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/28/c7b0dac902ccfd3d17007b1c38afc8/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/119cba6023617775e65acda6fa1b55/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/119cba6023617775e65acda6fa1b55/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/119cba6023617775e65acda6fa1b55/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/c7b0dac902ccfd3d17007b1c38afc8/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/3d93137fc0ce6a8b84c346e03a77c5/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)
07:29:28 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[2130000], rate=15975000.00/min 07:29:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 22Rv1_FFPE_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.
-22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns: identified 218 cancer introns
07:29:43 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim
07:29:43 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/prelim_introns.ok
07:29:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns
07:29:44 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns.prelim --min_total_reads 5 > 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns
07:29:44 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/introns_filtered.ok
07:29:44 : INFO : -found 83 cancer introns
07:29:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns --cancer_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
07:29:44 : INFO : Creating the BED File.
07:29:45 : INFO : Saving Bed File as 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
07:29:45 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns --cancer_introns 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed
07:29:45 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/intron_igv_bed.ok
07:29:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed --bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
07:29:51 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed --bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1
07:29:51 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/reads_alignments_extracted.ok
07:29:51 : INFO : Running: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.bam
07:29:51 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.bam
07:29:51 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/sort_cancer_intron_reads.ok
07:29:51 : INFO : Running: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.bam
07:29:56 : INFO : Execution Time = 0.09 minutes. CMD: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.bam
07:29:56 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/sort_gene_reads.ok
07:29:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam
Done with chr chr1.
Done with chr chr2.
Done with chr chr3.
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 chr14.
Done with chr chr15.
Done with chr chr16.
Done with chr chr17.
Done with chr chr19.
Done with chr chr20.
Done with chr chr22.
07:29:58 : INFO : Execution Time = 0.03 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.bam
07:29:58 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:29:58 : INFO : Running: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
07:29:59 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmp
07:29:59 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:29:59 : INFO : Running: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
07:29:59 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam
07:29:59 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:29:59 : INFO : Running: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
07:29:59 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam
07:29:59 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:29:59 : INFO : Running: create_report 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.ctat-splicing.igv.html --track-config 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1'
07:30:11 : INFO : Execution Time = 0.20 minutes. CMD: create_report 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.ctat-splicing.igv.html --track-config 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1'
07:30:11 : INFO : Running: touch /tmp/nxf.b79sDTTscV/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.chckpts/igv_create_html.ok
07:30:11 : INFO : done.