Microbiome analysis with QIIME2

…BRIEF INTRO IN PROGRESS…


A tentative snakemake workflow that defines qiime2 bioinformatics rules in a DAG (directed acyclic graph) format. A detailed interactive snakemake HTML report is available here. Use a wider screen to get a better interactive snakemake report.





Citation

Please consider citing the iMAP article[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.


References

[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4


Appendix

Project main tree

.
├── LICENSE.md
├── README.md
├── config
│   ├── config.yml
│   ├── pbs
│   ├── samples.tsv
│   ├── slurm
│   └── units.tsv
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── data
│   ├── barcodes.fastq.gz
│   ├── forward.fastq.gz
│   ├── logs
│   ├── metadata
│   ├── reads
│   ├── references
│   ├── reverse.fastq.gz
│   ├── sample_metadata.tsv
│   └── test
├── docs
│   ├── importable_formats.txt
│   ├── importable_types.txt
│   └── primers.md
├── images
│   ├── 16srrna.png
│   ├── bioinformatics.png
│   ├── bkgd.png
│   ├── empress-tree.png
│   ├── empress-tree.svg
│   ├── imap_part05.svg
│   └── smkreport
├── imap-bioinformatics-qiime2.Rproj
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── export.bib
│   ├── imap.bib
│   └── references.bib
├── qiime2_process
│   ├── aligned-rep-seqs.qza
│   ├── alpha-rarefaction.qzv
│   ├── alpha-rarefaction.zip
│   ├── alpha_diversity
│   ├── beta_diversity
│   ├── demux-subsample.qza
│   ├── demux-subsample.qzv
│   ├── demux-subsample.zip
│   ├── demux.qza
│   ├── demux.qzv
│   ├── demux.zip
│   ├── feature-table-genus.qza
│   ├── feature-table.qza
│   ├── feature-table.qzv
│   ├── interactive1
│   ├── interactive2
│   ├── masked-aligned-rep-seqs.qza
│   ├── masked-aligned-rep-seqs.qzv
│   ├── rarefy_interactive
│   ├── rep-seqs.qza
│   ├── rep-seqs.qzv
│   ├── rooted-tree
│   ├── rooted-tree.qza
│   ├── sample-metadata.qzv
│   ├── sample-metadata.tsv
│   ├── stats.qza
│   ├── stats.qzv
│   ├── taxonomy.qza
│   ├── taxonomy.qzv
│   ├── transformed
│   ├── tree.qzv
│   ├── tree.zip
│   ├── tree_interactive
│   ├── unrooted-tree
│   └── unrooted-tree.qza
├── qiime2_process_refer
│   ├── aligned-rep-seqs.qza
│   ├── alpha-rarefaction.qzv
│   ├── alpha_diversity
│   ├── beta_diversity
│   ├── demux.qza
│   ├── demux.qzv
│   ├── early-table.qza
│   ├── feature-table-dn-99.qza
│   ├── feature-table-genus.qza
│   ├── feature-table.qzv
│   ├── googlechrome.dmg
│   ├── masked-aligned-rep-seqs.qza
│   ├── masked-aligned-rep-seqs.qzv
│   ├── new-ref-seqs-or-85.qza
│   ├── rep-seqs-cr-85.qza
│   ├── rep-seqs-dn-99.qza
│   ├── rep-seqs-or-85.qza
│   ├── rep-seqs.qzv
│   ├── rooted-tree
│   ├── rooted-tree.qza
│   ├── sample-metadata.qzv
│   ├── sample-metadata.tsv
│   ├── sample-metadata.zip
│   ├── stats.qzv
│   ├── table-cr-85.qza
│   ├── table-or-85.qza
│   ├── transformed
│   ├── unmatched-cr-85.qza
│   ├── unrooted-tree
│   └── unrooted-tree.qza
├── report.html
├── resources
│   ├── gg_classifier
│   ├── metadata
│   ├── reads
│   ├── silva_classifier
│   └── test
├── results
│   ├── count_summary.html
│   └── project_tree.txt
├── styles.css
└── workflow
    ├── Snakefile
    ├── envs
    ├── report
    ├── rules
    └── scripts

43 directories, 82 files


Unlocking working directory.
Building DAG of jobs...
Creating report...
Missing metadata for file results/project_tree.txt. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
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Missing metadata for file resources/reads/SRR17868069_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868069_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868070_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868070_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868071_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868071_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868072_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868072_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868073_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868073_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868074_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868074_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868075_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868075_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868076_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868076_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868077_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868077_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868078_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868078_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868079_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868079_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868080_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868080_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868081_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868081_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868082_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868082_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868083_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868083_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868084_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868084_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868085_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868085_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868086_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868086_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868087_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868087_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868088_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868088_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868089_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868089_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868090_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868090_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868091_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868091_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868092_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868092_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868093_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868093_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868094_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR17868094_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602723_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602723_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602724_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602724_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602725_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602725_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602726_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602726_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602727_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602727_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602728_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602728_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602729_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602729_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602730_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602730_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602731_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602731_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602732_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602732_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602733_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602733_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602734_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602734_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602735_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602735_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602736_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602736_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602737_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602737_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602738_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602738_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602739_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602739_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602740_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602740_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602741_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602741_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602742_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602742_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602743_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602743_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602744_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602744_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602745_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602745_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602746_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602746_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602747_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602747_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602748_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602748_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602749_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602749_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602750_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602750_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602751_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602751_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602752_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602752_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602753_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602753_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602754_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602754_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602755_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602755_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602756_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602756_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602757_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602757_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602758_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602758_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602759_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602759_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602760_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602760_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602761_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602761_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602762_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602762_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602763_1.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/reads/SRR23602763_2.fastq.gz. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/demux.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file resources/metadata/qiime2_manifest_file.tsv. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/alpha_diversity/rarefied_table.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/alpha_diversity/faith_pd_vector.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/alpha_diversity/observed_features_vector.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/alpha_diversity/shannon_vector.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/alpha_diversity/evenness_vector.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/unweighted_unifrac.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/weighted_unifrac.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/jaccard.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/bray_curtis.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/unweighted_unifrac_pcoa.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/weighted_unifrac_pcoa.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/jaccard_pcoa.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/bray_curtis_pcoa.qza. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/unweighted_unifrac_emperor.qzv. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/weighted_unifrac_emperor.qzv. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/jaccard_emperor.qzv. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Missing metadata for file qiime2_process/beta_diversity/bray_curtis_emperor.qzv. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
Downloading resources and rendering HTML.
Report created: report.html.
[0417/025245.459208:ERROR:xattr.cc(63)] setxattr org.chromium.crashpad.database.initialized on file /var/folders/_6/mt8ts63j5c35k8kdk17yzq7h0000gn/T/: Operation not permitted (1)
[0417/025245.572702:ERROR:file_io.cc(91)] ReadExactly: expected 8, observed 0
[0417/025245.576628:ERROR:xattr.cc(63)] setxattr org.chromium.crashpad.database.initialized on file /var/folders/_6/mt8ts63j5c35k8kdk17yzq7h0000gn/T/: Operation not permitted (1)
[0417/025254.755110:INFO:headless_shell.cc(653)] Written to file /Users/tmbuza/Dropbox/MICROBIOME/imap-bioinformatics-qiime2/images/smkreport/screenshot.png.
Created 1 file(s):
    /Users/tmbuza/Dropbox/MICROBIOME/imap-bioinformatics-qiime2/images/smkreport/screenshot.png


Troubleshooting of FAQs

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