Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/2ef70cf7065bd9d936d0ee3996e6f0/tih_rna_sample_00701_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 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/0e/84d85eb67d3b7a8b38af5e982e534b/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/f6b41a64c9f5860de6113ac0f663ab/tih_rna_sample_00701_B23MVV7LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/f6b41a64c9f5860de6113ac0f663ab/tih_rna_sample_00701_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/84d85eb67d3b7a8b38af5e982e534b/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/f6b41a64c9f5860de6113ac0f663ab/tih_rna_sample_00701_B23MVV7LT4_1.Chimeric.out.junction ==> STAGING COMPLETE (7 inputs) 09:02:20 : INFO 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[9900000], rate=9281250.00/min [9910000], rate=9290625.00/min 09:03:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00701_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00701_B23MVV7LT4_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. -tih_rna_sample_00701_B23MVV7LT4_1.introns: identified 8482 cancer introns 09:03:38 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00701_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00701_B23MVV7LT4_1.cancer.introns.prelim 09:03:38 : INFO : Running: touch /tmp/nxf.Ml6QO6dXZt/tih_rna_sample_00701_B23MVV7LT4_1.chckpts/prelim_introns.ok 09:03:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00701_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00701_B23MVV7LT4_1.cancer.introns 09:03:39 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00701_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00701_B23MVV7LT4_1.cancer.introns 09:03:39 : INFO : Running: touch /tmp/nxf.Ml6QO6dXZt/tih_rna_sample_00701_B23MVV7LT4_1.chckpts/introns_filtered.ok 09:03:39 : INFO : -found 3759 cancer introns 09:03:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00701_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00701_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00701_B23MVV7LT4_1.introns.for_IGV.bed 09:03:39 : INFO : Creating the BED File. 09:03:50 : INFO : Saving Bed File as tih_rna_sample_00701_B23MVV7LT4_1.introns.for_IGV.bed 09:03:50 : INFO : Execution Time = 0.19 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00701_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00701_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00701_B23MVV7LT4_1.introns.for_IGV.bed 09:03:50 : INFO : Running: touch /tmp/nxf.Ml6QO6dXZt/tih_rna_sample_00701_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 09:03:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00701_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00701_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00701_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00701_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 09:34:40 : INFO : Execution Time = 30.83 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00701_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00701_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00701_B23MVV7LT4_1 09:34:40 : INFO : Running: touch /tmp/nxf.Ml6QO6dXZt/tih_rna_sample_00701_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 09:34:40 : INFO : Running: samtools sort -o tih_rna_sample_00701_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00701_B23MVV7LT4_1.cancer_intron_reads.bam 09:34:41 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o tih_rna_sample_00701_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00701_B23MVV7LT4_1.cancer_intron_reads.bam 09:34:41 : INFO : Running: touch /tmp/nxf.Ml6QO6dXZt/tih_rna_sample_00701_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 09:34:41 : INFO : Running: samtools sort -o tih_rna_sample_00701_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00701_B23MVV7LT4_1.gene_reads.bam