Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/047ba7c8aafd4f00175a73129e1472/FFPE_V4_0002_RNA_0001_B23MVV7LT4_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/91/113a1b8ec7dc4a119650c81b0371d5/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/047ba7c8aafd4f00175a73129e1472/FFPE_V4_0002_RNA_0001_B23MVV7LT4_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/91/113a1b8ec7dc4a119650c81b0371d5/.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 FFPE_V4_0002_RNA_0001_B23MVV7LT4_1 + all_qc -bam FFPE_V4_0002_RNA_0001_B23MVV7LT4_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 FFPE_V4_0002_RNA_0001_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 mkdir -p FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/full_bed.bed seqtool depth -bam FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam -bed FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.depth.gz saturation_plot -bams FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam -region chr20 -output FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam > FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/saturation_qc.tsv fragment_size -bams FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam -region chr20 -output_prefix FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam > FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.mpileup && contamination -input FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_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: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s] 151834it [00:00, 1517386.37it/s] 316079it [00:00, 1590850.31it/s] 484716it [00:00, 1634397.67it/s] 656737it [00:00, 1668144.64it/s] 826708it [00:00, 1679426.83it/s] 998488it [00:00, 1692428.78it/s] 1171190it [00:00, 1703608.07it/s] 1341552it [00:00, 1702249.46it/s] 1512348it [00:00, 1704009.92it/s] 1683326it [00:01, 1705765.87it/s] 1854135it [00:01, 1706371.64it/s] 2024773it [00:01, 1702731.22it/s] 2195048it [00:01, 1678635.27it/s] 2367950it [00:01, 1693666.41it/s] 2543473it [00:01, 1711844.17it/s] 2714815it [00:01, 1712295.58it/s] 2886088it [00:01, 1708344.12it/s] 3056954it [00:01, 1708284.36it/s] 3227804it [00:01, 1706023.41it/s] 3398422it [00:02, 1684937.52it/s] 3568904it [00:02, 1690748.89it/s] 3741151it [00:02, 1700137.07it/s] 3913306it [00:02, 1706513.81it/s] 4083991it [00:02, 1700025.12it/s] 4255726it [00:02, 1705075.76it/s] 4429404it [00:02, 1714522.83it/s] 4601939it [00:02, 1717600.00it/s] 4774505it [00:02, 1719996.71it/s] 4946515it [00:02, 1718342.91it/s] 5118357it [00:03, 1704790.23it/s] 5288864it [00:03, 1686474.40it/s] 5459753it [00:03, 1693070.59it/s] 5629106it [00:03, 1675983.86it/s] 5804248it [00:03, 1698170.98it/s] 5978536it [00:03, 1711271.31it/s] 6149969it [00:03, 1712160.22it/s] 6322608it [00:03, 1716270.51it/s] 6497519it [00:03, 1726052.05it/s] 6670150it [00:03, 1718638.94it/s] 6844392it [00:04, 1725720.73it/s] 7017444it [00:04, 1726726.66it/s] 7190131it [00:04, 1712792.22it/s] 7361443it [00:04, 1705008.86it/s] 7533158it [00:04, 1708591.96it/s] 7704038it [00:04, 1706972.30it/s] 7875321it [00:04, 1708694.84it/s] 8046202it [00:04, 1702478.68it/s] 8216461it [00:04, 1692122.74it/s] 8388591it [00:04, 1700745.92it/s] 8558685it [00:05, 1697870.59it/s] 8733053it [00:05, 1711527.74it/s] 8904558it [00:05, 1712562.86it/s] 9075826it [00:05, 1711510.38it/s] 9246985it [00:05, 1696627.64it/s] 9383462it [00:05, 1700988.78it/s] [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai tabix -s 1 -b 2 -e 2 FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.depth.gz seqtool depth_hist -nbins 500 FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.depth.gz > FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.depth_hist.tsv cat FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md -output FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/FFPE_V4_0002_RNA_0001_B23MVV7LT4_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 FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam > FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_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 FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam > FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.depth.gz> FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_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 FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam > FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_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: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bai cat FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md/qc_complete.txt + merge_qc -folders FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md -output FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1_full_basic_stats.tsv