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/8d/70f025ceed0e460b2324b3bccff693/.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/9b/153688ee2989d879459907d9e5bc17/aih-tih-sc-6734d6-R1_A23WJ53LT4_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/8d/70f025ceed0e460b2324b3bccff693/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/153688ee2989d879459907d9e5bc17/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bam 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-6734d6-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai 0it [00:00, ?it/s] 160118it [00:00, 1600746.45it/s] 328920it [00:00, 1652039.65it/s] 504374it [00:00, 1698809.34it/s] 678377it [00:00, 1715056.71it/s] 852480it [00:00, 1724372.64it/s] 1025984it [00:00, 1727936.90it/s] 1199734it [00:00, 1731040.73it/s] 1373949it [00:00, 1734447.43it/s] 1549430it [00:00, 1740792.30it/s] 1723510it [00:01, 1738143.26it/s] 1899291it [00:01, 1744133.28it/s] 2076053it [00:01, 1751252.84it/s] 2251180it [00:01, 1748058.50it/s] 2427612it [00:01, 1752942.45it/s] 2602909it [00:01, 1749586.68it/s] 2777871it [00:01, 1748940.93it/s] 2952767it [00:01, 1747049.23it/s] 3127810it [00:01, 1748041.09it/s] 3302616it [00:01, 1744772.25it/s] 3477096it [00:02, 1718518.50it/s] 3656280it [00:02, 1740227.68it/s] 3830389it [00:02, 1736139.58it/s] 4004062it [00:02, 1712662.01it/s] 4180278it [00:02, 1727271.49it/s] 4355492it [00:02, 1734633.98it/s] 4529027it [00:02, 1730239.58it/s] 4703232it [00:02, 1733741.19it/s] 4879062it [00:02, 1741050.85it/s] 5053197it [00:02, 1739328.24it/s] 5229200it [00:03, 1745488.61it/s] 5403766it [00:03, 1736842.61it/s] 5577470it [00:03, 1724110.94it/s] 5752008it [00:03, 1730414.61it/s] 5925312it [00:03, 1731111.76it/s] 6100202it [00:03, 1736405.90it/s] 6273858it [00:03, 1733081.13it/s] 6447178it [00:03, 1727383.38it/s] 6619927it [00:03, 1714436.45it/s] 6791395it [00:03, 1699196.12it/s] 6961350it [00:04, 1694625.17it/s] 7131034it [00:04, 1695263.90it/s] 7300577it [00:04, 1692255.02it/s] 7470530it [00:04, 1694397.40it/s] 7640882it [00:04, 1697099.28it/s] 7813599it [00:04, 1706073.93it/s] 7984500it [00:04, 1706838.76it/s] 8157609it [00:04, 1713932.72it/s] 8329024it [00:04, 1713981.17it/s] 8502300it [00:04, 1719508.54it/s] 8676110it [00:05, 1724893.05it/s] 8851690it [00:05, 1734145.91it/s] 9027281it [00:05, 1740588.59it/s] 9201342it [00:05, 1736036.04it/s] 9375608it [00:05, 1737999.82it/s] 9549606it [00:05, 1738576.14it/s] 9723466it [00:05, 1734158.92it/s] 9897264it [00:05, 1735284.31it/s] 10070796it [00:05, 1730762.70it/s] 10244429it [00:05, 1732412.22it/s] 10417674it [00:06, 1727879.60it/s] 10590467it [00:06, 1725464.63it/s] 10765965it [00:06, 1734274.23it/s] 10939599it [00:06, 1734865.77it/s] 11115442it [00:06, 1741901.51it/s] 11290433it [00:06, 1744279.33it/s] 11464864it [00:06, 1725282.28it/s] 11641269it [00:06, 1736794.01it/s] 11816588it [00:06, 1741598.17it/s] 11991445it [00:06, 1743659.31it/s] 12167958it [00:07, 1750065.03it/s] 12342983it [00:07, 1745871.29it/s] 12517585it [00:07, 1738472.58it/s] 12691448it [00:07, 1730136.29it/s] 12866442it [00:07, 1736011.68it/s] 13041183it [00:07, 1739352.96it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai 13215131it [00:07, 1734544.99it/s] 13388596it [00:07, 1722838.15it/s] 13560901it [00:07, 1701917.38it/s] 13731150it [00:07, 1700670.78it/s] 13903975it [00:08, 1708712.42it/s] 14075717it [00:08, 1711286.46it/s] 14246873it [00:08, 1708647.66it/s] 14417756it [00:08, 1674678.97it/s] 14588113it [00:08, 1683175.32it/s] 14759095it [00:08, 1691050.19it/s] 14929221it [00:08, 1694069.32it/s] 15101377it [00:08, 1702246.72it/s] 15272444it [00:08, 1704744.06it/s] 15446863it [00:08, 1716518.63it/s] 15618545it [00:09, 1706396.80it/s] 15791042it [00:09, 1711913.50it/s] 15964735it [00:09, 1719348.79it/s] 16137792it [00:09, 1722589.52it/s] 16311765it [00:09, 1727703.36it/s] 16319445it [00:09, 1724848.36it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md -output aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1.md -output aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_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-6734d6-R1_A23WJ53LT4_1/aih-tih-sc-6734d6-R1_A23WJ53LT4_1_full_basic_stats.tsv