Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/35c0e724ee5ae49cc30c6ed85ccc98/tih_rna_sample_00598_B23MVV7LT4_1.md.bam 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/8d/be8fb507ab60e53e9e4e283d496966/.command.sh 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/8d/be8fb507ab60e53e9e4e283d496966/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/35c0e724ee5ae49cc30c6ed85ccc98/tih_rna_sample_00598_B23MVV7LT4_1.md.bai 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 tih_rna_sample_00598_B23MVV7LT4_1 + all_qc -bam tih_rna_sample_00598_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_00598_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 mkdir -p tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/full_bed.bed seqtool depth -bam tih_rna_sample_00598_B23MVV7LT4_1.md.bam -bed tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth.gz saturation_plot -bams tih_rna_sample_00598_B23MVV7LT4_1.md.bam -region chr20 -output tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00598_B23MVV7LT4_1.md.bam > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/saturation_qc.tsv fragment_size -bams tih_rna_sample_00598_B23MVV7LT4_1.md.bam -region chr20 -output_prefix tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bam > tih_rna_sample_00598_B23MVV7LT4_1.md.mpileup && contamination -input tih_rna_sample_00598_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_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_00598_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_00598_B23MVV7LT4_1.md.bai 152513it [00:00, 1524956.94it/s] 320357it [00:00, 1614947.88it/s] 489157it [00:00, 1648170.67it/s] 662117it [00:00, 1680272.07it/s] 839604it [00:00, 1714336.47it/s] 1016344it [00:00, 1732332.30it/s] 1193478it [00:00, 1745046.40it/s] 1369724it [00:00, 1750555.70it/s] 1548787it [00:00, 1763051.81it/s] 1727983it [00:01, 1771946.43it/s] 1905178it [00:01, 1749080.80it/s] 2081790it [00:01, 1754187.65it/s] 2260226it [00:01, 1763240.14it/s] 2436904it [00:01, 1764264.63it/s] 2613360it [00:01, 1753381.31it/s] 2790162it [00:01, 1757724.18it/s] 2969045it [00:01, 1767001.18it/s] 3145768it [00:01, 1749136.04it/s] 3322065it [00:01, 1753217.68it/s] 3497427it [00:02, 1735313.21it/s] 3673809it [00:02, 1743743.48it/s] 3848235it [00:02, 1669097.55it/s] 4015810it [00:02, 1594381.98it/s] 4176219it [00:02, 1519296.16it/s] 4329246it [00:02, 1450755.68it/s] 4486878it [00:02, 1485166.02it/s] 4660926it [00:02, 1557016.17it/s] 4817827it [00:02, 1557486.19it/s] 4974417it [00:02, 1516101.28it/s] 5152832it [00:03, 1593066.03it/s] 5331976it [00:03, 1650755.38it/s] 5511122it [00:03, 1692038.56it/s] 5689210it [00:03, 1718260.45it/s] 5869182it [00:03, 1742390.80it/s] 6051101it [00:03, 1765226.77it/s] 6231753it [00:03, 1777387.18it/s] 6412287it [00:03, 1785707.82it/s] 6592501it [00:03, 1790590.52it/s] 6771660it [00:03, 1761938.59it/s] 6948023it [00:04, 1749191.76it/s] 7126048it [00:04, 1758345.69it/s] 7301983it [00:04, 1758575.99it/s] 7478190it [00:04, 1759583.60it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai 7655014it [00:04, 1762134.34it/s] 7831264it [00:04, 1720439.04it/s] 8003540it [00:04, 1713006.78it/s] 8174997it [00:04, 1705266.56it/s] 8348337it [00:04, 1713550.51it/s] 8522111it [00:05, 1720695.31it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai 8701339it [00:05, 1741983.21it/s] 8878427it [00:05, 1750578.47it/s] 8981284it [00:05, 1704623.01it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai tabix -s 1 -b 2 -e 2 tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth.gz seqtool depth_hist -nbins 500 tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth.gz > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth_hist.tsv cat tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00598_B23MVV7LT4_1.md -output tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bam > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bam > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/tih_rna_sample_00598_B23MVV7LT4_1.md.depth.gz> tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bam > tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00598_B23MVV7LT4_1.md.bai cat tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md/qc_complete.txt + merge_qc -folders tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1.md -output tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00598_B23MVV7LT4_1/tih_rna_sample_00598_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_00598_B23MVV7LT4_1/tih_rna_sample_00598_B23MVV7LT4_1_full_basic_stats.tsv