Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/242325e075b0fbf591816180526f9e/aih-tih-sc-51ee59-R1_B23WHYVLT4_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/42/a222865b19c8ff7742d747c72b385d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/242325e075b0fbf591816180526f9e/aih-tih-sc-51ee59-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/42/a222865b19c8ff7742d747c72b385d/.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-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir aih-tih-sc-51ee59-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-51ee59-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-51ee59-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-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-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-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-51ee59-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-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-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-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-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 141495it [00:00, 1412455.99it/s] 292943it [00:00, 1472384.00it/s] 449214it [00:00, 1513591.06it/s] 604948it [00:00, 1530838.62it/s] 760160it [00:00, 1538496.18it/s] 914012it [00:00, 1536968.76it/s] 1068482it [00:00, 1539482.87it/s] 1225119it [00:00, 1548024.39it/s] 1380399it [00:00, 1549392.56it/s] 1536181it [00:01, 1551871.76it/s] 1691472it [00:01, 1552094.78it/s] 1846682it [00:01, 1551876.26it/s] 2001870it [00:01, 1549059.15it/s] 2157031it [00:01, 1549812.25it/s] 2316048it [00:01, 1561849.88it/s] 2472235it [00:01, 1549952.65it/s] 2627252it [00:01, 1549747.46it/s] 2783878it [00:01, 1554674.30it/s] 2941262it [00:01, 1560396.06it/s] 3097312it [00:02, 1545703.91it/s] 3254478it [00:02, 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1564847.11it/s] 7978731it [00:05, 1567191.56it/s] 8136659it [00:05, 1570786.45it/s] 8296622it [00:05, 1579366.68it/s] 8457355it [00:05, 1587720.86it/s] 8620581it [00:05, 1601042.56it/s] 8780696it [00:05, 1600239.69it/s] 8940728it [00:05, 1599800.27it/s] 9100713it [00:05, 1595859.36it/s] 9260305it [00:05, 1595542.15it/s] 9419863it [00:06, 1595293.14it/s] 9579395it [00:06, 1584317.82it/s] 9737845it [00:06, 1581430.88it/s] 9896000it [00:06, 1579753.04it/s] 10056656it [00:06, 1587746.61it/s] 10215440it [00:06, 1577019.22it/s] 10373537it [00:06, 1578129.38it/s] 10531365it [00:06, 1568163.26it/s] 10690542it [00:06, 1575178.65it/s] 10848080it [00:06, 1574707.13it/s] 11005565it [00:07, 1567886.31it/s] 11162368it [00:07, 1563071.87it/s] 11318686it [00:07, 1559441.48it/s] 11474637it [00:07, 1557948.32it/s] 11630596it [00:07, 1558424.42it/s] 11786442it [00:07, 1553272.94it/s] 11941956it [00:07, 1553818.67it/s] 12099147it [00:07, 1559215.08it/s] 12255393it [00:07, 1560176.70it/s] 12412954it [00:07, 1564720.19it/s] 12569429it [00:08, 1562905.13it/s] 12727109it [00:08, 1566913.88it/s] 12883803it [00:08, 1563783.00it/s] 13040576it [00:08, 1564952.59it/s] 13197074it [00:08, 1555651.71it/s] 13352652it [00:08, 1553932.54it/s] 13511214it [00:08, 1563383.17it/s] 13555777it [00:08, 1564233.87it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md -output aih-tih-sc-51ee59-R1_B23WHYVLT4_1/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md/aih-tih-sc-51ee59-R1_B23WHYVLT4_1.md.depth.png