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/79/1b35d245d016b7f3e08e10537663a7/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/4c0a14033590134598dfb07ab67e08/659_b7Z-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.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/12/4c0a14033590134598dfb07ab67e08/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/1b35d245d016b7f3e08e10537663a7/.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_b7Z-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 154721it [00:00, 1547122.95it/s][W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai 321792it [00:00, 1619788.64it/s] 490325it [00:00, 1649637.21it/s] 659309it [00:00, 1665480.56it/s] 828366it [00:00, 1674503.75it/s] 998396it [00:00, 1683250.18it/s] 1166809it [00:00, 1683362.51it/s] 1338779it [00:00, 1694906.92it/s] 1508488it [00:00, 1695563.30it/s] 1678045it [00:01, 1694340.03it/s] 1847480it [00:01, 1692941.02it/s] 2016775it [00:01, 1690363.50it/s] 2186471it [00:01, 1692340.54it/s] 2357682it [00:01, 1698285.57it/s] 2533857it [00:01, 1717378.87it/s] 2705598it [00:01, 1717050.07it/s] 2877305it [00:01, 1708782.21it/s] 3048194it [00:01, 1707090.94it/s] 3218922it [00:01, 1707129.75it/s] 3389640it [00:02, 1685346.02it/s] 3558237it [00:02, 1639664.66it/s] 3722477it [00:02, 1590353.07it/s] 3881919it [00:02, 1581403.95it/s] 4045922it [00:02, 1598270.69it/s] 4205989it [00:02, 1585429.42it/s] 4364696it [00:02, 1577235.17it/s] 4522527it [00:02, 1570718.34it/s] 4679668it [00:02, 1529192.06it/s] 4839442it [00:02, 1549114.30it/s] 4994577it [00:03, 1514858.63it/s] 5146324it [00:03, 1490667.87it/s] 5314873it [00:03, 1547153.47it/s] 5483515it [00:03, 1587929.70it/s] 5656109it [00:03, 1628527.69it/s] 5823500it [00:03, 1641914.89it/s] 5991577it [00:03, 1653458.04it/s] 6159343it [00:03, 1660658.08it/s] 6328565it [00:03, 1670070.69it/s] 6496810it [00:03, 1673755.23it/s] 6664249it [00:04, 1669051.51it/s] 6832514it [00:04, 1673098.35it/s] 7000264it [00:04, 1674393.41it/s] 7169034it [00:04, 1678356.26it/s] 7337994it [00:04, 1681702.96it/s] 7508582it [00:04, 1688931.04it/s] 7678490it [00:04, 1691955.01it/s] 7848034it [00:04, 1692927.92it/s] 8018260it [00:04, 1695706.49it/s] 8189024it [00:04, 1699213.26it/s] 8358948it [00:05, 1697062.78it/s] 8529802it [00:05, 1700483.45it/s] 8699853it [00:05, 1699781.18it/s] 8869833it [00:05, 1685476.89it/s] 9039138it [00:05, 1687715.42it/s] 9209458it [00:05, 1692322.10it/s] 9382095it [00:05, 1702487.35it/s] 9552359it [00:05, 1701327.87it/s] 9725636it [00:05, 1710725.63it/s] 9897062it [00:05, 1711767.77it/s] 10068246it [00:06, 1709011.84it/s] 10239153it [00:06, 1703759.24it/s] 10409536it [00:06, 1695571.03it/s] 10581913it [00:06, 1703967.64it/s] 10754557it [00:06, 1710665.34it/s] 10925636it [00:06, 1705210.87it/s] 11096168it [00:06, 1700719.82it/s] 11266249it [00:06, 1699726.11it/s] 11436228it [00:06, 1698864.44it/s] 11607037it [00:06, 1701597.51it/s] 11778048it [00:07, 1704129.27it/s] 11951143it [00:07, 1712128.43it/s] 12122360it [00:07, 1706926.42it/s] 12293058it [00:07, 1703051.32it/s] 12443725it [00:07, 1668057.35it/s] [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md -output 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md -output 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv