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/c8/df1f42043faf347b6152170b79ce4b/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/825e6edc2b8d8b2b70055dde5a7a95/rna_s1200_S21.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/825e6edc2b8d8b2b70055dde5a7a95/rna_s1200_S21.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/825e6edc2b8d8b2b70055dde5a7a95/rna_s1200_S21.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/df1f42043faf347b6152170b79ce4b/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/f1149b8715780589b3b3ec8eaab375/rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai ==> STAGING COMPLETE (7 inputs) 04:04:47 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [160000], rate=9600000.00/min [170000], rate=10200000.00/min [180000], rate=10800000.00/min [190000], rate=11400000.00/min [200000], rate=12000000.00/min [210000], rate=12600000.00/min [220000], rate=13200000.00/min [230000], rate=13800000.00/min [240000], rate=14400000.00/min 04:04:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1200_S21.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > rna_s1200_S21.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. -rna_s1200_S21.introns: identified 1141 cancer introns 04:04:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1200_S21.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > rna_s1200_S21.cancer.introns.prelim 04:04:55 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/prelim_introns.ok 04:04:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1200_S21.cancer.introns.prelim --min_total_reads 5 > rna_s1200_S21.cancer.introns 04:04:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1200_S21.cancer.introns.prelim --min_total_reads 5 > rna_s1200_S21.cancer.introns 04:04:55 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/introns_filtered.ok 04:04:55 : INFO : -found 17 cancer introns 04:04:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1200_S21.introns --cancer_introns rna_s1200_S21.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed rna_s1200_S21.introns.for_IGV.bed 04:04:56 : INFO : Creating the BED File. 04:04:56 : INFO : Saving Bed File as rna_s1200_S21.introns.for_IGV.bed 04:04:56 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1200_S21.introns --cancer_introns rna_s1200_S21.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed rna_s1200_S21.introns.for_IGV.bed 04:04:56 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/intron_igv_bed.ok 04:04:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1200_S21.introns.for_IGV.bed --bam rna_s1200_S21.Aligned.sortedByCoord.out.bam --output_prefix rna_s1200_S21 [W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai 04:04:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1200_S21.introns.for_IGV.bed --bam rna_s1200_S21.Aligned.sortedByCoord.out.bam --output_prefix rna_s1200_S21 04:04:57 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/reads_alignments_extracted.ok 04:04:57 : INFO : Running: samtools sort -o rna_s1200_S21.cancer_intron_reads.sorted.bam rna_s1200_S21.cancer_intron_reads.bam 04:04:57 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1200_S21.cancer_intron_reads.sorted.bam rna_s1200_S21.cancer_intron_reads.bam 04:04:57 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/sort_cancer_intron_reads.ok 04:04:57 : INFO : Running: samtools sort -o rna_s1200_S21.gene_reads.sorted.bam rna_s1200_S21.gene_reads.bam 04:04:57 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o rna_s1200_S21.gene_reads.sorted.bam rna_s1200_S21.gene_reads.bam 04:04:57 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/sort_gene_reads.ok 04:04:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp --keep_secondary rna_s1200_S21.gene_reads.sorted.bam Done with chr chr1. Done with chr chr2. Done with chr chr6. Done with chr chr7. Done with chr chr8. Done with chr chr9. Done with chr chr12. Done with chr chr17. Done with chr chr20. 04:04:58 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp --keep_secondary rna_s1200_S21.gene_reads.sorted.bam 04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp.ok 04:04:58 : INFO : Running: samtools sort -o rna_s1200_S21.gene_reads.sorted.sifted.bam rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp 04:04:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1200_S21.gene_reads.sorted.sifted.bam rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp 04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.tmpsorted.ok 04:04:58 : INFO : Running: samtools index rna_s1200_S21.gene_reads.sorted.sifted.bam 04:04:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1200_S21.gene_reads.sorted.sifted.bam 04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.indexed.ok 04:04:58 : INFO : Running: samtools index rna_s1200_S21.cancer_intron_reads.sorted.bam 04:04:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1200_S21.cancer_intron_reads.sorted.bam 04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.cancer_intron_reads.sorted.bam.indexed.ok 04:04:58 : INFO : Running: create_report rna_s1200_S21.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output rna_s1200_S21.ctat-splicing.igv.html --track-config rna_s1200_S21.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: rna_s1200_S21' [W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi 04:05:01 : INFO : Execution Time = 0.04 minutes. CMD: create_report rna_s1200_S21.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output rna_s1200_S21.ctat-splicing.igv.html --track-config rna_s1200_S21.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: rna_s1200_S21' 04:05:01 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/igv_create_html.ok 04:05:01 : INFO : done.