Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/0f14dcd1e97d5fa480dbbabe1485b4/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bam 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/85/48fbdd3c660655f154e010b5c901b0/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/0f14dcd1e97d5fa480dbbabe1485b4/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict 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/85/48fbdd3c660655f154e010b5c901b0/.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_bld_01_A23WKFTLT4_2 + all_qc -bam BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2 -reference ref_genome.fa -region chr20 mkdir -p BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/full_bed.bed seqtool depth -bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bam -bed BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.depth.gz saturation_plot -bams BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bam -region chr20 -output BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bam > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/saturation_qc.tsv fragment_size -bams BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bam -region chr20 -output_prefix BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2.md.bam > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.mpileup && contamination -input BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai 77888it [00:00, 778812.04it/s] 168717it [00:00, 854937.32it/s] 254211it [00:00, 819070.99it/s] 336755it [00:00, 821370.10it/s] 421058it [00:00, 829019.77it/s] 507115it [00:00, 839496.75it/s] 597945it [00:00, 861797.65it/s] 684187it [00:00, 836319.72it/s] 768003it [00:00, 830852.09it/s] 852045it [00:01, 833715.86it/s] 945034it [00:01, 862631.55it/s] 1031405it [00:01, 861977.30it/s] 1117677it [00:01, 859888.55it/s] 1203717it [00:01, 851284.38it/s] 1288895it [00:01, 841796.94it/s] 1373123it [00:01, 829899.18it/s] 1458169it [00:01, 835922.20it/s] 1542041it [00:01, 836716.06it/s] 1627212it [00:01, 841147.26it/s] 1713829it [00:02, 848477.98it/s] 1808759it [00:02, 878554.53it/s] 1921930it [00:02, 954162.11it/s] 2039448it [00:02, 1020215.82it/s] 2166963it [00:02, 1096530.96it/s] 2306921it [00:02, 1187304.44it/s] 2448521it [00:02, 1255816.50it/s] 2579304it [00:02, 1271378.03it/s] 2707791it [00:02, 1275331.07it/s] 2841482it [00:02, 1293761.05it/s] 2970874it [00:03, 1246960.58it/s] 3104244it [00:03, 1272273.55it/s][W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai 3246337it [00:03, 1316021.47it/s] 3390629it [00:03, 1353489.25it/s] 3526244it [00:03, 1345973.49it/s] 3661032it [00:03, 1274031.71it/s] 3789314it [00:03, 1139721.86it/s] 3906226it [00:03, 1059215.42it/s] 4014800it [00:03, 995886.93it/s] 4116439it [00:04, 981820.33it/s] 4215914it [00:04, 954372.38it/s] 4312148it [00:04, 926493.40it/s][W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai 4405276it [00:04, 900254.87it/s] 4495571it [00:04, 898984.46it/s][W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai 4585647it [00:04, 892879.91it/s] 4675028it [00:04, 869258.25it/s] 4762047it [00:04, 861246.67it/s] 4851712it [00:04, 871360.53it/s] 4938924it [00:05, 866852.71it/s] 5027640it [00:05, 872754.77it/s] 5080307it [00:05, 978370.96it/s] [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai tabix -s 1 -b 2 -e 2 BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.depth.gz seqtool depth_hist -nbins 500 BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.depth.gz > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.depth_hist.tsv cat BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md -output BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2.md.bam > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2.md.bam > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.depth.gz> BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2.md.bam > BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bai cat BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md/qc_complete.txt + merge_qc -folders BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md -output BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2_full_basic_stats.tsv + head -n1 BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_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_01_A23WKFTLT4_2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2_full_basic_stats.tsv