Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/23677ccc4d2b40c8b99bdeb5215367/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  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/9c/23677ccc4d2b40c8b99bdeb5215367/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/2ba7f22da423ad5fa2a932d2bcbbfd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/23677ccc4d2b40c8b99bdeb5215367/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/cac338698952731907b7584bf502c1/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/2ba7f22da423ad5fa2a932d2bcbbfd/.command.run
==> STAGING COMPLETE (7 inputs)

07:26:14 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
07:26:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file A549_FFPE_01_RNA_0001_B23LG7FLT4_2.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > A549_FFPE_01_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.
-A549_FFPE_01_RNA_0001_B23LG7FLT4_2.introns: no cancer introns identified.
07:26:18 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file A549_FFPE_01_RNA_0001_B23LG7FLT4_2.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > A549_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim 
07:26:18 : INFO : Running: touch /tmp/nxf.5cggV2WirS/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/prelim_introns.ok
07:26:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates A549_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5  > A549_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns 
07:26:19 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates A549_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5  > A549_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns 
07:26:19 : INFO : Running: touch /tmp/nxf.5cggV2WirS/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/introns_filtered.ok
07:26:19 : INFO : -found 0 cancer introns
ls: cannot access '*.cancer_intron_reads.sorted.bam': No such file or directory
ls: cannot access '*.cancer_intron_reads.sorted.bam.bai': No such file or directory
ls: cannot access '*.gene_reads.sorted.sifted.bam': No such file or directory
ls: cannot access '*.gene_reads.sorted.sifted.bam.bai': No such file or directory
ls: cannot access '*.introns.for_IGV.bed': No such file or directory
ls: cannot access '*.ctat-splicing.igv.html': No such file or directory
ls: cannot access '*.igv.tracks': No such file or directory