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/7d/4c1ad0317915a9ecd033cbf05d9484/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/9c20cc1da1a66f7ec89d29846903f0/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai 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/7d/4c1ad0317915a9ecd033cbf05d9484/.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/ad/9c20cc1da1a66f7ec89d29846903f0/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir aih-tih-sc-758b5a-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-758b5a-R1_B23WHYVLT4_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 aih-tih-sc-758b5a-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_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: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 120366it [00:00, 1199440.24it/s] 244666it [00:00, 1224977.50it/s] 394116it [00:00, 1347921.85it/s] 556302it [00:00, 1455987.17it/s] 710011it [00:00, 1485203.80it/s] 860448it [00:00, 1491699.97it/s] 1013621it [00:00, 1504718.23it/s] 1164097it [00:00, 1478276.03it/s] 1325790it [00:00, 1521071.87it/s] 1488908it [00:01, 1554754.23it/s] 1655443it [00:01, 1588382.45it/s] 1814380it [00:01, 1579157.97it/s] 1974838it [00:01, 1586780.17it/s] 2135600it [00:01, 1593026.95it/s] 2294947it [00:01, 1591256.20it/s] 2456570it [00:01, 1598727.51it/s] 2624515it [00:01, 1622926.90it/s] 2790313it [00:01, 1633424.75it/s] 2953673it [00:01, 1620890.69it/s] 3115795it [00:02, 1597646.94it/s] 3275645it [00:02, 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1692367.62it/s] 8254106it [00:05, 1709333.70it/s] 8430154it [00:05, 1724633.27it/s] 8602628it [00:05, 1711132.26it/s] 8775633it [00:05, 1716748.73it/s] 8951320it [00:05, 1728712.60it/s] 9126937it [00:05, 1736901.74it/s] 9304062it [00:05, 1747164.71it/s] 9478794it [00:05, 1742362.47it/s] 9654874it [00:05, 1747735.56it/s] 9829659it [00:06, 1741321.41it/s] 10003803it [00:06, 1733104.45it/s] 10177128it [00:06, 1723940.45it/s] 10349538it [00:06, 1719481.87it/s] 10521497it [00:06, 1714029.20it/s] 10692907it [00:06, 1711465.28it/s] 10864058it [00:06, 1700504.66it/s] 11034446it [00:06, 1701488.23it/s] 11204605it [00:06, 1695034.82it/s] 11376226it [00:06, 1701322.53it/s] 11546369it [00:07, 1692714.80it/s] 11715654it [00:07, 1684352.89it/s] 11889134it [00:07, 1699337.50it/s] 12059090it [00:07, 1698341.67it/s] 12228939it [00:07, 1696770.05it/s] 12398626it [00:07, 1689388.23it/s] 12568493it [00:07, 1692135.51it/s] 12741351it [00:07, 1702999.53it/s] 12911663it [00:07, 1636221.83it/s] 13075838it [00:07, 1624303.59it/s] 13238643it [00:08, 1620132.11it/s] 13405027it [00:08, 1632948.63it/s] 13568528it [00:08, 1626725.75it/s] 13731342it [00:08, 1610567.00it/s] 13892514it [00:08, 1609642.87it/s] 14056069it [00:08, 1617303.77it/s] 14218452it [00:08, 1619225.83it/s] 14380422it [00:08, 1584619.00it/s] 14539160it [00:08, 1585413.97it/s] 14695176it [00:08, 1635311.77it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-758b5a-R1_B23WHYVLT4_1/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md/aih-tih-sc-758b5a-R1_B23WHYVLT4_1.md.depth_hist.tsv