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/e5/d081613f1aead6d6f9b374eda045ae/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/9e975f3166574e14c705024704f577/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam 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/e5/d081613f1aead6d6f9b374eda045ae/.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/10/9e975f3166574e14c705024704f577/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai 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-2b9bfa-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai 147281it [00:00, 1472765.76it/s] 310215it [00:00, 1564843.85it/s] 473062it [00:00, 1593878.06it/s] 640015it [00:00, 1623680.55it/s] 806204it [00:00, 1637442.34it/s] 972418it [00:00, 1645823.84it/s] 1138758it [00:00, 1651520.06it/s] 1306666it [00:00, 1660280.14it/s] 1476524it [00:00, 1672238.41it/s] 1643748it [00:01, 1671727.53it/s] 1811444it [00:01, 1673309.52it/s] 1978776it [00:01, 1656738.40it/s] 2144487it [00:01, 1641196.39it/s] 2313231it [00:01, 1654988.45it/s] 2479685it [00:01, 1657803.42it/s] 2646921it [00:01, 1662147.50it/s] 2821825it [00:01, 1688159.15it/s] 2991056it [00:01, 1689198.27it/s] 3159998it [00:01, 1677974.52it/s] 3327826it [00:02, 1657433.97it/s] 3496495it [00:02, 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[00:07, 1691333.59it/s] 13450528it [00:08, 1684772.04it/s] 13508536it [00:08, 1662623.10it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md -output aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md -output aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1_full_basic_stats.tsv