16:06:36 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

[90000], rate=5400000.00/min 
[100000], rate=6000000.00/min 
[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 
[240000], rate=14400000.00/min 16:06:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1200_S21.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > rna_s1200_S21.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.
-rna_s1200_S21.introns: identified 1141 cancer introns
16:06:41 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1200_S21.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > rna_s1200_S21.cancer.introns.prelim 
16:06:41 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/prelim_introns.ok
16:06:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1200_S21.cancer.introns.prelim --min_total_reads 5  > rna_s1200_S21.cancer.introns 
16:06:41 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1200_S21.cancer.introns.prelim --min_total_reads 5  > rna_s1200_S21.cancer.introns 
16:06:41 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/introns_filtered.ok
16:06:41 : INFO : -found 17 cancer introns
16:06:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1200_S21.introns  --cancer_introns rna_s1200_S21.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed rna_s1200_S21.introns.for_IGV.bed 
16:06:42 : INFO :  Creating the BED File.
16:06:42 : INFO : Saving Bed File as rna_s1200_S21.introns.for_IGV.bed
16:06:42 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1200_S21.introns  --cancer_introns rna_s1200_S21.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed rna_s1200_S21.introns.for_IGV.bed 
16:06:42 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/intron_igv_bed.ok
16:06:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1200_S21.introns.for_IGV.bed  --bam rna_s1200_S21.Aligned.sortedByCoord.out.bam  --output_prefix rna_s1200_S21 
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
16:06:43 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1200_S21.introns.for_IGV.bed  --bam rna_s1200_S21.Aligned.sortedByCoord.out.bam  --output_prefix rna_s1200_S21 
16:06:43 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/reads_alignments_extracted.ok
16:06:43 : INFO : Running: samtools sort -o rna_s1200_S21.cancer_intron_reads.sorted.bam rna_s1200_S21.cancer_intron_reads.bam
16:06:43 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1200_S21.cancer_intron_reads.sorted.bam rna_s1200_S21.cancer_intron_reads.bam
16:06:43 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/sort_cancer_intron_reads.ok
16:06:43 : INFO : Running: samtools sort -o rna_s1200_S21.gene_reads.sorted.bam rna_s1200_S21.gene_reads.bam
16:06:43 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o rna_s1200_S21.gene_reads.sorted.bam rna_s1200_S21.gene_reads.bam
16:06:43 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/sort_gene_reads.ok
16:06:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  rna_s1200_S21.gene_reads.sorted.bam 
16:06:43 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  rna_s1200_S21.gene_reads.sorted.bam 
16:06:43 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp.ok
16:06:43 : INFO : Running: samtools sort -o rna_s1200_S21.gene_reads.sorted.sifted.bam rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp
16:06:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1200_S21.gene_reads.sorted.sifted.bam rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp
16:06:44 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.tmpsorted.ok
16:06:44 : INFO : Running: samtools index rna_s1200_S21.gene_reads.sorted.sifted.bam 
16:06:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1200_S21.gene_reads.sorted.sifted.bam 
16:06:44 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.indexed.ok
16:06:44 : INFO : Running: samtools index rna_s1200_S21.cancer_intron_reads.sorted.bam 
16:06:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1200_S21.cancer_intron_reads.sorted.bam 
16:06:44 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/rna_s1200_S21.cancer_intron_reads.sorted.bam.indexed.ok
16:06:44 : INFO : Running: create_report rna_s1200_S21.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output rna_s1200_S21.ctat-splicing.igv.html  --track-config rna_s1200_S21.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: rna_s1200_S21' 
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
16:06:46 : INFO : Execution Time = 0.04 minutes. CMD: create_report rna_s1200_S21.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output rna_s1200_S21.ctat-splicing.igv.html  --track-config rna_s1200_S21.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: rna_s1200_S21' 
16:06:46 : INFO : Running: touch /tmp/nxf.GU94eNsyiz/rna_s1200_S21.chckpts/igv_create_html.ok
16:06:46 : INFO : done.