08:50:15 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10950000], rate=16425000.00/min
[10960000], rate=16440000.00/min
[10970000], rate=16455000.00/min
[10980000], rate=16470000.00/min
[10990000], rate=16485000.00/min
[11000000], rate=16500000.00/min
[11010000], rate=16515000.00/min
[11020000], rate=16530000.00/min
[11030000], rate=16545000.00/min
[11040000], rate=16560000.00/min
[11050000], rate=16575000.00/min
[11060000], rate=16590000.00/min
[11070000], rate=16605000.00/min
[11080000], rate=16620000.00/min
[11090000], rate=16635000.00/min
[11100000], rate=16650000.00/min
[11110000], rate=16665000.00/min
[11120000], rate=16680000.00/min 08:51:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_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.
-1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns: identified 5455 cancer introns
08:51:03 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim
08:51:03 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/prelim_introns.ok
08:51:03 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns
08:51:04 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns
08:51:04 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/introns_filtered.ok
08:51:04 : INFO : -found 1255 cancer introns
08:51:04 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
08:51:04 : INFO : Creating the BED File.
08:51:07 : INFO : Saving Bed File as 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
08:51:07 : INFO : Execution Time = 0.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
08:51:07 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/intron_igv_bed.ok
08:51:07 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2
[W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
09:07:15 : INFO : Execution Time = 16.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2
09:07:15 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/reads_alignments_extracted.ok
09:07:15 : INFO : Running: samtools sort -o 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam
09:07:15 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.bam
09:07:15 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_cancer_intron_reads.ok
09:07:15 : INFO : Running: samtools sort -o 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam
[bam_sort_core] merging from 71 files and 1 in-memory blocks...
09:25:12 : INFO : Execution Time = 17.96 minutes. CMD: samtools sort -o 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.bam
09:25:12 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/sort_gene_reads.ok
09:25:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam
09:30:32 : INFO : Execution Time = 5.33 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.bam
09:30:32 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
09:30:32 : INFO : Running: samtools sort -o 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
09:31:02 : INFO : Execution Time = 0.49 minutes. CMD: samtools sort -o 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmp
09:31:02 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:31:02 : INFO : Running: samtools index 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam
09:31:05 : INFO : Execution Time = 0.06 minutes. CMD: samtools index 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam
09:31:05 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
09:31:05 : INFO : Running: samtools index 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam
09:31:05 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam
09:31:05 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
09:31:05 : INFO : Running: create_report 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
09:35:41 : INFO : Execution Time = 4.60 minutes. CMD: create_report 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.ctat-splicing.igv.html --track-config 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2'
09:35:41 : INFO : Running: touch /tmp/nxf.lZ00dQoXYT/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/igv_create_html.ok
09:35:41 : INFO : done.