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/49/a9b28a6adf9c87fa473eca3b62c4db/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/0d67dff87d6c5050d9ca1997ced295/659_bMa-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/49/a9b28a6adf9c87fa473eca3b62c4db/.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-rnd-pltf-dev-nextflow-scratch-01/work/bf/0d67dff87d6c5050d9ca1997ced295/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir 659_bMa-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 164509it [00:00, 1644969.99it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai 341159it [00:00, 1716418.53it/s] 522613it [00:00, 1761195.52it/s] 705551it [00:00, 1788092.08it/s] 886659it [00:00, 1796289.45it/s] 1067079it [00:00, 1798957.62it/s] 1248532it [00:00, 1804032.07it/s] 1428936it [00:00, 1794921.23it/s] 1608862it [00:00, 1796254.70it/s] 1791060it [00:01, 1804157.99it/s] 1973069it [00:01, 1808947.21it/s] 2156321it [00:01, 1816093.05it/s] 2337935it [00:01, 1813668.15it/s] 2521287it [00:01, 1819506.57it/s] 2703648it [00:01, 1820720.38it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai 2885723it [00:01, 1816163.89it/s] 3067344it [00:01, 1792212.93it/s] 3247479it [00:01, 1794912.64it/s] 3429175it [00:01, 1801467.67it/s] 3609363it [00:02, 1786687.42it/s] 3790591it [00:02, 1794278.81it/s] 3971476it [00:02, 1798606.42it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai 4154386it [00:02, 1807696.37it/s] 4336616it [00:02, 1812048.80it/s] 4517841it [00:02, 1810129.11it/s] 4700830it [00:02, 1816028.72it/s] 4882445it [00:02, 1809922.47it/s] 5063666it [00:02, 1810591.36it/s] 5244734it [00:02, 1805145.83it/s] 5426723it [00:03, 1809538.44it/s] 5609185it [00:03, 1813905.02it/s] 5791387it [00:03, 1816321.04it/s] 5974267it [00:03, 1819928.84it/s] 6156264it [00:03, 1812266.65it/s] 6337501it [00:03, 1804229.90it/s] 6517936it [00:03, 1802969.87it/s] 6698241it [00:03, 1792946.96it/s] 6877550it [00:03, 1790803.75it/s] 7056640it [00:03, 1788344.22it/s] 7235481it [00:04, 1778602.87it/s] 7414664it [00:04, 1782514.52it/s] 7596055it [00:04, 1791860.80it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai 7777019it [00:04, 1797111.67it/s] 7961078it [00:04, 1810104.10it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai 8113870it [00:04, 1801320.16it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-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_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv