Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/a54da64b0d1af8c8bd15542567fbd9/659_bua-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/30/7c4688f9bcf609ebcf88882447527d/.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/30/7c4688f9bcf609ebcf88882447527d/.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/3a/a54da64b0d1af8c8bd15542567fbd9/659_bua-T1-TRNA-1_B23MHV2LT4_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 659_bua-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/659_bua-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai 157323it [00:00, 1573062.73it/s] 324325it [00:00, 1630035.40it/s] 494354it [00:00, 1662054.75it/s] 663704it [00:00, 1674426.47it/s] 834587it [00:00, 1686794.93it/s] 1004135it [00:00, 1689715.40it/s] 1173107it [00:00, 1686923.46it/s] 1342084it [00:00, 1687789.46it/s] 1510864it [00:00, 1669806.53it/s] 1677885it [00:01, 1629675.85it/s] 1841058it [00:01, 1483964.80it/s] 2000574it [00:01, 1515080.98it/s] 2168359it [00:01, 1561568.63it/s] 2337787it [00:01, 1600014.78it/s] 2511923it [00:01, 1641384.98it/s] 2691283it [00:01, 1686253.20it/s] 2866015it [00:01, 1704230.50it/s] 3037318it [00:01, 1706799.13it/s] 3208415it [00:01, 1707292.06it/s] 3379436it [00:02, 1699772.49it/s] 3549623it [00:02, 1700172.19it/s] 3720984it [00:02, 1704160.87it/s] 3891505it [00:02, 1679980.55it/s] 4059647it [00:02, 1666781.51it/s] 4234602it [00:02, 1691162.68it/s] 4405899it [00:02, 1697613.77it/s] 4576353it [00:02, 1699643.51it/s] 4749979it [00:02, 1710542.19it/s] 4922101it [00:02, 1713700.52it/s] 5093678it [00:03, 1714287.28it/s] 5265132it [00:03, 1711811.43it/s] 5439228it [00:03, 1720369.66it/s] 5611280it [00:03, 1697474.69it/s] 5781103it [00:03, 1686286.60it/s] 5949791it [00:03, 1659547.03it/s] 6118697it [00:03, 1668061.21it/s] 6290402it [00:03, 1682517.05it/s] 6464483it [00:03, 1699676.42it/s] 6636179it [00:03, 1704800.55it/s] 6808683it [00:04, 1710748.27it/s] 6982440it [00:04, 1718658.42it/s] 7155819it [00:04, 1723155.21it/s] 7328159it [00:04, 1721320.31it/s] 7500663it [00:04, 1722398.83it/s] 7672915it [00:04, 1722077.70it/s] 7845132it [00:04, 1719389.83it/s] 8020877it [00:04, 1730697.75it/s] 8196218it [00:04, 1737445.54it/s] 8371422it [00:04, 1741788.97it/s] 8547365it [00:05, 1747040.63it/s] 8726200it [00:05, 1759393.75it/s] 8902143it [00:05, 1753006.57it/s] 9077451it [00:05, 1709559.42it/s] 9248639it [00:05, 1674147.24it/s] 9420651it [00:05, 1687515.75it/s] 9591298it [00:05, 1693056.25it/s] 9762601it [00:05, 1698929.27it/s] 9932621it [00:05, 1686919.66it/s] 10107800it [00:05, 1706108.56it/s] 10281252it [00:06, 1714422.56it/s] 10452766it [00:06, 1711324.03it/s] 10625226it [00:06, 1715249.72it/s] 10802517it [00:06, 1732447.08it/s] 10976351it [00:06, 1734178.41it/s] 11149954it [00:06, 1734701.10it/s] 11324527it [00:06, 1737974.67it/s] 11498337it [00:06, 1733757.22it/s] 11671723it [00:06, 1727095.57it/s] 11844445it [00:07, 1662804.80it/s] 12014863it [00:07, 1674757.67it/s] 12186634it [00:07, 1687347.51it/s] 12360259it [00:07, 1701774.88it/s] 12538536it [00:07, 1725787.74it/s] 12713177it [00:07, 1731898.02it/s] 12887839it [00:07, 1736261.67it/s] 13062486it [00:07, 1739285.16it/s][W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai 13241545it [00:07, 1754606.90it/s] 13417058it [00:07, 1684411.02it/s] 13586126it [00:08, 1685156.91it/s] 13756404it [00:08, 1690301.73it/s] 13925754it [00:08, 1682595.36it/s] 14094236it [00:08, 1681680.22it/s] 14266941it [00:08, 1695107.70it/s] 14438023it [00:08, 1699760.14it/s] 14609865it [00:08, 1705301.31it/s] 14782616it [00:08, 1711830.03it/s] 14953847it [00:08, 1685161.35it/s] 14978869it [00:08, 1694111.82it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/659_bua-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/659_bua-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/659_bua-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/659_bua-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bua-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/659_bua-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-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_bua-T1-TRNA-1_B23MHV2LT4_1/659_bua-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv