Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/6c319c17dbcb663e1f33dd6c1cf5af/aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.SJ.out.tab
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/6c319c17dbcb663e1f33dd6c1cf5af/aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/eb38ee69cd6bd1e8b0068212db1064/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/6c319c17dbcb663e1f33dd6c1cf5af/aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/eaf36bc1ed5dbc4da7bf53d70bc527/aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/eb38ee69cd6bd1e8b0068212db1064/.command.run
==> STAGING COMPLETE (7 inputs)
08:46:41 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[9430000], rate=14889473.68/min 08:47:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-6cc13c-R1_A23YTGFLT4_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-6cc13c-R1_A23YTGFLT4_1.introns: identified 7136 cancer introns
08:47:31 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.cancer.introns.prelim
08:47:31 : INFO : Running: touch /tmp/nxf.upE9tDh21U/aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok
08:47:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.cancer.introns
08:47:31 : 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-6cc13c-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.cancer.introns
08:47:31 : INFO : Running: touch /tmp/nxf.upE9tDh21U/aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok
08:47:31 : INFO : -found 2663 cancer introns
08:47:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.introns.for_IGV.bed
08:47:32 : INFO : Creating the BED File.
08:47:37 : INFO : Saving Bed File as aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.introns.for_IGV.bed
08:47:37 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.introns.for_IGV.bed
08:47:37 : INFO : Running: touch /tmp/nxf.upE9tDh21U/aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok
08:47:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-6cc13c-R1_A23YTGFLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
09:11:51 : INFO : Execution Time = 24.22 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-6cc13c-R1_A23YTGFLT4_1
09:11:51 : INFO : Running: touch /tmp/nxf.upE9tDh21U/aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok
09:11:51 : INFO : Running: samtools sort -o aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.cancer_intron_reads.bam
09:11:51 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.cancer_intron_reads.bam
09:11:51 : INFO : Running: touch /tmp/nxf.upE9tDh21U/aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok
09:11:52 : INFO : Running: samtools sort -o aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.gene_reads.bam