Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/ffe166a882d857b809d9e6eb4bb0e9/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/99aaf7afdf6c020eef326e1796a9e6/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.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/08/c076e3b904d51ad75bf9e3056ed057/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/99aaf7afdf6c020eef326e1796a9e6/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/99aaf7afdf6c020eef326e1796a9e6/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/c076e3b904d51ad75bf9e3056ed057/.command.run
==> STAGING COMPLETE (7 inputs)
09:08:49 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[9850000], rate=21888888.89/min 09:09:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_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.
-FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns: identified 6500 cancer introns
09:09:25 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim
09:09:25 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/prelim_introns.ok
09:09:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer.introns
09:09:25 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer.introns
09:09:25 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/introns_filtered.ok
09:09:25 : INFO : -found 2906 cancer introns
09:09:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns --cancer_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
09:09:25 : INFO : Creating the BED File.
09:09:30 : INFO : Saving Bed File as FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
09:09:31 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns --cancer_introns FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
09:09:31 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
09:09:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed --bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix FFPE_V4_0001_RNA_0001_B23LG7FLT4_1
[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
09:27:21 : INFO : Execution Time = 17.84 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed --bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix FFPE_V4_0001_RNA_0001_B23LG7FLT4_1
09:27:21 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
09:27:21 : INFO : Running: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.bam
09:27:21 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.bam
09:27:21 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
09:27:21 : INFO : Running: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.bam
[bam_sort_core] merging from 100 files and 1 in-memory blocks...
09:47:44 : INFO : Execution Time = 20.38 minutes. CMD: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.bam
09:47:44 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
09:47:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary FFPE_V4_0001_RNA_0001_B23LG7FLT4_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.
09:54:59 : INFO : Execution Time = 7.24 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam
09:54:59 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
09:54:59 : INFO : Running: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
09:56:33 : INFO : Execution Time = 1.57 minutes. CMD: samtools sort -o FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
09:56:33 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
09:56:33 : INFO : Running: samtools index FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
09:56:44 : INFO : Execution Time = 0.17 minutes. CMD: samtools index FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
09:56:44 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
09:56:44 : INFO : Running: samtools index FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
09:56:44 : INFO : Execution Time = 0.00 minutes. CMD: samtools index FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
09:56:44 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
09:56:44 : INFO : Running: create_report FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.ctat-splicing.igv.html --track-config FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: FFPE_V4_0001_RNA_0001_B23LG7FLT4_1'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
10:02:57 : INFO : Execution Time = 6.23 minutes. CMD: create_report FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.ctat-splicing.igv.html --track-config FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: FFPE_V4_0001_RNA_0001_B23LG7FLT4_1'
10:02:57 : INFO : Running: touch /tmp/nxf.BOZOHLp3zQ/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.chckpts/igv_create_html.ok
10:02:57 : INFO : done.