Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/fb89939eba61d5b706cbb1ad481589/aih-tih-sc-2a5468-R1_B23WHYVLT4_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/e2/14ebd453fdd666330bfc7560796761/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/fb89939eba61d5b706cbb1ad481589/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/604a6926ab30f33787028fb774950e/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/14ebd453fdd666330bfc7560796761/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/fb89939eba61d5b706cbb1ad481589/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)
09:40:13 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10930000], rate=13116000.00/min 09:41:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-2a5468-R1_B23WHYVLT4_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.
-aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns: identified 7877 cancer introns
09:41:14 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns.prelim
09:41:14 : INFO : Running: touch /tmp/nxf.ghw27TllkF/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok
09:41:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns
09:41:14 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns
09:41:14 : INFO : Running: touch /tmp/nxf.ghw27TllkF/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok
09:41:14 : INFO : -found 3805 cancer introns
09:41:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:41:15 : INFO : Creating the BED File.
09:41:24 : INFO : Saving Bed File as aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:41:24 : INFO : Execution Time = 0.17 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-2a5468-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:41:24 : INFO : Running: touch /tmp/nxf.ghw27TllkF/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok
09:41:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-2a5468-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-2a5468-R1_B23WHYVLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai