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/4c/e118a997d4d35b91823f5a1058b8e2/.command.sh 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/3a/3cf1dababdb7b9c924b5e077a445e1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/e118a997d4d35b91823f5a1058b8e2/.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-rnd-pltf-dev-nextflow-scratch-01/work/3a/3cf1dababdb7b9c924b5e077a445e1/659_bGW-T1-TRNA-1_B23MHV2LT4_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_bGW-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bGW-T1-TRNA-1_B23MHV2LT4_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_bGW-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_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_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_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_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 155817it [00:00, 1558097.19it/s] 324138it [00:00, 1631427.06it/s] 492814it [00:00, 1656657.21it/s] 664348it [00:00, 1679798.19it/s] 836058it [00:00, 1693223.13it/s] 1008534it [00:00, 1703922.26it/s] 1179471it [00:00, 1705685.10it/s] 1350219it [00:00, 1706131.40it/s] 1521484it [00:00, 1708145.39it/s] 1693388it [00:01, 1711386.90it/s] 1864527it [00:01, 1709389.08it/s] 2039119it [00:01, 1720449.30it/s] 2215121it [00:01, 1732412.11it/s] 2388364it [00:01, 1730074.28it/s] 2561374it [00:01, 1723258.57it/s] 2735695it [00:01, 1729226.54it/s] 2908669it [00:01, 1729364.96it/s] 3081611it [00:01, 1725902.59it/s] 3254206it [00:01, 1721914.51it/s] 3426402it [00:02, 1708104.14it/s] 3598796it [00:02, 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1704387.43it/s] 8741472it [00:05, 1710218.51it/s] 8915593it [00:05, 1719470.47it/s] 9087585it [00:05, 1711328.29it/s] 9259002it [00:05, 1712018.71it/s] 9430232it [00:05, 1711712.88it/s] 9602756it [00:05, 1715647.09it/s] 9774336it [00:05, 1712244.98it/s] 9945572it [00:05, 1707118.03it/s] 10116626it [00:05, 1708121.51it/s] 10288454it [00:06, 1711042.57it/s] 10459565it [00:06, 1691474.59it/s] 10628764it [00:06, 1691305.90it/s] 10800983it [00:06, 1700490.78it/s] 10971380it [00:06, 1701509.48it/s] 11145636it [00:06, 1713765.65it/s] 11320368it [00:06, 1723789.12it/s] 11493523it [00:06, 1726095.54it/s] 11666145it [00:06, 1720405.74it/s] 11838624it [00:06, 1721701.42it/s] 12012984it [00:07, 1728232.33it/s] 12185815it [00:07, 1725366.67it/s] 12360145it [00:07, 1730714.01it/s] 12533222it [00:07, 1722533.94it/s] 12705487it [00:07, 1716638.04it/s] 12877161it [00:07, 1709916.14it/s] 13050303it [00:07, 1716304.37it/s][W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai 13222524it [00:07, 1718045.07it/s] 13394337it [00:07, 1698124.71it/s] 13564202it [00:07, 1694980.78it/s] 13733735it [00:08, 1693182.25it/s] 13903506it [00:08, 1694510.05it/s] 14072975it [00:08, 1673489.73it/s] 14241663it [00:08, 1677437.31it/s] 14410850it [00:08, 1681709.26it/s] 14579843it [00:08, 1684142.04it/s] 14750462it [00:08, 1690711.04it/s] 14921253it [00:08, 1695834.20it/s] 15090854it [00:08, 1690652.49it/s] 15265277it [00:08, 1706646.21it/s] 15439199it [00:09, 1716218.89it/s] 15611959it [00:09, 1719610.20it/s] 15783930it [00:09, 1713624.24it/s] 15956068it [00:09, 1715774.84it/s] 16127654it [00:09, 1712088.34it/s] 16143740it [00:09, 1705074.12it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/659_bGW-T1-TRNA-1_B23MHV2LT4_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_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_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_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_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_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_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_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_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_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGW-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bGW-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bGW-T1-TRNA-1_B23MHV2LT4_1/659_bGW-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv