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/cc/153e1e8a47476296bf5292838a63c5/.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/01/abfbefebb896799a5a678a07d0dacb/659_bNS-T1-TRNA-1_A23MVY2LT4_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/cc/153e1e8a47476296bf5292838a63c5/.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/01/abfbefebb896799a5a678a07d0dacb/659_bNS-T1-TRNA-1_A23MVY2LT4_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_bNS-T1-TRNA-1_A23MVY2LT4_1 + all_qc -bam 659_bNS-T1-TRNA-1_A23MVY2LT4_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_bNS-T1-TRNA-1_A23MVY2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/full_bed.bed seqtool depth -bam 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam -bed 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz saturation_plot -bams 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam -region chr20 -output 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam -region chr20 -output_prefix 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_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_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.mpileup && contamination -input 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_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_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai 0it [00:00, ?it/s] 155246it [00:00, 1552405.96it/s] 321316it [00:00, 1615936.10it/s] 489680it [00:00, 1646828.30it/s] 658273it [00:00, 1662246.34it/s] 826519it [00:00, 1669520.05it/s] 993472it [00:00, 1654387.57it/s] 1158937it [00:00, 1599057.68it/s] 1327839it [00:00, 1626903.93it/s] 1495947it [00:00, 1643478.92it/s] 1664530it [00:01, 1656368.99it/s] 1831868it [00:01, 1661509.99it/s] 1998852it [00:01, 1663862.86it/s] 2167799it [00:01, 1671450.84it/s] 2339059it [00:01, 1683828.16it/s] 2509944it [00:01, 1691339.39it/s] 2679254it [00:01, 1691854.43it/s] 2848467it [00:01, 1690445.06it/s] 3021139it [00:01, 1701315.93it/s] 3193673it [00:01, 1708458.76it/s] 3364530it [00:02, 1686387.23it/s] 3533240it [00:02, 1680782.35it/s] 3703253it [00:02, 1686520.79it/s] 3873989it [00:02, 1692721.37it/s] 4045789it [00:02, 1700198.85it/s] 4215835it [00:02, 1696994.50it/s] 4385553it [00:02, 1691993.75it/s] 4556410it [00:02, 1696931.29it/s] 4726116it [00:02, 1693400.10it/s] 4896630it [00:02, 1696896.22it/s] 5066328it [00:03, 1692051.10it/s] 5238148it [00:03, 1699789.92it/s] 5409329it [00:03, 1703373.27it/s] 5581684it [00:03, 1709401.81it/s] 5753702it [00:03, 1712620.41it/s] 5925724it [00:03, 1714885.15it/s] 6098348it [00:03, 1718276.32it/s] 6270179it [00:03, 1718161.62it/s] 6441997it [00:03, 1717021.00it/s] 6614362it [00:03, 1718996.45it/s] 6786263it [00:04, 1709827.42it/s] 6959396it [00:04, 1716166.64it/s] 7131731it [00:04, 1718304.83it/s] 7305155it [00:04, 1723063.81it/s] 7478227it [00:04, 1725345.54it/s] 7650767it [00:04, 1722049.95it/s] 7822977it [00:04, 1720347.50it/s] 7995016it [00:04, 1710837.56it/s] 8166113it [00:04, 1705794.11it/s] 8336702it [00:04, 1704163.04it/s] 8507336it [00:05, 1704796.51it/s] 8677821it [00:05, 1701233.00it/s] 8847949it [00:05, 1698710.59it/s] 9017823it [00:05, 1689823.53it/s] 9191298it [00:05, 1703202.88it/s] 9364845it [00:05, 1712822.57it/s] 9536142it [00:05, 1710477.87it/s] 9708456it [00:05, 1714243.05it/s] 9879889it [00:05, 1711473.71it/s] 10051043it [00:05, 1705057.52it/s] 10221558it [00:06, 1697080.21it/s] 10393620it [00:06, 1704083.76it/s] 10564724it [00:06, 1706148.30it/s] 10735349it [00:06, 1704470.55it/s] 10905803it [00:06, 1701429.21it/s] 11075951it [00:06, 1699294.63it/s] 11245884it [00:06, 1693804.96it/s] 11415270it [00:06, 1689877.64it/s] 11586245it [00:06, 1695712.31it/s] 11755827it [00:06, 1695709.93it/s] 11928103it [00:07, 1703745.22it/s] 12098482it [00:07, 1700406.84it/s] 12268756it [00:07, 1701092.12it/s] 12438869it [00:07, 1700399.82it/s] 12551319it [00:07, 1694868.65it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz > 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.depth_hist.tsv cat 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md -output 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/659_bNS-T1-TRNA-1_A23MVY2LT4_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_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_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_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_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_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz> 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_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_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_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_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_A23MVY2LT4_1.md.bai cat 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bNS-T1-TRNA-1_A23MVY2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1.md -output 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv + head -n1 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bNS-T1-TRNA-1_A23MVY2LT4_1/659_bNS-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv