document
  default <http://snakemake-provenance#>
  prefix crypto <http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#>
  prefix rdfs <http://www.w3.org/2000/01/rdf-schema#>
  
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/REF_aln.bam, samples/2VM-sim/20170904/alignments/rejects.bam, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/REF_aln.bam, samples/2VM-sim/20170904/alignments/full_aln.bam, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/REF_aln.bam, references/ALL_aln_majority.fasta, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/REF_aln.bam, references/ALL_aln_ambig.fasta, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/full_aln.bam.bai, samples/2VM-sim/20170904/alignments/full_aln.sam, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/full_aln.bam, samples/2VM-sim/20170904/alignments/full_aln.sam, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/rejects.bam.bai, samples/2VM-sim/20170904/alignments/rejects.sam, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/rejects.bam, samples/2VM-sim/20170904/alignments/rejects.sam, -, -, -)
  wasDerivedFrom(references/ALL_aln_ambig.fasta, references/HXB2.fasta, -, -, -)
  wasDerivedFrom(references/ALL_aln_ambig.fasta, samples/2VM-sim/20170904/references/ref_ambig.fasta, -, -, -)
  wasDerivedFrom(references/ALL_aln_majority.fasta, references/HXB2.fasta, -, -, -)
  wasDerivedFrom(references/ALL_aln_majority.fasta, samples/2VM-sim/20170904/references/ref_majority.fasta, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/references/ref_majority.fasta, samples/2VM-sim/20170904/preprocessed_data/R2.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/references/ref_majority.fasta, samples/2VM-sim/20170904/preprocessed_data/R1.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/references/ref_majority.fasta, samples/2VM-sim/20170904/references/initial_consensus.fasta, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/references/ref_ambig.fasta, samples/2VM-sim/20170904/preprocessed_data/R2.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/references/ref_ambig.fasta, samples/2VM-sim/20170904/preprocessed_data/R1.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/references/ref_ambig.fasta, samples/2VM-sim/20170904/references/initial_consensus.fasta, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/rejects.sam, samples/2VM-sim/20170904/preprocessed_data/R2.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/rejects.sam, samples/2VM-sim/20170904/preprocessed_data/R1.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/rejects.sam, samples/2VM-sim/20170904/references/initial_consensus.fasta, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/full_aln.sam, samples/2VM-sim/20170904/preprocessed_data/R2.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/full_aln.sam, samples/2VM-sim/20170904/preprocessed_data/R1.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/alignments/full_aln.sam, samples/2VM-sim/20170904/references/initial_consensus.fasta, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/references/initial_consensus.fasta, references/initial_aln_gap_removed.fasta, -, -, -)
  wasDerivedFrom(references/initial_aln_gap_removed.fasta, samples/2VM-sim/20170904/references/vicuna_consensus.fasta, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/references/vicuna_consensus.fasta, samples/2VM-sim/20170904/preprocessed_data/R2.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/references/vicuna_consensus.fasta, samples/2VM-sim/20170904/preprocessed_data/R1.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/references/vicuna_consensus.fasta, references/HXB2.fasta, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/preprocessed_data/R1.fastq, samples/2VM-sim/20170904/preprocessed_data/R1.fastq.gz, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/preprocessed_data/R2.fastq, samples/2VM-sim/20170904/preprocessed_data/R2.fastq.gz, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/preprocessed_data/R2.fastq.gz, samples/2VM-sim/20170904/extracted_data/R2.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/preprocessed_data/R2.fastq.gz, samples/2VM-sim/20170904/extracted_data/R1.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/preprocessed_data/R1.fastq.gz, samples/2VM-sim/20170904/extracted_data/R2.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/preprocessed_data/R1.fastq.gz, samples/2VM-sim/20170904/extracted_data/R1.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/extracted_data/R2.fastq, samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R2.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/extracted_data/R1.fastq, samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R1.fastq, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R1.fastq, samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R1.fastq.gz, -, -, -)
  wasDerivedFrom(samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R2.fastq, samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R2.fastq.gz, -, -, -)
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  wasGeneratedBy(samples/2VM-sim/20170904/alignments/full_aln.bam.bai, activity-sam2bam-231b5d2a-58d6-41bd-8f94-b4b3d452becb, -)
  wasGeneratedBy(samples/2VM-sim/20170904/alignments/full_aln.bam, activity-sam2bam-231b5d2a-58d6-41bd-8f94-b4b3d452becb, -)
  wasGeneratedBy(samples/2VM-sim/20170904/alignments/rejects.bam.bai, activity-sam2bam-42ed3490-c14e-472c-8324-32e08d3c71bb, -)
  wasGeneratedBy(samples/2VM-sim/20170904/alignments/rejects.bam, activity-sam2bam-42ed3490-c14e-472c-8324-32e08d3c71bb, -)
  wasGeneratedBy(references/ALL_aln_ambig.fasta, activity-msa-48d8d399-d6cd-45e7-bc1b-ec1777dace97, -)
  wasGeneratedBy(references/ALL_aln_majority.fasta, activity-msa-36eec256-11ee-465f-90e5-341eb23f5b54, -)
  wasGeneratedBy(samples/2VM-sim/20170904/references/ref_majority.fasta, activity-hmm_align-4a4a68e6-fa68-4be9-9892-af73802d36ed, -)
  wasGeneratedBy(samples/2VM-sim/20170904/references/ref_ambig.fasta, activity-hmm_align-4a4a68e6-fa68-4be9-9892-af73802d36ed, -)
  wasGeneratedBy(samples/2VM-sim/20170904/alignments/rejects.sam, activity-hmm_align-4a4a68e6-fa68-4be9-9892-af73802d36ed, -)
  wasGeneratedBy(samples/2VM-sim/20170904/alignments/full_aln.sam, activity-hmm_align-4a4a68e6-fa68-4be9-9892-af73802d36ed, -)
  wasGeneratedBy(samples/2VM-sim/20170904/references/initial_consensus.fasta, activity-create_vicuna_initial-2c966b37-b971-481e-b796-1cf496060b27, -)
  wasGeneratedBy(references/initial_aln_gap_removed.fasta, activity-initial_vicuna_msa-416c38f6-592f-4876-a9f4-baae66f8a748, -)
  wasGeneratedBy(samples/2VM-sim/20170904/references/vicuna_consensus.fasta, activity-initial_vicuna-ac2da80a-9a0b-41e9-8f7f-c17637d0363e, -)
  wasGeneratedBy(samples/2VM-sim/20170904/preprocessed_data/R1.fastq, activity-gunzip-4a61c654-a8ae-41a9-aaf2-3ab541a6818f, -)
  wasGeneratedBy(samples/2VM-sim/20170904/preprocessed_data/R2.fastq, activity-gunzip-799d4179-0470-4bad-b741-3c882ebcd14e, -)
  wasGeneratedBy(samples/2VM-sim/20170904/preprocessed_data/R2.fastq.gz, activity-preprocessing-73e31451-094a-4cad-94eb-201f065d0c7f, -)
  wasGeneratedBy(samples/2VM-sim/20170904/preprocessed_data/R1.fastq.gz, activity-preprocessing-73e31451-094a-4cad-94eb-201f065d0c7f, -)
  wasGeneratedBy(samples/2VM-sim/20170904/extracted_data/R2.fastq, activity-extract-05915f2a-a1c6-4033-ae19-eab204ab344e, -)
  wasGeneratedBy(samples/2VM-sim/20170904/extracted_data/R1.fastq, activity-extract-9bfbf4fe-c195-41c4-beb6-785bf0190a92, -)
  wasGeneratedBy(samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R1.fastq, activity-gunzip-36804754-fba7-4969-8b56-7c91907e9949, -)
  wasGeneratedBy(samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R2.fastq, activity-gunzip-bbb8a266-392a-4e67-9776-a46047ff2691, -)
  used(activity-all-7c122235-7cd0-409e-8dbe-9a0082bc8bf4, samples/2VM-sim/20170904/references/ref_majority.fasta, -)
  used(activity-all-7c122235-7cd0-409e-8dbe-9a0082bc8bf4, samples/2VM-sim/20170904/references/ref_ambig.fasta, -)
  used(activity-all-7c122235-7cd0-409e-8dbe-9a0082bc8bf4, samples/2VM-sim/20170904/alignments/REF_aln.bam, -)
  used(activity-convert_to_ref-e8ff9e0f-8a41-4443-bd7b-ba5dc6907c6b, samples/2VM-sim/20170904/alignments/rejects.bam, -)
  used(activity-convert_to_ref-e8ff9e0f-8a41-4443-bd7b-ba5dc6907c6b, samples/2VM-sim/20170904/alignments/full_aln.bam, -)
  used(activity-convert_to_ref-e8ff9e0f-8a41-4443-bd7b-ba5dc6907c6b, references/ALL_aln_majority.fasta, -)
  used(activity-convert_to_ref-e8ff9e0f-8a41-4443-bd7b-ba5dc6907c6b, references/ALL_aln_ambig.fasta, -)
  used(activity-sam2bam-231b5d2a-58d6-41bd-8f94-b4b3d452becb, samples/2VM-sim/20170904/alignments/full_aln.sam, -)
  used(activity-sam2bam-42ed3490-c14e-472c-8324-32e08d3c71bb, samples/2VM-sim/20170904/alignments/rejects.sam, -)
  used(activity-msa-48d8d399-d6cd-45e7-bc1b-ec1777dace97, references/HXB2.fasta, -)
  used(activity-msa-48d8d399-d6cd-45e7-bc1b-ec1777dace97, samples/2VM-sim/20170904/references/ref_ambig.fasta, -)
  used(activity-msa-36eec256-11ee-465f-90e5-341eb23f5b54, references/HXB2.fasta, -)
  used(activity-msa-36eec256-11ee-465f-90e5-341eb23f5b54, samples/2VM-sim/20170904/references/ref_majority.fasta, -)
  used(activity-hmm_align-4a4a68e6-fa68-4be9-9892-af73802d36ed, samples/2VM-sim/20170904/preprocessed_data/R2.fastq, -)
  used(activity-hmm_align-4a4a68e6-fa68-4be9-9892-af73802d36ed, samples/2VM-sim/20170904/preprocessed_data/R1.fastq, -)
  used(activity-hmm_align-4a4a68e6-fa68-4be9-9892-af73802d36ed, samples/2VM-sim/20170904/references/initial_consensus.fasta, -)
  used(activity-create_vicuna_initial-2c966b37-b971-481e-b796-1cf496060b27, references/initial_aln_gap_removed.fasta, -)
  used(activity-initial_vicuna_msa-416c38f6-592f-4876-a9f4-baae66f8a748, samples/2VM-sim/20170904/references/vicuna_consensus.fasta, -)
  used(activity-initial_vicuna-ac2da80a-9a0b-41e9-8f7f-c17637d0363e, samples/2VM-sim/20170904/preprocessed_data/R2.fastq, -)
  used(activity-initial_vicuna-ac2da80a-9a0b-41e9-8f7f-c17637d0363e, samples/2VM-sim/20170904/preprocessed_data/R1.fastq, -)
  used(activity-initial_vicuna-ac2da80a-9a0b-41e9-8f7f-c17637d0363e, references/HXB2.fasta, -)
  used(activity-gunzip-4a61c654-a8ae-41a9-aaf2-3ab541a6818f, samples/2VM-sim/20170904/preprocessed_data/R1.fastq.gz, -)
  used(activity-gunzip-799d4179-0470-4bad-b741-3c882ebcd14e, samples/2VM-sim/20170904/preprocessed_data/R2.fastq.gz, -)
  used(activity-preprocessing-73e31451-094a-4cad-94eb-201f065d0c7f, samples/2VM-sim/20170904/extracted_data/R2.fastq, -)
  used(activity-preprocessing-73e31451-094a-4cad-94eb-201f065d0c7f, samples/2VM-sim/20170904/extracted_data/R1.fastq, -)
  used(activity-extract-05915f2a-a1c6-4033-ae19-eab204ab344e, samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R2.fastq, -)
  used(activity-extract-9bfbf4fe-c195-41c4-beb6-785bf0190a92, samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R1.fastq, -)
  used(activity-gunzip-36804754-fba7-4969-8b56-7c91907e9949, samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R1.fastq.gz, -)
  used(activity-gunzip-bbb8a266-392a-4e67-9776-a46047ff2691, samples/2VM-sim/20170904/raw_data/2VirusMix_simulated_R2.fastq.gz, -)
  entity(samples/2VM-sim/20170904/alignments/REF_aln.bam)
  entity(samples/2VM-sim/20170904/alignments/REF_aln.bam)
  entity(samples/2VM-sim/20170904/alignments/full_aln.bam.bai)
  entity(samples/2VM-sim/20170904/alignments/full_aln.bam)
  entity(samples/2VM-sim/20170904/alignments/full_aln.bam)
  entity(samples/2VM-sim/20170904/alignments/rejects.bam.bai)
  entity(samples/2VM-sim/20170904/alignments/rejects.bam)
  entity(samples/2VM-sim/20170904/alignments/rejects.bam)
  entity(references/ALL_aln_ambig.fasta)
  entity(references/ALL_aln_ambig.fasta)
endDocument