Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_postQC_hg38.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/17fccdf819f8ec4c552cea4ecfb06f/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_coding_postQC_hg38.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/17fccdf819f8ec4c552cea4ecfb06f/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/foresight_clarity_targets_hg38.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/338c684915aa27a98142f0d8b75ab8/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/FINAL_hotspot_list_07302025_hg38_sorted.bed Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed Downloading: s3://natera-platform-sandbox/platform-users/ralla/nfcore_rnafusion_resources/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/338c684915aa27a98142f0d8b75ab8/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/dbsnp138_hg38_common.bed Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_noncoding_postQC_hg38.bed ==> STAGING COMPLETE (18 inputs) mkdir -p 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/ cat xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed altera_v3_targets_postQC_hg38.bed altera_v3_targets_coding_postQC_hg38.bed altera_v3_targets_noncoding_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed FINAL_hotspot_list_07302025_hg38_sorted.bed foresight_clarity_targets_hg38.bed | cut -f 1-3 | bedtools sort -g Homo_sapiens_assembly38.fasta.fai | bedtools merge > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed seqtool depth -bam 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam -bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz saturation_plot -bams 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam -region chr20 -output 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/saturation_qc.tsv fragment_size -bams 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam -region chr20 -output_prefix 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f Homo_sapiens_assembly38.fasta -l dbsnp_hg38_contam_sites.bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.mpileup && contamination -input 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/contamination.tsv seqtool noise -bam 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam -ref Homo_sapiens_assembly38.fasta -region chr20 -include_bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed -exclude_bed dbsnp138_hg38_common.bed -threads 1 > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.noise_summary.tsv [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [mpileup] 1 samples in 1 input files loading BEDs... [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.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: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s] 144597it [00:00, 1445892.09it/s] 304913it [00:00, 1538366.92it/s] 468437it [00:00, 1582471.63it/s] 632334it [00:00, 1604751.57it/s] 796188it [00:00, 1616917.80it/s] 960577it [00:00, 1626071.39it/s] 1127115it [00:00, 1638878.94it/s] 1294024it [00:00, 1648480.55it/s] 1458873it [00:00, 1638787.30it/s] 1625336it [00:01, 1646717.58it/s] 1790020it [00:01, 1645775.89it/s] 1954606it [00:01, 1620112.28it/s] 2116706it [00:01, 1606497.17it/s] 2283129it [00:01, 1623664.04it/s] 2445571it [00:01, 1578775.64it/s] 2603733it [00:01, 1579586.14it/s] 2771360it [00:01, 1608054.78it/s] 2938079it [00:01, 1625437.66it/s] 3106370it [00:01, 1642498.53it/s] 3270748it [00:02, 1629787.73it/s] 3437232it [00:02, 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1654306.22it/s] 8322438it [00:05, 1663109.30it/s] 8492251it [00:05, 1673580.85it/s] 8662739it [00:05, 1682946.72it/s] 8832017it [00:05, 1685878.80it/s] 9000632it [00:05, 1683420.44it/s] 9170037it [00:05, 1686443.58it/s] 9338696it [00:05, 1681435.26it/s] 9506853it [00:05, 1680974.92it/s] 9674960it [00:05, 1680648.84it/s] 9843031it [00:06, 1677532.95it/s] 10010790it [00:06, 1670378.50it/s] 10177837it [00:06, 1663593.32it/s] 10345840it [00:06, 1668481.28it/s] 10513215it [00:06, 1670038.86it/s] 10680227it [00:06, 1664399.99it/s] 10846675it [00:06, 1655159.97it/s] 11014400it [00:06, 1661727.71it/s]done loading BEDs. 11182241it [00:06, 1666693.84it/s] 11348923it [00:07, 1664774.15it/s] 11515409it [00:07, 1662161.31it/s] 11682673it [00:07, 1665279.29it/s] 11849207it [00:07, 1665199.32it/s] 12016139it [00:07, 1666418.41it/s] 12183615it [00:07, 1668900.47it/s] 12354241it [00:07, 1680082.47it/s] 12522252it [00:07, 1674946.43it/s] 12689752it [00:07, 1671615.41it/s] 12856944it [00:07, 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17719312it [00:10, 1663118.89it/s] 17886376it [00:10, 1665195.39it/s] 18052903it [00:11, 1663688.93it/s] 18219455it [00:11, 1664224.75it/s] 18388819it [00:11, 1673027.63it/s] 18557591it [00:11, 1677282.39it/s] 18725322it [00:11, 1676534.96it/s] 18892978it [00:11, 1663337.65it/s] 19059621it [00:11, 1664246.01it/s] 19226678it [00:11, 1666122.56it/s] 19393878it [00:11, 1667834.62it/s] 19560672it [00:11, 1665447.63it/s] 19727224it [00:12, 1659163.83it/s] 19896251it [00:12, 1668440.86it/s] 20064816it [00:12, 1673479.55it/s] 20234585it [00:12, 1680715.13it/s] 20403786it [00:12, 1684081.98it/s] 20572201it [00:12, 1681748.97it/s] 20740381it [00:12, 1667199.07it/s] 20907131it [00:12, 1647205.17it/s] 21071914it [00:12, 1627456.60it/s] 21238883it [00:12, 1639886.58it/s] 21408796it [00:13, 1657423.35it/s] 21576273it [00:13, 1662567.36it/s] 21742586it [00:13, 1605854.31it/s] 21903601it [00:13, 1590618.53it/s] 22071922it [00:13, 1617628.12it/s] 22238958it [00:13, 1633134.61it/s] 22403791it [00:13, 1637621.52it/s] 22569754it [00:13, 1644148.81it/s] 22736332it [00:13, 1650582.30it/s] 22904359it [00:13, 1659300.75it/s] 23070795it [00:14, 1660768.91it/s] 23236920it [00:14, 1655058.05it/s] 23406968it [00:14, 1668615.78it/s] 23575497it [00:14, 1673588.51it/s] 23742880it [00:14, 1658170.33it/s] 23909926it [00:14, 1661696.45it/s] 24076131it [00:14, 1629069.00it/s] 24243473it [00:14, 1642125.60it/s] 24410844it [00:14, 1651397.67it/s] 24578185it [00:14, 1657930.62it/s][W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 24744056it [00:15, 1653680.21it/s] 24911492it [00:15, 1659832.94it/s] 25078728it [00:15, 1663543.09it/s] 25245114it [00:15, 1662271.71it/s] 25412384it [00:15, 1665339.85it/s] 25579270it [00:15, 1666383.62it/s] 25747433it [00:15, 1670941.04it/s] 25915109it [00:15, 1672672.39it/s] 26082383it [00:15, 1668755.77it/s] 26249265it [00:15, 1665387.82it/s] 26340481it [00:16, 1642803.78it/s] [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai tabix -s 1 -b 2 -e 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz seqtool depth_hist -nbins 500 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv cat 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md -output 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_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 xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed -n_threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/read_qc.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.tsv seqtool reads_per_target -bed xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.tsv seqtool depth_stats -bed xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.tsv seqtool gc_bias -reference Homo_sapiens_assembly38.fasta -bed xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed -bin_size 0.05 -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.tsv seqtool read_qc -bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed -n_threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/read_qc.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.tsv seqtool reads_per_target -bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.tsv seqtool depth_stats -bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.tsv seqtool gc_bias -reference Homo_sapiens_assembly38.fasta -bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed -bin_size 0.05 -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.tsv seqtool read_qc -bed altera_v3_targets_postQC_hg38.bed -n_threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/read_qc.altera_v3_targets_postQC_hg38.bed.tsv seqtool reads_per_target -bed altera_v3_targets_postQC_hg38.bed -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.altera_v3_targets_postQC_hg38.bed.tsv seqtool depth_stats -bed altera_v3_targets_postQC_hg38.bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.altera_v3_targets_postQC_hg38.bed.tsv seqtool gc_bias -reference Homo_sapiens_assembly38.fasta -bed altera_v3_targets_postQC_hg38.bed -bin_size 0.05 -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_postQC_hg38.bed.tsv seqtool read_qc -bed altera_v3_targets_coding_postQC_hg38.bed -n_threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/read_qc.altera_v3_targets_coding_postQC_hg38.bed.tsv seqtool reads_per_target -bed altera_v3_targets_coding_postQC_hg38.bed -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.altera_v3_targets_coding_postQC_hg38.bed.tsv seqtool depth_stats -bed altera_v3_targets_coding_postQC_hg38.bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.altera_v3_targets_coding_postQC_hg38.bed.tsv seqtool gc_bias -reference Homo_sapiens_assembly38.fasta -bed altera_v3_targets_coding_postQC_hg38.bed -bin_size 0.05 -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_coding_postQC_hg38.bed.tsv seqtool read_qc -bed altera_v3_targets_noncoding_postQC_hg38.bed -n_threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/read_qc.altera_v3_targets_noncoding_postQC_hg38.bed.tsv seqtool reads_per_target -bed altera_v3_targets_noncoding_postQC_hg38.bed -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.altera_v3_targets_noncoding_postQC_hg38.bed.tsv seqtool depth_stats -bed altera_v3_targets_noncoding_postQC_hg38.bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.altera_v3_targets_noncoding_postQC_hg38.bed.tsv seqtool gc_bias -reference Homo_sapiens_assembly38.fasta -bed altera_v3_targets_noncoding_postQC_hg38.bed -bin_size 0.05 -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_noncoding_postQC_hg38.bed.tsv seqtool read_qc -bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed -n_threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/read_qc.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv seqtool reads_per_target -bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv seqtool depth_stats -bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv seqtool gc_bias -reference Homo_sapiens_assembly38.fasta -bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed -bin_size 0.05 -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv seqtool read_qc -bed FINAL_hotspot_list_07302025_hg38_sorted.bed -n_threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/read_qc.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv seqtool reads_per_target -bed FINAL_hotspot_list_07302025_hg38_sorted.bed -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv seqtool depth_stats -bed FINAL_hotspot_list_07302025_hg38_sorted.bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv seqtool gc_bias -reference Homo_sapiens_assembly38.fasta -bed FINAL_hotspot_list_07302025_hg38_sorted.bed -bin_size 0.05 -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool read_qc -bed foresight_clarity_targets_hg38.bed -n_threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/read_qc.foresight_clarity_targets_hg38.bed.tsv [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool reads_per_target -bed foresight_clarity_targets_hg38.bed -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.foresight_clarity_targets_hg38.bed.tsv [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool depth_stats -bed foresight_clarity_targets_hg38.bed 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.foresight_clarity_targets_hg38.bed.tsv [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool gc_bias -reference Homo_sapiens_assembly38.fasta -bed foresight_clarity_targets_hg38.bed -bin_size 0.05 -threads 1 -bam_threads 2 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.foresight_clarity_targets_hg38.bed.tsv [W::hts_idx_load3] The index file is older than the data file: 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai cat 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "FINAL_hotspot_list_07302025_hg38_sorted.bed" -output "1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.FINAL_hotspot_list_07302025_hg38_sorted.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.foresight_clarity_targets_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "foresight_clarity_targets_hg38.bed" -output "1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.foresight_clarity_targets_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_coding_postQC_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_coding_postQC_hg38.bed" -output "1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_coding_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_noncoding_postQC_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_noncoding_postQC_hg38.bed" -output "1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_noncoding_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_postQC_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_postQC_hg38.bed" -output "1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed" -output "1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed" -output "1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed" -output "1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/qc_complete.txt