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/6a/e847106c1b3d80baca25ed431cf97a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/d2836ec3337af420724590c84c657b/NTC_0001_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/d2836ec3337af420724590c84c657b/NTC_0001_0001_B23LG7FLT4_2.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/e847106c1b3d80baca25ed431cf97a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/4e939040807a352ed4d1ff26209595/NTC_0001_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/d2836ec3337af420724590c84c657b/NTC_0001_0001_B23LG7FLT4_2.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)

20:10:36 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
20:10:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file NTC_0001_0001_B23LG7FLT4_2.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > NTC_0001_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.
-NTC_0001_0001_B23LG7FLT4_2.introns: no cancer introns identified.
20:10:39 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file NTC_0001_0001_B23LG7FLT4_2.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > NTC_0001_0001_B23LG7FLT4_2.cancer.introns.prelim 
20:10:39 : INFO : Running: touch /tmp/nxf.Kn05GwSRWD/NTC_0001_0001_B23LG7FLT4_2.chckpts/prelim_introns.ok
20:10:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates NTC_0001_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5  > NTC_0001_0001_B23LG7FLT4_2.cancer.introns 
20:10:40 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates NTC_0001_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5  > NTC_0001_0001_B23LG7FLT4_2.cancer.introns 
20:10:40 : INFO : Running: touch /tmp/nxf.Kn05GwSRWD/NTC_0001_0001_B23LG7FLT4_2.chckpts/introns_filtered.ok
20:10:40 : 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