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/e8/8c59ebb3a01eb0db56bc30b61a10fc/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/df0c6bc4195efe00c3a134004f3c6d/KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/b8606c5ab4fbb4df33f6a24ea94bad/KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/b8606c5ab4fbb4df33f6a24ea94bad/KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/8c59ebb3a01eb0db56bc30b61a10fc/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/b8606c5ab4fbb4df33f6a24ea94bad/KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.SJ.out.tab
==> STAGING COMPLETE (7 inputs)
21:32:30 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10560000], rate=9051428.57/min
[10570000], rate=9060000.00/min
[10580000], rate=9068571.43/min
[10590000], rate=9077142.86/min
[10600000], rate=9085714.29/min
[10610000], rate=9094285.71/min
[10620000], rate=9102857.14/min
[10630000], rate=9111428.57/min
[10640000], rate=9120000.00/min
[10650000], rate=9128571.43/min
[10660000], rate=9137142.86/min 21:33:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > KG1_FFPE_01_RNA_0003_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.
-KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.introns: identified 6756 cancer introns
21:33:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.cancer.introns.prelim
21:33:57 : INFO : Running: touch /tmp/nxf.ENvlneYZ7e/KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.chckpts/prelim_introns.ok
21:33:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.cancer.introns
21:33:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.cancer.introns
21:33:57 : INFO : Running: touch /tmp/nxf.ENvlneYZ7e/KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.chckpts/introns_filtered.ok
21:33:57 : INFO : -found 3191 cancer introns
21:33:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.introns --cancer_introns KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.introns.for_IGV.bed
21:33:58 : INFO : Creating the BED File.
21:34:06 : INFO : Saving Bed File as KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.introns.for_IGV.bed
21:34:06 : INFO : Execution Time = 0.15 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.introns --cancer_introns KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.introns.for_IGV.bed
21:34:06 : INFO : Running: touch /tmp/nxf.ENvlneYZ7e/KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.chckpts/intron_igv_bed.ok
21:34:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.introns.for_IGV.bed --bam KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix KG1_FFPE_01_RNA_0003_B23LG7FLT4_2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai