08:42:58 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[9720000], rate=14953846.15/min 08:43:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00403_23H5VFLT4_s29.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00403_23H5VFLT4_s29.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_00403_23H5VFLT4_s29.introns: identified 5322 cancer introns
08:43:50 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00403_23H5VFLT4_s29.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00403_23H5VFLT4_s29.cancer.introns.prelim
08:43:50 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/prelim_introns.ok
08:43:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00403_23H5VFLT4_s29.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00403_23H5VFLT4_s29.cancer.introns
08:43:51 : 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_00403_23H5VFLT4_s29.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00403_23H5VFLT4_s29.cancer.introns
08:43:51 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/introns_filtered.ok
08:43:51 : INFO : -found 1817 cancer introns
08:43:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00403_23H5VFLT4_s29.introns --cancer_introns tih_rna_sample_00403_23H5VFLT4_s29.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00403_23H5VFLT4_s29.introns.for_IGV.bed
08:43:51 : INFO : Creating the BED File.
08:43:56 : INFO : Saving Bed File as tih_rna_sample_00403_23H5VFLT4_s29.introns.for_IGV.bed
08:43:56 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00403_23H5VFLT4_s29.introns --cancer_introns tih_rna_sample_00403_23H5VFLT4_s29.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00403_23H5VFLT4_s29.introns.for_IGV.bed
08:43:56 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/intron_igv_bed.ok
08:43:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00403_23H5VFLT4_s29.introns.for_IGV.bed --bam tih_rna_sample_00403_23H5VFLT4_s29.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00403_23H5VFLT4_s29
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00403_23H5VFLT4_s29.Aligned.sortedByCoord.out.bam.bai
08:57:20 : INFO : Execution Time = 13.40 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00403_23H5VFLT4_s29.introns.for_IGV.bed --bam tih_rna_sample_00403_23H5VFLT4_s29.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00403_23H5VFLT4_s29
08:57:20 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/reads_alignments_extracted.ok
08:57:20 : INFO : Running: samtools sort -o tih_rna_sample_00403_23H5VFLT4_s29.cancer_intron_reads.sorted.bam tih_rna_sample_00403_23H5VFLT4_s29.cancer_intron_reads.bam
08:57:21 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o tih_rna_sample_00403_23H5VFLT4_s29.cancer_intron_reads.sorted.bam tih_rna_sample_00403_23H5VFLT4_s29.cancer_intron_reads.bam
08:57:21 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/sort_cancer_intron_reads.ok
08:57:21 : INFO : Running: samtools sort -o tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.bam tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.bam
[bam_sort_core] merging from 77 files and 1 in-memory blocks...
09:15:16 : INFO : Execution Time = 17.92 minutes. CMD: samtools sort -o tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.bam tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.bam
09:15:16 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/sort_gene_reads.ok
09:15:16 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.bam
09:23:38 : INFO : Execution Time = 8.38 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.bam
09:23:38 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam.tmp.ok
09:23:38 : INFO : Running: samtools sort -o tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 7 files and 1 in-memory blocks...
09:25:36 : INFO : Execution Time = 1.96 minutes. CMD: samtools sort -o tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam.tmp
09:25:36 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:25:36 : INFO : Running: samtools index tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam
09:25:50 : INFO : Execution Time = 0.24 minutes. CMD: samtools index tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam
09:25:50 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/tih_rna_sample_00403_23H5VFLT4_s29.gene_reads.sorted.sifted.bam.indexed.ok
09:25:50 : INFO : Running: samtools index tih_rna_sample_00403_23H5VFLT4_s29.cancer_intron_reads.sorted.bam
09:25:50 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00403_23H5VFLT4_s29.cancer_intron_reads.sorted.bam
09:25:50 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/tih_rna_sample_00403_23H5VFLT4_s29.cancer_intron_reads.sorted.bam.indexed.ok
09:25:50 : INFO : Running: create_report tih_rna_sample_00403_23H5VFLT4_s29.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00403_23H5VFLT4_s29.ctat-splicing.igv.html --track-config tih_rna_sample_00403_23H5VFLT4_s29.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00403_23H5VFLT4_s29'
09:32:30 : INFO : Execution Time = 6.66 minutes. CMD: create_report tih_rna_sample_00403_23H5VFLT4_s29.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00403_23H5VFLT4_s29.ctat-splicing.igv.html --track-config tih_rna_sample_00403_23H5VFLT4_s29.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00403_23H5VFLT4_s29'
09:32:30 : INFO : Running: touch /tmp/nxf.UDKQzDBvps/tih_rna_sample_00403_23H5VFLT4_s29.chckpts/igv_create_html.ok
09:32:30 : INFO : done.