Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/818f69b5d637b0af4b7188bb507d94/659_bNS-T1-TRNA-1_B23MHV2LT4_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/cb/a6e32164572ea0cb98f1c5ee3fe63d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/818f69b5d637b0af4b7188bb507d94/659_bNS-T1-TRNA-1_B23MHV2LT4_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/cb/a6e32164572ea0cb98f1c5ee3fe63d/.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 659_bNS-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bNS-T1-TRNA-1_B23MHV2LT4_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 659_bNS-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_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: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 150761it [00:00, 1507528.77it/s] 316500it [00:00, 1595348.01it/s] 485348it [00:00, 1637746.41it/s] 654417it [00:00, 1658624.19it/s] 825437it [00:00, 1677203.04it/s] 994044it [00:00, 1680197.74it/s] 1165241it [00:00, 1690563.76it/s] 1335873it [00:00, 1695563.36it/s] 1506191it [00:00, 1697927.14it/s] 1676017it [00:01, 1698012.90it/s] 1845985it [00:01, 1698507.49it/s] 2015836it [00:01, 1698263.64it/s] 2186348it [00:01, 1700323.72it/s] 2362211it [00:01, 1717916.64it/s] 2534003it [00:01, 1714397.10it/s] 2705445it [00:01, 1712990.41it/s] 2876746it [00:01, 1710512.62it/s] 3050587it [00:01, 1718860.81it/s] 3224704it [00:01, 1725534.32it/s] 3397261it [00:02, 1701543.33it/s] 3567491it [00:02, 1700330.91it/s] 3739581it [00:02, 1706429.89it/s] 3910265it [00:02, 1705404.97it/s] 4080834it [00:02, 1697492.85it/s] 4250609it [00:02, 1697315.43it/s] 4420358it [00:02, 1696073.40it/s] 4590673it [00:02, 1698037.82it/s] 4760993it [00:02, 1699562.27it/s] 4930956it [00:02, 1696231.01it/s] 5100585it [00:03, 1690606.37it/s] 5270389it [00:03, 1692804.66it/s] 5441632it [00:03, 1698654.75it/s] 5611820it [00:03, 1699601.39it/s] 5782408it [00:03, 1701462.04it/s] 5952558it [00:03, 1701307.36it/s] 6122691it [00:03, 1692021.40it/s] 6292159it [00:03, 1692794.27it/s] 6461448it [00:03, 1686572.19it/s] 6630116it [00:03, 1686471.60it/s] 6798770it [00:04, 1678999.02it/s] 6968452it [00:04, 1684299.73it/s] 7141110it [00:04, 1696920.98it/s] 7312995it [00:04, 1703465.38it/s] 7486395it [00:04, 1712592.96it/s] 7659969it [00:04, 1719511.08it/s] 7831928it [00:04, 1718973.87it/s] 8003831it [00:04, 1716409.23it/s] 8175477it [00:04, 1715713.13it/s] 8347052it [00:04, 1713778.51it/s] 8518433it [00:05, 1709352.27it/s] 8689372it [00:05, 1708007.31it/s] 8860886it [00:05, 1710123.49it/s] 9031901it [00:05, 1706207.38it/s] 9206590it [00:05, 1718227.23it/s] 9379384it [00:05, 1720979.37it/s] 9553171it [00:05, 1726025.64it/s] 9726209it [00:05, 1727317.44it/s] 9898944it [00:05, 1722903.39it/s] 10071239it [00:05, 1717074.45it/s] 10242953it [00:06, 1714013.83it/s] 10416544it [00:06, 1720541.77it/s] 10588604it [00:06, 1717366.49it/s] 10760346it [00:06, 1715541.14it/s] 10931904it [00:06, 1713850.88it/s] 11103292it [00:06, 1712666.65it/s] 11274560it [00:06, 1707323.45it/s] 11446594it [00:06, 1711053.91it/s] 11620000it [00:06, 1717920.89it/s] 11791797it [00:06, 1716610.21it/s] 11963568it [00:07, 1716925.30it/s] 12135263it [00:07, 1715618.29it/s] 12229420it [00:07, 1703508.34it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_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 2 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_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 2 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_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 2 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_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: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bNS-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv