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/5b/891d8b49b678f18355de90381f876b/.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/15/0d44baeef2a729265f37c02c1337a3/659_bhK-T1-TRNA-1_A23MVY2LT4_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/5b/891d8b49b678f18355de90381f876b/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/0d44baeef2a729265f37c02c1337a3/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bam 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_bhK-T1-TRNA-1_A23MVY2LT4_1 + all_qc -bam 659_bhK-T1-TRNA-1_A23MVY2LT4_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_bhK-T1-TRNA-1_A23MVY2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/full_bed.bed seqtool depth -bam 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bam -bed 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz saturation_plot -bams 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bam -region chr20 -output 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bam -region chr20 -output_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_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_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.mpileup && contamination -input 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_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_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai 0it [00:00, ?it/s] 146332it [00:00, 1463237.67it/s] 309255it [00:00, 1560839.43it/s] 472516it [00:00, 1593576.52it/s] 639015it [00:00, 1621734.46it/s] 807573it [00:00, 1644729.18it/s] 976304it [00:00, 1659182.55it/s] 1143463it [00:00, 1663214.60it/s] 1313881it [00:00, 1676235.78it/s] 1481983it [00:00, 1677711.85it/s] 1650850it [00:01, 1681075.46it/s] 1819852it [00:01, 1683792.48it/s] 1988232it [00:01, 1678397.75it/s] 2156487it [00:01, 1679616.95it/s] 2329861it [00:01, 1695838.02it/s] 2500153it [00:01, 1697846.46it/s] 2669941it [00:01, 1692823.42it/s] 2839284it [00:01, 1692987.65it/s] 3011874it [00:01, 1702839.88it/s] 3182900it [00:01, 1704958.70it/s] 3353400it [00:02, 1673099.53it/s] 3521363it [00:02, 1675014.21it/s] 3690991it [00:02, 1681315.78it/s] 3859639it [00:02, 1682811.11it/s] 4027973it [00:02, 1671471.70it/s] 4195170it [00:02, 1668725.61it/s] 4362076it [00:02, 1666504.23it/s] 4528772it [00:02, 1666520.95it/s] 4695440it [00:02, 1664998.65it/s] 4862960it [00:02, 1667860.91it/s] 5029755it [00:03, 1644727.47it/s] 5197698it [00:03, 1654994.01it/s] 5365476it [00:03, 1661651.03it/s] 5533621it [00:03, 1667527.42it/s] 5704487it [00:03, 1679754.38it/s] 5873157it [00:03, 1681813.40it/s] 6041361it [00:03, 1678763.67it/s] 6209646it [00:03, 1679969.95it/s] 6378484it [00:03, 1682411.78it/s] 6546734it [00:03, 1675098.23it/s] 6714257it [00:04, 1665643.05it/s] 6886387it [00:04, 1682203.52it/s] 7057264it [00:04, 1690034.91it/s] 7231209it [00:04, 1704789.13it/s] 7404068it [00:04, 1711894.58it/s] 7575273it [00:04, 1710878.76it/s] 7746372it [00:04, 1708668.67it/s] 7917247it [00:04, 1702891.85it/s] 8087545it [00:04, 1694231.70it/s] 8256982it [00:04, 1692827.11it/s] 8427125it [00:05, 1695376.32it/s] 8596670it [00:05, 1688285.90it/s] 8767610it [00:05, 1694568.43it/s] 8937077it [00:05, 1677073.39it/s] 9108436it [00:05, 1687901.26it/s] 9280480it [00:05, 1697506.21it/s] 9453243it [00:05, 1706392.51it/s] 9624435it [00:05, 1708027.19it/s] 9795259it [00:05, 1704417.52it/s] 9965717it [00:05, 1697412.51it/s] 10135877it [00:06, 1698642.21it/s] 10305753it [00:06, 1698066.78it/s] 10475568it [00:06, 1693694.87it/s] 10644959it [00:06, 1693631.73it/s] 10814327it [00:06, 1693065.74it/s] 10983637it [00:06, 1692274.48it/s] 11152867it [00:06, 1687969.43it/s] 11321668it [00:06, 1683776.18it/s] 11490239it [00:06, 1684335.35it/s] 11660090it [00:06, 1688560.96it/s] 11828950it [00:07, 1683110.91it/s] 11997267it [00:07, 1682450.40it/s] 12124510it [00:07, 1681263.48it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz > 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.depth_hist.tsv cat 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md -output 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/659_bhK-T1-TRNA-1_A23MVY2LT4_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_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_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_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_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_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz> 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_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_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_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_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_1.md.bai cat 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bhK-T1-TRNA-1_A23MVY2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1.md -output 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv + head -n1 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bhK-T1-TRNA-1_A23MVY2LT4_1/659_bhK-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv