08:55:09 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[5840000], rate=20611764.71/min
[5850000], rate=20647058.82/min
[5860000], rate=20682352.94/min 08:55:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00479_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00479_B23WHTKLT4_2.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_00479_B23WHTKLT4_2.introns: identified 7131 cancer introns
08:55:34 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00479_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns.prelim
08:55:34 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/prelim_introns.ok
08:55:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns
08:55:34 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns
08:55:34 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/introns_filtered.ok
08:55:34 : INFO : -found 2663 cancer introns
08:55:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00479_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed
08:55:34 : INFO : Creating the BED File.
08:55:39 : INFO : Saving Bed File as tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed
08:55:39 : INFO : Execution Time = 0.08 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00479_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00479_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed
08:55:39 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/intron_igv_bed.ok
08:55:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00479_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00479_B23WHTKLT4_2
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00479_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam.bai
09:08:38 : INFO : Execution Time = 12.99 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00479_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00479_B23WHTKLT4_2
09:08:38 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/reads_alignments_extracted.ok
09:08:38 : INFO : Running: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.bam
09:08:39 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.bam
09:08:39 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/sort_cancer_intron_reads.ok
09:08:39 : INFO : Running: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.bam
[bam_sort_core] merging from 75 files and 1 in-memory blocks...
09:24:20 : INFO : Execution Time = 15.69 minutes. CMD: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.bam
09:24:20 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/sort_gene_reads.ok
09:24:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.bam
09:29:22 : INFO : Execution Time = 5.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.bam
09:29:22 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
09:29:22 : INFO : Running: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
09:29:58 : INFO : Execution Time = 0.60 minutes. CMD: samtools sort -o tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmp
09:29:58 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:29:58 : INFO : Running: samtools index tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam
09:30:03 : INFO : Execution Time = 0.07 minutes. CMD: samtools index tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam
09:30:03 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/tih_rna_sample_00479_B23WHTKLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
09:30:03 : INFO : Running: samtools index tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.sorted.bam
09:30:03 : INFO : Execution Time = 0.00 minutes. CMD: samtools index tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.sorted.bam
09:30:03 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/tih_rna_sample_00479_B23WHTKLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
09:30:03 : INFO : Running: create_report tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00479_B23WHTKLT4_2.ctat-splicing.igv.html --track-config tih_rna_sample_00479_B23WHTKLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00479_B23WHTKLT4_2'
09:35:44 : INFO : Execution Time = 5.68 minutes. CMD: create_report tih_rna_sample_00479_B23WHTKLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output tih_rna_sample_00479_B23WHTKLT4_2.ctat-splicing.igv.html --track-config tih_rna_sample_00479_B23WHTKLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: tih_rna_sample_00479_B23WHTKLT4_2'
09:35:44 : INFO : Running: touch /tmp/nxf.8NmWX74b3e/tih_rna_sample_00479_B23WHTKLT4_2.chckpts/igv_create_html.ok
09:35:44 : INFO : done.