Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/3a845f35d2b449c4f225bd8029ff40/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam 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/11/356aba0b44941bdb1ff909497fd1b2/.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/11/356aba0b44941bdb1ff909497fd1b2/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/3a845f35d2b449c4f225bd8029ff40/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai 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_2 + all_qc -bam A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_2 -reference ref_genome.fa -region chr20 mkdir -p A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.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_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/full_bed.bed seqtool depth -bam A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam -bed A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth.gz saturation_plot -bams A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam -region chr20 -output A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/saturation_qc.tsv fragment_size -bams A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam -region chr20 -output_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.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_2.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_2.md.mpileup && contamination -input A673_FFPE_RNA_0001_B23LG7FLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.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_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_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: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai 0it [00:00, ?it/s] 113865it [00:00, 1138558.79it/s] 229886it [00:00, 1151249.82it/s] 345011it [00:00, 1142600.56it/s] 460178it [00:00, 1145983.63it/s] 575926it [00:00, 1150094.44it/s] 691481it [00:00, 1151925.46it/s] 807399it [00:00, 1154272.68it/s] 923642it [00:00, 1156833.26it/s] 1039856it [00:00, 1158473.34it/s] 1156302it [00:01, 1160302.23it/s] 1272334it [00:01, 1156482.37it/s] 1389141it [00:01, 1159981.24it/s] 1505143it [00:01, 1155435.76it/s] 1621232it [00:01, 1157061.20it/s] 1737286it [00:01, 1158091.45it/s] 1853751it [00:01, 1160047.07it/s] 1970371it [00:01, 1161876.73it/s] 2086827it [00:01, 1162665.09it/s] 2203096it [00:01, 1161932.08it/s] 2319291it [00:02, 1150357.61it/s] 2434353it [00:02, 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[00:10, 1155173.35it/s] 12641129it [00:10, 1159815.63it/s] 12757115it [00:11, 1158717.85it/s] 12872990it [00:11, 1157497.62it/s] 12988778it [00:11, 1157595.84it/s] 13104591it [00:11, 1157729.67it/s] 13220434it [00:11, 1157924.93it/s] 13336343it [00:11, 1158258.73it/s] 13452657it [00:11, 1159706.71it/s] 13568973it [00:11, 1160725.11it/s] 13685220it [00:11, 1161232.12it/s] 13801344it [00:11, 1158628.33it/s] 13917209it [00:12, 1157004.42it/s] 14032911it [00:12, 1156337.66it/s] 14148546it [00:12, 1150623.22it/s] 14263726it [00:12, 1150962.59it/s] 14378827it [00:12, 1148631.29it/s] 14494067it [00:12, 1149747.28it/s] 14564283it [00:12, 1155100.79it/s] [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai tabix -s 1 -b 2 -e 2 A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth.gz seqtool depth_hist -nbins 500 A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth.gz > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth_hist.tsv cat A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title A673_FFPE_RNA_0001_B23LG7FLT4_2.md -output A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.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_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/A673_FFPE_RNA_0001_B23LG7FLT4_2.md.depth.gz> A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_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: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai cat A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.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_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.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_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md/qc_complete.txt + merge_qc -folders A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md -output A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv + head -n1 A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2_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_2/A673_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv