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/ed/b824a015c1741fa73eeef09243bdf9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/1832b6439c06db8f647edc539c8772/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/1832b6439c06db8f647edc539c8772/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/b824a015c1741fa73eeef09243bdf9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/1832b6439c06db8f647edc539c8772/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/f009dfff9b9a5372ceae69db50060b/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)

07:25:36 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

[270000], rate=16200000.00/min 
[280000], rate=16800000.00/min 
[290000], rate=17400000.00/min 
[300000], rate=18000000.00/min 
[310000], rate=18600000.00/min 
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[340000], rate=20400000.00/min 
[350000], rate=21000000.00/min 
[360000], rate=21600000.00/min 
[370000], rate=22200000.00/min 
[380000], rate=22800000.00/min 
[390000], rate=23400000.00/min 
[400000], rate=24000000.00/min 
[410000], rate=24600000.00/min 
[420000], rate=25200000.00/min 
[430000], rate=25800000.00/min 
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[450000], rate=27000000.00/min 
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[470000], rate=28200000.00/min 
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[500000], rate=30000000.00/min 
[510000], rate=30600000.00/min 
[520000], rate=31200000.00/min 
[530000], rate=31800000.00/min 07:25:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file A549_FFPE_01_RNA_0001_B23LG7FLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > A549_FFPE_01_RNA_0001_B23LG7FLT4_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.
-A549_FFPE_01_RNA_0001_B23LG7FLT4_1.introns: no cancer introns identified.
07:25:41 : 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_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > A549_FFPE_01_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim 
07:25:41 : INFO : Running: touch /tmp/nxf.ObJM3FZrIi/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.chckpts/prelim_introns.ok
07:25:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates A549_FFPE_01_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5  > A549_FFPE_01_RNA_0001_B23LG7FLT4_1.cancer.introns 
07:25:42 : 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_1.cancer.introns.prelim --min_total_reads 5  > A549_FFPE_01_RNA_0001_B23LG7FLT4_1.cancer.introns 
07:25:42 : INFO : Running: touch /tmp/nxf.ObJM3FZrIi/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.chckpts/introns_filtered.ok
07:25:42 : 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