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/d8/4a65ceb8438435e0339e8c688960be/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/2dec0c5dbb7ecaf3d462e5d8606fee/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/2dec0c5dbb7ecaf3d462e5d8606fee/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/5116b92af65cead81bc153a7f4d82b/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/4a65ceb8438435e0339e8c688960be/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/2dec0c5dbb7ecaf3d462e5d8606fee/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)
21:35:13 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[9430000], rate=10477777.78/min 21:36:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.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.
-FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns: identified 6167 cancer introns
21:36:21 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim
21:36:21 : INFO : Running: touch /tmp/nxf.OObM2lAgNO/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/prelim_introns.ok
21:36:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns
21:36:22 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns
21:36:22 : INFO : Running: touch /tmp/nxf.OObM2lAgNO/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/introns_filtered.ok
21:36:22 : INFO : -found 2885 cancer introns
21:36:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --cancer_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed
21:36:22 : INFO : Creating the BED File.
21:36:32 : INFO : Saving Bed File as FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed
21:36:32 : INFO : Execution Time = 0.17 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns --cancer_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed
21:36:32 : INFO : Running: touch /tmp/nxf.OObM2lAgNO/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/intron_igv_bed.ok
21:36:32 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix FFPE_V4_0001_RNA_0001_B23LG7FLT4_2
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
21:57:42 : INFO : Execution Time = 21.16 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix FFPE_V4_0001_RNA_0001_B23LG7FLT4_2
21:57:42 : INFO : Running: touch /tmp/nxf.OObM2lAgNO/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok
21:57:42 : INFO : Running: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam
21:57:43 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam
21:57:43 : INFO : Running: touch /tmp/nxf.OObM2lAgNO/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok
21:57:43 : INFO : Running: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_2.gene_reads.bam