Run the viral-ngs Snakemake pipelines inside a Docker environment

1. Pull the viral-ngs Docker Image

   docker pull quay.io/broadinstitute/viral-ngs
   
   docker run -t quay.io/broadinstitute/viral-ngs
   
   # Without /bin/bash → May run and exit immediately
   docker run -it quay.io/broadinstitute/viral-ngs
   # With /bin/bash → Stays open for interaction
   docker run -it --entrypoint /bin/bash quay.io/broadinstitute/viral-ngs
   docker run -it quay.io/broadinstitute/viral-ngs
   docker attach <container_id>
   
   docker run -v /home/jhuang/DATA/Data_Huang_Human_herpesvirus_3/viralngs_docker/data:/user-data -it quay.io/broadinstitute/viral-ngs
   
   snakemake --printshellcmds --cores 80
   
   # IMPORTANT_NOTE: we can have a look of the structure of env rkitchen/excerpt
   docker run -v ~/DATA/Data_Ute/Data_Ute_smallRNA_7/trimmed:/exceRptInput \
                       -v ~/DATA/Data_Ute/Data_Ute_smallRNA_7/results_exo5:/exceRptOutput \
                       -v /mnt/nvme0n1p1/MyexceRptDatabase:/exceRpt_DB \
                       --entrypoint /bin/bash -it rkitchen/excerpt #\
                       #INPUT_FILE_PATH=/exceRptInput/xxx.gz MAIN_ORGANISM_GENOME_ID=hg38 N_THREADS=50 JAVA_RAM='200G' MAP_EXOGENOUS=on
   
   docker inspect quay.io/broadinstitute/viral-ngs
               "Env": [
           "PATH=/opt/viral-ngs/source:/opt/miniconda/envs/viral-ngs-env/bin:/opt/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
           "LANG=en_US.UTF-8",
           "LANGUAGE=en_US:en",
           "LC_ALL=en_US.UTF-8",
           "MINICONDA_PATH=/opt/miniconda",
           "INSTALL_PATH=/opt/viral-ngs",
           "VIRAL_NGS_PATH=/opt/viral-ngs/source",
           "CONDA_DEFAULT_ENV=viral-ngs-env",
           "CONDA_PREFIX=/opt/miniconda/envs/viral-ngs-env",
           "JAVA_HOME=/opt/miniconda",
           "VIRAL_NGS_DOCKER_DATA_PATH=/user-data",
           "NOVOALIGN_PATH=/novoalign",
           "GATK_PATH=/gatk"
       ]
   

2. Set Up the Analysis Directory Structure

   The pipeline expects a specific directory structure. Inside your host machine (not the container), create:
   
   viralngs_docker/
   │── config.yaml          # Copy from viral-ngs/pipes/
   │── Snakefile            # Copy from viral-ngs/pipes/
   │── data/
   │   ├── 00_raw/          # Place input BAM files (e.g., `sample1.bam`)
   │   ├── 01_cleaned/
   │   ├── 01_per_sample/
   │   ├── 02_align_to_self/
   │   ├── 02_assembly/
   │   ├── 03_align_to_ref/
   │   ├── 03_interhost/
   │   ├── 04_intrahost/
   │── log/
   │── reports/
   │── tmp/
   │── samples-depletion.txt    # List samples (one per line, e.g., `sample1`)
   │── samples-assembly.txt     # List samples for assembly
   │── samples-runs.txt         # List samples for interhost analysis
   │── samples-assembly-failures.txt  # (Leave empty)
   
   Key Steps:
   
       Input BAMs: Place your .bam files in data/00_raw/ (e.g., sample1.bam).
   
       Sample Lists:
   
           samples-depletion.txt → Samples for depletion pipeline.
   
           samples-assembly.txt → Samples for assembly pipeline.
   
           samples-runs.txt → Samples for interhost analysis.
   

3. Run the Pipeline in Docker

   Mount your analysis directory into the container and execute Snakemake:
   
   cd /mnt/md1/DATA/Data_Huang_Human_herpesvirus_3
   docker run -it \
   -v "$(pwd)/viralngs_docker:/opt/viral-ngs-analysis" \
   -w /opt/viral-ngs-analysis \
   quay.io/broadinstitute/viral-ngs \
   snakemake --cores all --use-conda
   
   Flags Explained:
   Flag    Purpose
   -v $(pwd)/viralngs_docker:/opt/viral-ngs-analysis   Mounts your host directory into the container.
   -w /opt/viral-ngs-analysis  Sets the working directory inside the container.
   --cores all Uses all available CPU cores.
   --use-conda Ensures Conda environments are used (if specified in rules).
   

4. Customize config.yaml

   Edit the config.yaml file (copied from viral-ngs/pipes/) to match your project:
   
   # Example config.yaml adjustments:
   ref_genome: "path/to/reference.fasta"
   threads: 40  # Number of CPU threads
   

5. Monitor Pipeline Progress

   Logs: Check log/ for detailed logs.
   
   Snakemake Options:
   
       snakemake -n → Dry run (simulate pipeline).
   
       snakemake --dag | dot -Tpng > dag.png → Generate a workflow graph.
   

6. Post-Run Outputs

   Results will be organized in:
   
       data/02_assembly/ → Assembled genomes.
   
       data/03_interhost/ → Interhost variants.
   
       reports/ → Summary reports.
   

7. Troubleshooting

   Issue: Missing Dependencies

   If Snakemake fails due to missing tools, ensure Conda is available inside Docker:
   /user-data/viral_ngs_dbs/
   docker run -it \
   -v "$(pwd)/viralngs_docker:/opt/viral-ngs-analysis" \
   -w /opt/viral-ngs-analysis \
   quay.io/broadinstitute/viral-ngs \
   bash -c "conda install -y snakemake && snakemake --cores 20 --use-conda"
   #NOTE that we can also install tools inside Docker!!!!
   

   Issue: Permissions

   Ensure the container can write to your mounted directory:
   
   chmod -R a+rwx viralngs_docker
   

8. Alternative: Run Inside an Interactive Container (FINAL RUNNABLE)

   For debugging, start a shell and run Snakemake manually:

   #docker run -it \
   #-v "$(pwd)/viralngs_docker:/opt/viral-ngs-analysis" \
   #-w /opt/viral-ngs-analysis \
   #--entrypoint /bin/bash \
   #quay.io/broadinstitute/viral-ngs
   docker run \
   -v /mnt/md1/DATA/Data_Huang_Human_herpesvirus_3/viralngs_docker:/opt/viral-ngs-analysis \
   -v /home/jhuang/REFs:/user-data \
   -v /home/jhuang/Tools/novocraft_v3:/novoalign \
   -v /home/jhuang/Tools/GenomeAnalysisTK-3.6:/gatk \
   -w /opt/viral-ngs-analysis \
   --entrypoint /bin/bash \
   -it quay.io/broadinstitute/viral-ngs
   
   #Under viral-ngs-analysis
   ln -s /opt/viral-ngs/source bin
   
   # Inside the container:
   snakemake --cores 20 --use-conda
   

9. LOG

   root@37a95bb989f3:/opt/viral-ngs-analysis# snakemake --cores 20 --use-conda
   Building DAG of jobs...
   Using shell: /bin/bash
   Provided cores: 20
   Rules claiming more threads will be scaled down.
   Job counts:
           count   jobs
           1       all
           10      assemble_spades
           1       consolidate_fastqc_on_all_assemblies
           2       consolidate_fastqc_on_all_runs
           1       consolidate_spike_count
           10      depletion
           30      fastqc_report
           10      filter_to_taxon
           10      isnvs_per_sample
           1       isnvs_vcf
           10      map_reads_to_self
           20      merge_one_per_sample
           1       multi_align_mafft
           10      orient_and_impute
           10      refine_assembly_1
           10      refine_assembly_2
           10      spikein_report
           147
   
   [Thu Apr  3 11:52:51 2025]
   rule depletion:
       input: data/00_raw/PCC1_VZV_60_6.bam, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssd, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nin, sabeti-public-dbs/bwa/hg19.bwt, sabeti-public-dbs/bwa/hg19.amb, sabeti-public-dbs/bwa/hg19.ann, sabeti-public-dbs/bwa/hg19.pac, sabeti-public-dbs/bwa/hg19.sa
       output: tmp/01_cleaned/PCC1_VZV_60_6.bwa_depleted.bam, tmp/01_cleaned/PCC1_VZV_60_6.bmtagger_depleted.bam, tmp/01_cleaned/PCC1_VZV_60_6.rmdup.bam, data/01_cleaned/PCC1_VZV_60_6.cleaned.bam
       jobid: 128
       wildcards: sample=PCC1_VZV_60_6
       resources: mem_mb=15000, threads=15
   
   [Thu Apr  3 11:52:51 2025]
   rule depletion:
       input: data/00_raw/VZV_60c.bam, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssd, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nin, sabeti-public-dbs/bwa/hg19.bwt, sabeti-public-dbs/bwa/hg19.amb, sabeti-public-dbs/bwa/hg19.ann, sabeti-public-dbs/bwa/hg19.pac, sabeti-public-dbs/bwa/hg19.sa
       output: tmp/01_cleaned/VZV_60c.bwa_depleted.bam, tmp/01_cleaned/VZV_60c.bmtagger_depleted.bam, tmp/01_cleaned/VZV_60c.rmdup.bam, data/01_cleaned/VZV_60c.cleaned.bam
       jobid: 116
       wildcards: sample=VZV_60c
       resources: mem_mb=15000, threads=15
   
   [Thu Apr  3 11:52:51 2025]
   rule depletion:
       input: data/00_raw/VZV_20c.bam, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssd, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nin, sabeti-public-dbs/bwa/hg19.bwt, sabeti-public-dbs/bwa/hg19.amb, sabeti-public-dbs/bwa/hg19.ann, sabeti-public-dbs/bwa/hg19.pac, sabeti-public-dbs/bwa/hg19.sa
       output: tmp/01_cleaned/VZV_20c.bwa_depleted.bam, tmp/01_cleaned/VZV_20c.bmtagger_depleted.bam, tmp/01_cleaned/VZV_20c.rmdup.bam, data/01_cleaned/VZV_20c.cleaned.bam
       jobid: 112
       wildcards: sample=VZV_20c
       resources: mem_mb=15000, threads=15
   
   [Thu Apr  3 11:52:51 2025]
   rule depletion:
       input: data/00_raw/PCC1_VZV_20_2.bam, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssd, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nin, sabeti-public-dbs/bwa/hg19.bwt, sabeti-public-dbs/bwa/hg19.amb, sabeti-public-dbs/bwa/hg19.ann, sabeti-public-dbs/bwa/hg19.pac, sabeti-public-dbs/bwa/hg19.sa
       output: tmp/01_cleaned/PCC1_VZV_20_2.bwa_depleted.bam, tmp/01_cleaned/PCC1_VZV_20_2.bmtagger_depleted.bam, tmp/01_cleaned/PCC1_VZV_20_2.rmdup.bam, data/01_cleaned/PCC1_VZV_20_2.cleaned.bam
       jobid: 120
       wildcards: sample=PCC1_VZV_20_2
       resources: mem_mb=15000, threads=15
   
   [Thu Apr  3 11:52:51 2025]
   rule depletion:
       input: data/00_raw/PCC1_VZV_20_5.bam, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssd, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nin, sabeti-public-dbs/bwa/hg19.bwt, sabeti-public-dbs/bwa/hg19.amb, sabeti-public-dbs/bwa/hg19.ann, sabeti-public-dbs/bwa/hg19.pac, sabeti-public-dbs/bwa/hg19.sa
       output: tmp/01_cleaned/PCC1_VZV_20_5.bwa_depleted.bam, tmp/01_cleaned/PCC1_VZV_20_5.bmtagger_depleted.bam, tmp/01_cleaned/PCC1_VZV_20_5.rmdup.bam, data/01_cleaned/PCC1_VZV_20_5.cleaned.bam
       jobid: 122
       wildcards: sample=PCC1_VZV_20_5
       resources: mem_mb=15000, threads=15
   
   [Thu Apr  3 11:52:51 2025]
   rule depletion:
       input: data/00_raw/PCC1_VZV_60_4.bam, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssd, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nin, sabeti-public-dbs/bwa/hg19.bwt, sabeti-public-dbs/bwa/hg19.amb, sabeti-public-dbs/bwa/hg19.ann, sabeti-public-dbs/bwa/hg19.pac, sabeti-public-dbs/bwa/hg19.sa
       output: tmp/01_cleaned/PCC1_VZV_60_4.bwa_depleted.bam, tmp/01_cleaned/PCC1_VZV_60_4.bmtagger_depleted.bam, tmp/01_cleaned/PCC1_VZV_60_4.rmdup.bam, data/01_cleaned/PCC1_VZV_60_4.cleaned.bam
       jobid: 126
       wildcards: sample=PCC1_VZV_60_4
       resources: mem_mb=15000, threads=15
   
   [Thu Apr  3 11:52:51 2025]
   rule depletion:
       input: data/00_raw/VZV_60S.bam, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssd, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nin, sabeti-public-dbs/bwa/hg19.bwt, sabeti-public-dbs/bwa/hg19.amb, sabeti-public-dbs/bwa/hg19.ann, sabeti-public-dbs/bwa/hg19.pac, sabeti-public-dbs/bwa/hg19.sa
       output: tmp/01_cleaned/VZV_60S.bwa_depleted.bam, tmp/01_cleaned/VZV_60S.bmtagger_depleted.bam, tmp/01_cleaned/VZV_60S.rmdup.bam, data/01_cleaned/VZV_60S.cleaned.bam
       jobid: 114
       wildcards: sample=VZV_60S
       resources: mem_mb=15000, threads=15
   
   [Thu Apr  3 11:52:51 2025]
   rule depletion:
       input: data/00_raw/VZV_20S.bam, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssd, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nin, sabeti-public-dbs/bwa/hg19.bwt, sabeti-public-dbs/bwa/hg19.amb, sabeti-public-dbs/bwa/hg19.ann, sabeti-public-dbs/bwa/hg19.pac, sabeti-public-dbs/bwa/hg19.sa
       output: tmp/01_cleaned/VZV_20S.bwa_depleted.bam, tmp/01_cleaned/VZV_20S.bmtagger_depleted.bam, tmp/01_cleaned/VZV_20S.rmdup.bam, data/01_cleaned/VZV_20S.cleaned.bam
       jobid: 110
       wildcards: sample=VZV_20S
       resources: mem_mb=15000, threads=15
   
   [Thu Apr  3 11:52:51 2025]
   rule depletion:
       input: data/00_raw/PCC1_VZV_20_1.bam, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssd, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nin, sabeti-public-dbs/bwa/hg19.bwt, sabeti-public-dbs/bwa/hg19.amb, sabeti-public-dbs/bwa/hg19.ann, sabeti-public-dbs/bwa/hg19.pac, sabeti-public-dbs/bwa/hg19.sa
       output: tmp/01_cleaned/PCC1_VZV_20_1.bwa_depleted.bam, tmp/01_cleaned/PCC1_VZV_20_1.bmtagger_depleted.bam, tmp/01_cleaned/PCC1_VZV_20_1.rmdup.bam, data/01_cleaned/PCC1_VZV_20_1.cleaned.bam
       jobid: 118
       wildcards: sample=PCC1_VZV_20_1
       resources: mem_mb=15000, threads=15
   
   [Thu Apr  3 11:52:51 2025]
   rule depletion:
       input: data/00_raw/PCC1_VZV_60_1.bam, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/hg19.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA.srprism.ssd, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.bitmask, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssa, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.imp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.idx, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.map, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ss, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.amp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.rmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.pmp, /user-data/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3.srprism.ssd, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nhr, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nsq, /user-data/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters.nin, sabeti-public-dbs/bwa/hg19.bwt, sabeti-public-dbs/bwa/hg19.amb, sabeti-public-dbs/bwa/hg19.ann, sabeti-public-dbs/bwa/hg19.pac, sabeti-public-dbs/bwa/hg19.sa
       output: tmp/01_cleaned/PCC1_VZV_60_1.bwa_depleted.bam, tmp/01_cleaned/PCC1_VZV_60_1.bmtagger_depleted.bam, tmp/01_cleaned/PCC1_VZV_60_1.rmdup.bam, data/01_cleaned/PCC1_VZV_60_1.cleaned.bam
       jobid: 124
       wildcards: sample=PCC1_VZV_60_1
       resources: mem_mb=15000, threads=15
   
   Job counts:
           count   jobs
           1       depletion
           1
   

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