Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/80c7a3c2df156fb3104ea9d1721b43/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_postQC_hg38.bed Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_coding_postQC_hg38.bed 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/c8/b82f0cb896b4d0d3d3fabd0aa7dd79/.command.sh 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/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/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/80c7a3c2df156fb3104ea9d1721b43/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam 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/c8/b82f0cb896b4d0d3d3fabd0aa7dd79/.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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed seqtool depth -bam 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam -bed 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz saturation_plot -bams 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam -region chr20 -output 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/saturation_qc.tsv fragment_size -bams 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam -region chr20 -output_prefix 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.mpileup && contamination -input 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/contamination.tsv seqtool noise -bam 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam -ref Homo_sapiens_assembly38.fasta -region chr20 -include_bed 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed -exclude_bed dbsnp138_hg38_common.bed -threads 1 > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.noise_summary.tsv [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-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: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-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: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 141681it [00:00, 1416720.15it/s] 300983it [00:00, 1520093.66it/s] 462876it [00:00, 1565186.76it/s] 624137it [00:00, 1583830.28it/s] 788295it [00:00, 1604506.34it/s] 949476it [00:00, 1606968.97it/s] 1112795it [00:00, 1615519.58it/s] 1274347it [00:00, 1610369.83it/s] 1436043it [00:00, 1612369.53it/s] 1599820it [00:01, 1620181.45it/s] 1763529it [00:01, 1625332.16it/s] 1927607it [00:01, 1630008.31it/s] 2091211it [00:01, 1631817.32it/s] 2254395it [00:01, 1612739.85it/s] 2417615it [00:01, 1618539.22it/s] 2579510it [00:01, 1618511.34it/s] 2741390it [00:01, 1614892.94it/s] 2902900it [00:01, 1583624.37it/s] 3061399it [00:01, 1579976.91it/s] 3219489it [00:02, 1557516.95it/s] 3382288it [00:02, 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1666018.29it/s] 22127529it [00:13, 1672546.65it/s] 22295675it [00:13, 1675192.45it/s] 22463229it [00:13, 1671567.51it/s] 22631057it [00:14, 1673433.82it/s] 22798419it [00:14, 1672285.54it/s] 22965660it [00:14, 1651731.93it/s] 23130895it [00:14, 1613690.31it/s] 23294102it [00:14, 1619014.65it/s] 23456158it [00:14, 1602930.80it/s] 23619300it [00:14, 1611302.28it/s] 23780531it [00:14, 1595150.84it/s] 23944553it [00:14, 1608435.98it/s] 24108026it [00:15, 1616218.44it/s] 24272097it [00:15, 1623435.14it/s] 24435142it [00:15, 1625368.47it/s] 24598858it [00:15, 1628876.82it/s] 24762636it [00:15, 1631527.76it/s] 24927920it [00:15, 1637841.17it/s] 25092507it [00:15, 1640235.09it/s] 25256542it [00:15, 1613115.47it/s] 25419086it [00:15, 1616755.05it/s] 25583083it [00:15, 1623648.00it/s] 25747906it [00:16, 1630964.17it/s] 25912252it [00:16, 1634522.71it/s][W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 26076969it [00:16, 1638233.27it/s] 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1582152.09it/s] 31025467it [00:19, 1598197.12it/s] 31191134it [00:19, 1615332.98it/s] 31358636it [00:19, 1633000.39it/s] 31525930it [00:19, 1644856.55it/s] 31690501it [00:19, 1622251.10it/s] 31852844it [00:19, 1520447.11it/s] 32010714it [00:19, 1536950.06it/s] 32176434it [00:19, 1571475.04it/s] 32341598it [00:20, 1594844.41it/s] 32506072it [00:20, 1609502.40it/s] 32667860it [00:20, 1611960.13it/s] 32831308it [00:20, 1618554.03it/s] 32993771it [00:20, 1620339.56it/s] 33156927it [00:20, 1623665.78it/s] 33322463it [00:20, 1632997.03it/s] 33486838it [00:20, 1636167.72it/s] 33650518it [00:20, 1635859.96it/s] 33814149it [00:20, 1627635.49it/s] 33977379it [00:21, 1628998.76it/s] 34145178it [00:21, 1643530.98it/s] 34309556it [00:21, 1643291.71it/s] 34473940it [00:21, 1643412.96it/s] 34638294it [00:21, 1620917.01it/s] 34800607it [00:21, 1621508.98it/s] 34962812it [00:21, 1586112.38it/s] 35123795it [00:21, 1593062.59it/s] 35287085it [00:21, 1604826.08it/s] 35451466it [00:21, 1616382.83it/s] 35616094it [00:22, 1625225.74it/s] 35780979it [00:22, 1632255.53it/s] 35944350it [00:22, 1632667.51it/s] 36107656it [00:22, 1626040.47it/s] 36271784it [00:22, 1630572.98it/s] 36436790it [00:22, 1636263.99it/s] 36601141it [00:22, 1638412.12it/s][W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 36765314it [00:22, 1639387.57it/s] 36929263it [00:22, 1634740.14it/s] 37093641it [00:22, 1637425.08it/s] 37257391it [00:23, 1637280.85it/s] 37422571it [00:23, 1641608.44it/s] 37588384it [00:23, 1646540.27it/s] 37754948it [00:23, 1652246.41it/s] 37920176it [00:23, 1642778.39it/s] 38084468it [00:23, 1640825.42it/s] 38249328it [00:23, 1643129.21it/s] 38413649it [00:23, 1634101.97it/s] 38534400it [00:23, 1614267.14it/s] [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai tabix -s 1 -b 2 -e 2 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz seqtool depth_hist -nbins 500 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv cat 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md -output 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool read_qc -bed foresight_clarity_targets_hg38.bed -n_threads 1 -bam_threads 2 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool reads_per_target -bed foresight_clarity_targets_hg38.bed -threads 1 -bam_threads 2 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool depth_stats -bed foresight_clarity_targets_hg38.bed 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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: 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai cat 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 "1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "FINAL_hotspot_list_07302025_hg38_sorted.bed" -output "1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.FINAL_hotspot_list_07302025_hg38_sorted.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.foresight_clarity_targets_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "foresight_clarity_targets_hg38.bed" -output "1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.foresight_clarity_targets_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 "1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_coding_postQC_hg38.bed" -output "1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_coding_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 "1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_noncoding_postQC_hg38.bed" -output "1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_noncoding_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 "1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_postQC_hg38.bed" -output "1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 "1029_FZX-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 "1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 "1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed" -output "1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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 "1029_FZX-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 "1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-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` > 1029_FZX-T1-TDNA-1_A23MHWWLT4_1/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md/qc_complete.txt