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/0f/03f5a1a0ef5a86fa0e544c3a15ea8a/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/40017f562c364c231d4b4714b754bd/659_bGc-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/3a/40017f562c364c231d4b4714b754bd/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/03f5a1a0ef5a86fa0e544c3a15ea8a/.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_bGc-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 156013it [00:00, 1560045.94it/s] 323584it [00:00, 1627774.84it/s] 494481it [00:00, 1664819.55it/s] 666368it [00:00, 1686133.21it/s] 838364it [00:00, 1698303.51it/s] 1010715it [00:00, 1706851.73it/s] 1184931it [00:00, 1718368.10it/s] 1357356it [00:00, 1720221.48it/s] 1529379it [00:00, 1719687.63it/s] 1702304it [00:01, 1722619.25it/s] 1874567it [00:01, 1715864.46it/s] 2047888it [00:01, 1721109.17it/s] 2221549it [00:01, 1725777.37it/s] 2400381it [00:01, 1744623.47it/s] 2574850it [00:01, 1740656.15it/s] 2748922it [00:01, 1735313.27it/s] 2922461it [00:01, 1728142.06it/s] 3098160it [00:01, 1736744.56it/s] 3275138it [00:01, 1746611.04it/s] 3449811it [00:02, 1720835.94it/s] 3622170it [00:02, 1721632.26it/s] 3796591it [00:02, 1728297.47it/s] 3970421it [00:02, 1731233.27it/s] 4143924it [00:02, 1732343.44it/s] 4317185it [00:02, 1730481.08it/s] 4490252it [00:02, 1727359.42it/s] 4663494it [00:02, 1728847.27it/s] 4836389it [00:02, 1717622.62it/s] 5009752it [00:02, 1722376.14it/s] 5184624it [00:03, 1730187.66it/s] 5357659it [00:03, 1726743.55it/s] 5531535it [00:03, 1730270.80it/s] 5704572it [00:03, 1728336.67it/s] 5877413it [00:03, 1716549.97it/s] 6049089it [00:03, 1713345.50it/s] 6220575it [00:03, 1713768.39it/s] 6391962it [00:03, 1708236.40it/s] 6562862it [00:03, 1708301.89it/s] 6733699it [00:03, 1707406.56it/s] 6904444it [00:04, 1702708.76it/s] 7075576it [00:04, 1705264.02it/s] 7247591it [00:04, 1709589.67it/s] 7419010it [00:04, 1710798.94it/s] 7592625it [00:04, 1718373.78it/s] 7764805it [00:04, 1719383.86it/s] 7940869it [00:04, 1731614.62it/s] 8117030it [00:04, 1740591.14it/s] 8291092it [00:04, 1735585.90it/s] 8464656it [00:04, 1733211.79it/s] 8637981it [00:05, 1732694.65it/s] 8811253it [00:05, 1730532.36it/s] 8984309it [00:05, 1725678.04it/s] 9156881it [00:05, 1711287.16it/s] 9333367it [00:05, 1727208.13it/s] 9508887it [00:05, 1735540.87it/s] 9682468it [00:05, 1733737.23it/s] 9858293it [00:05, 1741049.85it/s] 10032414it [00:05, 1739063.54it/s] 10206332it [00:05, 1736161.03it/s] 10379957it [00:06, 1731487.53it/s] 10555659it [00:06, 1739099.75it/s] 10729578it [00:06, 1737861.69it/s] 10903428it [00:06, 1737994.93it/s] 11077232it [00:06, 1736386.06it/s] 11250874it [00:06, 1732368.62it/s] 11424115it [00:06, 1729824.19it/s] 11599087it [00:06, 1735758.86it/s] 11772667it [00:06, 1734068.73it/s] 11949307it [00:06, 1743729.75it/s] 12123684it [00:07, 1740257.51it/s] 12297714it [00:07, 1739867.28it/s] 12458173it [00:07, 1724991.56it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-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_bGc-T1-TRNA-1_B23MHV2LT4_1/659_bGc-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv