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/b1/e3a88ccf9a319530b7e0b429cb7f39/.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/0f/b137a04b7f21e2224c28ccf75d243c/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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/b1/e3a88ccf9a319530b7e0b429cb7f39/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/b137a04b7f21e2224c28ccf75d243c/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai 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_bld_02_A23WKFTLT4_2 + all_qc -bam BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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_bld_02_A23WKFTLT4_2 -reference ref_genome.fa -region chr20 mkdir -p BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/full_bed.bed seqtool depth -bam BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bam -bed BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.depth.gz saturation_plot -bams BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bam -region chr20 -output BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bam > BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/saturation_qc.tsv fragment_size -bams BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bam -region chr20 -output_prefix BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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_bld_02_A23WKFTLT4_2.md.bam > BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.mpileup && contamination -input BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai 0it [00:00, ?it/s] 149189it [00:00, 1491809.62it/s] 305903it [00:00, 1536084.86it/s] 470661it [00:00, 1586965.95it/s] 640443it [00:00, 1630707.88it/s] 809855it [00:00, 1653385.70it/s] 975194it [00:00, 1633555.62it/s] 1144459it [00:00, 1652692.16it/s] 1315962it [00:00, 1672328.65it/s] 1489279it [00:00, 1691253.74it/s] 1660070it [00:01, 1696357.57it/s] 1829733it [00:01, 1696386.93it/s] 1999391it [00:01, 1687587.60it/s] 2173762it [00:01, 1704488.48it/s] 2346675it [00:01, 1711889.61it/s] 2521494it [00:01, 1722707.50it/s] 2693780it [00:01, 1719705.51it/s] 2865762it [00:01, 1718519.82it/s] 3037622it [00:01, 1716218.16it/s] 3209250it [00:01, 1707905.91it/s] 3380052it [00:02, 1685677.57it/s] 3550228it [00:02, 1690423.74it/s] 3719321it [00:02, 1685278.18it/s] 3889940it [00:02, 1691456.39it/s] 4062825it [00:02, 1702561.81it/s] 4233109it [00:02, 1688754.58it/s] 4402024it [00:02, 1683106.67it/s] 4570362it [00:02, 1551276.68it/s] 4727473it [00:02, 1505368.89it/s] 4883907it [00:02, 1521834.53it/s] 5037235it [00:03, 1520215.46it/s] 5207037it [00:03, 1571541.18it/s] 5370947it [00:03, 1591263.37it/s] 5530649it [00:03, 1551183.29it/s] 5686338it [00:03, 1522237.79it/s] 5851541it [00:03, 1559755.78it/s] 6024084it [00:03, 1608161.89it/s] 6190246it [00:03, 1623883.04it/s] 6358201it [00:03, 1640348.34it/s] 6527061it [00:03, 1654617.80it/s] 6695757it [00:04, 1664243.88it/s] 6862322it [00:04, 1664069.46it/s] 7035427it [00:04, 1684009.77it/s] 7205088it [00:04, 1687730.81it/s] 7374501it [00:04, 1689554.94it/s] 7545625it [00:04, 1696031.25it/s] 7717815it [00:04, 1703768.66it/s] 7891070it [00:04, 1712381.18it/s] 8062323it [00:04, 1710108.18it/s] 8235463it [00:04, 1716474.74it/s] 8409428it [00:05, 1723405.68it/s] 8583264it [00:05, 1727795.81it/s] 8756049it [00:05, 1712468.74it/s] 8927687it [00:05, 1713500.97it/s] 9099062it [00:05, 1706194.20it/s] 9270012it [00:05, 1707168.07it/s] 9442996it [00:05, 1713923.07it/s] 9615484it [00:05, 1717135.57it/s] 9787209it [00:05, 1713898.29it/s] 9959018it [00:05, 1715136.78it/s] 10132445it [00:06, 1720850.92it/s] 10308794it [00:06, 1733610.12it/s] 10482289it [00:06, 1733997.31it/s] 10656097it [00:06, 1735206.87it/s] 10834239it [00:06, 1749043.12it/s] 11009146it [00:06, 1745714.03it/s] 11183721it [00:06, 1736495.48it/s] 11357383it [00:06, 1733384.39it/s] 11530730it [00:06, 1724040.44it/s] 11703148it [00:06, 1717776.31it/s] 11876994it [00:07, 1723921.95it/s] 12049398it [00:07, 1714372.77it/s] 12222414it [00:07, 1719058.89it/s] 12395671it [00:07, 1722920.75it/s] 12568209it [00:07, 1723639.02it/s] 12740582it [00:07, 1722271.07it/s] 12912816it [00:07, 1702900.13it/s] 13083156it [00:07, 1696056.64it/s][W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai 13254040it [00:07, 1699843.23it/s] 13424053it [00:07, 1684516.54it/s] 13592791it [00:08, 1685335.54it/s] 13761949it [00:08, 1687167.21it/s] 13930689it [00:08, 1676234.00it/s] 14104510it [00:08, 1694654.15it/s] 14275634it [00:08, 1699534.54it/s] 14449382it [00:08, 1710790.78it/s] 14623160it [00:08, 1718846.95it/s] 14795064it [00:08, 1715215.29it/s] 14852659it [00:08, 1681238.48it/s] [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai tabix -s 1 -b 2 -e 2 BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.depth.gz seqtool depth_hist -nbins 500 BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.depth.gz > BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.depth_hist.tsv cat BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md -output BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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_bld_02_A23WKFTLT4_2.md.bam > BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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_bld_02_A23WKFTLT4_2.md.bam > BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.depth.gz> BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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_bld_02_A23WKFTLT4_2.md.bam > BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.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_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md.bai cat BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md/qc_complete.txt + merge_qc -folders BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.md -output BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2_full_basic_stats.tsv + head -n1 BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2_full_basic_stats.tsv