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/dc/1242d2d19987f20c4e02cf31feef6d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/45e986371be9a37b017c7d8bb67dba/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/13/45e986371be9a37b017c7d8bb67dba/659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/1242d2d19987f20c4e02cf31feef6d/.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 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 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 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 0it [00:00, ?it/s] 129529it [00:00, 1295176.98it/s][W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.md.bai 278410it [00:00, 1409020.13it/s] 433261it [00:00, 1472667.30it/s] 590487it [00:00, 1511944.43it/s] 750159it [00:00, 1542466.56it/s] 906396it [00:00, 1549182.43it/s] 1061315it [00:00, 1503410.44it/s] 1211919it [00:00, 1490765.39it/s] 1361174it [00:00, 1473250.80it/s] 1508633it [00:01, 1422888.53it/s] 1651280it [00:01, 1317010.22it/s] 1784478it [00:01, 1260694.92it/s] 1911742it [00:01, 1185346.45it/s] 2031536it [00:01, 1101581.05it/s] 2143129it [00:01, 1027952.02it/s] 2247241it [00:01, 978992.15it/s] 2345991it [00:01, 953528.33it/s] 2447963it [00:01, 970895.36it/s] 2589851it [00:02, 1093913.38it/s] 2746297it [00:02, 1226486.77it/s] 2887022it [00:02, 1278319.84it/s] 3031011it [00:02, 1325260.03it/s] 3193789it [00:02, 1413938.87it/s] 3360714it [00:02, 1489309.21it/s] 3510516it [00:02, 1469464.21it/s] 3658119it [00:02, 1447058.84it/s] 3803330it [00:02, 1419600.13it/s] 3968906it [00:03, 1488196.56it/s] 4131737it [00:03, 1529149.27it/s] 4285662it [00:03, 1532081.02it/s] 4439189it [00:03, 1518686.25it/s] 4591295it [00:03, 1517173.28it/s] 4743177it [00:03, 1484206.60it/s] 4891842it [00:03, 1440021.53it/s] 5036218it [00:03, 1365398.66it/s] 5173617it [00:03, 1334352.05it/s] 5307639it [00:03, 1327341.27it/s] 5464218it [00:04, 1395356.79it/s] 5604365it [00:04, 1388093.65it/s] 5743588it [00:04, 1320693.86it/s] 5893234it [00:04, 1370491.91it/s] 6050662it [00:04, 1429202.62it/s] 6208526it [00:04, 1472745.25it/s] 6360891it [00:04, 1487686.93it/s] 6510194it [00:04, 1482002.98it/s] 6677305it [00:04, 1537953.69it/s] 6846387it [00:04, 1583307.07it/s] 7012410it [00:05, 1606203.00it/s] 7182284it [00:05, 1633805.74it/s] 7347324it [00:05, 1638734.52it/s] 7514356it [00:05, 1648152.59it/s] 7680761it [00:05, 1652878.01it/s] 7852750it [00:05, 1672928.02it/s] 8027382it [00:05, 1694793.75it/s] 8198291it [00:05, 1699047.64it/s] 8368978it [00:05, 1701367.01it/s] 8541126it [00:05, 1707372.57it/s] 8713729it [00:06, 1712939.55it/s] 8885031it [00:06, 1694665.66it/s] 9055901it [00:06, 1698812.98it/s] 9226302it [00:06, 1700337.60it/s] 9402930it [00:06, 1720020.47it/s] 9576078it [00:06, 1723422.65it/s] 9750268it [00:06, 1728793.07it/s] 9925017it [00:06, 1734228.94it/s] 10100324it [00:06, 1739851.07it/s] 10274318it [00:06, 1737955.34it/s] 10448120it [00:07, 1730116.22it/s] 10623593it [00:07, 1737401.50it/s] 10797345it [00:07, 1736910.97it/s] 10971044it [00:07, 1582817.46it/s] 11131953it [00:07, 1577087.75it/s] 11301784it [00:07, 1611530.66it/s] 11464395it [00:07, 1468981.85it/s] 11614470it [00:07, 1412432.50it/s] 11758028it [00:07, 1372178.64it/s] 11896802it [00:08, 1352747.68it/s] 12033066it [00:08, 1322791.15it/s] 12165980it [00:08, 1309543.17it/s] 12297317it [00:08, 1301274.87it/s] 12456930it [00:08, 1385488.26it/s] 12458173it [00:08, 1464220.01it/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