.command.log - Workdir - DAQ:BAM_POSTDEDUP_QC:SEQTOOL (659_bgw-T1-TDNA-1_A23MHWWLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/e53d7766982e1f18acfd8cba247f67/.command.log
Size: 32.0 KB
Task: DAQ:BAM_POSTDEDUP_QC:SEQTOOL (659_bgw-T1-TDNA-1_A23MHWWLT4_1)
Attempt
Content

  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

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[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