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/usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_dts-T1-TRNA-1_B23MHV2LT4_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. -659_dts-T1-TRNA-1_B23MHV2LT4_1.introns: identified 7878 cancer introns 08:53:11 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 08:53:11 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 08:53:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:53:11 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:53:11 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 08:53:11 : INFO : -found 2724 cancer introns 08:53:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:53:12 : INFO : Creating the BED File. 08:53:21 : INFO : Saving Bed File as 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:53:22 : INFO : Execution Time = 0.18 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:53:22 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 08:53:22 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_dts-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_dts-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 09:21:02 : INFO : Execution Time = 27.67 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_dts-T1-TRNA-1_B23MHV2LT4_1 09:21:02 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 09:21:02 : INFO : Running: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:21:03 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:21:03 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 09:21:03 : INFO : Running: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam [bam_sort_core] merging from 95 files and 1 in-memory blocks... 09:49:01 : INFO : Execution Time = 27.97 minutes. CMD: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam 09:49:01 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_gene_reads.ok 09:49:01 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 09:56:07 : INFO : Execution Time = 7.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 09:56:07 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:56:07 : INFO : Running: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:57:04 : INFO : Execution Time = 0.95 minutes. CMD: samtools sort -o 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp 09:57:04 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:57:04 : INFO : Running: samtools index 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 09:57:10 : INFO : Execution Time = 0.10 minutes. CMD: samtools index 659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 09:57:10 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_dts-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:57:10 : INFO : Running: samtools index 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 09:57:10 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 09:57:10 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_dts-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:57:10 : INFO : Running: create_report 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_dts-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_dts-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_dts-T1-TRNA-1_B23MHV2LT4_1' 10:03:38 : INFO : Execution Time = 6.46 minutes. CMD: create_report 659_dts-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_dts-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_dts-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_dts-T1-TRNA-1_B23MHV2LT4_1' 10:03:38 : INFO : Running: touch /tmp/nxf.WOz7zuwY7T/659_dts-T1-TRNA-1_B23MHV2LT4_1.chckpts/igv_create_html.ok 10:03:38 : INFO : done.