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/2c/52a8bbd0928a71f22facd49ea7e5b8/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/f75e2719d3e9d36bc6490dbb4a8d62/BreastNP_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.dict Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/f75e2719d3e9d36bc6490dbb4a8d62/BreastNP_FFPE_L03_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/2c/52a8bbd0928a71f22facd49ea7e5b8/.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_L03_RNA_01_B23LG7FLT4_1 + all_qc -bam BreastNP_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1 -reference ref_genome.fa -region chr20 mkdir -p BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_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 > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/full_bed.bed saturation_plot -bams BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam -region chr20 -output BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam -bed BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/saturation_qc.tsv fragment_size -bams BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam -region chr20 -output_prefix BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.mpileup && contamination -input BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: BreastNP_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: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_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: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 0it [00:00, ?it/s] 118808it [00:00, 1187948.02it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 237603it [00:00, 1159253.98it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 364830it [00:00, 1210143.91it/s] 493045it [00:00, 1238312.28it/s] 623276it [00:00, 1261054.77it/s] 751569it [00:00, 1268431.47it/s] 882192it [00:00, 1280728.37it/s] 1012640it [00:00, 1288245.35it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 1141488it [00:00, 1222810.77it/s] 1264438it [00:01, 1103954.54it/s] 1377177it [00:01, 1002129.15it/s] 1480230it [00:01, 950708.30it/s] 1577309it [00:01, 919732.65it/s] 1670537it [00:01, 893596.65it/s] 1760643it [00:01, 865708.46it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 1847647it [00:01, 853058.60it/s] 1933168it [00:01, 846774.85it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 2017952it [00:01, 828000.46it/s] 2101679it [00:02, 830587.58it/s] 2185841it [00:02, 833735.30it/s] 2269951it [00:02, 835765.05it/s] 2354200it [00:02, 837716.20it/s] 2438006it [00:02, 836938.83it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 2522006it [00:02, 837770.22it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 2608362it [00:02, 845417.73it/s] 2694949it [00:02, 851405.65it/s] 2781965it [00:02, 856910.88it/s] 2867670it [00:02, 855799.95it/s] 2953260it [00:03, 855442.16it/s] 3040295it [00:03, 859875.53it/s] 3127694it [00:03, 864029.92it/s] 3215240it [00:03, 867413.90it/s] 3301986it [00:03, 867042.58it/s] 3388693it [00:03, 863755.76it/s] 3475209it [00:03, 864056.37it/s] 3561734it [00:03, 864380.53it/s] 3648175it [00:03, 857626.09it/s] 3733951it [00:03, 845290.13it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 3819220it [00:04, 847458.93it/s] 3907709it [00:04, 858547.64it/s] 3994208it [00:04, 860429.75it/s] 4081610it [00:04, 864464.41it/s] 4170692it [00:04, 872315.74it/s] 4258763it [00:04, 874804.68it/s] 4346797it [00:04, 876431.84it/s] 4434450it [00:04, 872069.15it/s] 4521668it [00:04, 866899.18it/s] 4609630it [00:04, 870615.58it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai 4697909it [00:05, 874221.93it/s] 4785721it [00:05, 875366.75it/s] 4861965it [00:05, 920416.71it/s] [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai tabix -s 1 -b 2 -e 2 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz seqtool depth_hist -nbins 500 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv cat BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md -output BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz> BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_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: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai cat BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_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 "BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_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` > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/qc_complete.txt + merge_qc -folders BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md -output BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv + head -n1 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv