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/13/8a4a1fdb15286e082382b2dbec6eca/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/c8590f94f58d2b099e8ed73390973f/aih-tih-sc-3cac57-R1_A23WJ53LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/c8590f94f58d2b099e8ed73390973f/aih-tih-sc-3cac57-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/8a4a1fdb15286e082382b2dbec6eca/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/c8590f94f58d2b099e8ed73390973f/aih-tih-sc-3cac57-R1_A23WJ53LT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/eac41c56d0abac9ed1b3e0d848ceb4/aih-tih-sc-3cac57-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai ==> STAGING COMPLETE (7 inputs) 08:57:44 : INFO 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rate=18688235.29/min [10600000], rate=18705882.35/min [10610000], rate=18188571.43/min 08:58:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3cac57-R1_A23WJ53LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3cac57-R1_A23WJ53LT4_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-3cac57-R1_A23WJ53LT4_1.introns: identified 7512 cancer introns 08:58:28 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-3cac57-R1_A23WJ53LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-3cac57-R1_A23WJ53LT4_1.cancer.introns.prelim 08:58:28 : INFO : Running: touch /tmp/nxf.In7VXAxr5Q/aih-tih-sc-3cac57-R1_A23WJ53LT4_1.chckpts/prelim_introns.ok 08:58:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-3cac57-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3cac57-R1_A23WJ53LT4_1.cancer.introns 08:58:28 : 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-3cac57-R1_A23WJ53LT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-3cac57-R1_A23WJ53LT4_1.cancer.introns 08:58:28 : INFO : Running: touch /tmp/nxf.In7VXAxr5Q/aih-tih-sc-3cac57-R1_A23WJ53LT4_1.chckpts/introns_filtered.ok 08:58:28 : INFO : -found 3306 cancer introns 08:58:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3cac57-R1_A23WJ53LT4_1.introns --cancer_introns aih-tih-sc-3cac57-R1_A23WJ53LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3cac57-R1_A23WJ53LT4_1.introns.for_IGV.bed 08:58:28 : INFO : Creating the BED File. 08:58:36 : INFO : Saving Bed File as aih-tih-sc-3cac57-R1_A23WJ53LT4_1.introns.for_IGV.bed 08:58:36 : INFO : Execution Time = 0.13 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-3cac57-R1_A23WJ53LT4_1.introns --cancer_introns aih-tih-sc-3cac57-R1_A23WJ53LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-3cac57-R1_A23WJ53LT4_1.introns.for_IGV.bed 08:58:36 : INFO : Running: touch /tmp/nxf.In7VXAxr5Q/aih-tih-sc-3cac57-R1_A23WJ53LT4_1.chckpts/intron_igv_bed.ok 08:58:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3cac57-R1_A23WJ53LT4_1.introns.for_IGV.bed --bam aih-tih-sc-3cac57-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3cac57-R1_A23WJ53LT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai 09:22:55 : INFO : Execution Time = 24.31 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-3cac57-R1_A23WJ53LT4_1.introns.for_IGV.bed --bam aih-tih-sc-3cac57-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-3cac57-R1_A23WJ53LT4_1 09:22:55 : INFO : Running: touch /tmp/nxf.In7VXAxr5Q/aih-tih-sc-3cac57-R1_A23WJ53LT4_1.chckpts/reads_alignments_extracted.ok 09:22:55 : INFO : Running: samtools sort -o aih-tih-sc-3cac57-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3cac57-R1_A23WJ53LT4_1.cancer_intron_reads.bam 09:22:55 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-3cac57-R1_A23WJ53LT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-3cac57-R1_A23WJ53LT4_1.cancer_intron_reads.bam 09:22:55 : INFO : Running: touch /tmp/nxf.In7VXAxr5Q/aih-tih-sc-3cac57-R1_A23WJ53LT4_1.chckpts/sort_cancer_intron_reads.ok 09:22:55 : INFO : Running: samtools sort -o aih-tih-sc-3cac57-R1_A23WJ53LT4_1.gene_reads.sorted.bam aih-tih-sc-3cac57-R1_A23WJ53LT4_1.gene_reads.bam