21:19:43 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[13650000], rate=18613636.36/min 21:20:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.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.
-EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns: identified 1646 cancer introns
21:20:33 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer.introns.prelim
21:20:33 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/prelim_introns.ok
21:20:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer.introns
21:20:34 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer.introns
21:20:34 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/introns_filtered.ok
21:20:34 : INFO : -found 1064 cancer introns
21:20:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns --cancer_introns EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
21:20:34 : INFO : Creating the BED File.
21:20:37 : INFO : Saving Bed File as EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
21:20:37 : INFO : Execution Time = 0.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns --cancer_introns EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed
21:20:37 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
21:20:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1
[W::hts_idx_load3] The index file is older than the data file: EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
21:32:21 : INFO : Execution Time = 11.73 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed --bam EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1
21:32:21 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
21:32:21 : INFO : Running: samtools sort -o EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
21:32:21 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer_intron_reads.bam
21:32:21 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
21:32:21 : INFO : Running: samtools sort -o EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.bam
[bam_sort_core] merging from 61 files and 1 in-memory blocks...
21:46:30 : INFO : Execution Time = 14.14 minutes. CMD: samtools sort -o EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.bam
21:46:30 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
21:46:30 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam
21:51:03 : INFO : Execution Time = 4.56 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.bam
21:51:03 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
21:51:04 : INFO : Running: samtools sort -o EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
21:51:59 : INFO : Execution Time = 0.93 minutes. CMD: samtools sort -o EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
21:51:59 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
21:51:59 : INFO : Running: samtools index EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
21:52:05 : INFO : Execution Time = 0.10 minutes. CMD: samtools index EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
21:52:05 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
21:52:05 : INFO : Running: samtools index EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
21:52:06 : INFO : Execution Time = 0.00 minutes. CMD: samtools index EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
21:52:06 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
21:52:06 : INFO : Running: create_report EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1'
21:57:08 : INFO : Execution Time = 5.04 minutes. CMD: create_report EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.ctat-splicing.igv.html --track-config EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1'
21:57:08 : INFO : Running: touch /tmp/nxf.uINhFlAYit/EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.chckpts/igv_create_html.ok
21:57:08 : INFO : done.