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-rnd-pltf-dev-nextflow-scratch-01/work/12/b67be7e02742b3f5c7d852dac7c92d/659_bgw-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-rnd-pltf-dev-nextflow-scratch-01/work/12/b67be7e02742b3f5c7d852dac7c92d/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam 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/23/e53d7766982e1f18acfd8cba247f67/.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/23/e53d7766982e1f18acfd8cba247f67/.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 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed seqtool depth -bam 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam -bed 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz saturation_plot -bams 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam -region chr20 -output 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/saturation_qc.tsv fragment_size -bams 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam -region chr20 -output_prefix 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.mpileup && contamination -input 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/contamination.tsv seqtool noise -bam 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam -ref Homo_sapiens_assembly38.fasta -region chr20 -include_bed 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed -exclude_bed dbsnp138_hg38_common.bed -threads 1 > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.noise_summary.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-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: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-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: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s] 152444it [00:00, 1524376.03it/s] 316011it [00:00, 1589811.62it/s] 484721it [00:00, 1634208.69it/s] 652577it [00:00, 1651698.12it/s] 822195it [00:00, 1667585.44it/s] 991875it [00:00, 1677500.54it/s] 1163828it [00:00, 1691126.03it/s] 1334832it [00:00, 1697049.46it/s] 1504537it [00:00, 1692108.04it/s] 1675104it [00:01, 1696272.97it/s] 1844735it [00:01, 1665108.16it/s] 2011369it [00:01, 1644261.20it/s] 2178527it [00:01, 1652372.11it/s] 2343862it [00:01, 1621269.18it/s] 2506151it [00:01, 1588221.51it/s] 2671479it [00:01, 1607182.17it/s] 2841318it [00:01, 1634011.58it/s] 3011859it [00:01, 1655079.05it/s] 3183056it [00:01, 1671968.96it/s] 3350389it [00:02, 1665621.17it/s] 3519648it [00:02, 1673567.43it/s] 3687079it [00:02, 1659380.13it/s] 3853089it [00:02, 1604535.21it/s] 4017325it [00:02, 1615528.13it/s] 4179191it [00:02, 1586471.73it/s] 4345348it [00:02, 1608360.33it/s] 4506445it [00:02, 1600971.09it/s] 4674908it [00:02, 1625599.73it/s] 4839325it [00:02, 1631045.24it/s] 5002612it [00:03, 1631436.86it/s] 5165843it [00:03, 1599154.89it/s] 5334099it [00:03, 1623708.39it/s] 5501131it [00:03, 1637500.47it/s] 5665023it [00:03, 1636850.95it/s] 5828807it [00:03, 1610867.82it/s] 5990041it [00:03, 1593357.47it/s] 6153793it [00:03, 1606322.67it/s] 6320302it [00:03, 1623689.08it/s] 6482771it [00:03, 1620810.67it/s] 6648461it [00:04, 1631465.68it/s] 6816101it [00:04, 1644849.24it/s] 6980634it [00:04, 1594071.13it/s] 7140400it [00:04, 1500418.96it/s] 7291662it [00:04, 1491980.28it/s] 7446353it [00:04, 1507660.50it/s] 7613696it [00:04, 1555558.12it/s] 7784085it [00:04, 1598974.00it/s] 7954733it [00:04, 1630640.46it/s] 8122649it [00:05, 1645009.32it/s] 8290597it [00:05, 1655242.02it/s] 8458398it [00:05, 1662006.66it/s] 8629444it [00:05, 1676469.81it/s] 8800321it [00:05, 1686066.04it/s] 8974428it [00:05, 1702420.64it/s] 9149719it [00:05, 1717485.23it/s] 9325007it [00:05, 1728076.75it/s] 9497850it [00:05, 1718913.84it/s] 9670764it [00:05, 1721955.54it/s] 9842986it [00:06, 1721736.78it/s] 10015178it [00:06, 1721476.38it/s] 10187339it [00:06, 1708750.69it/s] 10358243it [00:06, 1700373.50it/s] 10528305it [00:06, 1692785.14it/s] 10697603it [00:06, 1689649.71it/s] 10866642it [00:06, 1689857.43it/s] 11035637it [00:06, 1685895.83it/s] 11204233it [00:06, 1679957.30it/s]done loading BEDs. 11373372it [00:06, 1683353.18it/s] 11543602it [00:07, 1688998.55it/s] 11712509it [00:07, 1681800.95it/s] 11882039it [00:07, 1685815.97it/s] 12052292it [00:07, 1690792.10it/s] 12221618it [00:07, 1691515.39it/s] 12391824it [00:07, 1694655.47it/s] 12565228it [00:07, 1706444.30it/s] 12739963it [00:07, 1718693.38it/s] 12911837it [00:07, 1709635.24it/s] 13083023it [00:07, 1710288.21it/s] 13254454it [00:08, 1711479.53it/s] 13425610it [00:08, 1707377.52it/s] 13596355it [00:08, 1660088.82it/s] 13762643it [00:08, 1635687.65it/s] 13934710it [00:08, 1660509.02it/s] 14105769it [00:08, 1675246.40it/s] 14274211it [00:08, 1677949.34it/s] 14442140it [00:08, 1673530.13it/s][W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 14609586it [00:08, 1650088.35it/s] 14783894it [00:08, 1677534.04it/s] 14958609it [00:09, 1698174.07it/s] 15134783it [00:09, 1717083.26it/s] 15307328it [00:09, 1719566.55it/s] 15482279it [00:09, 1728473.63it/s] 15656899it [00:09, 1733763.99it/s] 15830313it [00:09, 1705499.81it/s] 16000988it [00:09, 1690429.38it/s] 16172877it [00:09, 1698822.69it/s] 16342843it [00:09, 1682881.74it/s] 16511208it [00:09, 1682742.80it/s] 16679536it [00:10, 1680096.80it/s] 16849562it [00:10, 1686085.28it/s] 17018408it [00:10, 1686780.83it/s] 17187108it [00:10, 1673534.53it/s] 17354568it [00:10, 1673836.53it/s] 17523648it [00:10, 1678879.32it/s] 17693376it [00:10, 1684355.54it/s] 17862783it [00:10, 1687230.58it/s] 18032490it [00:10, 1690158.73it/s] 18201752it [00:10, 1690878.42it/s] 18375809it [00:11, 1705618.84it/s] 18548886it [00:11, 1713139.23it/s] 18720607it [00:11, 1714343.12it/s] 18893255it [00:11, 1717962.37it/s] 19065054it [00:11, 1703368.55it/s] 19235421it [00:11, 1701866.86it/s] 19405628it [00:11, 1697141.26it/s] 19575665it [00:11, 1698089.38it/s] 19745485it [00:11, 1688293.72it/s] 19914332it [00:11, 1686012.21it/s] 20086689it [00:12, 1697203.84it/s] 20258635it [00:12, 1703728.27it/s] 20429586it [00:12, 1705358.59it/s] 20600132it [00:12, 1698250.75it/s] 20769969it [00:12, 1688967.73it/s] 20938882it [00:12, 1667707.75it/s] 21105712it [00:12, 1652343.72it/s] 21275867it [00:12, 1666854.08it/s] 21444240it [00:12, 1671845.72it/s] 21616528it [00:12, 1687021.25it/s] 21785277it [00:13, 1649014.20it/s] 21950383it [00:13, 1580247.83it/s] 22122311it [00:13, 1620073.72it/s] 22291627it [00:13, 1641310.02it/s] 22458807it [00:13, 1650243.87it/s] 22626947it [00:13, 1659433.27it/s] 22793170it [00:13, 1656909.79it/s] 22962742it [00:13, 1668384.50it/s] 23131563it [00:13, 1674265.09it/s] 23299096it [00:13, 1659978.77it/s] 23471063it [00:14, 1677708.04it/s] 23642376it [00:14, 1688227.72it/s] 23811265it [00:14, 1680211.06it/s] 23980816it [00:14, 1684755.33it/s] 24149331it [00:14, 1662420.75it/s] 24315659it [00:14, 1661406.18it/s] 24484736it [00:14, 1670118.92it/s] 24655503it [00:14, 1681158.73it/s] 24824755it [00:14, 1684537.22it/s] 24995687it [00:15, 1691934.79it/s] 25165504it [00:15, 1693655.27it/s] 25334887it [00:15, 1690188.80it/s] 25503919it [00:15, 1689236.78it/s] 25675749it [00:15, 1697925.68it/s] 25845550it [00:15, 1690292.51it/s] 26014592it [00:15, 1685917.24it/s] 26183194it [00:15, 1677078.75it/s] 26227675it [00:15, 1666728.29it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai tabix -s 1 -b 2 -e 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv cat 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md -output 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool gc_bias -reference Homo_sapiens_assembly38.fasta -bed FINAL_hotspot_list_07302025_hg38_sorted.bed -bin_size 0.05 -threads 1 -bam_threads 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool read_qc -bed foresight_clarity_targets_hg38.bed -n_threads 1 -bam_threads 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool reads_per_target -bed foresight_clarity_targets_hg38.bed -threads 1 -bam_threads 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool depth_stats -bed foresight_clarity_targets_hg38.bed 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_bgw-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 2 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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: 659_bgw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai cat 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 "659_bgw-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "FINAL_hotspot_list_07302025_hg38_sorted.bed" -output "659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.FINAL_hotspot_list_07302025_hg38_sorted.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.foresight_clarity_targets_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bgw-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "foresight_clarity_targets_hg38.bed" -output "659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.foresight_clarity_targets_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 "659_bgw-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_noncoding_postQC_hg38.bed" -output "659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_noncoding_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 "659_bgw-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_coding_postQC_hg38.bed" -output "659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_coding_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 "659_bgw-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_postQC_hg38.bed" -output "659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 "659_bgw-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed" -output "659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 "659_bgw-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 "659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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 "659_bgw-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 "659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-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` > 659_bgw-T1-TDNA-1_A23MHWWLT4_1/659_bgw-T1-TDNA-1_A23MHWWLT4_1.md/qc_complete.txt