Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/ce393d6c57309e5285ad2026222f1c/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/93bb5d7938365e62ce15598e4864f4/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz 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/22/93bb5d7938365e62ce15598e4864f4/.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/1d/ce393d6c57309e5285ad2026222f1c/659_bCu-T1-TRNA-1_B23WHTKLT4_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_bCu-T1-TRNA-1_B23WHTKLT4_1 + all_qc -bam 659_bCu-T1-TRNA-1_B23WHTKLT4_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_bCu-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed saturation_plot -bams 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam -bed 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/saturation_qc.tsv fragment_size -bams 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output_prefix 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_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_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.mpileup && contamination -input 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_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_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai 135134it [00:00, 1351202.76it/s] 282497it [00:00, 1423148.71it/s] 424812it [00:00, 1418384.90it/s] 566653it [00:00, 1315547.13it/s] 704977it [00:00, 1338732.81it/s] 839618it [00:00, 1310282.32it/s] 985712it [00:00, 1357606.62it/s] 1122622it [00:00, 1361138.19it/s] 1259121it [00:00, 1302956.42it/s] 1390105it [00:01, 1297308.40it/s] 1524309it [00:01, 1310499.41it/s] 1655724it [00:01, 1294791.29it/s] 1785466it [00:01, 1291009.96it/s] 1927418it [00:01, 1329005.26it/s] 2070885it [00:01, 1360368.69it/s][W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai 2216724it [00:01, 1389542.98it/s] 2359234it [00:01, 1400137.02it/s] 2499368it [00:01, 1358722.35it/s] 2635576it [00:01, 1255765.79it/s] 2762772it [00:02, 1203808.47it/s] 2884468it [00:02, 1179987.10it/s] 3003321it [00:02, 1163197.91it/s][W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai 3120177it [00:02, 1148021.37it/s] 3235308it [00:02, 1144343.35it/s] 3280276it [00:02, 1277791.30it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz > 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv cat 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md -output 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/659_bCu-T1-TRNA-1_B23WHTKLT4_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_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_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_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_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_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz> 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_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_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_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_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bai cat 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bCu-T1-TRNA-1_B23WHTKLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md/qc_complete.txt + merge_qc -folders 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1.md -output 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv + head -n1 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bCu-T1-TRNA-1_B23WHTKLT4_1/659_bCu-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv