Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/e7e472702900f870eec5eb9cd82518/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/af/e7e472702900f870eec5eb9cd82518/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/8eec97d104e056aec065ea23a517cf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/e7e472702900f870eec5eb9cd82518/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/3231eeede2403a4f3cb44acb9111a7/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/8eec97d104e056aec065ea23a517cf/.command.run
==> STAGING COMPLETE (7 inputs)

20:09:53 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

[110000], rate=6600000.00/min 
[120000], rate=7200000.00/min 
[130000], rate=7800000.00/min 
[140000], rate=8400000.00/min 
[150000], rate=9000000.00/min 
[160000], rate=9600000.00/min 
[170000], rate=10200000.00/min 
[180000], rate=10800000.00/min 
[190000], rate=11400000.00/min 
[200000], rate=12000000.00/min 
[210000], rate=12600000.00/min 
[220000], rate=13200000.00/min 
[230000], rate=13800000.00/min 20:09:57 : 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.
20:09:57 : 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 
20:09:57 : INFO : Running: touch /tmp/nxf.lpjnw7M8aA/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/prelim_introns.ok
20:09:57 : 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 
20:09:57 : 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 
20:09:57 : INFO : Running: touch /tmp/nxf.lpjnw7M8aA/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/introns_filtered.ok
20:09:57 : 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