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/1e/5e06d055f9176537f30e7bdaf93187/.command.sh 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/fb/d7d2801b210e9db9056abad315e950/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 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/1e/5e06d055f9176537f30e7bdaf93187/.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/fb/d7d2801b210e9db9056abad315e950/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bam 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_CRL_T1_RNA_SLD_01_A23T55JLT4_1 + all_qc -bam 1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed saturation_plot -bams 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -region chr20 -output 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -bed 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_qc.tsv fragment_size -bams 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -region chr20 -output_prefix 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup && contamination -input 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 0it [00:00, ?it/s] 142084it [00:00, 1420492.52it/s] 296064it [00:00, 1490616.99it/s] 458913it [00:00, 1553529.91it/s] 623386it [00:00, 1589397.03it/s] 786574it [00:00, 1604682.73it/s] 952015it [00:00, 1621563.02it/s] 1116515it [00:00, 1629197.23it/s] 1282906it [00:00, 1640218.16it/s] 1448634it [00:00, 1645489.64it/s] 1614053it [00:01, 1648146.83it/s] 1778868it [00:01, 1638517.04it/s] 1943678it [00:01, 1641395.87it/s] 2110296it [00:01, 1648861.34it/s] 2279408it [00:01, 1661578.71it/s] 2447426it [00:01, 1667022.70it/s] 2615100it [00:01, 1669919.86it/s] 2782098it [00:01, 1641146.84it/s] 2950276it [00:01, 1653174.69it/s] 3115688it [00:01, 1648919.51it/s] 3280645it [00:02, 1618849.68it/s] 3442677it [00:02, 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1664697.64it/s] 17812990it [00:11, 1668227.86it/s] 17980815it [00:11, 1671196.95it/s] 18147946it [00:11, 1663321.31it/s] 18315398it [00:11, 1666490.01it/s] 18485634it [00:11, 1677182.11it/s] 18653696it [00:11, 1678184.79it/s] 18821524it [00:11, 1554030.42it/s] 18990519it [00:11, 1592551.27it/s] 19155214it [00:11, 1608077.01it/s] 19324682it [00:11, 1633320.48it/s] 19492468it [00:12, 1646396.17it/s] 19664145it [00:12, 1667191.11it/s] 19834508it [00:12, 1677917.17it/s] 20003532it [00:12, 1681566.70it/s] 20171925it [00:12, 1677996.58it/s] 20345281it [00:12, 1694557.81it/s] 20514862it [00:12, 1691102.42it/s] 20688753it [00:12, 1705357.18it/s] 20861295it [00:12, 1711284.69it/s] 21032473it [00:12, 1705324.14it/s] 21203044it [00:13, 1700318.24it/s] 21377029it [00:13, 1712098.68it/s] 21548265it [00:13, 1648069.20it/s] 21718402it [00:13, 1663575.26it/s] 21869929it [00:13, 1623415.05it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai tabix -s 1 -b 2 -e 2 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz seqtool depth_hist -nbins 500 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv cat 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz> 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md.bai cat 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md/qc_complete.txt + merge_qc -folders 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv + head -n1 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv