Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/455c82d48c8981709b731bd1143182/659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/b6c1775dba548abce19250c188a082/.command.sh 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/aa/b6c1775dba548abce19250c188a082/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/455c82d48c8981709b731bd1143182/659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam 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 659_6i-T1-TRNA-1_B23WHTKLT4_1 + all_qc -bam 659_6i-T1-TRNA-1_B23WHTKLT4_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 659_6i-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed seqtool depth -bam 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam -bed 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/659_6i-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz saturation_plot -bams 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/saturation_qc.tsv fragment_size -bams 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output_prefix 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.mpileup && contamination -input 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.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: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai 0it [00:00, ?it/s] 165032it [00:00, 1649794.50it/s] 340748it [00:00, 1712890.51it/s] 520279it [00:00, 1750484.33it/s] 700169it [00:00, 1769562.72it/s] 881907it [00:00, 1786774.93it/s] 1062573it [00:00, 1793511.42it/s] 1242479it [00:00, 1795303.48it/s] 1422010it [00:00, 1793559.57it/s] 1602382it [00:00, 1796605.75it/s] 1782044it [00:01, 1793813.05it/s] 1961832it [00:01, 1795027.69it/s] 2142376it [00:01, 1798041.40it/s] 2322182it [00:01, 1796953.00it/s] 2501879it [00:01, 1796355.10it/s] 2681515it [00:01, 1768258.71it/s] 2858438it [00:01, 1754651.15it/s] 3033980it [00:01, 1653104.78it/s] 3209407it [00:01, 1681941.21it/s] 3385537it [00:01, 1704893.03it/s] 3556787it [00:02, 1701089.74it/s] 3735719it [00:02, 1726970.74it/s] 3913934it [00:02, 1743264.83it/s] 4093350it [00:02, 1758355.96it/s] 4270534it [00:02, 1762334.82it/s] 4446938it [00:02, 1746729.19it/s] 4625351it [00:02, 1757717.71it/s] 4804040it [00:02, 1766380.27it/s] 4981837it [00:02, 1769668.15it/s] 5160301it [00:02, 1773973.84it/s] 5337743it [00:03, 1755308.98it/s] 5516620it [00:03, 1765130.41it/s] 5697203it [00:03, 1777234.87it/s][W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai 5877434it [00:03, 1784648.56it/s] 6055937it [00:03, 1771999.66it/s] 6233181it [00:03, 1760179.28it/s] 6410213it [00:03, 1763165.90it/s] 6588289it [00:03, 1768337.84it/s] 6767487it [00:03, 1775372.44it/s] 6946107it [00:03, 1778584.74it/s] 7123982it [00:04, 1680613.12it/s] 7300692it [00:04, 1705464.03it/s] 7474187it [00:04, 1714028.94it/s][W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai 7648225it [00:04, 1721746.34it/s] 7826885it [00:04, 1740846.07it/s] 8006372it [00:04, 1756861.46it/s] 8186484it [00:04, 1770016.86it/s] 8363681it [00:04, 1766870.89it/s] 8540505it [00:04, 1757469.14it/s] 8716355it [00:04, 1755746.01it/s] 8892001it [00:05, 1750708.02it/s] 9069141it [00:05, 1756758.45it/s] 9250385it [00:05, 1773354.84it/s][W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai 9427756it [00:05, 1749167.82it/s] 9433693it [00:05, 1755237.33it/s] [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai tabix -s 1 -b 2 -e 2 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/659_6i-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/659_6i-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz > 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/659_6i-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv cat 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/659_6i-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_6i-T1-TRNA-1_B23WHTKLT4_1.md -output 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/659_6i-T1-TRNA-1_B23WHTKLT4_1.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 2 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_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 2 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/659_6i-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz> 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_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 2 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.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: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_B23WHTKLT4_1.md.bai cat 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_6i-T1-TRNA-1_B23WHTKLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md/qc_complete.txt + merge_qc -folders 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1.md -output 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv + head -n1 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_6i-T1-TRNA-1_B23WHTKLT4_1/659_6i-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv