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/f0/ca19577faa75f36672226207c80d50/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/3a660e64d6089d3d18b9bf2b3930cd/aih-tih-sc-1d9134-R1_B23WHYVLT4_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-rnd-pltf-dev-nextflow-scratch-01/work/4a/3a660e64d6089d3d18b9bf2b3930cd/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai 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/f0/ca19577faa75f36672226207c80d50/.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 aih-tih-sc-1d9134-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai 151908it [00:00, 1518994.53it/s] 317690it [00:00, 1600612.93it/s] 485015it [00:00, 1633746.57it/s] 654251it [00:00, 1656845.92it/s] 825845it [00:00, 1678125.24it/s] 994546it [00:00, 1681121.98it/s] 1164286it [00:00, 1686346.74it/s] 1335141it [00:00, 1693392.14it/s] 1508241it [00:00, 1704996.35it/s] 1678741it [00:01, 1703647.59it/s] 1849106it [00:01, 1700061.01it/s] 2021731it [00:01, 1707850.18it/s] 2192519it [00:01, 1685046.51it/s] 2361655it [00:01, 1686912.64it/s] 2532704it [00:01, 1693939.59it/s] 2703279it [00:01, 1697455.11it/s] 2873054it [00:01, 1664298.35it/s] 3039638it [00:01, 1625454.41it/s] 3202438it [00:01, 1609059.93it/s] 3363517it [00:02, 1569827.32it/s] 3520740it [00:02, 1495042.72it/s] 3670950it [00:02, 1337255.05it/s] 3836376it [00:02, 1421183.17it/s] 4004354it [00:02, 1492107.13it/s] 4173947it [00:02, 1549487.67it/s] 4340915it [00:02, 1583945.31it/s] 4509135it [00:02, 1612368.84it/s] 4679130it [00:02, 1637938.57it/s] 4848118it [00:02, 1653169.49it/s] 5014182it [00:03, 1637695.44it/s] 5178496it [00:03, 1630695.10it/s] 5345888it [00:03, 1643448.42it/s] 5513265it [00:03, 1652418.60it/s] 5678715it [00:03, 1652432.35it/s] 5844132it [00:03, 1652917.28it/s] 6012447it [00:03, 1661795.50it/s] 6183870it [00:03, 1677458.38it/s] 6352349it [00:03, 1679625.47it/s] 6520352it [00:03, 1677870.26it/s] 6688168it [00:04, 1664766.46it/s] 6854686it [00:04, 1661019.47it/s] 7026014it [00:04, 1676444.01it/s] 7193688it [00:04, 1566160.77it/s] 7351759it [00:04, 1533544.41it/s] 7520870it [00:04, 1578351.40it/s] 7691560it [00:04, 1615417.12it/s] 7863664it [00:04, 1646249.33it/s] 8035347it [00:04, 1666927.62it/s] 8072219it [00:04, 1628846.90it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md -output aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1.md -output aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-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-1d9134-R1_B23WHYVLT4_1/aih-tih-sc-1d9134-R1_B23WHYVLT4_1_full_basic_stats.tsv