Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/cc2a5c6e84922391637d3d4c17a549/659_bjQ-T1-TRNA-1_B23MHV2LT4_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/39/11a58bb2ae38aa448f1a62a37b0bbc/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/cc2a5c6e84922391637d3d4c17a549/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai 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/39/11a58bb2ae38aa448f1a62a37b0bbc/.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 659_bjQ-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 144721it [00:00, 1447121.67it/s] 299546it [00:00, 1506561.79it/s] 458101it [00:00, 1542583.71it/s] 616262it [00:00, 1557951.30it/s] 778132it [00:00, 1579676.79it/s] 940792it [00:00, 1595590.82it/s] 1101506it [00:00, 1599329.31it/s] 1263036it [00:00, 1604375.98it/s] 1423475it [00:00, 1604350.95it/s] 1585868it [00:01, 1610364.71it/s] 1753478it [00:01, 1630452.76it/s] 1916882it [00:01, 1631426.14it/s] 2080025it [00:01, 1620320.40it/s] 2242075it [00:01, 1607791.09it/s] 2406984it [00:01, 1619954.23it/s] 2569010it [00:01, 1616474.76it/s] 2732231it [00:01, 1621144.16it/s] 2894363it [00:01, 1608593.85it/s] 3055252it [00:01, 1603404.15it/s] 3215613it [00:02, 1592842.18it/s] 3378346it [00:02, 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1590651.59it/s] 8184711it [00:05, 1592739.06it/s] 8344016it [00:05, 1577004.67it/s] 8506544it [00:05, 1591276.59it/s] 8670024it [00:05, 1604185.81it/s] 8834286it [00:05, 1615616.01it/s] 8997901it [00:05, 1621695.11it/s] 9166308it [00:05, 1640319.23it/s] 9330367it [00:05, 1635910.09it/s] 9493979it [00:05, 1623840.22it/s] 9658707it [00:06, 1630795.04it/s] 9824121it [00:06, 1637733.73it/s] 9987917it [00:06, 1635650.26it/s] 10152837it [00:06, 1639674.37it/s] 10318135it [00:06, 1643630.78it/s] 10482508it [00:06, 1637174.51it/s] 10646237it [00:06, 1632971.49it/s] 10813044it [00:06, 1643423.72it/s] 10977398it [00:06, 1640468.42it/s] 11142704it [00:06, 1644207.19it/s] 11308588it [00:07, 1648481.87it/s] 11473443it [00:07, 1642870.16it/s] 11638260it [00:07, 1644429.00it/s] 11802709it [00:07, 1642836.18it/s] 11966997it [00:07, 1640535.70it/s] 12131054it [00:07, 1581789.03it/s] 12289675it [00:07, 1492744.99it/s] 12451641it [00:07, 1528521.76it/s] 12614723it [00:07, 1557886.61it/s] 12776892it [00:08, 1576429.18it/s] 12942528it [00:08, 1599871.95it/s] 13103029it [00:08, 1583786.91it/s] 13265120it [00:08, 1594527.93it/s] 13428163it [00:08, 1605134.10it/s] 13596460it [00:08, 1628190.46it/s] 13762050it [00:08, 1636419.18it/s] 13925816it [00:08, 1632254.06it/s] 14090426it [00:08, 1636261.39it/s] 14183067it [00:08, 1597403.44it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv