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/31/ae424395332ad619ca1bb21c05bbf4/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/bc062d4a07fcb36798b25cb03e64f1/659_bCu-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-rnd-pltf-dev-nextflow-scratch-01/work/7a/bc062d4a07fcb36798b25cb03e64f1/659_bCu-T1-TRNA-1_B23MHV2LT4_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/31/ae424395332ad619ca1bb21c05bbf4/.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_bCu-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 157929it [00:00, 1579208.67it/s] 329556it [00:00, 1659797.29it/s] 505714it [00:00, 1706241.53it/s] 681957it [00:00, 1728398.18it/s] 858357it [00:00, 1741212.78it/s] 1032479it [00:00, 1738913.97it/s] 1208033it [00:00, 1744321.93it/s] 1385497it [00:00, 1753800.62it/s] 1563254it [00:00, 1761205.82it/s] 1739376it [00:01, 1756323.30it/s] 1915012it [00:01, 1756125.32it/s] 2090627it [00:01, 1750965.20it/s] 2267339it [00:01, 1755823.85it/s] 2448509it [00:01, 1772646.40it/s] 2627740it [00:01, 1778545.76it/s] 2805601it [00:01, 1775068.85it/s] 2984069it [00:01, 1777894.73it/s] 3161863it [00:01, 1772552.94it/s] 3339125it [00:01, 1771937.33it/s] 3516323it [00:02, 1754335.22it/s] 3694117it [00:02, 1761341.95it/s] 3870685it [00:02, 1762617.62it/s] 4046971it [00:02, 1762473.33it/s] 4225066it [00:02, 1767981.82it/s] 4402203it [00:02, 1768977.76it/s] 4579111it [00:02, 1765830.66it/s] 4755702it [00:02, 1756122.31it/s] 4932791it [00:02, 1760511.45it/s] 5111075it [00:02, 1767166.01it/s] 5287804it [00:03, 1764855.70it/s] 5464450it [00:03, 1765318.52it/s] 5640988it [00:03, 1765147.16it/s] 5817507it [00:03, 1763529.40it/s] 5993863it [00:03, 1762792.64it/s] 6170145it [00:03, 1760864.60it/s] 6346524it [00:03, 1761722.28it/s] 6522698it [00:03, 1757703.83it/s] 6698471it [00:03, 1754163.99it/s] 6873890it [00:03, 1747555.96it/s] 7048652it [00:04, 1739745.62it/s] 7224562it [00:04, 1745492.17it/s] 7401199it [00:04, 1751703.57it/s] 7578577it [00:04, 1758283.06it/s] 7754415it [00:04, 1755163.69it/s] 7929939it [00:04, 1752039.29it/s] 8105686it [00:04, 1753639.96it/s] 8281118it [00:04, 1753735.13it/s] 8456783it [00:04, 1754587.35it/s] 8635320it [00:04, 1763788.01it/s] 8812403it [00:05, 1765877.92it/s] 8988993it [00:05, 1763775.70it/s] 9166983it [00:05, 1768586.00it/s] 9345055it [00:05, 1772200.71it/s] 9523109it [00:05, 1774683.68it/s] 9700579it [00:05, 1771405.19it/s] 9877722it [00:05, 1758351.84it/s] 10054470it [00:05, 1761022.24it/s] 10230840it [00:05, 1761803.69it/s] 10407033it [00:05, 1761397.37it/s][W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai 10583182it [00:06, 1755926.29it/s] 10758784it [00:06, 1752926.02it/s] 10934083it [00:06, 1748626.30it/s] 11110059it [00:06, 1751932.08it/s] 11287616it [00:06, 1758979.19it/s] 11464450it [00:06, 1761757.86it/s] 11640631it [00:06, 1750300.50it/s] 11739404it [00:06, 1757149.88it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv