Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/7011b0e6abc29d062de47eb63b19ce/BreastNB_FFPE_L01_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-rnd-pltf-dev-nextflow-scratch-01/work/8d/a3b5141ff9d51b382b710f012c2281/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/7011b0e6abc29d062de47eb63b19ce/BreastNB_FFPE_L01_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/8d/a3b5141ff9d51b382b710f012c2281/.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_L01_RNA_01_B23LG7FLT4_1 + all_qc -bam BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1 -reference ref_genome.fa -region chr20 mkdir -p BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/full_bed.bed seqtool depth -bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam -bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth.gz saturation_plot -bams BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam -region chr20 -output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/saturation_qc.tsv fragment_size -bams BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam -region chr20 -output_prefix BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.mpileup && contamination -input BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1.md.bai 0it [00:00, ?it/s] 94199it [00:00, 941901.07it/s] 212187it [00:00, 1081839.84it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai 329790it [00:00, 1124806.06it/s] 444996it [00:00, 1135527.04it/s] 558549it [00:00, 1042026.06it/s] 663943it [00:00, 991930.88it/s] 764148it [00:00, 947669.32it/s] 859718it [00:00, 909133.04it/s] 955218it [00:00, 922195.98it/s] 1055830it [00:01, 946472.28it/s] 1156859it [00:01, 965123.22it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai 1259240it [00:01, 982361.43it/s] 1375767it [00:01, 1036532.28it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai 1492627it [00:01, 1075788.44it/s] 1615816it [00:01, 1122310.04it/s] 1734570it [00:01, 1141697.09it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai 1856667it [00:01, 1165382.32it/s] 1977491it [00:01, 1178190.31it/s] 2097643it [00:01, 1185157.71it/s] 2216242it [00:02, 1157373.13it/s] 2332178it [00:02, 1114637.70it/s] 2444061it [00:02, 1099418.30it/s] 2530074it [00:02, 1061376.33it/s] [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai tabix -s 1 -b 2 -e 2 BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth.gz seqtool depth_hist -nbins 500 BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth.gz > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv cat BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md -output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth.gz> BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai cat BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/qc_complete.txt + merge_qc -folders BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md -output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv + head -n1 BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_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_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv