Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/af15205b816de8ba91fc11855d08b8/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Chimeric.out.junction
  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/30/af15205b816de8ba91fc11855d08b8/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/275410acb28cd31f03c858bc858265/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/c7a87fa19da268b4b93df294774db1/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/af15205b816de8ba91fc11855d08b8/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/275410acb28cd31f03c858bc858265/.command.run
==> STAGING COMPLETE (7 inputs)

07:47:20 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

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[4320000], rate=10368000.00/min 07:47:52 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_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.
-BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns: identified 1349 cancer introns
07:47:53 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns.prelim 
07:47:53 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/prelim_introns.ok
07:47:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns.prelim --min_total_reads 5  > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns 
07:47:53 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns.prelim --min_total_reads 5  > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns 
07:47:53 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/introns_filtered.ok
07:47:53 : INFO : -found 865 cancer introns
07:47:53 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns  --cancer_introns BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed 
07:47:54 : INFO :  Creating the BED File.
07:47:57 : INFO : Saving Bed File as BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed
07:47:58 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns  --cancer_introns BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed 
07:47:58 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/intron_igv_bed.ok
07:47:58 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed  --bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam  --output_prefix BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2 
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
07:51:41 : INFO : Execution Time = 3.72 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed  --bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam  --output_prefix BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2 
07:51:41 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/reads_alignments_extracted.ok
07:51:41 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.bam
07:51:41 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.bam
07:51:41 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/sort_cancer_intron_reads.ok
07:51:41 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.bam
[bam_sort_core] merging from 12 files and 1 in-memory blocks...
07:55:46 : INFO : Execution Time = 4.09 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.bam
07:55:46 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/sort_gene_reads.ok
07:55:46 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  BVT_FFPE_TRNA_bld_01_A23WKFTLT4_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.
Done with chr chrX.
07:56:53 : INFO : Execution Time = 1.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.bam 
07:56:53 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
07:56:53 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmp
07:57:05 : INFO : Execution Time = 0.21 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmp
07:57:05 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:57:05 : INFO : Running: samtools index BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam 
07:57:07 : INFO : Execution Time = 0.03 minutes. CMD: samtools index BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam 
07:57:07 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
07:57:07 : INFO : Running: samtools index BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.sorted.bam 
07:57:07 : INFO : Execution Time = 0.00 minutes. CMD: samtools index BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.sorted.bam 
07:57:07 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
07:57:07 : INFO : Running: create_report BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.ctat-splicing.igv.html  --track-config BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2' 
07:58:36 : INFO : Execution Time = 1.49 minutes. CMD: create_report BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.ctat-splicing.igv.html  --track-config BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2' 
07:58:36 : INFO : Running: touch /tmp/nxf.RdlGvObuYe/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.chckpts/igv_create_html.ok
07:58:36 : INFO : done.