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/26/5737d6ddee60f4ba408d85642f0bf1/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/cb1409ec2dda9ccb426dc8c78e8422/tih_rna_sample_00479_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/3b79ebd02c2a998719f23406a2c845/tih_rna_sample_00479_B23WHTKLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/3b79ebd02c2a998719f23406a2c845/tih_rna_sample_00479_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/3b79ebd02c2a998719f23406a2c845/tih_rna_sample_00479_B23WHTKLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/5737d6ddee60f4ba408d85642f0bf1/.command.run
==> STAGING COMPLETE (7 inputs)
09:01:48 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[8740000], rate=15423529.41/min 09:02:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00479_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00479_B23WHTKLT4_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_00479_B23WHTKLT4_1.introns: identified 6930 cancer introns
09:02:32 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00479_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00479_B23WHTKLT4_1.cancer.introns.prelim
09:02:32 : INFO : Running: touch /tmp/nxf.drri540x4W/tih_rna_sample_00479_B23WHTKLT4_1.chckpts/prelim_introns.ok
09:02:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00479_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00479_B23WHTKLT4_1.cancer.introns
09:02:32 : 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_00479_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00479_B23WHTKLT4_1.cancer.introns
09:02:32 : INFO : Running: touch /tmp/nxf.drri540x4W/tih_rna_sample_00479_B23WHTKLT4_1.chckpts/introns_filtered.ok
09:02:32 : INFO : -found 3896 cancer introns
09:02:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00479_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00479_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00479_B23WHTKLT4_1.introns.for_IGV.bed
09:02:33 : INFO : Creating the BED File.
09:02:41 : INFO : Saving Bed File as tih_rna_sample_00479_B23WHTKLT4_1.introns.for_IGV.bed
09:02:41 : INFO : Execution Time = 0.15 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00479_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00479_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00479_B23WHTKLT4_1.introns.for_IGV.bed
09:02:41 : INFO : Running: touch /tmp/nxf.drri540x4W/tih_rna_sample_00479_B23WHTKLT4_1.chckpts/intron_igv_bed.ok
09:02:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00479_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00479_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00479_B23WHTKLT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00479_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
09:27:26 : INFO : Execution Time = 24.75 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00479_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00479_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00479_B23WHTKLT4_1
09:27:26 : INFO : Running: touch /tmp/nxf.drri540x4W/tih_rna_sample_00479_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok
09:27:27 : INFO : Running: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00479_B23WHTKLT4_1.cancer_intron_reads.bam
09:27:28 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00479_B23WHTKLT4_1.cancer_intron_reads.bam
09:27:28 : INFO : Running: touch /tmp/nxf.drri540x4W/tih_rna_sample_00479_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok
09:27:28 : INFO : Running: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_1.gene_reads.sorted.bam tih_rna_sample_00479_B23WHTKLT4_1.gene_reads.bam