Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/2b1613fd25c028ed511af70ba39c6e/GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz 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/20/bd3591537778e3285a9a6d2ed3e829/.command.sh 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/20/bd3591537778e3285a9a6d2ed3e829/.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-rnd-pltf-dev-nextflow-scratch-01/work/10/2b1613fd25c028ed511af70ba39c6e/GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai 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 GM24385_0001_RNA_0001_23H5VFLT4_s32 + all_qc -bam GM24385_0001_RNA_0001_23H5VFLT4_s32.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 GM24385_0001_RNA_0001_23H5VFLT4_s32 -reference ref_genome.fa -region chr20 mkdir -p GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/full_bed.bed seqtool depth -bam GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bam -bed GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/GM24385_0001_RNA_0001_23H5VFLT4_s32.md.depth.gz saturation_plot -bams GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bam -region chr20 -output GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/saturation_qc.tsv fragment_size -bams GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bam -region chr20 -output_prefix GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s32.md.mpileup && contamination -input GM24385_0001_RNA_0001_23H5VFLT4_s32.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.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: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai 0it [00:00, ?it/s] 136608it [00:00, 1365999.88it/s] 280063it [00:00, 1406279.91it/s] 428254it [00:00, 1440777.73it/s] 578555it [00:00, 1465259.19it/s] 728007it [00:00, 1475738.42it/s] 878882it [00:00, 1486929.53it/s] 1031910it [00:00, 1501079.18it/s] 1187469it [00:00, 1518409.33it/s] 1339310it [00:00, 1515164.53it/s] 1490828it [00:01, 1504856.55it/s] 1641329it [00:01, 1499825.63it/s] 1791323it [00:01, 1494130.02it/s] 1945783it [00:01, 1509288.14it/s] 2100235it [00:01, 1519818.47it/s] 2252235it [00:01, 1513327.53it/s] 2403584it [00:01, 1492451.00it/s] 2556289it [00:01, 1502684.93it/s] 2709800it [00:01, 1512210.55it/s] 2861072it [00:01, 1499981.96it/s] 3011180it [00:02, 1500151.35it/s] 3164595it [00:02, 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6961284it [00:05, 1052534.49it/s] 7066561it [00:05, 1046958.61it/s] 7171261it [00:05, 1041294.26it/s] 7275385it [00:05, 1038776.26it/s] 7379254it [00:05, 1035031.28it/s] 7484960it [00:05, 1041431.87it/s] 7589154it [00:06, 1041540.95it/s] 7694726it [00:06, 1045742.41it/s] 7799305it [00:06, 1042906.39it/s] 7905983it [00:06, 1050007.23it/s] 8024909it [00:06, 1091510.05it/s] 8176907it [00:06, 1219661.23it/s] 8327741it [00:06, 1306060.45it/s] 8477722it [00:06, 1364080.13it/s] 8628844it [00:06, 1408155.63it/s] 8779630it [00:06, 1437934.81it/s] 8929382it [00:07, 1455674.89it/s] 9080322it [00:07, 1471676.15it/s] 9232115it [00:07, 1485523.20it/s] 9382509it [00:07, 1490452.48it/s] 9532811it [00:07, 1494200.04it/s] 9682236it [00:07, 1436693.16it/s] 9826382it [00:07, 1398317.25it/s] 9974404it [00:07, 1421916.01it/s] 10118605it [00:07, 1427680.99it/s] 10261688it [00:07, 1422539.51it/s] 10417576it [00:08, 1462740.94it/s] 10573627it [00:08, 1491706.83it/s] 10727704it [00:08, 1506253.83it/s] 10878473it [00:08, 1490250.41it/s] 11027629it [00:08, 1489067.59it/s] 11180463it [00:08, 1500605.92it/s] 11303018it [00:08, 1307782.49it/s] [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai tabix -s 1 -b 2 -e 2 GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/GM24385_0001_RNA_0001_23H5VFLT4_s32.md.depth.gz seqtool depth_hist -nbins 500 GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/GM24385_0001_RNA_0001_23H5VFLT4_s32.md.depth.gz > GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/GM24385_0001_RNA_0001_23H5VFLT4_s32.md.depth_hist.tsv cat GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/GM24385_0001_RNA_0001_23H5VFLT4_s32.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title GM24385_0001_RNA_0001_23H5VFLT4_s32.md -output GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/GM24385_0001_RNA_0001_23H5VFLT4_s32.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 GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.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 GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/GM24385_0001_RNA_0001_23H5VFLT4_s32.md.depth.gz> GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.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 GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.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: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.md.bai cat GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "GM24385_0001_RNA_0001_23H5VFLT4_s32.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md/qc_complete.txt + merge_qc -folders GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32.md -output GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32_full_basic_stats.tsv + head -n1 GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed GM24385_0001_RNA_0001_23H5VFLT4_s32/GM24385_0001_RNA_0001_23H5VFLT4_s32_full_basic_stats.tsv