Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/9869c7965692d85b59cdf992458358/659_buD-T1-TRNA-1_B23WHTKLT4_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/92/fb481a6fb4afc04ad5b4779fe2cfe7/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/9869c7965692d85b59cdf992458358/659_buD-T1-TRNA-1_B23WHTKLT4_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/92/fb481a6fb4afc04ad5b4779fe2cfe7/.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_buD-T1-TRNA-1_B23WHTKLT4_1 + all_qc -bam 659_buD-T1-TRNA-1_B23WHTKLT4_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_buD-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed seqtool depth -bam 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bam -bed 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/659_buD-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz saturation_plot -bams 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/saturation_plot.png -threads 1 fragment_size -bams 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output_prefix 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/fragsize -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/saturation_qc.tsv samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.mpileup && contamination -input 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_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_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai 0it [00:00, ?it/s] 147741it [00:00, 1477312.79it/s] 312328it [00:00, 1576418.07it/s] 480741it [00:00, 1625567.23it/s] 651199it [00:00, 1656733.76it/s] 822988it [00:00, 1678696.15it/s] 996494it [00:00, 1697841.51it/s] 1169853it [00:00, 1709421.97it/s] 1342016it [00:00, 1713196.84it/s] 1513336it [00:00, 1710322.75it/s] 1687625it [00:01, 1720341.08it/s] 1860415it [00:01, 1722556.32it/s] 2032673it [00:01, 1700076.31it/s] 2206981it [00:01, 1712956.07it/s] 2379175it [00:01, 1715632.29it/s] 2553357it [00:01, 1723467.22it/s] 2726906it [00:01, 1727052.39it/s] 2899636it [00:01, 1721306.14it/s] 3071787it [00:01, 1716202.16it/s] 3243423it [00:01, 1693097.96it/s] 3412804it [00:02, 1645631.92it/s] 3577657it [00:02, 1510935.79it/s] 3745166it [00:02, 1556309.43it/s] 3914101it [00:02, 1593965.50it/s] 4085720it [00:02, 1629123.28it/s] 4256332it [00:02, 1651539.14it/s] 4429116it [00:02, 1673957.32it/s] 4601373it [00:02, 1688320.34it/s] 4774251it [00:02, 1700325.00it/s] 4945802it [00:02, 1704795.94it/s] 5116540it [00:03, 1645426.23it/s] 5281691it [00:03, 1599099.77it/s] 5453998it [00:03, 1634763.42it/s] 5624676it [00:03, 1655721.58it/s] 5796235it [00:03, 1673288.82it/s] 5967036it [00:03, 1683529.85it/s] 6136842it [00:03, 1687735.69it/s] 6305807it [00:03, 1682793.42it/s] 6476681it [00:03, 1690496.19it/s] 6647735it [00:03, 1696381.37it/s] 6823164it [00:04, 1713669.66it/s] 6994589it [00:04, 1609683.16it/s] 7156870it [00:04, 1551591.82it/s] 7326340it [00:04, 1591985.95it/s] 7495194it [00:04, 1619727.14it/s] 7664670it [00:04, 1641555.97it/s] 7838776it [00:04, 1670756.15it/s] 8009963it [00:04, 1682889.87it/s] 8182438it [00:04, 1695303.66it/s] 8355344it [00:05, 1705342.65it/s] 8528970it [00:05, 1714553.75it/s] 8703639it [00:05, 1724144.46it/s] 8876163it [00:05, 1718300.28it/s][W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai 9049605it [00:05, 1723036.25it/s] 9221967it [00:05, 1718339.42it/s] 9393844it [00:05, 1696367.62it/s] 9444184it [00:05, 1671768.07it/s] [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai tabix -s 1 -b 2 -e 2 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/659_buD-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/659_buD-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz > 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/659_buD-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv cat 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/659_buD-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_buD-T1-TRNA-1_B23WHTKLT4_1.md -output 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/659_buD-T1-TRNA-1_B23WHTKLT4_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_buD-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_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_buD-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_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_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/659_buD-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz> 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_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_buD-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_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_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai cat 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_buD-T1-TRNA-1_B23WHTKLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md/qc_complete.txt + merge_qc -folders 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md -output 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv + head -n1 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv