Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/82d3b82ba79d285fb61633dd0fb778/A673_FFPE_RNA_0001_B23LG7FLT4_3.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/82d3b82ba79d285fb61633dd0fb778/A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam 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/13/c0bbf0cfa54676cc4b654af4bf5482/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/c0bbf0cfa54676cc4b654af4bf5482/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/82d3b82ba79d285fb61633dd0fb778/A673_FFPE_RNA_0001_B23LG7FLT4_3.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/3d013309291690d8fb86b67138cdef/A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai ==> STAGING COMPLETE (7 inputs) 21:23:25 : INFO : 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rate=12689361.70/min [9950000], rate=12702127.66/min [9960000], rate=12714893.62/min 21:24:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file A673_FFPE_RNA_0001_B23LG7FLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > A673_FFPE_RNA_0001_B23LG7FLT4_3.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. -A673_FFPE_RNA_0001_B23LG7FLT4_3.introns: identified 7289 cancer introns 21:24:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file A673_FFPE_RNA_0001_B23LG7FLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim 21:24:24 : INFO : Running: touch /tmp/nxf.sVSRoTHnn6/A673_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/prelim_introns.ok 21:24:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim --min_total_reads 5 > A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns 21:24:24 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim --min_total_reads 5 > A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns 21:24:24 : INFO : Running: touch /tmp/nxf.sVSRoTHnn6/A673_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/introns_filtered.ok 21:24:24 : INFO : -found 3626 cancer introns 21:24:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns A673_FFPE_RNA_0001_B23LG7FLT4_3.introns --cancer_introns A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed A673_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed 21:24:25 : INFO : Creating the BED File. 21:24:34 : INFO : Saving Bed File as A673_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed 21:24:34 : INFO : Execution Time = 0.17 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns A673_FFPE_RNA_0001_B23LG7FLT4_3.introns --cancer_introns A673_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed A673_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed 21:24:34 : INFO : Running: touch /tmp/nxf.sVSRoTHnn6/A673_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/intron_igv_bed.ok 21:24:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed A673_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed --bam A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --output_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai