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/2d/641b7ce469098a4f6903468c83166c/.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/6e/9144a24a50586790b611a5c668803f/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/641b7ce469098a4f6903468c83166c/.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-rnd-pltf-dev-nextflow-scratch-01/work/6e/9144a24a50586790b611a5c668803f/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir aih-tih-sc-b845f7-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-b845f7-R1_B23WHYVLT4_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 aih-tih-sc-b845f7-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_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: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai 138436it [00:00, 1384298.61it/s] 290224it [00:00, 1462846.56it/s] 454644it [00:00, 1545625.06it/s] 612844it [00:00, 1559963.70it/s] 782400it [00:00, 1608832.42it/s] 948816it [00:00, 1627529.08it/s] 1119208it [00:00, 1652477.48it/s] 1285611it [00:00, 1656132.93it/s] 1455151it [00:00, 1668389.69it/s] 1623620it [00:01, 1673400.05it/s] 1790961it [00:01, 1667495.29it/s] 1957716it [00:01, 1666440.54it/s] 2124364it [00:01, 1664587.52it/s] 2290826it [00:01, 1651459.20it/s] 2466955it [00:01, 1684236.24it/s] 2640078it [00:01, 1698122.71it/s] 2809924it [00:01, 1694673.64it/s] 2979416it [00:01, 1687316.67it/s] 3151250it [00:01, 1696459.43it/s] 3320917it [00:02, 1679467.39it/s] 3488911it [00:02, 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1735981.93it/s] 8525162it [00:05, 1733123.94it/s] 8698755it [00:05, 1733944.45it/s] 8872159it [00:05, 1708286.69it/s] 9043076it [00:05, 1692883.90it/s] 9212442it [00:05, 1669259.70it/s] 9379465it [00:05, 1667367.03it/s] 9547744it [00:05, 1671896.54it/s] 9717011it [00:05, 1677926.52it/s] 9889553it [00:05, 1692046.70it/s] 10058799it [00:06, 1686146.93it/s] 10231657it [00:06, 1698779.35it/s] 10401564it [00:06, 1694531.96it/s] 10575619it [00:06, 1708248.12it/s] 10747221it [00:06, 1710405.22it/s] 10918278it [00:06, 1705542.33it/s] 11088846it [00:06, 1704878.12it/s] 11259343it [00:06, 1702869.44it/s] 11431267it [00:06, 1707728.05it/s] 11602046it [00:06, 1706010.55it/s] 11772652it [00:07, 1703519.96it/s] 11943355it [00:07, 1704550.13it/s] 12113884it [00:07, 1704617.62it/s] 12285433it [00:07, 1707793.83it/s] 12456214it [00:07, 1702696.28it/s] 12628086it [00:07, 1707465.06it/s] 12798837it [00:07, 1703023.34it/s] 12972988it [00:07, 1714507.37it/s] 13144446it [00:07, 1706194.93it/s] 13315675it [00:07, 1707996.61it/s] 13486485it [00:08, 1707279.62it/s] 13657220it [00:08, 1686855.04it/s] 13704839it [00:08, 1670065.87it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md -output aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/aih-tih-sc-b845f7-R1_B23WHYVLT4_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 aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_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 aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_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 aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_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: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1.md -output aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-b845f7-R1_B23WHYVLT4_1/aih-tih-sc-b845f7-R1_B23WHYVLT4_1_full_basic_stats.tsv