Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/3f9b8fcca2aee8f8e9e55406e975c2/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai 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/7f/d7c88e002b98064e5561f615e17014/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/3f9b8fcca2aee8f8e9e55406e975c2/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bam 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/7f/d7c88e002b98064e5561f615e17014/.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 aih-tih-sc-3e91d2-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-3e91d2-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-3e91d2-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-3e91d2-R1_B23WHYVLT4_1/aih-tih-sc-3e91d2-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-3e91d2-R1_B23WHYVLT4_1/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-3e91d2-R1_B23WHYVLT4_1/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-3e91d2-R1_B23WHYVLT4_1/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-3e91d2-R1_B23WHYVLT4_1/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-3e91d2-R1_B23WHYVLT4_1/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-3e91d2-R1_B23WHYVLT4_1/aih-tih-sc-3e91d2-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-3e91d2-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-3e91d2-R1_B23WHYVLT4_1/aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-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-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-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-3e91d2-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-3e91d2-R1_B23WHYVLT4_1.md.bai 152190it [00:00, 1521854.28it/s] 317258it [00:00, 1597595.99it/s] 481766it [00:00, 1619207.96it/s] 643687it [00:00, 1531265.76it/s] 812678it [00:00, 1586392.90it/s] 971952it [00:00, 1562971.97it/s] 1134713it [00:00, 1583442.90it/s] 1299536it [00:00, 1603673.68it/s] 1465775it [00:00, 1621774.54it/s] 1631261it [00:01, 1631805.50it/s] 1797498it [00:01, 1641086.58it/s] 1965182it [00:01, 1651900.84it/s] 2130457it [00:01, 1648443.73it/s] 2301791it [00:01, 1667958.11it/s] 2470759it [00:01, 1674474.89it/s] 2639262it [00:01, 1677625.06it/s] 2807051it [00:01, 1671105.09it/s] 2974185it [00:01, 1666136.83it/s] 3140817it [00:01, 1661462.45it/s] 3306977it [00:02, 1555359.25it/s] 3475365it [00:02, 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1620612.42it/s] 17168832it [00:10, 1625126.56it/s] 17331362it [00:10, 1618264.21it/s] 17494052it [00:10, 1620824.05it/s] 17659787it [00:10, 1631710.55it/s] 17822973it [00:11, 1622297.51it/s] 17986241it [00:11, 1625377.97it/s] 18148795it [00:11, 1621692.13it/s] 18314772it [00:11, 1633047.11it/s] 18481193it [00:11, 1642219.08it/s] 18645428it [00:11, 1641888.55it/s] 18713543it [00:11, 1617295.08it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.md.bai