Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/9c43bdb841910e432b707a3371459c/659_Kh-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/9c43bdb841910e432b707a3371459c/659_Kh-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/33a784a3cd26ed1cb8a13bde2ed4ac/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/b9af0b97cfaeebcf285c1d1979f78f/659_Kh-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/9c43bdb841910e432b707a3371459c/659_Kh-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/33a784a3cd26ed1cb8a13bde2ed4ac/.command.run
==> STAGING COMPLETE (7 inputs)

20:22:08 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
20:22:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > 659_Kh-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_Kh-T1-TRNA-1_B23MHV2LT4_1.introns: identified 81 cancer introns
20:22:12 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 
20:22:12 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok
20:22:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5  > 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 
20:22:12 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5  > 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 
20:22:12 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok
20:22:12 : INFO : -found 42 cancer introns
20:22:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns  --cancer_introns 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 
20:22:12 : INFO :  Creating the BED File.
20:22:12 : INFO : Saving Bed File as 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
20:22:12 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns  --cancer_introns 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 
20:22:12 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok
20:22:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed  --bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam  --output_prefix 659_Kh-T1-TRNA-1_B23MHV2LT4_1 
[W::hts_idx_load3] The index file is older than the data file: 659_Kh-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
20:22:13 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed  --bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam  --output_prefix 659_Kh-T1-TRNA-1_B23MHV2LT4_1 
20:22:13 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok
20:22:13 : INFO : Running: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam
20:22:13 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam
20:22:13 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok
20:22:13 : INFO : Running: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam
20:22:13 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam
20:22:13 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_gene_reads.ok
20:22:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  659_Kh-T1-TRNA-1_B23MHV2LT4_1.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 chr11.
Done with chr chr14.
Done with chr chr16.
Done with chr chr17.
Done with chr chr19.
Done with chr chr21.
Done with chr chr22.
20:22:14 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 
20:22:14 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok
20:22:14 : INFO : Running: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp
20:22:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp
20:22:14 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
20:22:14 : INFO : Running: samtools index 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 
20:22:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 
20:22:14 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_Kh-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok
20:22:14 : INFO : Running: samtools index 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 
20:22:14 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 
20:22:14 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_Kh-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok
20:22:14 : INFO : Running: create_report 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output 659_Kh-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html  --track-config 659_Kh-T1-TRNA-1_B23MHV2LT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: 659_Kh-T1-TRNA-1_B23MHV2LT4_1' 
20:22:20 : INFO : Execution Time = 0.10 minutes. CMD: create_report 659_Kh-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output 659_Kh-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html  --track-config 659_Kh-T1-TRNA-1_B23MHV2LT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: 659_Kh-T1-TRNA-1_B23MHV2LT4_1' 
20:22:20 : INFO : Running: touch /tmp/nxf.E6NqxtOn3r/659_Kh-T1-TRNA-1_B23MHV2LT4_1.chckpts/igv_create_html.ok
20:22:20 : INFO : done.