04:04:47 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [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 04:04:54 : 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 04:04:55 : 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 04:04:55 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/prelim_introns.ok 04:04:55 : 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 04:04:55 : 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 04:04:55 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/introns_filtered.ok 04:04:55 : INFO : -found 17 cancer introns 04:04:55 : 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 04:04:56 : INFO : Creating the BED File. 04:04:56 : INFO : Saving Bed File as rna_s1200_S21.introns.for_IGV.bed 04:04:56 : 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 04:04:56 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/intron_igv_bed.ok 04:04:56 : 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 04:04:57 : 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 04:04:57 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/reads_alignments_extracted.ok 04:04:57 : INFO : Running: samtools sort -o rna_s1200_S21.cancer_intron_reads.sorted.bam rna_s1200_S21.cancer_intron_reads.bam 04:04:57 : 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 04:04:57 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/sort_cancer_intron_reads.ok 04:04:57 : INFO : Running: samtools sort -o rna_s1200_S21.gene_reads.sorted.bam rna_s1200_S21.gene_reads.bam 04:04:57 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o rna_s1200_S21.gene_reads.sorted.bam rna_s1200_S21.gene_reads.bam 04:04:57 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/sort_gene_reads.ok 04:04:58 : 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 04:04:58 : 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 04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp.ok 04:04:58 : INFO : Running: samtools sort -o rna_s1200_S21.gene_reads.sorted.sifted.bam rna_s1200_S21.gene_reads.sorted.sifted.bam.tmp 04:04:58 : 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 04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.tmpsorted.ok 04:04:58 : INFO : Running: samtools index rna_s1200_S21.gene_reads.sorted.sifted.bam 04:04:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1200_S21.gene_reads.sorted.sifted.bam 04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.gene_reads.sorted.sifted.bam.indexed.ok 04:04:58 : INFO : Running: samtools index rna_s1200_S21.cancer_intron_reads.sorted.bam 04:04:58 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1200_S21.cancer_intron_reads.sorted.bam 04:04:58 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/rna_s1200_S21.cancer_intron_reads.sorted.bam.indexed.ok 04:04:58 : 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 04:05:01 : 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' 04:05:01 : INFO : Running: touch /tmp/nxf.go0PY1ss5R/rna_s1200_S21.chckpts/igv_create_html.ok 04:05:01 : INFO : done.