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-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/c3/2c2cff51aae440b36f404cca7a7f09/.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-rnd-pltf-dev-nextflow-scratch-01/work/1d/3fa7431e6c620d4369640253248aa8/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 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/1d/3fa7431e6c620d4369640253248aa8/1136_6TL-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/c3/2c2cff51aae440b36f404cca7a7f09/.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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed seqtool depth -bam 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam -bed 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz saturation_plot -bams 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam -region chr20 -output 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/saturation_qc.tsv fragment_size -bams 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam -region chr20 -output_prefix 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.mpileup && contamination -input 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/contamination.tsv seqtool noise -bam 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam -ref Homo_sapiens_assembly38.fasta -region chr20 -include_bed 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed -exclude_bed dbsnp138_hg38_common.bed -threads 1 > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.noise_summary.tsv [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s] 149746it [00:00, 1497108.06it/s] 312119it [00:00, 1571558.78it/s] 478423it [00:00, 1613153.55it/s] 645249it [00:00, 1634888.88it/s] 812945it [00:00, 1650042.47it/s] 981734it [00:00, 1662894.32it/s] 1148024it [00:00, 1661592.56it/s] 1314184it [00:00, 1636729.98it/s] 1477934it [00:00, 1624933.36it/s] 1645758it [00:01, 1641056.03it/s] 1809925it [00:01, 1601283.00it/s] 1970273it [00:01, 1589836.17it/s] 2140320it [00:01, 1622526.77it/s] 2310006it [00:01, 1644625.99it/s] 2480952it [00:01, 1663892.16it/s] 2647470it [00:01, 1659869.81it/s] 2815821it [00:01, 1666718.51it/s] 2982560it [00:01, 1588460.06it/s] 3145423it [00:01, 1600068.19it/s] 3306027it [00:02, 1559357.12it/s] 3463770it [00:02, 1564447.45it/s] 3629722it [00:02, 1592098.54it/s] 3795083it [00:02, 1610203.08it/s] 3956391it [00:02, 1600046.30it/s] 4118458it [00:02, 1606133.74it/s] 4285665it [00:02, 1625573.37it/s] 4453059it [00:02, 1639967.70it/s] 4617154it [00:02, 1601023.58it/s] 4777514it [00:02, 1587075.66it/s] 4936404it [00:03, 1580378.63it/s] 5094563it [00:03, 1579087.39it/s] 5256933it [00:03, 1592279.49it/s] 5416237it [00:03, 1559681.72it/s] 5572381it [00:03, 1466109.84it/s] 5720125it [00:03, 1455180.52it/s] 5882599it [00:03, 1503621.15it/s] 6051703it [00:03, 1557940.05it/s] 6219022it [00:03, 1591542.22it/s] 6384791it [00:03, 1610989.83it/s] 6553524it [00:04, 1633605.97it/s] 6723307it [00:04, 1652700.76it/s] 6894469it [00:04, 1670112.84it/s] 7066946it [00:04, 1686343.33it/s] 7235999it [00:04, 1687581.64it/s] 7405188it [00:04, 1688859.87it/s] 7574143it [00:04, 1688008.58it/s] 7742992it [00:04, 1683362.24it/s] 7911364it [00:04, 1674750.40it/s] 8078872it [00:04, 1673871.89it/s][W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 8246570it [00:05, 1674786.36it/s] 8414065it [00:05, 1667289.10it/s] 8582236it [00:05, 1671461.96it/s] 8750433it [00:05, 1674588.57it/s] 8917903it [00:05, 1674064.70it/s] 9085540it [00:05, 1674743.36it/s] 9253020it [00:05, 1672669.02it/s] 9422333it [00:05, 1678691.83it/s] 9590207it [00:05, 1677370.86it/s] 9758404it [00:05, 1678693.84it/s] 9926276it [00:06, 1675490.34it/s] 10093828it [00:06, 1668873.26it/s] 10260722it [00:06, 1598027.84it/s] 10426578it [00:06, 1615574.75it/s] 10588629it [00:06, 1616851.78it/s] 10750663it [00:06, 1600269.11it/s] 10910949it [00:06, 1582644.24it/s]done loading BEDs. 11078383it [00:06, 1609405.43it/s] 11246062it [00:06, 1629299.34it/s] 11412970it [00:07, 1641082.78it/s] 11580720it [00:07, 1651874.43it/s] 11746007it [00:07, 1650176.14it/s] 11911094it [00:07, 1630801.67it/s] 12074267it [00:07, 1626473.06it/s] 12236977it [00:07, 1625085.61it/s] 12404482it [00:07, 1639946.59it/s] 12571739it [00:07, 1649611.65it/s] 12740282it [00:07, 1660244.20it/s] 12906335it [00:07, 1642704.62it/s] 13074639it [00:08, 1654653.84it/s] 13243314it [00:08, 1664192.59it/s] 13410818it [00:08, 1667412.05it/s] 13577591it [00:08, 1660454.59it/s] 13747944it [00:08, 1673211.18it/s] 13917302it [00:08, 1679282.85it/s] 14085742it [00:08, 1680797.68it/s] 14254169it [00:08, 1681656.66it/s] 14422345it [00:08, 1670235.10it/s] 14590072it [00:08, 1672314.93it/s] 14757575it [00:09, 1673107.58it/s] 14924899it [00:09, 1671943.26it/s] 15093224it [00:09, 1675310.60it/s] 15264223it [00:09, 1685681.08it/s] 15433535it [00:09, 1687892.41it/s] 15602330it [00:09, 1683108.54it/s] 15770648it [00:09, 1661255.22it/s] 15936837it [00:09, 1645012.22it/s] 16106029it [00:09, 1658864.37it/s] 16277491it [00:09, 1675401.95it/s] 16445095it [00:10, 1626230.48it/s] 16608048it [00:10, 1578722.71it/s] 16776689it [00:10, 1609754.32it/s] 16942895it [00:10, 1624997.99it/s] 17109104it [00:10, 1635813.64it/s] 17277020it [00:10, 1648624.81it/s] 17443021it [00:10, 1651994.85it/s] 17613426it [00:10, 1667432.06it/s] 17783776it [00:10, 1678185.36it/s] 17951678it [00:10, 1664556.16it/s] 18118214it [00:11, 1662427.67it/s] 18284512it [00:11, 1637980.41it/s] 18453151it [00:11, 1652244.98it/s] 18621038it [00:11, 1659978.89it/s] 18789347it [00:11, 1666815.49it/s] 18957670it [00:11, 1671603.59it/s] 19125749it [00:11, 1674211.23it/s] 19266369it [00:11, 1638169.72it/s] [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai tabix -s 1 -b 2 -e 2 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz seqtool depth_hist -nbins 500 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv cat 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md -output 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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 reads_per_target -bed FINAL_hotspot_list_07302025_hg38_sorted.bed -threads 1 -bam_threads 2 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv seqtool read_qc -bed FINAL_hotspot_list_07302025_hg38_sorted.bed -n_threads 1 -bam_threads 2 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/read_qc.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv seqtool depth_stats -bed FINAL_hotspot_list_07302025_hg38_sorted.bed 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-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 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool read_qc -bed foresight_clarity_targets_hg38.bed -n_threads 1 -bam_threads 2 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool reads_per_target -bed foresight_clarity_targets_hg38.bed -threads 1 -bam_threads 2 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai seqtool depth_stats -bed foresight_clarity_targets_hg38.bed 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai cat 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "FINAL_hotspot_list_07302025_hg38_sorted.bed" -output "1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "foresight_clarity_targets_hg38.bed" -output "1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.foresight_clarity_targets_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_noncoding_postQC_hg38.bed" -output "1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_coding_postQC_hg38.bed" -output "1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_postQC_hg38.bed" -output "1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_postQC_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" cat 1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed" -output "1136_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-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_6TL-T1-TDNA-1_A23MHWWLT4_1/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md/qc_complete.txt