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/04/01b9f29fb12fa74e719915afaa3459/.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/58/6edd781c757f8d46f3202100ea9e9e/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.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/04/01b9f29fb12fa74e719915afaa3459/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/6edd781c757f8d46f3202100ea9e9e/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2 + all_qc -bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2 -reference ref_genome.fa -region chr20 mkdir -p 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/full_bed.bed seqtool depth -bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz saturation_plot -bams 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -region chr20 -output 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/saturation_qc.tsv fragment_size -bams 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -region chr20 -output_prefix 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.mpileup && contamination -input 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.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: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 0it [00:00, ?it/s] 163639it [00:00, 1636301.83it/s] 332400it [00:00, 1666441.31it/s] 499045it [00:00, 1661244.75it/s] 671294it [00:00, 1685216.74it/s] 844379it [00:00, 1701475.16it/s] 1016690it [00:00, 1708799.94it/s] 1190212it [00:00, 1717408.34it/s] 1364319it [00:00, 1724909.54it/s] 1536813it [00:00, 1724309.30it/s] 1710261it [00:01, 1727425.39it/s] 1884490it [00:01, 1731951.01it/s] 2057687it [00:01, 1731102.45it/s] 2232577it [00:01, 1736469.15it/s] 2406442it [00:01, 1737043.10it/s] 2580147it [00:01, 1736613.98it/s] 2753809it [00:01, 1734252.49it/s] 2927236it [00:01, 1698719.46it/s] 3105876it [00:01, 1724639.26it/s] 3278491it [00:01, 1713643.83it/s] 3449967it [00:02, 1701767.42it/s] 3621083it 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1721521.91it/s] 8715816it [00:05, 1722249.61it/s] 8889292it [00:05, 1725949.80it/s] 9061937it [00:05, 1712462.43it/s] 9233420it [00:05, 1713142.07it/s] 9406656it [00:05, 1718857.55it/s] 9580888it [00:05, 1725848.50it/s] 9754272it [00:05, 1728209.29it/s] 9928974it [00:05, 1733816.07it/s] 10102369it [00:05, 1730074.13it/s] 10275387it [00:06, 1728529.86it/s] 10448248it [00:06, 1727359.80it/s] 10621208it [00:06, 1727995.21it/s] 10794012it [00:06, 1722638.66it/s] 10966282it [00:06, 1715742.28it/s] 11140214it [00:06, 1722754.67it/s] 11312499it [00:06, 1713555.63it/s] 11488767it [00:06, 1728170.84it/s] 11661813it [00:06, 1728826.75it/s] 11834710it [00:06, 1724416.49it/s] 12009922it [00:07, 1732667.94it/s] 12183200it [00:07, 1730384.10it/s] 12357339it [00:07, 1733650.86it/s] 12531012it [00:07, 1734543.50it/s] 12704471it [00:07, 1731038.02it/s] 12879264it [00:07, 1736066.56it/s] 13053297it [00:07, 1737227.30it/s] 13227023it [00:07, 1736952.21it/s] 13400721it [00:07, 1736087.71it/s] 13574332it [00:07, 1713300.81it/s] 13747118it [00:08, 1717600.04it/s] 13918929it [00:08, 1717037.80it/s] 14090669it [00:08, 1710949.80it/s] 14261791it [00:08, 1706849.80it/s] 14432495it [00:08, 1706649.78it/s] 14606058it [00:08, 1715167.39it/s] 14777588it [00:08, 1712259.03it/s] 14948823it [00:08, 1673787.34it/s] 15119679it [00:08, 1684005.06it/s][W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 15291164it [00:08, 1693114.18it/s] 15460592it [00:09, 1679537.49it/s] 15628642it [00:09, 1668743.77it/s] 15801873it [00:09, 1687540.75it/s] 15973535it [00:09, 1696125.80it/s] 16145464it [00:09, 1703000.21it/s] 16163795it [00:09, 1699344.06it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai tabix -s 1 -b 2 -e 2 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz seqtool depth_hist -nbins 500 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.depth_hist.tsv cat 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz> 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.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: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md.bai cat 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md/qc_complete.txt + merge_qc -folders 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv + head -n1 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv