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/52/7c820d47a52d194d9771d7857d819d/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/3ab7b14fc9d28e11740fb0abdee03b/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/42bd1b06b412c4a605aba47fa94679/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/3ab7b14fc9d28e11740fb0abdee03b/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/42bd1b06b412c4a605aba47fa94679/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/3ab7b14fc9d28e11740fb0abdee03b/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.SJ.out.tab
==> STAGING COMPLETE (7 inputs)

08:52:17 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

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[22400000], rate=21333333.33/min 08:53:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.
-1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 5075 cancer introns
08:53:27 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim 
08:53:27 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok
08:53:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5  > 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 
08:53:27 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5  > 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 
08:53:27 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok
08:53:27 : INFO : -found 1476 cancer introns
08:53:27 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns  --cancer_introns 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 
08:53:28 : INFO :  Creating the BED File.
08:53:31 : INFO : Saving Bed File as 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
08:53:31 : INFO : Execution Time = 0.06 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns  --cancer_introns 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 
08:53:31 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok
08:53:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed  --bam 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 
[W::hts_idx_load3] The index file is older than the data file: 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
09:10:38 : INFO : Execution Time = 17.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed  --bam 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam  --output_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 
09:10:38 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok
09:10:38 : INFO : Running: samtools sort -o 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
09:10:39 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
09:10:39 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok
09:10:39 : INFO : Running: samtools sort -o 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
[bam_sort_core] merging from 79 files and 1 in-memory blocks...
09:30:00 : INFO : Execution Time = 19.36 minutes. CMD: samtools sort -o 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam
09:30:00 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_gene_reads.ok
09:30:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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 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.
09:35:19 : INFO : Execution Time = 5.31 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 
09:35:19 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
09:35:19 : INFO : Running: samtools sort -o 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
09:35:55 : INFO : Execution Time = 0.61 minutes. CMD: samtools sort -o 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmp
09:35:55 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:35:55 : INFO : Running: samtools index 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 
09:35:59 : INFO : Execution Time = 0.07 minutes. CMD: samtools index 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam 
09:35:59 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
09:35:59 : INFO : Running: samtools index 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 
09:35:59 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 
09:35:59 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
09:35:59 : INFO : Running: create_report 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html  --track-config 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1' 
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
09:41:07 : INFO : Execution Time = 5.13 minutes. CMD: create_report 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.ctat-splicing.igv.html  --track-config 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1' 
09:41:07 : INFO : Running: touch /tmp/nxf.adPVeJLeRH/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/igv_create_html.ok
09:41:07 : INFO : done.