Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/0a480b68974d6270a7bd11f47d6bc4/aih-tih-sc-070e1d-R1_B23WHYVLT4_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/13/b1507f3bfa0a300e71d3a13b929c97/.command.sh 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/13/b1507f3bfa0a300e71d3a13b929c97/.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/e9/0a480b68974d6270a7bd11f47d6bc4/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bam 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-070e1d-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 140716it [00:00, 1407087.54it/s] 307955it [00:00, 1563110.30it/s] 472473it [00:00, 1600551.76it/s] 634206it [00:00, 1607148.82it/s] 798857it [00:00, 1621317.83it/s] 963048it [00:00, 1628298.39it/s] 1130349it [00:00, 1642894.01it/s] 1296214it [00:00, 1647894.07it/s] 1463919it [00:00, 1656992.86it/s] 1630944it [00:01, 1661070.11it/s] 1803346it [00:01, 1680320.13it/s] 1971379it [00:01, 1678620.39it/s] 2139242it [00:01, 1662906.32it/s] 2305565it [00:01, 1645504.98it/s] 2473125it [00:01, 1654451.42it/s] 2638618it [00:01, 1643220.86it/s] 2802982it [00:01, 1639324.85it/s] 2966942it [00:01, 1631312.92it/s] 3130094it [00:01, 1628978.71it/s] 3293005it [00:02, 1584337.69it/s] 3451685it [00:02, 1523798.08it/s] 3604613it [00:02, 1515997.89it/s] 3767637it [00:02, 1549031.08it/s] 3931489it [00:02, 1575183.27it/s] 4092782it [00:02, 1586291.64it/s] 4257687it [00:02, 1604862.05it/s] 4419460it [00:02, 1608672.89it/s] 4581808it [00:02, 1613071.91it/s] 4743732it [00:02, 1614861.84it/s] 4911806it [00:03, 1634428.67it/s] 5077243it [00:03, 1640377.24it/s] 5244834it [00:03, 1651005.61it/s] 5411166it [00:03, 1654680.98it/s] 5583833it [00:03, 1676231.49it/s] 5758508it [00:03, 1697352.74it/s] 5931675it [00:03, 1707621.12it/s] 6104414it [00:03, 1713528.51it/s] 6278627it [00:03, 1722086.71it/s] 6453810it [00:03, 1730987.76it/s] 6626913it [00:04, 1714221.17it/s] 6798375it [00:04, 1702893.88it/s] 6970610it [00:04, 1708517.18it/s] 7141494it [00:04, 1700166.05it/s] 7311537it [00:04, 1694964.06it/s] 7481298it [00:04, 1695730.39it/s] 7650885it [00:04, 1669256.34it/s] 7817900it [00:04, 1639475.12it/s] 7981990it [00:04, 1632739.66it/s] 8145355it [00:04, 1631426.39it/s] 8308559it [00:05, 1624153.44it/s] 8471015it [00:05, 1611152.34it/s] 8632637it [00:05, 1612633.38it/s] 8793928it [00:05, 1605702.99it/s] 8956946it [00:05, 1612951.90it/s] 9119164it [00:05, 1615581.24it/s] 9282456it [00:05, 1620736.78it/s] 9444544it [00:05, 1603905.55it/s] 9606737it [00:05, 1609245.26it/s] 9768583it [00:05, 1611973.83it/s] 9929808it [00:06, 1608662.92it/s] 10090694it [00:06, 1599550.43it/s] 10251427it [00:06, 1601851.54it/s] 10412170it [00:06, 1603499.71it/s] 10573505it [00:06, 1606427.27it/s] 10734158it [00:06, 1595344.47it/s] 10893715it [00:06, 1587008.35it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai 11052436it [00:06, 1586525.27it/s] 11211103it [00:06, 1580263.21it/s] 11369271it [00:06, 1580672.23it/s] 11530657it [00:07, 1590563.85it/s] 11693161it [00:07, 1600854.05it/s] 11854408it [00:07, 1604310.17it/s] 12016437it [00:07, 1609079.09it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai 12180906it [00:07, 1619734.82it/s] 12346048it [00:07, 1629216.41it/s] 12491187it [00:07, 1629487.48it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md -output aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1.md -output aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-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-070e1d-R1_B23WHYVLT4_1/aih-tih-sc-070e1d-R1_B23WHYVLT4_1_full_basic_stats.tsv