09:08:18 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[15150000], rate=34961538.46/min 09:08:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_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.
-1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 4662 cancer introns
09:08:51 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim
09:08:51 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok
09:08:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns
09:08:51 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns
09:08:51 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok
09:08:51 : INFO : -found 1309 cancer introns
09:08:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
09:08:51 : INFO : Creating the BED File.
09:08:53 : INFO : Saving Bed File as 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
09:08:53 : INFO : Execution Time = 0.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
09:08:53 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok
09:08:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1
[W::hts_idx_load3] The index file is older than the data file: 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
09:18:33 : INFO : Execution Time = 9.67 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1
09:18:33 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok
09:18:33 : INFO : Running: samtools sort -o 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
09:18:34 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
09:18:34 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok
09:18:34 : INFO : Running: samtools sort -o 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
[bam_sort_core] merging from 78 files and 1 in-memory blocks...
09:31:00 : INFO : Execution Time = 12.44 minutes. CMD: samtools sort -o 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
09:31:00 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok
09:31:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam
09:34:42 : INFO : Execution Time = 3.71 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam
09:34:42 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
09:34:42 : INFO : Running: samtools sort -o 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
09:35:05 : INFO : Execution Time = 0.38 minutes. CMD: samtools sort -o 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
09:35:05 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:35:05 : INFO : Running: samtools index 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam
09:35:08 : INFO : Execution Time = 0.04 minutes. CMD: samtools index 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam
09:35:08 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
09:35:08 : INFO : Running: samtools index 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam
09:35:08 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam
09:35:08 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
09:35:08 : INFO : Running: create_report 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1'
09:38:05 : INFO : Execution Time = 2.95 minutes. CMD: create_report 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html --track-config 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1'
09:38:05 : INFO : Running: touch /tmp/nxf.khaWBcHSLC/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok
09:38:05 : INFO : done.