09:08:17 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10980000], rate=11557894.74/min
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[11590000], rate=11400000.00/min
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[11640000], rate=11449180.33/min 09:09:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > RT4_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.
-RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns: identified 7286 cancer introns
09:09:30 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim
09:09:30 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/prelim_introns.ok
09:09:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim --min_total_reads 5 > RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns
09:09:30 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns.prelim --min_total_reads 5 > RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns
09:09:30 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/introns_filtered.ok
09:09:31 : INFO : -found 3298 cancer introns
09:09:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns --cancer_introns RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
09:09:31 : INFO : Creating the BED File.
09:09:40 : INFO : Saving Bed File as RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
09:09:41 : INFO : Execution Time = 0.17 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns --cancer_introns RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed
09:09:41 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/intron_igv_bed.ok
09:09:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed --bam RT4_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --output_prefix RT4_FFPE_RNA_0001_B23LG7FLT4_3
[W::hts_idx_load3] The index file is older than the data file: RT4_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
09:40:11 : INFO : Execution Time = 30.50 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed --bam RT4_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --output_prefix RT4_FFPE_RNA_0001_B23LG7FLT4_3
09:40:11 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/reads_alignments_extracted.ok
09:40:11 : INFO : Running: samtools sort -o RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.bam
09:40:12 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.bam
09:40:12 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/sort_cancer_intron_reads.ok
09:40:12 : INFO : Running: samtools sort -o RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.bam
[bam_sort_core] merging from 119 files and 1 in-memory blocks...
10:10:37 : INFO : Execution Time = 30.41 minutes. CMD: samtools sort -o RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.bam
10:10:37 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/sort_gene_reads.ok
10:10:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp --keep_secondary RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam
10:21:30 : INFO : Execution Time = 10.88 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp --keep_secondary RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.bam
10:21:30 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp.ok
10:21:30 : INFO : Running: samtools sort -o RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 8 files and 1 in-memory blocks...
10:23:54 : INFO : Execution Time = 2.41 minutes. CMD: samtools sort -o RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmp
10:23:54 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:23:54 : INFO : Running: samtools index RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam
10:24:09 : INFO : Execution Time = 0.25 minutes. CMD: samtools index RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam
10:24:09 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/RT4_FFPE_RNA_0001_B23LG7FLT4_3.gene_reads.sorted.sifted.bam.indexed.ok
10:24:09 : INFO : Running: samtools index RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam
10:24:10 : INFO : Execution Time = 0.00 minutes. CMD: samtools index RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam
10:24:10 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/RT4_FFPE_RNA_0001_B23LG7FLT4_3.cancer_intron_reads.sorted.bam.indexed.ok
10:24:10 : INFO : Running: create_report RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output RT4_FFPE_RNA_0001_B23LG7FLT4_3.ctat-splicing.igv.html --track-config RT4_FFPE_RNA_0001_B23LG7FLT4_3.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: RT4_FFPE_RNA_0001_B23LG7FLT4_3'
10:32:51 : INFO : Execution Time = 8.70 minutes. CMD: create_report RT4_FFPE_RNA_0001_B23LG7FLT4_3.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output RT4_FFPE_RNA_0001_B23LG7FLT4_3.ctat-splicing.igv.html --track-config RT4_FFPE_RNA_0001_B23LG7FLT4_3.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: RT4_FFPE_RNA_0001_B23LG7FLT4_3'
10:32:51 : INFO : Running: touch /tmp/nxf.O4imf3Hv5T/RT4_FFPE_RNA_0001_B23LG7FLT4_3.chckpts/igv_create_html.ok
10:32:52 : INFO : done.