07:48:03 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[8640000], rate=12342857.14/min 07:48:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00378_23H5VFLT4_s24.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00378_23H5VFLT4_s24.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.
-tih_rna_sample_00378_23H5VFLT4_s24.introns: identified 4801 cancer introns
07:48:59 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00378_23H5VFLT4_s24.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns.prelim
07:48:59 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/prelim_introns.ok
07:48:59 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns
07:49:00 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns
07:49:00 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/introns_filtered.ok
07:49:00 : INFO : -found 1540 cancer introns
07:49:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00378_23H5VFLT4_s24.introns --cancer_introns tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed
07:49:00 : INFO : Creating the BED File.
07:49:06 : INFO : Saving Bed File as tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed
07:49:06 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00378_23H5VFLT4_s24.introns --cancer_introns tih_rna_sample_00378_23H5VFLT4_s24.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed
07:49:06 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/intron_igv_bed.ok
07:49:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed --bam tih_rna_sample_00378_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00378_23H5VFLT4_s24
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00378_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
08:00:34 : INFO : Execution Time = 11.45 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed --bam tih_rna_sample_00378_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00378_23H5VFLT4_s24
08:00:34 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/reads_alignments_extracted.ok
08:00:34 : INFO : Running: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.sorted.bam tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.bam
08:00:34 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.sorted.bam tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.bam
08:00:34 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/sort_cancer_intron_reads.ok
08:00:34 : INFO : Running: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.bam tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.bam
[bam_sort_core] merging from 40 files and 1 in-memory blocks...
08:12:06 : INFO : Execution Time = 11.54 minutes. CMD: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.bam tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.bam
08:12:06 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/sort_gene_reads.ok
08:12:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.bam
08:16:32 : INFO : Execution Time = 4.43 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.bam
08:16:32 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp.ok
08:16:32 : INFO : Running: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
08:18:19 : INFO : Execution Time = 1.77 minutes. CMD: samtools sort -o tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmp
08:18:19 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.tmpsorted.ok
08:18:19 : INFO : Running: samtools index tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam
08:18:30 : INFO : Execution Time = 0.19 minutes. CMD: samtools index tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam
08:18:30 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/tih_rna_sample_00378_23H5VFLT4_s24.gene_reads.sorted.sifted.bam.indexed.ok
08:18:30 : INFO : Running: samtools index tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.sorted.bam
08:18:30 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.sorted.bam
08:18:30 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/tih_rna_sample_00378_23H5VFLT4_s24.cancer_intron_reads.sorted.bam.indexed.ok
08:18:30 : INFO : Running: create_report tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00378_23H5VFLT4_s24.ctat-splicing.igv.html --track-config tih_rna_sample_00378_23H5VFLT4_s24.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00378_23H5VFLT4_s24'
08:25:13 : INFO : Execution Time = 6.71 minutes. CMD: create_report tih_rna_sample_00378_23H5VFLT4_s24.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00378_23H5VFLT4_s24.ctat-splicing.igv.html --track-config tih_rna_sample_00378_23H5VFLT4_s24.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00378_23H5VFLT4_s24'
08:25:13 : INFO : Running: touch /tmp/nxf.BPBrgHoCad/tih_rna_sample_00378_23H5VFLT4_s24.chckpts/igv_create_html.ok
08:25:13 : INFO : done.