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rate=16200000.00/min [10270000], rate=16215789.47/min [10280000], rate=16231578.95/min [10290000], rate=16247368.42/min [10300000], rate=16263157.89/min [10310000], rate=16278947.37/min [10320000], rate=16294736.84/min [10330000], rate=16310526.32/min [10340000], rate=16326315.79/min 09:44:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bua-T1-TRNA-1_A23MVY2LT4_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. -659_bua-T1-TRNA-1_A23MVY2LT4_2.introns: identified 5941 cancer introns 09:44:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer.introns.prelim 09:44:57 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/prelim_introns.ok 09:44:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer.introns.prelim --min_total_reads 5 > 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer.introns 09:44:57 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer.introns.prelim --min_total_reads 5 > 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer.introns 09:44:57 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/introns_filtered.ok 09:44:57 : INFO : -found 3080 cancer introns 09:44:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns --cancer_introns 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed 09:44:58 : INFO : Creating the BED File. 09:45:06 : INFO : Saving Bed File as 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed 09:45:06 : INFO : Execution Time = 0.15 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns --cancer_introns 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed 09:45:06 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/intron_igv_bed.ok 09:45:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed --bam 659_bua-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam --output_prefix 659_bua-T1-TRNA-1_A23MVY2LT4_2 [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam.bai 10:12:42 : INFO : Execution Time = 27.60 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed --bam 659_bua-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam --output_prefix 659_bua-T1-TRNA-1_A23MVY2LT4_2 10:12:42 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/reads_alignments_extracted.ok 10:12:42 : INFO : Running: samtools sort -o 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.bam 10:12:43 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.bam 10:12:43 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/sort_cancer_intron_reads.ok 10:12:43 : INFO : Running: samtools sort -o 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.bam 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.bam [bam_sort_core] merging from 126 files and 1 in-memory blocks... 10:42:29 : INFO : Execution Time = 29.77 minutes. CMD: samtools sort -o 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.bam 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.bam 10:42:29 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/sort_gene_reads.ok 10:42:29 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.bam Done with chr chr1. Done with chr chr2. Done with chr chr3. Done with chr chr4. Done with chr chr5. Done with chr chr6. Done with chr chr7. Done with chr chr8. Done with chr chr9. Done with chr chr10. Done with chr chr11. Done with chr chr12. Done with chr chr13. Done with chr chr14. Done with chr chr15. Done with chr chr16. Done with chr chr17. Done with chr chr18. Done with chr chr19. Done with chr chr20. Done with chr chr21. Done with chr chr22. 10:50:50 : INFO : Execution Time = 8.35 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.bam 10:50:50 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmp.ok 10:50:50 : INFO : Running: samtools sort -o 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 10:51:47 : INFO : Execution Time = 0.96 minutes. CMD: samtools sort -o 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmp 10:51:47 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok 10:51:47 : INFO : Running: samtools index 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam 10:51:54 : INFO : Execution Time = 0.11 minutes. CMD: samtools index 659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam 10:51:54 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/659_bua-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.indexed.ok 10:51:54 : INFO : Running: samtools index 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam 10:51:54 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam 10:51:54 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/659_bua-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam.indexed.ok 10:51:54 : INFO : Running: create_report 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bua-T1-TRNA-1_A23MVY2LT4_2.ctat-splicing.igv.html --track-config 659_bua-T1-TRNA-1_A23MVY2LT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bua-T1-TRNA-1_A23MVY2LT4_2' 10:58:26 : INFO : Execution Time = 6.52 minutes. CMD: create_report 659_bua-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bua-T1-TRNA-1_A23MVY2LT4_2.ctat-splicing.igv.html --track-config 659_bua-T1-TRNA-1_A23MVY2LT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bua-T1-TRNA-1_A23MVY2LT4_2' 10:58:26 : INFO : Running: touch /tmp/nxf.tXSJWdfyC3/659_bua-T1-TRNA-1_A23MVY2LT4_2.chckpts/igv_create_html.ok 10:58:26 : INFO : done.