21:57:40 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -mapping reads to genes [220000], rate=13200000.00/min [230000], rate=13800000.00/min [240000], rate=14400000.00/min [250000], rate=15000000.00/min [260000], rate=15600000.00/min [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 [320000], rate=19200000.00/min [330000], rate=19800000.00/min [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 [440000], rate=26400000.00/min [450000], rate=27000000.00/min [460000], rate=27600000.00/min [470000], rate=28200000.00/min [480000], rate=28800000.00/min [490000], rate=29400000.00/min [500000], rate=30000000.00/min [510000], rate=30600000.00/min [520000], rate=31200000.00/min [530000], rate=31800000.00/min [540000], rate=32400000.00/min [550000], rate=33000000.00/min 21:57:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1221_S42.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > rna_s1221_S42.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_s1221_S42.introns: identified 1033 cancer introns 21:57:45 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file rna_s1221_S42.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > rna_s1221_S42.cancer.introns.prelim 21:57:45 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/prelim_introns.ok 21:57:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1221_S42.cancer.introns.prelim --min_total_reads 5 > rna_s1221_S42.cancer.introns 21:57:45 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates rna_s1221_S42.cancer.introns.prelim --min_total_reads 5 > rna_s1221_S42.cancer.introns 21:57:45 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/introns_filtered.ok 21:57:45 : INFO : -found 28 cancer introns 21:57:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1221_S42.introns --cancer_introns rna_s1221_S42.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed rna_s1221_S42.introns.for_IGV.bed 21:57:45 : INFO : Creating the BED File. 21:57:46 : INFO : Saving Bed File as rna_s1221_S42.introns.for_IGV.bed 21:57:46 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns rna_s1221_S42.introns --cancer_introns rna_s1221_S42.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed rna_s1221_S42.introns.for_IGV.bed 21:57:46 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/intron_igv_bed.ok 21:57:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1221_S42.introns.for_IGV.bed --bam rna_s1221_S42.Aligned.sortedByCoord.out.bam --output_prefix rna_s1221_S42 [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai 21:57:46 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed rna_s1221_S42.introns.for_IGV.bed --bam rna_s1221_S42.Aligned.sortedByCoord.out.bam --output_prefix rna_s1221_S42 21:57:46 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/reads_alignments_extracted.ok 21:57:46 : INFO : Running: samtools sort -o rna_s1221_S42.cancer_intron_reads.sorted.bam rna_s1221_S42.cancer_intron_reads.bam 21:57:46 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1221_S42.cancer_intron_reads.sorted.bam rna_s1221_S42.cancer_intron_reads.bam 21:57:46 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/sort_cancer_intron_reads.ok 21:57:46 : INFO : Running: samtools sort -o rna_s1221_S42.gene_reads.sorted.bam rna_s1221_S42.gene_reads.bam 21:57:47 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o rna_s1221_S42.gene_reads.sorted.bam rna_s1221_S42.gene_reads.bam 21:57:47 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/sort_gene_reads.ok 21:57:47 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp --keep_secondary rna_s1221_S42.gene_reads.sorted.bam 21:57:47 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp --keep_secondary rna_s1221_S42.gene_reads.sorted.bam 21:57:47 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp.ok 21:57:47 : INFO : Running: samtools sort -o rna_s1221_S42.gene_reads.sorted.sifted.bam rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp 21:57:48 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o rna_s1221_S42.gene_reads.sorted.sifted.bam rna_s1221_S42.gene_reads.sorted.sifted.bam.tmp 21:57:48 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.tmpsorted.ok 21:57:48 : INFO : Running: samtools index rna_s1221_S42.gene_reads.sorted.sifted.bam 21:57:48 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1221_S42.gene_reads.sorted.sifted.bam 21:57:48 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/rna_s1221_S42.gene_reads.sorted.sifted.bam.indexed.ok 21:57:48 : INFO : Running: samtools index rna_s1221_S42.cancer_intron_reads.sorted.bam 21:57:48 : INFO : Execution Time = 0.00 minutes. CMD: samtools index rna_s1221_S42.cancer_intron_reads.sorted.bam 21:57:48 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/rna_s1221_S42.cancer_intron_reads.sorted.bam.indexed.ok 21:57:48 : INFO : Running: create_report rna_s1221_S42.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output rna_s1221_S42.ctat-splicing.igv.html --track-config rna_s1221_S42.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: rna_s1221_S42' 21:57:51 : INFO : Execution Time = 0.05 minutes. CMD: create_report rna_s1221_S42.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output rna_s1221_S42.ctat-splicing.igv.html --track-config rna_s1221_S42.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: rna_s1221_S42' 21:57:51 : INFO : Running: touch /tmp/nxf.UW1TgExS9J/rna_s1221_S42.chckpts/igv_create_html.ok 21:57:51 : INFO : done.