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/ea/abbb0318749574827ce9af71e7a552/.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/4e/52f0e74e859e1fa835638eeddd156d/659_1q-T1-TRNA-1_B23MHV2LT4_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/ea/abbb0318749574827ce9af71e7a552/.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/4e/52f0e74e859e1fa835638eeddd156d/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/659_1q-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 156384it [00:00, 1563752.01it/s] 325525it [00:00, 1638802.76it/s] 497618it [00:00, 1676241.49it/s] 668373it [00:00, 1688565.35it/s] 838264it [00:00, 1692265.60it/s] 1008004it [00:00, 1693984.32it/s] 1177403it [00:00, 1692106.01it/s] 1348082it [00:00, 1696633.44it/s] 1517746it [00:00, 1693560.42it/s] 1687993it [00:01, 1696209.69it/s] 1857616it [00:01, 1694544.20it/s] 2030462it [00:01, 1704820.66it/s] 2200947it [00:01, 1697307.45it/s] 2373440it [00:01, 1705485.99it/s] 2546612it [00:01, 1713346.84it/s] 2719014it [00:01, 1716530.42it/s] 2891706it [00:01, 1719622.51it/s] 3063674it [00:01, 1717594.63it/s] 3235438it [00:01, 1707956.51it/s] 3406248it [00:02, 1702501.85it/s] 3582424it [00:02, 1720161.80it/s] 3755255it [00:02, 1722574.51it/s] 3927526it [00:02, 1716502.40it/s] 4104709it [00:02, 1733007.88it/s] 4280537it [00:02, 1740539.89it/s] 4456350it [00:02, 1745782.56it/s] 4630940it [00:02, 1743319.41it/s] 4805280it [00:02, 1734504.19it/s] 4978745it [00:02, 1724592.97it/s] 5151223it [00:03, 1724059.24it/s] 5324764it [00:03, 1727421.62it/s] 5497517it [00:03, 1724195.38it/s] 5670543it [00:03, 1725961.20it/s] 5843146it [00:03, 1722103.49it/s] 6015362it [00:03, 1721726.98it/s] 6187539it [00:03, 1713219.63it/s] 6358871it [00:03, 1702032.26it/s] 6529093it [00:03, 1700788.12it/s] 6699216it [00:03, 1700742.64it/s] 6869299it [00:04, 1693494.73it/s] 7040419it [00:04, 1698751.05it/s] 7214204it [00:04, 1710402.31it/s] 7386582it [00:04, 1714381.85it/s] 7559895it [00:04, 1719972.61it/s] 7732567it [00:04, 1721969.66it/s] 7905852it [00:04, 1725211.04it/s] 8079450it [00:04, 1728420.01it/s] 8253174it [00:04, 1731035.38it/s] 8427139it [00:04, 1733594.47it/s] 8600770it [00:05, 1734373.43it/s] 8777284it [00:05, 1743578.26it/s] 8951643it [00:05, 1741804.75it/s] 9125825it [00:05, 1724392.79it/s] 9298304it [00:05, 1722990.10it/s] 9471892it [00:05, 1726811.25it/s] 9644595it [00:05, 1723013.72it/s] 9818071it [00:05, 1726496.45it/s] 9991092it [00:05, 1727586.55it/s] 10165702it [00:05, 1733104.00it/s] 10341491it [00:06, 1740503.79it/s] 10515548it [00:06, 1740024.37it/s] 10689555it [00:06, 1736341.21it/s] 10865101it [00:06, 1742040.03it/s] 11039310it [00:06, 1733869.34it/s] 11212708it [00:06, 1731104.48it/s] 11385826it [00:06, 1724433.58it/s] 11558278it [00:06, 1717461.89it/s] 11731541it [00:06, 1721958.67it/s] 11907073it [00:06, 1731778.02it/s] 12080262it [00:07, 1728882.61it/s] 12253159it [00:07, 1727777.58it/s] 12426961it [00:07, 1730818.26it/s] 12600048it [00:07, 1730463.70it/s] 12773191it [00:07, 1730731.37it/s] 12946267it [00:07, 1727093.00it/s] 13118980it [00:07, 1721813.60it/s] 13292698it [00:07, 1726384.66it/s] 13465342it [00:07, 1724137.35it/s] 13640486it [00:07, 1732277.64it/s] 13815831it [00:08, 1738451.21it/s] 13989681it [00:08, 1730876.97it/s] 14162779it [00:08, 1724390.48it/s] 14282442it [00:08, 1719728.29it/s] [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/659_1q-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/659_1q-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/659_1q-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/659_1q-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_1q-T1-TRNA-1_B23MHV2LT4_1.md -output 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/659_1q-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md -output 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-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_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv