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/fb/2f82be859249429b5e15d23e19cd42/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/db656108731ba2de3a43e386ace28f/FFPE_HD789_01_RNA_13_B23MVV7LT4_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-rnd-pltf-dev-nextflow-scratch-01/work/79/db656108731ba2de3a43e386ace28f/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam 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/fb/2f82be859249429b5e15d23e19cd42/.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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1 + all_qc -bam FFPE_HD789_01_RNA_13_B23MVV7LT4_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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 mkdir -p FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/full_bed.bed seqtool depth -bam FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam -bed FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth.gz saturation_plot -bams FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam -region chr20 -output FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/saturation_qc.tsv fragment_size -bams FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam -region chr20 -output_prefix FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam > FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.mpileup && contamination -input FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_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: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai 90817it [00:00, 908092.92it/s] 225656it [00:00, 1148048.92it/s] 363869it [00:00, 1253719.76it/s] 508170it [00:00, 1328004.67it/s] 658928it [00:00, 1392087.33it/s] 798162it [00:00, 1366198.18it/s] 964142it [00:00, 1460775.68it/s] 1119233it [00:00, 1489157.90it/s] 1278189it [00:00, 1520294.94it/s] 1433222it [00:01, 1529489.25it/s] 1586270it [00:01, 1514547.26it/s] 1737822it [00:01, 1511178.08it/s] 1889006it [00:01, 1489635.61it/s] 2047480it [00:01, 1517869.99it/s] 2199381it [00:01, 1483762.05it/s] 2353425it [00:01, 1500281.17it/s] 2513208it [00:01, 1529088.20it/s] 2672683it [00:01, 1548550.76it/s] 2827689it [00:01, 1388158.88it/s] 2969657it [00:02, 1373740.71it/s] 3109176it [00:02, 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1629432.04it/s] 7698951it [00:05, 1609149.14it/s] 7860559it [00:05, 1611151.61it/s] 8021810it [00:05, 1606663.49it/s] 8182568it [00:05, 1602729.72it/s] 8349254it [00:05, 1621728.47it/s] 8516228it [00:05, 1635993.43it/s] 8685093it [00:05, 1651546.58it/s] 8853836it [00:05, 1662245.55it/s] 9021368it [00:06, 1666126.78it/s] 9191977it [00:06, 1678059.67it/s] 9359805it [00:06, 1672483.93it/s] 9527072it [00:06, 1667774.76it/s] 9695814it [00:06, 1673611.23it/s] 9863188it [00:06, 1673000.04it/s] 10031104it [00:06, 1674809.42it/s] 10198592it [00:06, 1660018.00it/s] 10364626it [00:06, 1638656.64it/s] 10534440it [00:06, 1656214.15it/s] 10704377it [00:07, 1669000.86it/s] 10872102it [00:07, 1671424.21it/s] 11039292it [00:07, 1671275.29it/s] 11208428it [00:07, 1677244.83it/s] 11379326it [00:07, 1686705.62it/s] 11548795it [00:07, 1689063.36it/s] 11717716it [00:07, 1688367.24it/s] 11886563it [00:07, 1658770.45it/s] 12052561it [00:07, 1652830.44it/s] 12221887it [00:07, 1664780.05it/s] 12388437it [00:08, 1548272.19it/s] 12553017it [00:08, 1575753.75it/s] 12719873it [00:08, 1602417.24it/s] 12881133it [00:08, 1594491.97it/s] 13045001it [00:08, 1607389.71it/s] 13212536it [00:08, 1627389.42it/s] 13378793it [00:08, 1637784.69it/s] 13542866it [00:08, 1623190.68it/s] 13705411it [00:08, 1606467.39it/s] 13866237it [00:09, 1499471.57it/s] 14030074it [00:09, 1538561.38it/s] 14193288it [00:09, 1565357.29it/s] 14357244it [00:09, 1586926.95it/s] 14524853it [00:09, 1613079.83it/s] 14687653it [00:09, 1617461.20it/s] 14849820it [00:09, 1615979.85it/s] 15018438it [00:09, 1636821.11it/s] 15185717it [00:09, 1647514.62it/s] 15301882it [00:09, 1541552.37it/s] [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai tabix -s 1 -b 2 -e 2 FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth.gz seqtool depth_hist -nbins 500 FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth.gz > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth_hist.tsv cat FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md -output FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth.gz> FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_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: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai cat FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/qc_complete.txt + merge_qc -folders FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md -output FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1_full_basic_stats.tsv