Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/cbe97971bb7a8dda6ad832113e1794/1173_FM_T1_RNA_SLD_01_A23T55JLT4_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/8b/49a14ee615eada2269b23311e4ce2f/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/cbe97971bb7a8dda6ad832113e1794/1173_FM_T1_RNA_SLD_01_A23T55JLT4_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/8b/49a14ee615eada2269b23311e4ce2f/.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 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1 + all_qc -bam 1173_FM_T1_RNA_SLD_01_A23T55JLT4_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 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed saturation_plot -bams 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -region chr20 -output 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -bed 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_qc.tsv fragment_size -bams 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -region chr20 -output_prefix 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup && contamination -input 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_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: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 0it [00:00, ?it/s] 153526it [00:00, 1535173.62it/s] 325444it [00:00, 1643362.68it/s] 500997it [00:00, 1694546.72it/s] 678136it [00:00, 1724849.27it/s] 855375it [00:00, 1741964.42it/s] 1031834it [00:00, 1749624.84it/s] 1208146it [00:00, 1754011.15it/s] 1385267it [00:00, 1759462.77it/s] 1561641it [00:00, 1760774.13it/s] 1739567it [00:01, 1766459.34it/s] 1916213it [00:01, 1766356.95it/s] 2094419it [00:01, 1771111.08it/s] 2271531it [00:01, 1767449.52it/s] 2448278it [00:01, 1764193.40it/s] 2624768it [00:01, 1764383.63it/s] 2804250it [00:01, 1773506.38it/s] 2983421it [00:01, 1778838.10it/s] 3162524it [00:01, 1782477.30it/s] 3340774it [00:01, 1774885.20it/s] 3518271it [00:02, 1764478.56it/s] 3694736it [00:02, 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[00:07, 1752323.53it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai tabix -s 1 -b 2 -e 2 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz seqtool depth_hist -nbins 500 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz > 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv cat 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_FM_T1_RNA_SLD_01_A23T55JLT4_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 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_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 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz> 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_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 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_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: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md.bai cat 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md/qc_complete.txt + merge_qc -folders 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv + head -n1 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv