Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/7206381a0dcf13079d775f1600d86a/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_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/c1/ee603ecae47debe23f71f4374509b1/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/7206381a0dcf13079d775f1600d86a/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/1b4d36560b17fde41db58926c426e7/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/7206381a0dcf13079d775f1600d86a/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/ee603ecae47debe23f71f4374509b1/.command.run
==> STAGING COMPLETE (7 inputs)
08:55:38 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10380000], rate=11323636.36/min
[10390000], rate=11334545.45/min
[10400000], rate=11345454.55/min
[10410000], rate=11356363.64/min
[10420000], rate=11367272.73/min
[10430000], rate=11378181.82/min
[10440000], rate=11389090.91/min
[10450000], rate=11400000.00/min
[10460000], rate=11410909.09/min
[10470000], rate=11421818.18/min
[10480000], rate=11432727.27/min
[10490000], rate=11443636.36/min
[10500000], rate=11454545.45/min
[10510000], rate=11465454.55/min
[10520000], rate=11476363.64/min
[10530000], rate=11487272.73/min 08:56:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_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.
-SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns: identified 7732 cancer introns
08:56:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim
08:56:44 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/prelim_introns.ok
08:56:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns
08:56:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns.prelim --min_total_reads 5 > SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns
08:56:44 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/introns_filtered.ok
08:56:44 : INFO : -found 3460 cancer introns
08:56:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns --cancer_introns SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed
08:56:45 : INFO : Creating the BED File.
08:56:56 : INFO : Saving Bed File as SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed
08:56:57 : INFO : Execution Time = 0.21 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns --cancer_introns SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed
08:56:57 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/intron_igv_bed.ok
08:56:57 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2
[W::hts_idx_load3] The index file is older than the data file: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
09:30:56 : INFO : Execution Time = 33.99 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed --bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --output_prefix SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2
09:30:56 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/reads_alignments_extracted.ok
09:30:56 : INFO : Running: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam
09:30:57 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.bam
09:30:57 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/sort_cancer_intron_reads.ok
09:30:57 : INFO : Running: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.bam
[bam_sort_core] merging from 139 files and 1 in-memory blocks...
10:05:42 : INFO : Execution Time = 34.76 minutes. CMD: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.bam
10:05:42 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/sort_gene_reads.ok
10:05:42 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_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.
10:16:15 : INFO : Execution Time = 10.54 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.bam
10:16:15 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp.ok
10:16:15 : INFO : Running: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 7 files and 1 in-memory blocks...
10:18:15 : INFO : Execution Time = 2.01 minutes. CMD: samtools sort -o SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmp
10:18:15 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:18:15 : INFO : Running: samtools index SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam
10:18:28 : INFO : Execution Time = 0.21 minutes. CMD: samtools index SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam
10:18:28 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.gene_reads.sorted.sifted.bam.indexed.ok
10:18:28 : INFO : Running: samtools index SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam
10:18:28 : INFO : Execution Time = 0.00 minutes. CMD: samtools index SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam
10:18:28 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.cancer_intron_reads.sorted.bam.indexed.ok
10:18:28 : INFO : Running: create_report SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.ctat-splicing.igv.html --track-config SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2'
10:26:19 : INFO : Execution Time = 7.86 minutes. CMD: create_report SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.ctat-splicing.igv.html --track-config SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2'
10:26:19 : INFO : Running: touch /tmp/nxf.ET42Z3HQu8/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.chckpts/igv_create_html.ok
10:26:19 : INFO : done.