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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