Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/46cb1e6c507644a5e13c6a27819c8c/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.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/f0/6dc86f6435572c89bd7bb2714ae73a/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/46cb1e6c507644a5e13c6a27819c8c/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 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/f0/6dc86f6435572c89bd7bb2714ae73a/.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 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1 + all_qc -bam BreastNB_FFPE_L03_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 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1 -reference ref_genome.fa -region chr20 mkdir -p BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_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 > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/full_bed.bed seqtool depth -bam BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam -bed BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz saturation_plot -bams BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam -region chr20 -output BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/saturation_qc.tsv fragment_size -bams BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam -region chr20 -output_prefix BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_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 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.mpileup && contamination -input BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_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: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_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: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 117791it [00:00, 1177824.07it/s] 244802it [00:00, 1232072.69it/s] 374791it [00:00, 1263001.93it/s] 503333it [00:00, 1271824.95it/s] 632400it [00:00, 1278595.52it/s] 760260it [00:00, 1277897.22it/s] 888920it [00:00, 1280716.69it/s] 1018773it [00:00, 1286353.21it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 1147409it [00:00, 1286146.78it/s] 1276024it [00:01, 1276427.66it/s] 1403683it [00:01, 1275577.65it/s] 1531252it [00:01, 1266745.48it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 1657945it [00:01, 1260462.34it/s] 1786551it [00:01, 1268102.49it/s] 1914669it [00:01, 1271996.40it/s] 2044574it [00:01, 1280081.05it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 2174588it [00:01, 1286076.01it/s] 2303334it [00:01, 1286462.84it/s] 2431989it [00:01, 1284935.85it/s] 2562401it [00:02, 1290661.91it/s] 2691473it [00:02, 1286416.53it/s] 2820248it [00:02, 1286795.60it/s] 2948933it [00:02, 1286085.19it/s] 3078495it [00:02, 1288847.87it/s] 3207383it [00:02, 1204160.21it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 3328918it [00:02, 1155492.41it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 3454790it [00:02, 1184466.75it/s] 3580218it [00:02, 1204411.07it/s] 3656640it [00:02, 1257941.54it/s] [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai tabix -s 1 -b 2 -e 2 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz seqtool depth_hist -nbins 500 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv cat BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md -output BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L03_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 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_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 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_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 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz> BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_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 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_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: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai cat BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_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 "BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md/qc_complete.txt + merge_qc -folders BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md -output BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv + head -n1 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_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 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv