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/b3/fe0e6f0b46b136ba5ae57554247de3/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/8d0d96a6ef1dae44f84274179cfa2d/rna_s1221_S42.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/ed/8d0d96a6ef1dae44f84274179cfa2d/rna_s1221_S42.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/b3/fe0e6f0b46b136ba5ae57554247de3/.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 rna_s1221_S42 + all_qc -bam rna_s1221_S42.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 rna_s1221_S42 -reference ref_genome.fa -region chr20 mkdir -p rna_s1221_S42/rna_s1221_S42.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > rna_s1221_S42/rna_s1221_S42.md/full_bed.bed seqtool depth -bam rna_s1221_S42.md.bam -bed rna_s1221_S42/rna_s1221_S42.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth.gz saturation_plot -bams rna_s1221_S42.md.bam -region chr20 -output rna_s1221_S42/rna_s1221_S42.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 rna_s1221_S42.md.bam > rna_s1221_S42/rna_s1221_S42.md/saturation_qc.tsv fragment_size -bams rna_s1221_S42.md.bam -region chr20 -output_prefix rna_s1221_S42/rna_s1221_S42.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed rna_s1221_S42.md.bam > rna_s1221_S42.md.mpileup && contamination -input rna_s1221_S42.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > rna_s1221_S42/rna_s1221_S42.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai /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 [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai 153541it [00:00, 1534994.26it/s] 320738it [00:00, 1615528.43it/s][W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai 460613it [00:00, 1627554.34it/s] [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai tabix -s 1 -b 2 -e 2 rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth.gz seqtool depth_hist -nbins 500 rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth.gz > rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth_hist.tsv cat rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title rna_s1221_S42.md -output rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth.png [W::hts_idx_load3] The index file is older than the data file: Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi seqtool read_qc -bed Twist_rna_exome_AND_fusion_hg38.bed -n_threads 1 -bam_threads 2 rna_s1221_S42.md.bam > rna_s1221_S42/rna_s1221_S42.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 rna_s1221_S42.md.bam > rna_s1221_S42/rna_s1221_S42.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed rna_s1221_S42/rna_s1221_S42.md/rna_s1221_S42.md.depth.gz> rna_s1221_S42/rna_s1221_S42.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 rna_s1221_S42.md.bam > rna_s1221_S42/rna_s1221_S42.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai [W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai cat rna_s1221_S42/rna_s1221_S42.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "rna_s1221_S42.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "rna_s1221_S42/rna_s1221_S42.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > rna_s1221_S42/rna_s1221_S42.md/qc_complete.txt + merge_qc -folders rna_s1221_S42/rna_s1221_S42.md -output rna_s1221_S42/rna_s1221_S42_full_basic_stats.tsv + head -n1 rna_s1221_S42/rna_s1221_S42_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed rna_s1221_S42/rna_s1221_S42_full_basic_stats.tsv