Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/a079c3293495e6b0304c312fc5c9ff/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai 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/26/2b7976bdfa672b0ef2d2f758136b7c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/a079c3293495e6b0304c312fc5c9ff/A673_FFPE_RNA_0001_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-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/2b7976bdfa672b0ef2d2f758136b7c/.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 A673_FFPE_RNA_0001_B23LG7FLT4_1 + all_qc -bam A673_FFPE_RNA_0001_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 A673_FFPE_RNA_0001_B23LG7FLT4_1 -reference ref_genome.fa -region chr20 mkdir -p A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/full_bed.bed seqtool depth -bam A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -bed A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz saturation_plot -bams A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/saturation_qc.tsv fragment_size -bams A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output_prefix A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_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 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1.md.mpileup && contamination -input A673_FFPE_RNA_0001_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_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: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai 157903it [00:00, 1578952.45it/s] 323728it [00:00, 1625570.68it/s] 491333it [00:00, 1648602.91it/s] 662282it [00:00, 1672442.30it/s] 833810it [00:00, 1687854.29it/s] 1004571it [00:00, 1694557.58it/s] 1174952it [00:00, 1697569.55it/s] 1344709it [00:00, 1695989.50it/s] 1514309it [00:00, 1690743.17it/s] 1685474it [00:01, 1697167.53it/s] 1856301it [00:01, 1700541.21it/s] 2026359it [00:01, 1697786.37it/s] 2196636it [00:01, 1699281.28it/s] 2367922it [00:01, 1703363.92it/s] 2538261it [00:01, 1699329.06it/s] 2708903it [00:01, 1701282.28it/s] 2879035it [00:01, 1695781.67it/s] 3048748it [00:01, 1696062.40it/s] 3219591it [00:01, 1699756.04it/s] 3389571it [00:02, 1683805.47it/s] 3558146it [00:02, 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1700981.29it/s] 8669511it [00:05, 1697348.55it/s] 8840431it [00:05, 1700883.11it/s] 9010523it [00:05, 1700525.47it/s] 9180578it [00:05, 1697701.51it/s] 9350351it [00:05, 1696978.91it/s] 9520051it [00:05, 1690500.28it/s] 9691303it [00:05, 1697041.07it/s] 9861014it [00:05, 1696207.99it/s] 10030649it [00:05, 1696236.45it/s] 10200276it [00:06, 1693916.00it/s] 10369754it [00:06, 1694157.00it/s] 10539172it [00:06, 1680314.09it/s] 10709151it [00:06, 1686104.68it/s] 10881527it [00:06, 1697334.85it/s] 11051281it [00:06, 1696912.80it/s] 11223014it [00:06, 1703008.34it/s] 11394350it [00:06, 1706096.62it/s] 11568115it [00:06, 1715535.34it/s] 11739676it [00:06, 1713260.13it/s] 11911661it [00:07, 1715134.06it/s] 12083179it [00:07, 1711245.80it/s] 12254309it [00:07, 1709850.89it/s] 12425298it [00:07, 1703426.23it/s] 12597124it [00:07, 1707844.73it/s] 12767915it [00:07, 1702809.43it/s] 12938203it [00:07, 1700759.43it/s] 13108284it [00:07, 1698959.09it/s] 13278337it [00:07, 1699417.14it/s] 13448281it [00:07, 1697816.81it/s] 13619216it [00:08, 1701257.08it/s] 13789344it [00:08, 1694540.17it/s] 13958805it [00:08, 1681588.90it/s] 14126987it [00:08, 1676235.29it/s] 14294626it [00:08, 1674955.43it/s] 14462132it [00:08, 1674887.07it/s] 14550647it [00:08, 1694072.71it/s] [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai tabix -s 1 -b 2 -e 2 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz seqtool depth_hist -nbins 500 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv cat A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title A673_FFPE_RNA_0001_B23LG7FLT4_1.md -output A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_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 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_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 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_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 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/A673_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz> A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_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 A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_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: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai cat A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "A673_FFPE_RNA_0001_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md/qc_complete.txt + merge_qc -folders A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md -output A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv + head -n1 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv