Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/2e9263d06d21050652c9fc2b0879ff/A673_FFPE_RNA_0001_B23LG7FLT4_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/4d/1d30c22abf4bf029871d09917e911c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/2e9263d06d21050652c9fc2b0879ff/A673_FFPE_RNA_0001_B23LG7FLT4_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-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/1d30c22abf4bf029871d09917e911c/.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 A673_FFPE_RNA_0001_B23LG7FLT4_1 + all_qc -bam A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_1 -reference ref_genome.fa -region chr20 mkdir -p A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/full_bed.bed seqtool depth -bam A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -bed A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz saturation_plot -bams A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/saturation_qc.tsv fragment_size -bams A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output_prefix A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1.md.mpileup && contamination -input A673_FFPE_RNA_0001_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_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: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai 0it [00:00, ?it/s] 83941it [00:00, 839318.75it/s] 171038it [00:00, 857900.69it/s] 258576it [00:00, 865851.01it/s] 345162it [00:00, 857366.51it/s] 436816it [00:00, 878508.76it/s] 524689it [00:00, 867182.54it/s] 611445it [00:00, 801665.39it/s] 695044it [00:00, 811911.41it/s] 784116it [00:00, 835479.84it/s] 874861it [00:01, 857008.87it/s] 964995it [00:01, 870275.67it/s] 1053559it [00:01, 874861.56it/s] 1142948it [00:01, 880526.18it/s] 1232099it [00:01, 883797.41it/s] 1320603it [00:01, 862538.83it/s] 1407049it [00:01, 832783.23it/s] 1490634it [00:01, 832061.83it/s] 1574052it [00:01, 823174.48it/s] 1659077it [00:01, 831056.24it/s] 1747146it [00:02, 845606.88it/s] 1831824it [00:02, 809438.42it/s] 1913140it [00:02, 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12394194it [00:14, 878464.51it/s] 12482081it [00:14, 877368.26it/s] 12570984it [00:14, 880831.94it/s] 12661160it [00:14, 887070.27it/s] 12749884it [00:15, 881621.94it/s] 12838065it [00:15, 872874.59it/s] 12925381it [00:15, 850668.03it/s] 13014946it [00:15, 863691.60it/s] 13102200it [00:15, 866279.75it/s] 13188917it [00:15, 857374.13it/s] 13276364it [00:15, 862396.50it/s] 13362663it [00:15, 846009.13it/s] 13451815it [00:15, 859353.57it/s] 13537846it [00:15, 855840.35it/s] 13625162it [00:16, 860946.69it/s] 13712618it [00:16, 864976.62it/s] 13799157it [00:16, 860622.99it/s] 13892289it [00:16, 881631.02it/s] 13980492it [00:16, 855919.64it/s] 14071064it [00:16, 870445.38it/s] 14158427it [00:16, 871368.35it/s] 14247493it [00:16, 877067.34it/s] 14337643it [00:16, 884314.32it/s] 14426143it [00:16, 868598.65it/s] 14515243it [00:17, 875188.36it/s] 14550647it [00:17, 850315.20it/s] [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai tabix -s 1 -b 2 -e 2 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz seqtool depth_hist -nbins 500 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv cat A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title A673_FFPE_RNA_0001_B23LG7FLT4_1.md -output A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz> A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_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: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai cat A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "A673_FFPE_RNA_0001_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/qc_complete.txt + merge_qc -folders A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md -output A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv + head -n1 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv