Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/d7aa7634806624172b79dea4547fc8/.command.sh 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/c4/6a7b2e356432420f49d53a3cf94049/BreastNP_FFPE_L04_RNA_01_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-rnd-pltf-dev-nextflow-scratch-01/work/c4/6a7b2e356432420f49d53a3cf94049/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_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/09/d7aa7634806624172b79dea4547fc8/.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 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1 + all_qc -bam BreastNP_FFPE_L04_RNA_01_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 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1 -reference ref_genome.fa -region chr20 mkdir -p BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/full_bed.bed seqtool depth -bam BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam -bed BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.depth.gz fragment_size -bams BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam -region chr20 -output_prefix BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/fragsize -threads 1 saturation_plot -bams BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam -region chr20 -output BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/saturation_qc.tsv samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.mpileup && contamination -input BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_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: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai 0it [00:00, ?it/s] 62180it [00:00, 621713.14it/s] 126942it [00:00, 634608.67it/s] 196259it [00:00, 661262.59it/s] 264217it [00:00, 668456.95it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai 342136it [00:00, 708325.25it/s] 421728it [00:00, 738063.65it/s] 498569it [00:00, 747954.50it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai 580437it [00:00, 770439.52it/s] 667838it [00:00, 802781.86it/s] 750537it [00:01, 807240.62it/s] 831260it [00:01, 792558.19it/s] 910570it [00:01, 761474.33it/s] 986975it [00:01, 706740.59it/s] 1058469it [00:01, 700107.30it/s] 1129019it [00:01, 644729.89it/s] 1203022it [00:01, 670463.13it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai 1271067it [00:01, 670578.43it/s] 1343665it [00:01, 686245.17it/s] 1416458it [00:01, 698249.59it/s] 1487896it [00:02, 702934.62it/s] 1562180it [00:02, 714655.01it/s] 1633902it [00:02, 699921.34it/s] 1700726it [00:02, 713810.94it/s] [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai tabix -s 1 -b 2 -e 2 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.depth.gz seqtool depth_hist -nbins 500 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.depth.gz > BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv cat BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md -output BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L04_RNA_01_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 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_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 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_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 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.depth.gz> BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_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 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_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: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai cat BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md/qc_complete.txt + merge_qc -folders BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md -output BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv + head -n1 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv