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/2b/2e9bea3f0f3ebf6d3251724fa15deb/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/86add9b17813b45e84d18e5cb10cd6/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/86add9b17813b45e84d18e5cb10cd6/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/86add9b17813b45e84d18e5cb10cd6/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/a4e75ed89709eedd79b430f560b57d/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/2e9bea3f0f3ebf6d3251724fa15deb/.command.run ==> STAGING COMPLETE (7 inputs) 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rate=23400000.00/min [10930000], rate=23421428.57/min [10940000], rate=23442857.14/min [10950000], rate=23464285.71/min [10960000], rate=23485714.29/min [10970000], rate=23507142.86/min [10980000], rate=23528571.43/min [10990000], rate=23550000.00/min [11000000], rate=23571428.57/min [11010000], rate=23592857.14/min [11020000], rate=23614285.71/min [11030000], rate=23635714.29/min [11040000], rate=23657142.86/min [11050000], rate=23678571.43/min [11060000], rate=23700000.00/min [11070000], rate=23721428.57/min [11080000], rate=23742857.14/min 08:24:16 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_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. -1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 3776 cancer introns 08:24:17 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim 08:24:17 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok 08:24:17 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 08:24:17 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 08:24:17 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok 08:24:17 : INFO : -found 1314 cancer introns 08:24:17 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 08:24:17 : INFO : Creating the BED File. 08:24:20 : INFO : Saving Bed File as 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 08:24:20 : INFO : Execution Time = 0.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 08:24:20 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok 08:24:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1 [W::hts_idx_load3] The index file is older than the data file: 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai 08:31:08 : INFO : Execution Time = 6.79 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1 08:31:08 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok 08:31:08 : INFO : Running: samtools sort -o 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 08:31:08 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 08:31:08 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok 08:31:08 : INFO : Running: samtools sort -o 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam [bam_sort_core] merging from 38 files and 1 in-memory blocks... 08:40:02 : INFO : Execution Time = 8.89 minutes. CMD: samtools sort -o 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam 08:40:02 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok 08:40:02 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_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. Done with chr chr22. 08:43:50 : INFO : Execution Time = 3.81 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 08:43:50 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok 08:43:50 : INFO : Running: samtools sort -o 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 1 files and 1 in-memory blocks... 08:44:13 : INFO : Execution Time = 0.38 minutes. CMD: samtools sort -o 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp 08:44:13 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 08:44:13 : INFO : Running: samtools index 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 08:44:16 : INFO : Execution Time = 0.04 minutes. CMD: samtools index 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 08:44:16 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok 08:44:16 : INFO : Running: samtools index 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 08:44:16 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 08:44:16 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok 08:44:16 : INFO : Running: create_report 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1' 08:46:31 : INFO : Execution Time = 2.24 minutes. CMD: create_report 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1' 08:46:31 : INFO : Running: touch /tmp/nxf.YTddoY4kMG/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok 08:46:31 : INFO : done.