Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/65317c0d7e01654d97a67aea9d5671/tih_rna_sample_00089_23H5VFLT4_s39.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/1f/65317c0d7e01654d97a67aea9d5671/tih_rna_sample_00089_23H5VFLT4_s39.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/1daa411ced78e9759de9102dda91e3/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/65317c0d7e01654d97a67aea9d5671/tih_rna_sample_00089_23H5VFLT4_s39.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/1daa411ced78e9759de9102dda91e3/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/60cca2875f49132e8930798965d69a/tih_rna_sample_00089_23H5VFLT4_s39.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)
08:35:18 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[8650000], rate=17896551.72/min 08:35:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00089_23H5VFLT4_s39.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00089_23H5VFLT4_s39.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_00089_23H5VFLT4_s39.introns: identified 7862 cancer introns
08:35:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00089_23H5VFLT4_s39.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00089_23H5VFLT4_s39.cancer.introns.prelim
08:35:57 : INFO : Running: touch /tmp/nxf.TqcNSDldqo/tih_rna_sample_00089_23H5VFLT4_s39.chckpts/prelim_introns.ok
08:35:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00089_23H5VFLT4_s39.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00089_23H5VFLT4_s39.cancer.introns
08:35:57 : 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_00089_23H5VFLT4_s39.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00089_23H5VFLT4_s39.cancer.introns
08:35:57 : INFO : Running: touch /tmp/nxf.TqcNSDldqo/tih_rna_sample_00089_23H5VFLT4_s39.chckpts/introns_filtered.ok
08:35:57 : INFO : -found 3251 cancer introns
08:35:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00089_23H5VFLT4_s39.introns --cancer_introns tih_rna_sample_00089_23H5VFLT4_s39.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00089_23H5VFLT4_s39.introns.for_IGV.bed
08:35:57 : INFO : Creating the BED File.
08:36:04 : INFO : Saving Bed File as tih_rna_sample_00089_23H5VFLT4_s39.introns.for_IGV.bed
08:36:04 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00089_23H5VFLT4_s39.introns --cancer_introns tih_rna_sample_00089_23H5VFLT4_s39.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00089_23H5VFLT4_s39.introns.for_IGV.bed
08:36:04 : INFO : Running: touch /tmp/nxf.TqcNSDldqo/tih_rna_sample_00089_23H5VFLT4_s39.chckpts/intron_igv_bed.ok
08:36:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00089_23H5VFLT4_s39.introns.for_IGV.bed --bam tih_rna_sample_00089_23H5VFLT4_s39.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00089_23H5VFLT4_s39
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.Aligned.sortedByCoord.out.bam.bai
08:55:31 : INFO : Execution Time = 19.45 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00089_23H5VFLT4_s39.introns.for_IGV.bed --bam tih_rna_sample_00089_23H5VFLT4_s39.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00089_23H5VFLT4_s39
08:55:31 : INFO : Running: touch /tmp/nxf.TqcNSDldqo/tih_rna_sample_00089_23H5VFLT4_s39.chckpts/reads_alignments_extracted.ok
08:55:31 : INFO : Running: samtools sort -o tih_rna_sample_00089_23H5VFLT4_s39.cancer_intron_reads.sorted.bam tih_rna_sample_00089_23H5VFLT4_s39.cancer_intron_reads.bam
08:55:31 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00089_23H5VFLT4_s39.cancer_intron_reads.sorted.bam tih_rna_sample_00089_23H5VFLT4_s39.cancer_intron_reads.bam
08:55:31 : INFO : Running: touch /tmp/nxf.TqcNSDldqo/tih_rna_sample_00089_23H5VFLT4_s39.chckpts/sort_cancer_intron_reads.ok
08:55:31 : INFO : Running: samtools sort -o tih_rna_sample_00089_23H5VFLT4_s39.gene_reads.sorted.bam tih_rna_sample_00089_23H5VFLT4_s39.gene_reads.bam