Run the viral-ngs Snakemake pipelines inside a Docker environment

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  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
    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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