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/0c/92d282f03a18e21f66bc1f7a92921c/.command.sh 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/38/c1b4f3d48c340fe1f0156a1af813f9/aih-tih-sc-18a6f2-R1_B23WHYVLT4_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/0c/92d282f03a18e21f66bc1f7a92921c/.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-rnd-pltf-dev-nextflow-scratch-01/work/38/c1b4f3d48c340fe1f0156a1af813f9/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai 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 aih-tih-sc-18a6f2-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-18a6f2-R1_B23WHYVLT4_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 aih-tih-sc-18a6f2-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_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: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 136247it [00:00, 1362357.62it/s] 301477it [00:00, 1532857.58it/s] 477604it [00:00, 1637113.27it/s] 654424it [00:00, 1688815.94it/s] 831947it [00:00, 1719942.79it/s] 1010632it [00:00, 1742658.46it/s] 1186053it [00:00, 1746251.59it/s] 1363021it [00:00, 1753680.60it/s] 1540687it [00:00, 1760831.46it/s] 1719681it [00:01, 1769789.13it/s] 1898378it [00:01, 1774872.75it/s] 2077402it [00:01, 1779517.96it/s] 2259072it [00:01, 1790747.62it/s] 2438147it [00:01, 1787748.08it/s] 2616923it [00:01, 1783807.27it/s] 2795307it [00:01, 1780254.05it/s] 2973335it [00:01, 1765701.59it/s] 3149930it [00:01, 1735029.53it/s] 3323548it [00:01, 1729110.81it/s] 3500153it [00:02, 1740009.96it/s] 3677869it [00:02, 1750787.49it/s] 3853007it [00:02, 1749286.15it/s] 4029793it [00:02, 1754791.07it/s] 4205951it [00:02, 1756780.08it/s] 4381653it [00:02, 1744320.21it/s] 4557021it [00:02, 1747076.82it/s] 4735714it [00:02, 1758932.15it/s] 4911631it [00:02, 1718609.26it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai 5083701it [00:02, 1595271.84it/s] 5252490it [00:03, 1621237.50it/s] 5418292it [00:03, 1631730.77it/s] 5592243it [00:03, 1662970.15it/s] 5759373it [00:03, 1649402.99it/s] 5928475it [00:03, 1661568.60it/s] 6095068it [00:03, 1619389.65it/s] 6261136it [00:03, 1631369.71it/s] 6436410it [00:03, 1666986.56it/s] 6610085it [00:03, 1687562.32it/s] 6779111it [00:03, 1663641.52it/s] 6953367it [00:04, 1686765.22it/s] 7130017it [00:04, 1710297.21it/s] 7307593it [00:04, 1729734.98it/s] 7483130it [00:04, 1737347.71it/s] 7660575it [00:04, 1748400.77it/s] 7836764it [00:04, 1752384.46it/s] 7907517it [00:04, 1715799.80it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md -output aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/aih-tih-sc-18a6f2-R1_B23WHYVLT4_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 aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_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 aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_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 aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_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: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.md -output aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-18a6f2-R1_B23WHYVLT4_1/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1_full_basic_stats.tsv