08:49:43 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10140000], rate=16443243.24/min 08:50:28 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file A673_FFPE_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > A673_FFPE_RNA_0001_B23LG7FLT4_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.
-A673_FFPE_RNA_0001_B23LG7FLT4_2.introns: identified 7371 cancer introns
08:50:29 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file A673_FFPE_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim
08:50:29 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/prelim_introns.ok
08:50:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer.introns
08:50:29 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer.introns
08:50:29 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/introns_filtered.ok
08:50:29 : INFO : -found 3620 cancer introns
08:50:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns A673_FFPE_RNA_0001_B23LG7FLT4_2.introns --cancer_introns A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed A673_FFPE_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed
08:50:29 : INFO : Creating the BED File.
08:50:37 : INFO : Saving Bed File as A673_FFPE_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed
08:50:37 : INFO : Execution Time = 0.14 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns A673_FFPE_RNA_0001_B23LG7FLT4_2.introns --cancer_introns A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed A673_FFPE_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed
08:50:37 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/intron_igv_bed.ok
08:50:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed A673_FFPE_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam A673_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
09:13:43 : INFO : Execution Time = 23.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed A673_FFPE_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam A673_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2
09:13:43 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok
09:13:43 : INFO : Running: samtools sort -o A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam
09:13:44 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam
09:13:44 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok
09:13:44 : INFO : Running: samtools sort -o A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.bam
[bam_sort_core] merging from 94 files and 1 in-memory blocks...
09:38:53 : INFO : Execution Time = 25.14 minutes. CMD: samtools sort -o A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.bam
09:38:53 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/sort_gene_reads.ok
09:38:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam
09:47:20 : INFO : Execution Time = 8.46 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam
09:47:20 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
09:47:20 : INFO : Running: samtools sort -o A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
09:49:19 : INFO : Execution Time = 1.97 minutes. CMD: samtools sort -o A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp
09:49:19 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:49:19 : INFO : Running: samtools index A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam
09:49:31 : INFO : Execution Time = 0.20 minutes. CMD: samtools index A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam
09:49:31 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/A673_FFPE_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
09:49:31 : INFO : Running: samtools index A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam
09:49:31 : INFO : Execution Time = 0.00 minutes. CMD: samtools index A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam
09:49:31 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/A673_FFPE_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
09:49:31 : INFO : Running: create_report A673_FFPE_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output A673_FFPE_RNA_0001_B23LG7FLT4_2.ctat-splicing.igv.html --track-config A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: A673_FFPE_RNA_0001_B23LG7FLT4_2'
09:55:11 : INFO : Execution Time = 5.67 minutes. CMD: create_report A673_FFPE_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output A673_FFPE_RNA_0001_B23LG7FLT4_2.ctat-splicing.igv.html --track-config A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: A673_FFPE_RNA_0001_B23LG7FLT4_2'
09:55:11 : INFO : Running: touch /tmp/nxf.sGZmmRp0Mb/A673_FFPE_RNA_0001_B23LG7FLT4_2.chckpts/igv_create_html.ok
09:55:11 : INFO : done.