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/d8/c2d4f22bd5b989c7bf08e3d4fe438a/.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/ab/3e4f7767ff443caa676188dd4df574/aih-tih-sc-16054b-R1_B23WHYVLT4_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/d8/c2d4f22bd5b989c7bf08e3d4fe438a/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/3e4f7767ff443caa676188dd4df574/aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bam 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-16054b-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-16054b-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-16054b-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-16054b-R1_B23WHYVLT4_1/aih-tih-sc-16054b-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-16054b-R1_B23WHYVLT4_1/aih-tih-sc-16054b-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-16054b-R1_B23WHYVLT4_1/aih-tih-sc-16054b-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-16054b-R1_B23WHYVLT4_1/aih-tih-sc-16054b-R1_B23WHYVLT4_1.md/aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-16054b-R1_B23WHYVLT4_1/aih-tih-sc-16054b-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-16054b-R1_B23WHYVLT4_1/aih-tih-sc-16054b-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-16054b-R1_B23WHYVLT4_1/aih-tih-sc-16054b-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-16054b-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-16054b-R1_B23WHYVLT4_1/aih-tih-sc-16054b-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-16054b-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-16054b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-16054b-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-16054b-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bai 140698it [00:00, 1406850.53it/s] 287062it [00:00, 1439896.20it/s] 447212it [00:00, 1513649.04it/s] 610850it [00:00, 1562069.40it/s] 775878it [00:00, 1593694.61it/s] 940988it [00:00, 1613190.92it/s] 1107320it [00:00, 1629557.95it/s] 1274264it [00:00, 1642224.17it/s] 1438487it [00:00, 1633879.09it/s] 1603090it [00:01, 1637512.96it/s] 1768846it [00:01, 1643615.47it/s] 1933215it [00:01, 1621821.43it/s] 2095463it [00:01, 1608576.02it/s] 2257106it [00:01, 1610899.29it/s] 2423095it [00:01, 1625515.88it/s] 2590380it [00:01, 1639651.90it/s] 2759432it [00:01, 1654860.04it/s] 2924953it [00:01, 1653925.94it/s] 3090370it [00:01, 1651527.38it/s] 3255540it [00:02, 1636536.07it/s] 3423690it [00:02, 1649898.45it/s] 3589110it [00:02, 1651128.22it/s] 3754251it [00:02, 1644066.55it/s] 3918682it [00:02, 1616723.72it/s] 4082555it [00:02, 1623163.84it/s] 4246049it [00:02, 1626625.72it/s] 4408919it [00:02, 1627196.26it/s] 4571683it [00:02, 1611484.01it/s] 4741862it [00:02, 1638252.26it/s] 4905757it [00:03, 1562820.24it/s] 5062777it [00:03, 1464968.72it/s] 5229368it [00:03, 1520895.72it/s] 5398285it [00:03, 1568658.77it/s] 5566491it [00:03, 1601402.14it/s] 5735812it [00:03, 1628193.63it/s] 5906049it [00:03, 1650003.30it/s] 6075045it [00:03, 1661760.16it/s] 6244001it [00:03, 1669988.16it/s] 6411311it [00:03, 1661014.52it/s] 6578066it [00:04, 1662872.65it/s] 6744889it [00:04, 1664437.41it/s] 6911541it [00:04, 1664915.33it/s] 7078112it [00:04, 1659595.05it/s] 7245969it [00:04, 1665241.15it/s] 7412536it [00:04, 1662145.18it/s] 7581985it [00:04, 1671783.56it/s] 7750124it [00:04, 1674630.07it/s] 7920367it [00:04, 1682883.68it/s] 8088670it [00:04, 1681549.01it/s] 8256835it [00:05, 1681296.35it/s] 8424972it [00:05, 1676814.49it/s] 8592661it [00:05, 1663425.51it/s] 8759030it [00:05, 1626529.49it/s] 8924393it [00:05, 1634464.15it/s] 9090320it [00:05, 1641772.62it/s] 9254817it [00:05, 1642699.11it/s] 9419346it [00:05, 1643389.51it/s] 9584555it [00:05, 1645960.94it/s] 9749191it [00:05, 1640365.26it/s] 9915093it [00:06, 1645906.26it/s] 10080698it [00:06, 1648911.03it/s] 10249157it [00:06, 1659562.84it/s] 10415366it [00:06, 1660299.99it/s] 10581407it [00:06, 1643524.94it/s] 10747536it [00:06, 1648790.28it/s] 10775796it [00:06, 1632393.76it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-16054b-R1_B23WHYVLT4_1.md.bai