxf.zmpF1WqQ98/dna_s770.chckpts/igv_create_html.ok
07:59:50 : INFO : done.