Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/22651477babce313966489c4b0345b/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.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/ff/45b1d98dfb08792955ae675f70cabc/.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/ff/45b1d98dfb08792955ae675f70cabc/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/22651477babce313966489c4b0345b/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.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 aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai 160920it [00:00, 1609132.48it/s] 329606it [00:00, 1654822.20it/s] 502101it [00:00, 1686822.09it/s] 676839it [00:00, 1710710.53it/s] 849114it [00:00, 1715037.81it/s] 1020618it [00:00, 1713622.25it/s] 1192384it [00:00, 1714924.70it/s] 1364344it [00:00, 1716397.40it/s] 1535984it [00:00, 1715385.13it/s] 1708645it [00:01, 1718676.97it/s] 1880806it [00:01, 1719412.92it/s] 2052748it [00:01, 1717448.23it/s] 2224494it [00:01, 1715051.80it/s] 2397697it [00:01, 1720159.30it/s] 2569715it [00:01, 1716265.74it/s] 2741345it [00:01, 1713354.80it/s] 2915644it [00:01, 1722226.04it/s] 3088890it [00:01, 1725200.50it/s] 3261414it [00:01, 1715630.92it/s] 3432991it [00:02, 1702336.87it/s] 3605860it [00:02, 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1730262.23it/s] 8789259it [00:05, 1732961.56it/s] 8962558it [00:05, 1723660.17it/s] 9135323it [00:05, 1724841.37it/s] 9308748it [00:05, 1727642.32it/s] 9482089it [00:05, 1729358.31it/s] 9655031it [00:05, 1724732.26it/s] 9830433it [00:05, 1733483.44it/s] 10004188it [00:05, 1734623.39it/s] 10178749it [00:05, 1737902.60it/s] 10352544it [00:06, 1732548.39it/s] 10525805it [00:06, 1722326.60it/s] 10698262it [00:06, 1722984.94it/s] 10871697it [00:06, 1726367.90it/s] 11044344it [00:06, 1724669.78it/s] 11216818it [00:06, 1719193.07it/s] 11388745it [00:06, 1704507.43it/s] 11562263it [00:06, 1713496.19it/s] 11735365it [00:06, 1718566.63it/s] 11909571it [00:06, 1725568.65it/s] 12086323it [00:07, 1738101.11it/s] 12261082it [00:07, 1740929.53it/s] 12435188it [00:07, 1733723.62it/s] 12612231it [00:07, 1744679.47it/s] 12786714it [00:07, 1743087.65it/s] 12961544it [00:07, 1744636.54it/s] 13136016it [00:07, 1737840.62it/s] 13309811it [00:07, 1734652.27it/s] 13483284it [00:07, 1729885.15it/s] 13657528it [00:07, 1733621.61it/s] 13830897it [00:08, 1733034.75it/s] 14004205it [00:08, 1730113.77it/s] 14177220it [00:08, 1729445.57it/s] 14350167it [00:08, 1729436.10it/s] 14523119it [00:08, 1729449.37it/s] 14696065it [00:08, 1728317.10it/s] 14868898it [00:08, 1724869.01it/s] 15041387it [00:08, 1724179.39it/s] 15213823it [00:08, 1724222.88it/s] 15388717it [00:08, 1731617.52it/s] 15561881it [00:09, 1730083.09it/s] 15734891it [00:09, 1728866.00it/s] 15908186it [00:09, 1730077.64it/s] 16081195it [00:09, 1727802.74it/s] 16253977it [00:09, 1727231.16it/s] 16427268it [00:09, 1728923.11it/s] 16600183it [00:09, 1728978.02it/s] 16773082it [00:09, 1725910.35it/s] 16793613it [00:09, 1722652.90it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md -output aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.md -output aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_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-2a8dd7-R1_A23WJ53LT4_1/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1_full_basic_stats.tsv