Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/a23f8eb676d3c5a2ac8d553b1b202c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/2d4782d6c78a62e1676360a88bbbc2/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/2d4782d6c78a62e1676360a88bbbc2/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/a23f8eb676d3c5a2ac8d553b1b202c/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/twist/Twist_rna_exome_AND_fusion_hg38.bed Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir A549_FFPE_01_RNA_0001_B23LG7FLT4_1 + all_qc -bam A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam -beds Twist_rna_exome_AND_fusion_hg38.bed -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz -contamination_bed dbsnp_hg38_contam_sites.bed -output_folder A549_FFPE_01_RNA_0001_B23LG7FLT4_1 -reference ref_genome.fa -region chr20 mkdir -p A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/full_bed.bed seqtool depth -bam A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam -bed A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.depth.gz saturation_plot -bams A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam > A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/saturation_qc.tsv fragment_size -bams A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output_prefix A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam > A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.mpileup && contamination -input A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/contamination.tsv [mpileup] 1 samples in 1 input files /opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. import pkg_resources /opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. import pkg_resources 0it [00:00, ?it/s] 28846it [00:00, 1101220.49it/s] [W::hts_idx_load3] The index file is older than the data file: Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi tabix -s 1 -b 2 -e 2 A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.depth.gz seqtool depth_hist -nbins 500 A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.depth.gz > A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv cat A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md -output A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.depth.png seqtool read_qc -bed Twist_rna_exome_AND_fusion_hg38.bed -n_threads 1 -bam_threads 2 A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam > A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/read_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool reads_per_target -bed Twist_rna_exome_AND_fusion_hg38.bed -threads 1 -bam_threads 2 A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam > A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.depth.gz> A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/depth_stats.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool gc_bias -reference ref_genome.fa -bed Twist_rna_exome_AND_fusion_hg38.bed -bin_size 0.05 -threads 1 -bam_threads 2 A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam > A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv cat A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md/qc_complete.txt + merge_qc -folders A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md -output A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv + head -n1 A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed A549_FFPE_01_RNA_0001_B23LG7FLT4_1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv