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/1c/0f71a0c154cf351fb20ae48f0bca50/tih_rna_sample_00582_B23MVV7LT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/1b3971b41839d22775677faac33180/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/0f71a0c154cf351fb20ae48f0bca50/tih_rna_sample_00582_B23MVV7LT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/0f71a0c154cf351fb20ae48f0bca50/tih_rna_sample_00582_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/06c2d4721a1880f0c93d310501f4f9/tih_rna_sample_00582_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/1b3971b41839d22775677faac33180/.command.run
==> STAGING COMPLETE (7 inputs)
08:43:39 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[12100000], rate=15446808.51/min 08:44:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00582_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00582_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_00582_B23MVV7LT4_1.introns: identified 6087 cancer introns
08:44:36 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00582_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00582_B23MVV7LT4_1.cancer.introns.prelim
08:44:36 : INFO : Running: touch /tmp/nxf.NCrei3xTdY/tih_rna_sample_00582_B23MVV7LT4_1.chckpts/prelim_introns.ok
08:44:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00582_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00582_B23MVV7LT4_1.cancer.introns
08:44:36 : 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_00582_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00582_B23MVV7LT4_1.cancer.introns
08:44:36 : INFO : Running: touch /tmp/nxf.NCrei3xTdY/tih_rna_sample_00582_B23MVV7LT4_1.chckpts/introns_filtered.ok
08:44:36 : INFO : -found 2518 cancer introns
08:44:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00582_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00582_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00582_B23MVV7LT4_1.introns.for_IGV.bed
08:44:37 : INFO : Creating the BED File.
08:44:43 : INFO : Saving Bed File as tih_rna_sample_00582_B23MVV7LT4_1.introns.for_IGV.bed
08:44:43 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00582_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00582_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00582_B23MVV7LT4_1.introns.for_IGV.bed
08:44:43 : INFO : Running: touch /tmp/nxf.NCrei3xTdY/tih_rna_sample_00582_B23MVV7LT4_1.chckpts/intron_igv_bed.ok
08:44:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00582_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00582_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00582_B23MVV7LT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
09:05:33 : INFO : Execution Time = 20.84 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00582_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00582_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00582_B23MVV7LT4_1
09:05:33 : INFO : Running: touch /tmp/nxf.NCrei3xTdY/tih_rna_sample_00582_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok
09:05:33 : INFO : Running: samtools sort -o tih_rna_sample_00582_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00582_B23MVV7LT4_1.cancer_intron_reads.bam
09:05:34 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00582_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00582_B23MVV7LT4_1.cancer_intron_reads.bam
09:05:34 : INFO : Running: touch /tmp/nxf.NCrei3xTdY/tih_rna_sample_00582_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok
09:05:34 : INFO : Running: samtools sort -o tih_rna_sample_00582_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00582_B23MVV7LT4_1.gene_reads.bam