21:44:41 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[8740000], rate=13800000.00/min 21:45:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.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.
-NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns: identified 8024 cancer introns
21:45:29 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim
21:45:29 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/prelim_introns.ok
21:45:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim --min_total_reads 5 > NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns
21:45:29 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim --min_total_reads 5 > NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns
21:45:29 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/introns_filtered.ok
21:45:29 : INFO : -found 3607 cancer introns
21:45:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns --cancer_introns NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
21:45:30 : INFO : Creating the BED File.
21:45:39 : INFO : Saving Bed File as NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
21:45:39 : INFO : Execution Time = 0.16 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns --cancer_introns NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
21:45:39 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/intron_igv_bed.ok
21:45:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed --bam NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --output_prefix NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3
[W::hts_idx_load3] The index file is older than the data file: NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
22:10:25 : INFO : Execution Time = 24.76 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed --bam NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --output_prefix NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3
22:10:25 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/reads_alignments_extracted.ok
22:10:25 : INFO : Running: samtools sort -o NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.bam
22:10:26 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.bam
22:10:26 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/sort_cancer_intron_reads.ok
22:10:26 : INFO : Running: samtools sort -o NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.bam
[bam_sort_core] merging from 109 files and 1 in-memory blocks...
22:39:07 : INFO : Execution Time = 28.69 minutes. CMD: samtools sort -o NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.bam
22:39:07 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/sort_gene_reads.ok
22:39:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp --keep_secondary NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam
22:49:22 : INFO : Execution Time = 10.25 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp --keep_secondary NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam
22:49:22 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp.ok
22:49:22 : INFO : Running: samtools sort -o NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 5 files and 1 in-memory blocks...
22:51:06 : INFO : Execution Time = 1.73 minutes. CMD: samtools sort -o NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp
22:51:06 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmpsorted.ok
22:51:06 : INFO : Running: samtools index NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam
22:51:16 : INFO : Execution Time = 0.17 minutes. CMD: samtools index NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam
22:51:16 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.indexed.ok
22:51:16 : INFO : Running: samtools index NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam
22:51:17 : INFO : Execution Time = 0.00 minutes. CMD: samtools index NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam
22:51:17 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam.indexed.ok
22:51:17 : INFO : Running: create_report NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.ctat-splicing.igv.html --track-config NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3'
22:56:23 : INFO : Execution Time = 5.11 minutes. CMD: create_report NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.ctat-splicing.igv.html --track-config NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3'
22:56:23 : INFO : Running: touch /tmp/nxf.Zo5KLqMehO/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/igv_create_html.ok
22:56:23 : INFO : done.