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/10/ae49b282e8494bd76bbc65b1b1f49e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/f4e3624337ff0a3086ae93922f5c8d/659_d0V-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/f4e3624337ff0a3086ae93922f5c8d/659_d0V-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/4c2a93992182abded4c23bfd01a8fa/659_d0V-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/ae49b282e8494bd76bbc65b1b1f49e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/f4e3624337ff0a3086ae93922f5c8d/659_d0V-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (7 inputs)

20:23:03 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
20:23:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_d0V-T1-TRNA-1_B23MHV2LT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > 659_d0V-T1-TRNA-1_B23MHV2LT4_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.
-659_d0V-T1-TRNA-1_B23MHV2LT4_1.introns: no cancer introns identified.
20:23:05 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_d0V-T1-TRNA-1_B23MHV2LT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > 659_d0V-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 
20:23:05 : INFO : Running: touch /tmp/nxf.u60mCCW2Ei/659_d0V-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok
20:23:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_d0V-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5  > 659_d0V-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 
20:23:05 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_d0V-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5  > 659_d0V-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 
20:23:05 : INFO : Running: touch /tmp/nxf.u60mCCW2Ei/659_d0V-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok
20:23:05 : 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