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/65/cd5a88b83df2533aa011d840efe82a/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/d87df96d0681a710629f79dc302b5d/tih_rna_sample_00574_B23MVV7LT4_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/65/cd5a88b83df2533aa011d840efe82a/.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-rnd-pltf-dev-nextflow-scratch-01/work/a5/d87df96d0681a710629f79dc302b5d/tih_rna_sample_00574_B23MVV7LT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir tih_rna_sample_00574_B23MVV7LT4_1 + all_qc -bam tih_rna_sample_00574_B23MVV7LT4_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 tih_rna_sample_00574_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 mkdir -p tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/full_bed.bed seqtool depth -bam tih_rna_sample_00574_B23MVV7LT4_1.md.bam -bed tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/tih_rna_sample_00574_B23MVV7LT4_1.md.depth.gz saturation_plot -bams tih_rna_sample_00574_B23MVV7LT4_1.md.bam -region chr20 -output tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00574_B23MVV7LT4_1.md.bam > tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/saturation_qc.tsv fragment_size -bams tih_rna_sample_00574_B23MVV7LT4_1.md.bam -region chr20 -output_prefix tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed tih_rna_sample_00574_B23MVV7LT4_1.md.bam > tih_rna_sample_00574_B23MVV7LT4_1.md.mpileup && contamination -input tih_rna_sample_00574_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_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: tih_rna_sample_00574_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai 148000it [00:00, 1479772.09it/s] 309041it [00:00, 1556578.99it/s] 475903it [00:00, 1607714.85it/s] 640799it [00:00, 1623978.12it/s] 809277it [00:00, 1645756.46it/s] 976571it [00:00, 1654982.59it/s] 1147404it [00:00, 1672229.70it/s] 1317740it [00:00, 1682004.13it/s] 1488544it [00:00, 1690127.61it/s] 1658047it [00:01, 1691626.49it/s] 1827896it [00:01, 1693711.35it/s] 1998314it [00:01, 1696880.33it/s] 2170880it [00:01, 1705582.77it/s] 2341439it [00:01, 1687593.58it/s] 2513601it [00:01, 1697721.30it/s] 2685456it [00:01, 1703845.38it/s] 2860653it [00:01, 1718251.08it/s] 3032504it [00:01, 1714721.96it/s] 3203996it [00:01, 1707206.54it/s] 3374736it [00:02, 1687732.64it/s] 3546238it [00:02, 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1661473.46it/s] 8691324it [00:05, 1676064.82it/s] 8862029it [00:05, 1685224.56it/s] 9031096it [00:05, 1677442.44it/s] 9201941it [00:05, 1686634.96it/s] 9372731it [00:05, 1692951.91it/s] 9542226it [00:05, 1691848.79it/s] 9713864it [00:05, 1699165.12it/s] 9884283it [00:05, 1700654.00it/s] 10056933it [00:05, 1708238.34it/s] 10230822it [00:06, 1717368.68it/s] 10402596it [00:06, 1714368.06it/s] 10580031it [00:06, 1732310.41it/s] 10753285it [00:06, 1721029.13it/s] 10925420it [00:06, 1716521.40it/s] 11099850it [00:06, 1724786.34it/s] 11274692it [00:06, 1731830.80it/s] 11447893it [00:06, 1730136.39it/s] 11620919it [00:06, 1726329.37it/s] 11793562it [00:06, 1717318.88it/s] 11965309it [00:07, 1708980.27it/s] 12136222it [00:07, 1702820.40it/s] 12309745it [00:07, 1712452.12it/s] 12481006it [00:07, 1691236.67it/s] 12650189it [00:07, 1687939.16it/s] 12821451it [00:07, 1695250.90it/s] 12993221it [00:07, 1701920.49it/s] 13165031it [00:07, 1706735.60it/s] 13337167it [00:07, 1711091.90it/s] 13508294it [00:07, 1702882.85it/s] 13678602it [00:08, 1701595.74it/s] 13848775it [00:08, 1679679.80it/s] 14023322it [00:08, 1699162.01it/s] 14194669it [00:08, 1703400.66it/s] 14365061it [00:08, 1701022.18it/s] 14539214it [00:08, 1713094.95it/s] 14710555it [00:08, 1708754.58it/s] 14881666it [00:08, 1709442.78it/s] 15053807it [00:08, 1713005.34it/s] 15225121it [00:09, 1701783.25it/s] 15395323it [00:09, 1696562.15it/s] 15465894it [00:09, 1690357.73it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai tabix -s 1 -b 2 -e 2 tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/tih_rna_sample_00574_B23MVV7LT4_1.md.depth.gz seqtool depth_hist -nbins 500 tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/tih_rna_sample_00574_B23MVV7LT4_1.md.depth.gz > tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/tih_rna_sample_00574_B23MVV7LT4_1.md.depth_hist.tsv cat tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/tih_rna_sample_00574_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00574_B23MVV7LT4_1.md -output tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/tih_rna_sample_00574_B23MVV7LT4_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 tih_rna_sample_00574_B23MVV7LT4_1.md.bam > tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_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 tih_rna_sample_00574_B23MVV7LT4_1.md.bam > tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/tih_rna_sample_00574_B23MVV7LT4_1.md.depth.gz> tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_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 tih_rna_sample_00574_B23MVV7LT4_1.md.bam > tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_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: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai cat tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "tih_rna_sample_00574_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md/qc_complete.txt + merge_qc -folders tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md -output tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1_full_basic_stats.tsv