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/a1/8a4d2f5193fd038a4d96c466c247f5/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/3315d0b46f11063838d47d8afce264/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai 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/36/3315d0b46f11063838d47d8afce264/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bam 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/a1/8a4d2f5193fd038a4d96c466c247f5/.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 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3 + all_qc -bam BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.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 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3 -reference ref_genome.fa -region chr20 mkdir -p BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/full_bed.bed seqtool depth -bam BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bam -bed BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.depth.gz saturation_plot -bams BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bam -region chr20 -output BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bam > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/saturation_qc.tsv fragment_size -bams BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bam -region chr20 -output_prefix BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bam > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.mpileup && contamination -input BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.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: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai 0it [00:00, ?it/s] 169166it [00:00, 1691488.20it/s] 349417it [00:00, 1756751.51it/s] 534097it [00:00, 1797841.47it/s] 717214it [00:00, 1810939.83it/s] 900844it [00:00, 1820066.37it/s] 1082851it [00:00, 1816988.47it/s] 1266908it [00:00, 1824668.13it/s] 1449377it [00:00, 1821869.38it/s] 1633074it [00:00, 1826438.95it/s] 1815720it [00:01, 1820534.10it/s] 1997779it [00:01, 1816779.77it/s] 2180782it [00:01, 1820775.72it/s] 2362864it [00:01, 1819976.68it/s] 2548455it [00:01, 1830783.50it/s] 2732524it [00:01, 1833744.78it/s] 2915902it [00:01, 1832840.05it/s] 3099189it [00:01, 1831108.07it/s] 3282406it [00:01, 1831407.59it/s] 3465549it [00:01, 1827824.29it/s] 3648334it [00:02, 1807117.28it/s] 3829097it [00:02, 1803017.64it/s] 4009433it [00:02, 1793541.18it/s] 4188815it [00:02, 1785576.82it/s] 4367393it [00:02, 1784323.15it/s] 4545839it [00:02, 1782750.43it/s] 4727507it [00:02, 1792853.72it/s] 4908393it [00:02, 1797535.65it/s] 5092415it [00:02, 1810285.54it/s] 5275098it [00:02, 1815219.99it/s] 5460441it [00:03, 1826647.74it/s] 5643352it [00:03, 1827358.78it/s] 5827243it [00:03, 1830801.28it/s] 6011371it [00:03, 1833922.86it/s] 6194767it [00:03, 1821516.32it/s] 6376940it [00:03, 1814682.88it/s] 6558426it [00:03, 1811897.46it/s] 6739788it [00:03, 1812301.07it/s] 6921027it [00:03, 1809800.73it/s] 7102013it [00:03, 1805310.96it/s][W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai 7282549it [00:04, 1800746.51it/s] 7463476it [00:04, 1803275.13it/s] 7643808it [00:04, 1795550.45it/s] 7823372it [00:04, 1792766.68it/s] 8003155it [00:04, 1794258.38it/s] 8186887it [00:04, 1807108.85it/s] 8367862it [00:04, 1807871.43it/s][W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai 8548655it [00:04, 1647912.04it/s] 8727630it [00:04, 1687689.75it/s] 8910894it [00:04, 1729144.29it/s] 9094248it [00:05, 1759410.81it/s] 9279045it [00:05, 1785198.72it/s] 9460962it [00:05, 1795202.93it/s] 9642187it [00:05, 1800169.31it/s] 9825429it [00:05, 1809741.69it/s] 10008451it [00:05, 1815831.10it/s] 10190287it [00:05, 1808299.04it/s] 10371299it [00:05, 1797112.34it/s] 10553595it [00:05, 1804776.22it/s] 10734982it [00:05, 1807466.24it/s] 10916714it [00:06, 1810260.55it/s] 11097795it [00:06, 1810406.03it/s] 11278873it [00:06, 1805532.85it/s] 11462111it [00:06, 1813536.47it/s] 11645113it [00:06, 1818449.30it/s] 11826975it [00:06, 1817356.41it/s] 12008723it [00:06, 1808164.55it/s] 12193246it [00:06, 1819211.69it/s] 12375300it [00:06, 1819587.33it/s] 12559944it [00:06, 1827605.37it/s] 12742716it [00:07, 1827261.83it/s] 12826657it [00:07, 1805074.92it/s] [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai tabix -s 1 -b 2 -e 2 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.depth.gz seqtool depth_hist -nbins 500 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.depth.gz > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.depth_hist.tsv cat BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md -output BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.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 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bam > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.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 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bam > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.depth.gz> BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.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 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bam > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.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: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md.bai cat BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md/qc_complete.txt + merge_qc -folders BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.md -output BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3_full_basic_stats.tsv + head -n1 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3_full_basic_stats.tsv