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/fe/ca45974e14aec3eaac0039f5e94522/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/438350ea9655e318412c098d495d49/HD789_0002_RNA_0008_23H5VFLT4_s19.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/60e97305b1009e7f5b3994b3470288/HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/438350ea9655e318412c098d495d49/HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/ca45974e14aec3eaac0039f5e94522/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/438350ea9655e318412c098d495d49/HD789_0002_RNA_0008_23H5VFLT4_s19.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)
09:06:29 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[8110000], rate=15696774.19/min 09:07:08 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file HD789_0002_RNA_0008_23H5VFLT4_s19.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > HD789_0002_RNA_0008_23H5VFLT4_s19.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.
-HD789_0002_RNA_0008_23H5VFLT4_s19.introns: identified 9612 cancer introns
09:07:09 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file HD789_0002_RNA_0008_23H5VFLT4_s19.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > HD789_0002_RNA_0008_23H5VFLT4_s19.cancer.introns.prelim
09:07:09 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/prelim_introns.ok
09:07:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates HD789_0002_RNA_0008_23H5VFLT4_s19.cancer.introns.prelim --min_total_reads 5 > HD789_0002_RNA_0008_23H5VFLT4_s19.cancer.introns
09:07:09 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates HD789_0002_RNA_0008_23H5VFLT4_s19.cancer.introns.prelim --min_total_reads 5 > HD789_0002_RNA_0008_23H5VFLT4_s19.cancer.introns
09:07:09 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/introns_filtered.ok
09:07:09 : INFO : -found 5401 cancer introns
09:07:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns HD789_0002_RNA_0008_23H5VFLT4_s19.introns --cancer_introns HD789_0002_RNA_0008_23H5VFLT4_s19.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed HD789_0002_RNA_0008_23H5VFLT4_s19.introns.for_IGV.bed
09:07:10 : INFO : Creating the BED File.
09:07:20 : INFO : Saving Bed File as HD789_0002_RNA_0008_23H5VFLT4_s19.introns.for_IGV.bed
09:07:21 : INFO : Execution Time = 0.18 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns HD789_0002_RNA_0008_23H5VFLT4_s19.introns --cancer_introns HD789_0002_RNA_0008_23H5VFLT4_s19.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed HD789_0002_RNA_0008_23H5VFLT4_s19.introns.for_IGV.bed
09:07:21 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/intron_igv_bed.ok
09:07:21 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed HD789_0002_RNA_0008_23H5VFLT4_s19.introns.for_IGV.bed --bam HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam --output_prefix HD789_0002_RNA_0008_23H5VFLT4_s19
[W::hts_idx_load3] The index file is older than the data file: HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam.bai
09:39:27 : INFO : Execution Time = 32.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed HD789_0002_RNA_0008_23H5VFLT4_s19.introns.for_IGV.bed --bam HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam --output_prefix HD789_0002_RNA_0008_23H5VFLT4_s19
09:39:27 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/reads_alignments_extracted.ok
09:39:27 : INFO : Running: samtools sort -o HD789_0002_RNA_0008_23H5VFLT4_s19.cancer_intron_reads.sorted.bam HD789_0002_RNA_0008_23H5VFLT4_s19.cancer_intron_reads.bam
09:39:28 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o HD789_0002_RNA_0008_23H5VFLT4_s19.cancer_intron_reads.sorted.bam HD789_0002_RNA_0008_23H5VFLT4_s19.cancer_intron_reads.bam
09:39:28 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/sort_cancer_intron_reads.ok
09:39:28 : INFO : Running: samtools sort -o HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.bam HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.bam
[bam_sort_core] merging from 151 files and 1 in-memory blocks...
10:13:05 : INFO : Execution Time = 33.62 minutes. CMD: samtools sort -o HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.bam HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.bam
10:13:05 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/sort_gene_reads.ok
10:13:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam.tmp --keep_secondary HD789_0002_RNA_0008_23H5VFLT4_s19.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.
10:24:21 : INFO : Execution Time = 11.27 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam.tmp --keep_secondary HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.bam
10:24:21 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam.tmp.ok
10:24:21 : INFO : Running: samtools sort -o HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 9 files and 1 in-memory blocks...
10:26:48 : INFO : Execution Time = 2.46 minutes. CMD: samtools sort -o HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam.tmp
10:26:48 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:26:48 : INFO : Running: samtools index HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam
10:27:04 : INFO : Execution Time = 0.26 minutes. CMD: samtools index HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam
10:27:04 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/HD789_0002_RNA_0008_23H5VFLT4_s19.gene_reads.sorted.sifted.bam.indexed.ok
10:27:04 : INFO : Running: samtools index HD789_0002_RNA_0008_23H5VFLT4_s19.cancer_intron_reads.sorted.bam
10:27:04 : INFO : Execution Time = 0.00 minutes. CMD: samtools index HD789_0002_RNA_0008_23H5VFLT4_s19.cancer_intron_reads.sorted.bam
10:27:04 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/HD789_0002_RNA_0008_23H5VFLT4_s19.cancer_intron_reads.sorted.bam.indexed.ok
10:27:04 : INFO : Running: create_report HD789_0002_RNA_0008_23H5VFLT4_s19.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output HD789_0002_RNA_0008_23H5VFLT4_s19.ctat-splicing.igv.html --track-config HD789_0002_RNA_0008_23H5VFLT4_s19.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: HD789_0002_RNA_0008_23H5VFLT4_s19'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
10:36:33 : INFO : Execution Time = 9.48 minutes. CMD: create_report HD789_0002_RNA_0008_23H5VFLT4_s19.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output HD789_0002_RNA_0008_23H5VFLT4_s19.ctat-splicing.igv.html --track-config HD789_0002_RNA_0008_23H5VFLT4_s19.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: HD789_0002_RNA_0008_23H5VFLT4_s19'
10:36:33 : INFO : Running: touch /tmp/nxf.NNkNUkLMqQ/HD789_0002_RNA_0008_23H5VFLT4_s19.chckpts/igv_create_html.ok
10:36:33 : INFO : done.