Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/e937969fa28045989dc6ed308c1651/FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.Chimeric.out.junction
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/e4/f923b7d0477d3b3224d6743a8423ca/FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/ce612de34e10e22ed53e183659d210/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/e937969fa28045989dc6ed308c1651/FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/ce612de34e10e22ed53e183659d210/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/e937969fa28045989dc6ed308c1651/FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.SJ.out.tab
==> STAGING COMPLETE (7 inputs)
08:50:03 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[9010000], rate=10011111.11/min 08:51:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_HD789_02_RNA_0015_B23MHV2LT4_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.
-FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.introns: identified 9675 cancer introns
08:51:09 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.cancer.introns.prelim
08:51:09 : INFO : Running: touch /tmp/nxf.AHn2cxwj1Y/FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.chckpts/prelim_introns.ok
08:51:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.cancer.introns
08:51:10 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.cancer.introns
08:51:10 : INFO : Running: touch /tmp/nxf.AHn2cxwj1Y/FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.chckpts/introns_filtered.ok
08:51:10 : INFO : -found 5088 cancer introns
08:51:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.introns --cancer_introns FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.introns.for_IGV.bed
08:51:10 : INFO : Creating the BED File.
08:51:25 : INFO : Saving Bed File as FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.introns.for_IGV.bed
08:51:26 : INFO : Execution Time = 0.27 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.introns --cancer_introns FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.introns.for_IGV.bed
08:51:26 : INFO : Running: touch /tmp/nxf.AHn2cxwj1Y/FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.chckpts/intron_igv_bed.ok
08:51:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.introns.for_IGV.bed --bam FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix FFPE_HD789_02_RNA_0015_B23MHV2LT4_1
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai