07:20:38 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

[150000], rate=9000000.00/min 
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[480000], rate=28800000.00/min 
[490000], rate=29400000.00/min 
[500000], rate=30000000.00/min 
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[520000], rate=31200000.00/min 
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[640000], rate=19200000.00/min 
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[680000], rate=20400000.00/min 
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[700000], rate=21000000.00/min 
[710000], rate=21300000.00/min 
[720000], rate=21600000.00/min 
[730000], rate=21900000.00/min 07:20:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file dna_s739.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > dna_s739.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.
-dna_s739.introns: identified 5 cancer introns
07:20:43 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file dna_s739.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > dna_s739.cancer.introns.prelim 
07:20:43 : INFO : Running: touch /tmp/nxf.9CRPltkDRS/dna_s739.chckpts/prelim_introns.ok
07:20:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates dna_s739.cancer.introns.prelim --min_total_reads 5  > dna_s739.cancer.introns 
07:20:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates dna_s739.cancer.introns.prelim --min_total_reads 5  > dna_s739.cancer.introns 
07:20:44 : INFO : Running: touch /tmp/nxf.9CRPltkDRS/dna_s739.chckpts/introns_filtered.ok
07:20:44 : 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