From 39d95275755dd514abd214f39a9cf3a900c7ac6a Mon Sep 17 00:00:00 2001 From: Devon O'Rourke Date: Thu, 17 Dec 2020 12:28:39 -0500 Subject: [PATCH] resolved diversity doc with r script and manuscript --- .../VERSION | 3 - .../checksums.md5 | 99 -------- .../data/tree.nwk | 1 - .../metadata.yaml | 3 - .../provenance/VERSION | 3 - .../provenance/action/action.yaml | 160 ------------- .../VERSION | 3 - .../action/action.yaml | 182 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 182 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 160 ------------- .../citations.bib | 13 - .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 160 ------------- .../citations.bib | 13 - .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 182 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 160 ------------- .../citations.bib | 13 - .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 182 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 160 ------------- .../citations.bib | 13 - .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 182 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 172 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 171 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 160 ------------- .../citations.bib | 13 - .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 160 ------------- .../citations.bib | 13 - .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 223 ------------------ .../citations.bib | 22 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 182 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 160 ------------- .../citations.bib | 13 - .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 182 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 160 ------------- .../citations.bib | 13 - .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 182 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 182 -------------- .../citations.bib | 25 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 174 -------------- .../citations.bib | 24 -- .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 170 ------------- .../citations.bib | 13 - .../metadata.yaml | 3 - .../VERSION | 3 - .../action/action.yaml | 160 ------------- .../citations.bib | 13 - .../metadata.yaml | 3 - .../provenance/citations.bib | 13 - 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diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/metadata.yaml deleted file mode 100644 index cfefc8e..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 0dc9056e-4a2f-46da-b816-d5b6182f7dcd -type: Phylogeny[Rooted] -format: NewickDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/action/action.yaml deleted file mode 100644 index 7451f94..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/action/action.yaml +++ /dev/null @@ -1,160 +0,0 @@ -execution: - uuid: fe720c38-f063-4a2e-8811-0a530d17cd1a - runtime: - start: 2019-07-06T15:10:32.679355-04:00 - end: 2019-07-06T15:15:49.048203-04:00 - duration: 5 minutes, 16 seconds, and 368848 microseconds - -action: - type: pipeline - plugin: !ref 'environment:plugins:phylogeny' - action: align_to_tree_mafft_fasttree - inputs: - - sequences: be6cc846-b284-458b-824d-66f0666f3ed8 - parameters: - - n_threads: 24 - - mask_max_gap_frequency: 1.0 - - mask_min_conservation: 0.4 - output-name: rooted_tree - alias-of: f394d4c6-4c1b-4548-b3ef-96091164dca5 - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - phylogeny: - version: 2019.4.0 - website: https://github.com/qiime2/q2-phylogeny - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/action/action.yaml deleted file mode 100644 index 69f358a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/action/action.yaml +++ /dev/null @@ -1,182 +0,0 @@ -execution: - uuid: 7d289a6b-5af8-46bf-89ea-731f40e428ce - runtime: - start: 2019-07-02T22:09:21.116299-04:00 - end: 2019-07-02T22:12:09.994295-04:00 - duration: 2 minutes, 48 seconds, and 877996 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:dada2' - action: denoise_paired - inputs: - - demultiplexed_seqs: 0a43c585-7504-4d5f-a43b-facd4baa29bb - parameters: - - trunc_len_f: 181 - - trunc_len_r: 181 - - trim_left_f: 0 - - trim_left_r: 0 - - max_ee: 2.0 - - trunc_q: 2 - - chimera_method: consensus - - min_fold_parent_over_abundance: 1.0 - - n_threads: 24 - - n_reads_learn: 1000000 - - hashed_feature_ids: true - output-name: representative_sequences - -transformers: - inputs: - demultiplexed_seqs: - - from: SingleLanePerSamplePairedEndFastqDirFmt - to: SingleLanePerSamplePairedEndFastqDirFmt - output: - - from: q2_types.feature_data._transformer:DNAIterator - to: DNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - dada2: - version: 2019.4.0 - website: http://benjjneb.github.io/dada2/ - citations: - - !cite 'plugin|dada2:2019.4.0|0' - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/citations.bib deleted file mode 100644 index a0814b0..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{plugin|dada2:2019.4.0|0, - author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P}, - doi = {10.1038/nmeth.3869}, - journal = {Nature methods}, - number = {7}, - pages = {581}, - publisher = {Nature Publishing Group}, - title = {DADA2: high-resolution sample inference from Illumina amplicon data}, - volume = {13}, - year = {2016} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/metadata.yaml deleted file mode 100644 index fa8fdd9..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/01a01d8c-998b-447e-9e4c-0aaf88e3b0f3/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 01a01d8c-998b-447e-9e4c-0aaf88e3b0f3 -type: FeatureData[Sequence] -format: DNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/action/action.yaml deleted file mode 100644 index 0363f1f..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/action/action.yaml +++ /dev/null @@ -1,182 +0,0 @@ -execution: - uuid: 1b6c7441-c1a7-4242-992d-23c1bd70da7d - runtime: - start: 2019-07-02T22:09:21.117078-04:00 - end: 2019-07-02T22:21:05.954826-04:00 - duration: 11 minutes, 44 seconds, and 837748 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:dada2' - action: denoise_paired - inputs: - - demultiplexed_seqs: 8a7bb656-825b-4d8e-b29d-9ea52316a52c - parameters: - - trunc_len_f: 181 - - trunc_len_r: 181 - - trim_left_f: 0 - - trim_left_r: 0 - - max_ee: 2.0 - - trunc_q: 2 - - chimera_method: consensus - - min_fold_parent_over_abundance: 1.0 - - n_threads: 24 - - n_reads_learn: 1000000 - - hashed_feature_ids: true - output-name: representative_sequences - -transformers: - inputs: - demultiplexed_seqs: - - from: SingleLanePerSamplePairedEndFastqDirFmt - to: SingleLanePerSamplePairedEndFastqDirFmt - output: - - from: q2_types.feature_data._transformer:DNAIterator - to: DNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - dada2: - version: 2019.4.0 - website: http://benjjneb.github.io/dada2/ - citations: - - !cite 'plugin|dada2:2019.4.0|0' - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/citations.bib deleted file mode 100644 index a0814b0..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{plugin|dada2:2019.4.0|0, - author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P}, - doi = {10.1038/nmeth.3869}, - journal = {Nature methods}, - number = {7}, - pages = {581}, - publisher = {Nature Publishing Group}, - title = {DADA2: high-resolution sample inference from Illumina amplicon data}, - volume = {13}, - year = {2016} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/metadata.yaml deleted file mode 100644 index 95e1820..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0340c5c5-602b-42dc-83f2-115ddd213754/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 0340c5c5-602b-42dc-83f2-115ddd213754 -type: FeatureData[Sequence] -format: DNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/action/action.yaml deleted file mode 100644 index ef4202e..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/action/action.yaml +++ /dev/null @@ -1,160 +0,0 @@ -execution: - uuid: 258cef9a-f8ea-4351-bde4-abc98c34d8e7 - runtime: - start: 2019-07-01T16:33:04.115196-04:00 - end: 2019-07-01T16:33:07.001343-04:00 - duration: 2 seconds, and 886147 microseconds - -action: - type: import - format: PairedEndFastqManifestPhred33 - manifest: - - name: p31.manifest.file - md5sum: d841ec9b508142c361a2dfc900023e99 - -transformers: - output: - - from: PairedEndFastqManifestPhred33 - to: SingleLanePerSamplePairedEndFastqDirFmt - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.3.9 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/metadata.yaml deleted file mode 100644 index f09a325..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/05dbf8d8-290b-4d52-80ed-bb6520a624a3/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 05dbf8d8-290b-4d52-80ed-bb6520a624a3 -type: SampleData[PairedEndSequencesWithQuality] -format: SingleLanePerSamplePairedEndFastqDirFmt diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/action/action.yaml deleted file mode 100644 index 726c1e6..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/action/action.yaml +++ /dev/null @@ -1,160 +0,0 @@ -execution: - uuid: afd2b8c2-db36-4905-9cdc-6c0342df9d97 - runtime: - start: 2019-07-01T16:34:18.821155-04:00 - end: 2019-07-01T16:34:20.916766-04:00 - duration: 2 seconds, and 95611 microseconds - -action: - type: import - format: PairedEndFastqManifestPhred33 - manifest: - - name: p52.manifest.file - md5sum: cb9a8e7e36e13f7e411ce5123d5e5a61 - -transformers: - output: - - from: PairedEndFastqManifestPhred33 - to: SingleLanePerSamplePairedEndFastqDirFmt - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.3.9 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/metadata.yaml deleted file mode 100644 index a697377..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0a43c585-7504-4d5f-a43b-facd4baa29bb/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 0a43c585-7504-4d5f-a43b-facd4baa29bb -type: SampleData[PairedEndSequencesWithQuality] -format: SingleLanePerSamplePairedEndFastqDirFmt diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/action/action.yaml deleted file mode 100644 index b9286f6..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/action/action.yaml +++ /dev/null @@ -1,182 +0,0 @@ -execution: - uuid: 3895480a-eff2-4bfa-80ff-97f17d2e9dc6 - runtime: - start: 2019-07-02T22:07:46.071789-04:00 - end: 2019-07-02T22:11:24.333349-04:00 - duration: 3 minutes, 38 seconds, and 261560 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:dada2' - action: denoise_paired - inputs: - - demultiplexed_seqs: 4fc2db6c-abf1-4122-bd38-a2a1d3931a7b - parameters: - - trunc_len_f: 181 - - trunc_len_r: 181 - - trim_left_f: 0 - - trim_left_r: 0 - - max_ee: 2.0 - - trunc_q: 2 - - chimera_method: consensus - - min_fold_parent_over_abundance: 1.0 - - n_threads: 24 - - n_reads_learn: 1000000 - - hashed_feature_ids: true - output-name: representative_sequences - -transformers: - inputs: - demultiplexed_seqs: - - from: SingleLanePerSamplePairedEndFastqDirFmt - to: SingleLanePerSamplePairedEndFastqDirFmt - output: - - from: q2_types.feature_data._transformer:DNAIterator - to: DNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - dada2: - version: 2019.4.0 - website: http://benjjneb.github.io/dada2/ - citations: - - !cite 'plugin|dada2:2019.4.0|0' - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/citations.bib deleted file mode 100644 index a0814b0..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{plugin|dada2:2019.4.0|0, - author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P}, - doi = {10.1038/nmeth.3869}, - journal = {Nature methods}, - number = {7}, - pages = {581}, - publisher = {Nature Publishing Group}, - title = {DADA2: high-resolution sample inference from Illumina amplicon data}, - volume = {13}, - year = {2016} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/metadata.yaml deleted file mode 100644 index 25d7705..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/0d93b954-da68-406c-879b-841e63d57a2e/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 0d93b954-da68-406c-879b-841e63d57a2e -type: FeatureData[Sequence] -format: DNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/action/action.yaml deleted file mode 100644 index 4423f18..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/action/action.yaml +++ /dev/null @@ -1,160 +0,0 @@ -execution: - uuid: fd734369-8e20-40f9-aadc-2919495f3d06 - runtime: - start: 2019-07-01T16:41:28.990477-04:00 - end: 2019-07-01T16:41:32.186151-04:00 - duration: 3 seconds, and 195674 microseconds - -action: - type: import - format: PairedEndFastqManifestPhred33 - manifest: - - name: p71.manifest.file - md5sum: 4759d3822f7e985c16ede7500369f1f2 - -transformers: - output: - - from: PairedEndFastqManifestPhred33 - to: SingleLanePerSamplePairedEndFastqDirFmt - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.3.9 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/metadata.yaml deleted file mode 100644 index bf65c05..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/33c2d1a3-1578-4614-8525-1d94dde3f1fa/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 33c2d1a3-1578-4614-8525-1d94dde3f1fa -type: SampleData[PairedEndSequencesWithQuality] -format: SingleLanePerSamplePairedEndFastqDirFmt diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/action/action.yaml deleted file mode 100644 index 1613f16..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/action/action.yaml +++ /dev/null @@ -1,182 +0,0 @@ -execution: - uuid: e08f36cd-8dad-4477-80c4-8c2a13cd31aa - runtime: - start: 2019-07-02T22:07:58.651937-04:00 - end: 2019-07-02T22:19:22.236004-04:00 - duration: 11 minutes, 23 seconds, and 584067 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:dada2' - action: denoise_paired - inputs: - - demultiplexed_seqs: e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4 - parameters: - - trunc_len_f: 181 - - trunc_len_r: 181 - - trim_left_f: 0 - - trim_left_r: 0 - - max_ee: 2.0 - - trunc_q: 2 - - chimera_method: consensus - - min_fold_parent_over_abundance: 1.0 - - n_threads: 24 - - n_reads_learn: 1000000 - - hashed_feature_ids: true - output-name: representative_sequences - -transformers: - inputs: - demultiplexed_seqs: - - from: SingleLanePerSamplePairedEndFastqDirFmt - to: SingleLanePerSamplePairedEndFastqDirFmt - output: - - from: q2_types.feature_data._transformer:DNAIterator - to: DNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - dada2: - version: 2019.4.0 - website: http://benjjneb.github.io/dada2/ - citations: - - !cite 'plugin|dada2:2019.4.0|0' - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/citations.bib deleted file mode 100644 index a0814b0..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{plugin|dada2:2019.4.0|0, - author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P}, - doi = {10.1038/nmeth.3869}, - journal = {Nature methods}, - number = {7}, - pages = {581}, - publisher = {Nature Publishing Group}, - title = {DADA2: high-resolution sample inference from Illumina amplicon data}, - volume = {13}, - year = {2016} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/metadata.yaml deleted file mode 100644 index 5b3a023..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/376e617e-42cb-4151-bf30-30cc62f0d350/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 376e617e-42cb-4151-bf30-30cc62f0d350 -type: FeatureData[Sequence] -format: DNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/action/action.yaml deleted file mode 100644 index f137af3..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/action/action.yaml +++ /dev/null @@ -1,160 +0,0 @@ -execution: - uuid: 4a982bdb-9cec-4df9-a569-4cdc7f2f5f2a - runtime: - start: 2019-07-01T16:34:18.824974-04:00 - end: 2019-07-01T16:34:20.907406-04:00 - duration: 2 seconds, and 82432 microseconds - -action: - type: import - format: PairedEndFastqManifestPhred33 - manifest: - - name: p32.manifest.file - md5sum: 477a1746b3419e9137f3011768200578 - -transformers: - output: - - from: PairedEndFastqManifestPhred33 - to: SingleLanePerSamplePairedEndFastqDirFmt - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.3.9 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/metadata.yaml deleted file mode 100644 index 4b82ba7..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/4fc2db6c-abf1-4122-bd38-a2a1d3931a7b/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 4fc2db6c-abf1-4122-bd38-a2a1d3931a7b -type: SampleData[PairedEndSequencesWithQuality] -format: SingleLanePerSamplePairedEndFastqDirFmt diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/action/action.yaml deleted file mode 100644 index adb13e7..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/action/action.yaml +++ /dev/null @@ -1,182 +0,0 @@ -execution: - uuid: 44dd93b0-34aa-43ec-9ddc-121f57d9a8cf - runtime: - start: 2019-07-02T22:09:21.108368-04:00 - end: 2019-07-02T22:17:26.201578-04:00 - duration: 8 minutes, 5 seconds, and 93210 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:dada2' - action: denoise_paired - inputs: - - demultiplexed_seqs: 33c2d1a3-1578-4614-8525-1d94dde3f1fa - parameters: - - trunc_len_f: 181 - - trunc_len_r: 181 - - trim_left_f: 0 - - trim_left_r: 0 - - max_ee: 2.0 - - trunc_q: 2 - - chimera_method: consensus - - min_fold_parent_over_abundance: 1.0 - - n_threads: 24 - - n_reads_learn: 1000000 - - hashed_feature_ids: true - output-name: representative_sequences - -transformers: - inputs: - demultiplexed_seqs: - - from: SingleLanePerSamplePairedEndFastqDirFmt - to: SingleLanePerSamplePairedEndFastqDirFmt - output: - - from: q2_types.feature_data._transformer:DNAIterator - to: DNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - dada2: - version: 2019.4.0 - website: http://benjjneb.github.io/dada2/ - citations: - - !cite 'plugin|dada2:2019.4.0|0' - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/citations.bib deleted file mode 100644 index a0814b0..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{plugin|dada2:2019.4.0|0, - author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P}, - doi = {10.1038/nmeth.3869}, - journal = {Nature methods}, - number = {7}, - pages = {581}, - publisher = {Nature Publishing Group}, - title = {DADA2: high-resolution sample inference from Illumina amplicon data}, - volume = {13}, - year = {2016} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/metadata.yaml deleted file mode 100644 index c2bb3fe..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/65a03d2f-ff9c-4015-be7e-3e6876e4ec6c/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 65a03d2f-ff9c-4015-be7e-3e6876e4ec6c -type: FeatureData[Sequence] -format: DNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/action/action.yaml deleted file mode 100644 index 157d0d8..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/action/action.yaml +++ /dev/null @@ -1,172 +0,0 @@ -execution: - uuid: 2f86945a-fc9d-43b0-8cb5-2753bfdc1fc0 - runtime: - start: 2019-07-06T15:10:32.693265-04:00 - end: 2019-07-06T15:11:27.546275-04:00 - duration: 54 seconds, and 853010 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:alignment' - action: mafft - inputs: - - sequences: be6cc846-b284-458b-824d-66f0666f3ed8 - parameters: - - n_threads: 24 - - parttree: false - output-name: alignment - citations: - - !cite 'action|alignment:2019.4.0|method:mafft|0' - -transformers: - inputs: - sequences: - - from: DNASequencesDirectoryFormat - to: DNAFASTAFormat - output: - - from: AlignedDNAFASTAFormat - to: AlignedDNASequencesDirectoryFormat - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - alignment: - version: 2019.4.0 - website: https://github.com/qiime2/q2-alignment - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 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b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/citations.bib deleted file mode 100644 index 992ecc6..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{action|alignment:2019.4.0|method:mafft|0, - author = {Katoh, Kazutaka and Standley, Daron M}, - doi = {10.1093/molbev/mst010}, - journal = {Molecular biology and evolution}, - number = {4}, - pages = {772--780}, - publisher = {Society for Molecular Biology and Evolution}, - title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability}, - volume = {30}, - year = {2013} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/metadata.yaml deleted file mode 100644 index ce55283..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/77238308-4c92-42e9-b123-83970d4d7153/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 77238308-4c92-42e9-b123-83970d4d7153 -type: FeatureData[AlignedSequence] -format: AlignedDNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/action/action.yaml deleted file mode 100644 index 2053023..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/action/action.yaml +++ /dev/null @@ -1,171 +0,0 @@ -execution: - uuid: a6a85cf1-4aae-42a8-a1e0-4b7daae37f4b - runtime: - start: 2019-07-06T15:13:09.250747-04:00 - end: 2019-07-06T15:15:47.225606-04:00 - duration: 2 minutes, 37 seconds, and 974859 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:phylogeny' - action: fasttree - inputs: - - alignment: f3089593-c794-4c0a-9c80-4bad185405f1 - parameters: - - n_threads: 24 - output-name: tree - citations: - - !cite 'action|phylogeny:2019.4.0|method:fasttree|0' - -transformers: - inputs: - alignment: - - from: AlignedDNASequencesDirectoryFormat - to: AlignedDNAFASTAFormat - output: - - from: NewickFormat - to: NewickDirectoryFormat - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - phylogeny: - version: 2019.4.0 - website: https://github.com/qiime2/q2-phylogeny - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/citations.bib deleted file mode 100644 index f6781aa..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{action|phylogeny:2019.4.0|method:fasttree|0, - author = {Price, Morgan N and Dehal, Paramvir S and Arkin, Adam P}, - doi = {10.1371/journal.pone.0009490}, - journal = {PloS one}, - number = {3}, - pages = {e9490}, - publisher = {Public Library of Science}, - title = {FastTree 2--approximately maximum-likelihood trees for large alignments}, - volume = {5}, - year = {2010} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/metadata.yaml deleted file mode 100644 index 5589686..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/86b13f5f-42e2-48be-8a0f-db5316a18460/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 86b13f5f-42e2-48be-8a0f-db5316a18460 -type: Phylogeny[Unrooted] -format: NewickDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/action/action.yaml deleted file mode 100644 index acd1c29..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/action/action.yaml +++ /dev/null @@ -1,160 +0,0 @@ -execution: - uuid: 0678bf4a-186a-421a-abc0-15189ff371d7 - runtime: - start: 2019-07-01T16:37:04.883116-04:00 - end: 2019-07-01T16:37:07.583850-04:00 - duration: 2 seconds, and 700734 microseconds - -action: - type: import - format: PairedEndFastqManifestPhred33 - manifest: - - name: p51.manifest.file - md5sum: e7efd06fbc1647bbbef8d9c4a098a183 - -transformers: - output: - - from: PairedEndFastqManifestPhred33 - to: SingleLanePerSamplePairedEndFastqDirFmt - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.3.9 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/metadata.yaml deleted file mode 100644 index 6fb0076..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/874a5680-3feb-4813-97b2-85b28f6bbf52/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 874a5680-3feb-4813-97b2-85b28f6bbf52 -type: SampleData[PairedEndSequencesWithQuality] -format: SingleLanePerSamplePairedEndFastqDirFmt diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/action/action.yaml deleted file mode 100644 index 5a41aaf..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/action/action.yaml +++ /dev/null @@ -1,160 +0,0 @@ -execution: - uuid: 0a3c7256-a5b7-462c-9d0c-26fa261d3e31 - runtime: - start: 2019-07-01T16:42:45.044286-04:00 - end: 2019-07-01T16:42:48.186479-04:00 - duration: 3 seconds, and 142193 microseconds - -action: - type: import - format: PairedEndFastqManifestPhred33 - manifest: - - name: p72.manifest.file - md5sum: d793b8c2d1e1908b9da4ea0637fbf098 - -transformers: - output: - - from: PairedEndFastqManifestPhred33 - to: SingleLanePerSamplePairedEndFastqDirFmt - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.3.9 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/metadata.yaml deleted file mode 100644 index 0ee440a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/8a7bb656-825b-4d8e-b29d-9ea52316a52c/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 8a7bb656-825b-4d8e-b29d-9ea52316a52c -type: SampleData[PairedEndSequencesWithQuality] -format: SingleLanePerSamplePairedEndFastqDirFmt diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/action/action.yaml deleted file mode 100644 index b642b38..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/action/action.yaml +++ /dev/null @@ -1,223 +0,0 @@ -execution: - uuid: 628ff890-1fbb-4b95-93d9-6ca00849916c - runtime: - start: 2019-07-06T15:00:36.221935-04:00 - end: 2019-07-06T15:00:41.560989-04:00 - duration: 5 seconds, and 339054 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:feature-table' - action: merge_seqs - inputs: - - data: - - cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56 - - f101df0c-2ea0-483e-bfd6-91ca23727b1e - - 0d93b954-da68-406c-879b-841e63d57a2e - - d706caa6-60fc-41fd-aaa1-d719b7d8ef6e - - 376e617e-42cb-4151-bf30-30cc62f0d350 - - f178655c-6ef9-40d0-ba07-46822a870048 - - 01a01d8c-998b-447e-9e4c-0aaf88e3b0f3 - - 65a03d2f-ff9c-4015-be7e-3e6876e4ec6c - - 0340c5c5-602b-42dc-83f2-115ddd213754 - parameters: [] - output-name: merged_data - -transformers: - inputs: - data: - - from: DNASequencesDirectoryFormat - to: pandas.core.series:Series - plugin: !ref 'environment:plugins:types' - citations: - - !cite 'view|types:2019.4.1|pandas.core.series:Series|0' - - from: DNASequencesDirectoryFormat - to: pandas.core.series:Series - plugin: !ref 'environment:plugins:types' - citations: - - !cite 'view|types:2019.4.1|pandas.core.series:Series|0' - - from: DNASequencesDirectoryFormat - to: pandas.core.series:Series - plugin: !ref 'environment:plugins:types' - citations: - - !cite 'view|types:2019.4.1|pandas.core.series:Series|0' - - from: DNASequencesDirectoryFormat - to: pandas.core.series:Series - plugin: !ref 'environment:plugins:types' - citations: - - !cite 'view|types:2019.4.1|pandas.core.series:Series|0' - - from: DNASequencesDirectoryFormat - to: pandas.core.series:Series - plugin: !ref 'environment:plugins:types' - citations: - - !cite 'view|types:2019.4.1|pandas.core.series:Series|0' - - from: DNASequencesDirectoryFormat - to: pandas.core.series:Series - plugin: !ref 'environment:plugins:types' - citations: - - !cite 'view|types:2019.4.1|pandas.core.series:Series|0' - - from: DNASequencesDirectoryFormat - to: pandas.core.series:Series - plugin: !ref 'environment:plugins:types' - citations: - - !cite 'view|types:2019.4.1|pandas.core.series:Series|0' - - from: DNASequencesDirectoryFormat - to: pandas.core.series:Series - plugin: !ref 'environment:plugins:types' - citations: - - !cite 'view|types:2019.4.1|pandas.core.series:Series|0' - - from: DNASequencesDirectoryFormat - to: pandas.core.series:Series - plugin: !ref 'environment:plugins:types' - citations: - - !cite 'view|types:2019.4.1|pandas.core.series:Series|0' - output: - - from: pandas.core.series:Series - to: DNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - citations: - - !cite 'view|types:2019.4.1|pandas.core.series:Series|0' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - feature-table: - version: 2019.4.0 - website: https://github.com/qiime2/q2-feature-table - 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'0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/citations.bib deleted file mode 100644 index e44523a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/citations.bib +++ /dev/null @@ -1,22 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@inproceedings{view|types:2019.4.1|pandas.core.series:Series|0, - author = { Wes McKinney }, - booktitle = { Proceedings of the 9th Python in Science Conference }, - editor = { Stéfan van der Walt and Jarrod Millman }, - pages = { 51 -- 56 }, - title = { Data Structures for Statistical Computing in Python }, - year = { 2010 } -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/metadata.yaml deleted file mode 100644 index 9494aa9..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/be6cc846-b284-458b-824d-66f0666f3ed8/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: be6cc846-b284-458b-824d-66f0666f3ed8 -type: FeatureData[Sequence] -format: DNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/action/action.yaml deleted file mode 100644 index af3fc9e..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/action/action.yaml +++ /dev/null @@ -1,182 +0,0 @@ -execution: - uuid: 1d94bf73-61aa-4205-b35d-71266930a779 - runtime: - start: 2019-07-02T20:59:16.195196-04:00 - end: 2019-07-02T21:03:59.905116-04:00 - duration: 4 minutes, 43 seconds, and 709920 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:dada2' - action: denoise_paired - inputs: - - demultiplexed_seqs: ceff0eae-c33c-49e4-9f5b-69415cabfd09 - parameters: - - trunc_len_f: 181 - - trunc_len_r: 181 - - trim_left_f: 0 - - trim_left_r: 0 - - max_ee: 2.0 - - trunc_q: 2 - - chimera_method: consensus - - min_fold_parent_over_abundance: 1.0 - - n_threads: 24 - - n_reads_learn: 1000000 - - hashed_feature_ids: true - output-name: representative_sequences - -transformers: - inputs: - demultiplexed_seqs: - - from: SingleLanePerSamplePairedEndFastqDirFmt - to: SingleLanePerSamplePairedEndFastqDirFmt - output: - - from: q2_types.feature_data._transformer:DNAIterator - to: DNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - dada2: - version: 2019.4.0 - website: http://benjjneb.github.io/dada2/ - citations: - - !cite 'plugin|dada2:2019.4.0|0' - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/citations.bib deleted file mode 100644 index a0814b0..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{plugin|dada2:2019.4.0|0, - author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P}, - doi = {10.1038/nmeth.3869}, - journal = {Nature methods}, - number = {7}, - pages = {581}, - publisher = {Nature Publishing Group}, - title = {DADA2: high-resolution sample inference from Illumina amplicon data}, - volume = {13}, - year = {2016} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/metadata.yaml deleted file mode 100644 index dc436bd..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: cd9ccb56-2f4c-47c0-b2c3-dd5b5440fd56 -type: FeatureData[Sequence] -format: DNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/action/action.yaml deleted file mode 100644 index 738f7d3..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/action/action.yaml +++ /dev/null @@ -1,160 +0,0 @@ -execution: - uuid: 95a6241c-4e42-400f-b2c3-31227b55dd4f - runtime: - start: 2019-07-01T15:28:11.499591-04:00 - end: 2019-07-01T15:28:37.930628-04:00 - duration: 26 seconds, and 431037 microseconds - -action: - type: import - format: PairedEndFastqManifestPhred33 - manifest: - - name: p12.manifest.file - md5sum: 14eb43307ee43f907ea16540853e5d8d - -transformers: - output: - - from: PairedEndFastqManifestPhred33 - to: SingleLanePerSamplePairedEndFastqDirFmt - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.3.9 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/metadata.yaml deleted file mode 100644 index 15582b5..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ceff0eae-c33c-49e4-9f5b-69415cabfd09/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: ceff0eae-c33c-49e4-9f5b-69415cabfd09 -type: SampleData[PairedEndSequencesWithQuality] -format: SingleLanePerSamplePairedEndFastqDirFmt diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/action/action.yaml deleted file mode 100644 index ab18012..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/action/action.yaml +++ /dev/null @@ -1,182 +0,0 @@ -execution: - uuid: 24f28f43-e36a-4dfc-891f-878da4236723 - runtime: - start: 2019-07-02T22:08:21.905317-04:00 - end: 2019-07-02T22:19:45.469348-04:00 - duration: 11 minutes, 23 seconds, and 564031 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:dada2' - action: denoise_paired - inputs: - - demultiplexed_seqs: ffbbd0dd-d70b-460d-8e62-9e2393cd0edf - parameters: - - trunc_len_f: 181 - - trunc_len_r: 181 - - trim_left_f: 0 - - trim_left_r: 0 - - max_ee: 2.0 - - trunc_q: 2 - - chimera_method: consensus - - min_fold_parent_over_abundance: 1.0 - - n_threads: 24 - - n_reads_learn: 1000000 - - hashed_feature_ids: true - output-name: representative_sequences - -transformers: - inputs: - demultiplexed_seqs: - - from: SingleLanePerSamplePairedEndFastqDirFmt - to: SingleLanePerSamplePairedEndFastqDirFmt - output: - - from: q2_types.feature_data._transformer:DNAIterator - to: DNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - dada2: - version: 2019.4.0 - website: http://benjjneb.github.io/dada2/ - citations: - - !cite 'plugin|dada2:2019.4.0|0' - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/citations.bib deleted file mode 100644 index a0814b0..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{plugin|dada2:2019.4.0|0, - author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P}, - doi = {10.1038/nmeth.3869}, - journal = {Nature methods}, - number = {7}, - pages = {581}, - publisher = {Nature Publishing Group}, - title = {DADA2: high-resolution sample inference from Illumina amplicon data}, - volume = {13}, - year = {2016} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/metadata.yaml deleted file mode 100644 index 473da81..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/d706caa6-60fc-41fd-aaa1-d719b7d8ef6e/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: d706caa6-60fc-41fd-aaa1-d719b7d8ef6e -type: FeatureData[Sequence] -format: DNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/action/action.yaml deleted file mode 100644 index ee8794b..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/action/action.yaml +++ /dev/null @@ -1,160 +0,0 @@ -execution: - uuid: df169ee6-8f46-4fa4-83cd-bffcf06e9046 - runtime: - start: 2019-07-01T16:42:45.052299-04:00 - end: 2019-07-01T16:42:48.721668-04:00 - duration: 3 seconds, and 669369 microseconds - -action: - type: import - format: PairedEndFastqManifestPhred33 - manifest: - - name: p42.manifest.file - md5sum: 5e7d4f5921a9ab880a742b5e62cfe184 - -transformers: - output: - - from: PairedEndFastqManifestPhred33 - to: SingleLanePerSamplePairedEndFastqDirFmt - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.3.9 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/metadata.yaml deleted file mode 100644 index dbf8f47..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: e158b0fa-f44c-48f7-bdcd-61f3a2bb21e4 -type: SampleData[PairedEndSequencesWithQuality] -format: SingleLanePerSamplePairedEndFastqDirFmt diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/action/action.yaml deleted file mode 100644 index 81eb22d..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/action/action.yaml +++ /dev/null @@ -1,182 +0,0 @@ -execution: - uuid: d7f4488f-a10d-4000-bdf7-b0bdcf2c14e7 - runtime: - start: 2019-07-02T22:08:21.875389-04:00 - end: 2019-07-02T22:12:55.617546-04:00 - duration: 4 minutes, 33 seconds, and 742157 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:dada2' - action: denoise_paired - inputs: - - demultiplexed_seqs: 05dbf8d8-290b-4d52-80ed-bb6520a624a3 - parameters: - - trunc_len_f: 181 - - trunc_len_r: 181 - - trim_left_f: 0 - - trim_left_r: 0 - - max_ee: 2.0 - - trunc_q: 2 - - chimera_method: consensus - - min_fold_parent_over_abundance: 1.0 - - n_threads: 24 - - n_reads_learn: 1000000 - - hashed_feature_ids: true - output-name: representative_sequences - -transformers: - inputs: - demultiplexed_seqs: - - from: SingleLanePerSamplePairedEndFastqDirFmt - to: SingleLanePerSamplePairedEndFastqDirFmt - output: - - from: q2_types.feature_data._transformer:DNAIterator - to: DNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - dada2: - version: 2019.4.0 - website: http://benjjneb.github.io/dada2/ - citations: - - !cite 'plugin|dada2:2019.4.0|0' - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/citations.bib deleted file mode 100644 index a0814b0..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{plugin|dada2:2019.4.0|0, - author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P}, - doi = {10.1038/nmeth.3869}, - journal = {Nature methods}, - number = {7}, - pages = {581}, - publisher = {Nature Publishing Group}, - title = {DADA2: high-resolution sample inference from Illumina amplicon data}, - volume = {13}, - year = {2016} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/metadata.yaml deleted file mode 100644 index 3c92fc3..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f101df0c-2ea0-483e-bfd6-91ca23727b1e/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: f101df0c-2ea0-483e-bfd6-91ca23727b1e -type: FeatureData[Sequence] -format: DNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/action/action.yaml deleted file mode 100644 index 1bb0c5f..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/action/action.yaml +++ /dev/null @@ -1,182 +0,0 @@ -execution: - uuid: f3f376ac-a853-4a53-87a8-2aab9cc3d86a - runtime: - start: 2019-07-02T22:09:21.123123-04:00 - end: 2019-07-02T22:15:29.162403-04:00 - duration: 6 minutes, 8 seconds, and 39280 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:dada2' - action: denoise_paired - inputs: - - demultiplexed_seqs: 874a5680-3feb-4813-97b2-85b28f6bbf52 - parameters: - - trunc_len_f: 181 - - trunc_len_r: 181 - - trim_left_f: 0 - - trim_left_r: 0 - - max_ee: 2.0 - - trunc_q: 2 - - chimera_method: consensus - - min_fold_parent_over_abundance: 1.0 - - n_threads: 24 - - n_reads_learn: 1000000 - - hashed_feature_ids: true - output-name: representative_sequences - -transformers: - inputs: - demultiplexed_seqs: - - from: SingleLanePerSamplePairedEndFastqDirFmt - to: SingleLanePerSamplePairedEndFastqDirFmt - output: - - from: q2_types.feature_data._transformer:DNAIterator - to: DNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - dada2: - version: 2019.4.0 - website: http://benjjneb.github.io/dada2/ - citations: - - !cite 'plugin|dada2:2019.4.0|0' - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/citations.bib deleted file mode 100644 index a0814b0..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/citations.bib +++ /dev/null @@ -1,25 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@article{plugin|dada2:2019.4.0|0, - author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P}, - doi = {10.1038/nmeth.3869}, - journal = {Nature methods}, - number = {7}, - pages = {581}, - publisher = {Nature Publishing Group}, - title = {DADA2: high-resolution sample inference from Illumina amplicon data}, - volume = {13}, - year = {2016} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/metadata.yaml deleted file mode 100644 index 87b87c9..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f178655c-6ef9-40d0-ba07-46822a870048/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: f178655c-6ef9-40d0-ba07-46822a870048 -type: FeatureData[Sequence] -format: DNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/action/action.yaml deleted file mode 100644 index 54c6a5b..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/action/action.yaml +++ /dev/null @@ -1,174 +0,0 @@ -execution: - uuid: 647698ef-4e0a-469c-8d25-560cd200bcd1 - runtime: - start: 2019-07-06T15:11:27.589638-04:00 - end: 2019-07-06T15:13:09.215409-04:00 - duration: 1 minute, 41 seconds, and 625771 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:alignment' - action: mask - inputs: - - alignment: 77238308-4c92-42e9-b123-83970d4d7153 - parameters: - - max_gap_frequency: 1.0 - - min_conservation: 0.4 - output-name: masked_alignment - citations: - - !cite 'action|alignment:2019.4.0|method:mask|0' - -transformers: - inputs: - alignment: - - from: AlignedDNASequencesDirectoryFormat - to: skbio.alignment._tabular_msa:TabularMSA - plugin: !ref 'environment:plugins:types' - output: - - from: skbio.alignment._tabular_msa:TabularMSA - to: AlignedDNASequencesDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - alignment: - version: 2019.4.0 - website: https://github.com/qiime2/q2-alignment - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/citations.bib deleted file mode 100644 index 93ef7e2..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/citations.bib +++ /dev/null @@ -1,24 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - -@incollection{action|alignment:2019.4.0|method:mask|0, - address = {New York}, - author = {Lane, DJ}, - booktitle = {Nucleic Acid Techniques in Bacterial Systematics}, - editor = {Stackebrandt, E and Goodfellow, M}, - pages = {115--175}, - publisher = {John Wiley and Sons}, - title = {16S/23S rRNA sequencing}, - year = {1991} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/metadata.yaml deleted file mode 100644 index 3da7c5d..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f3089593-c794-4c0a-9c80-4bad185405f1/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: f3089593-c794-4c0a-9c80-4bad185405f1 -type: FeatureData[AlignedSequence] -format: AlignedDNASequencesDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/action/action.yaml deleted file mode 100644 index e44fc6e..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/action/action.yaml +++ /dev/null @@ -1,170 +0,0 @@ -execution: - uuid: a01b4ace-6894-4bcf-94b0-3c497e08d2e8 - runtime: - start: 2019-07-06T15:15:47.259813-04:00 - end: 2019-07-06T15:15:48.901120-04:00 - duration: 1 second, and 641307 microseconds - -action: - type: method - plugin: !ref 'environment:plugins:phylogeny' - action: midpoint_root - inputs: - - tree: 86b13f5f-42e2-48be-8a0f-db5316a18460 - parameters: [] - output-name: rooted_tree - -transformers: - inputs: - tree: - - from: NewickDirectoryFormat - to: skbio.tree._tree:TreeNode - plugin: !ref 'environment:plugins:types' - output: - - from: skbio.tree._tree:TreeNode - to: NewickDirectoryFormat - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - phylogeny: - version: 2019.4.0 - website: https://github.com/qiime2/q2-phylogeny - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.6.16 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/metadata.yaml deleted file mode 100644 index e08bca7..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/f394d4c6-4c1b-4548-b3ef-96091164dca5/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: f394d4c6-4c1b-4548-b3ef-96091164dca5 -type: Phylogeny[Rooted] -format: NewickDirectoryFormat diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/VERSION b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/VERSION deleted file mode 100644 index 7183f9c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/VERSION +++ /dev/null @@ -1,3 +0,0 @@ -QIIME 2 -archive: 5 -framework: 2019.4.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/action/action.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/action/action.yaml deleted file mode 100644 index 2b141d7..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/action/action.yaml +++ /dev/null @@ -1,160 +0,0 @@ -execution: - uuid: 00dcbe95-ca64-4a6c-b882-b4949496301e - runtime: - start: 2019-07-01T16:42:45.055507-04:00 - end: 2019-07-01T16:42:48.743290-04:00 - duration: 3 seconds, and 687783 microseconds - -action: - type: import - format: PairedEndFastqManifestPhred33 - manifest: - - name: p41.manifest.file - md5sum: 43b88a89466f90b7402efcc79f83a7ed - -transformers: - output: - - from: PairedEndFastqManifestPhred33 - to: SingleLanePerSamplePairedEndFastqDirFmt - plugin: !ref 'environment:plugins:types' - -environment: - platform: linux-x86_64 - python: |- - 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) - [GCC 7.3.0] - framework: - version: 2019.4.0 - website: https://qiime2.org - citations: - - !cite 'framework|qiime2:2019.4.0|0' - plugins: - types: - version: 2019.4.1 - website: https://github.com/qiime2/q2-types - python-packages: - xopen: 0.5.1 - widgetsnbextension: 3.4.2 - wheel: 0.33.1 - webencodings: 0.5.1 - wcwidth: 0.1.7 - urllib3: 1.24.2 - unifrac: 0.9.2 - tzlocal: 1.5.1 - traitlets: 4.3.2 - tornado: 6.0.2 - testpath: 0.4.2 - terminado: 0.8.2 - statsmodels: 0.9.0 - six: 1.12.0 - setuptools: 41.0.1 - Send2Trash: 1.5.0 - seaborn: 0.9.0 - scipy: 1.2.1 - scikit-learn: 0.20.2 - scikit-bio: 0.5.5 - requests: 2.21.0 - qiime2: 2019.4.0 - q2templates: 2019.4.0 - q2cli: 2019.4.0 - q2-vsearch: 2019.4.0 - q2-types: 2019.4.1 - q2-taxa: 2019.4.0 - q2-sample-classifier: 2019.4.0 - q2-quality-filter: 2019.4.0 - q2-quality-control: 2019.4.0 - q2-phylogeny: 2019.4.0 - q2-metadata: 2019.4.0 - q2-longitudinal: 2019.4.0 - q2-gneiss: 2019.4.0 - q2-fragment-insertion: 2019.4.0 - q2-feature-table: 2019.4.0 - q2-feature-classifier: 2019.4.0 - q2-emperor: 2019.4.0 - q2-diversity: 2019.4.0 - q2-demux: 2019.4.1 - q2-deblur: 2019.4.0 - q2-dada2: 2019.4.0 - q2-cutadapt: 2019.4.0 - q2-composition: 2019.4.0 - q2-alignment: 2019.4.0 - pyzmq: 18.0.1 - PyYAML: 5.1.1 - pytz: '2019.1' - python-dateutil: 2.8.0 - pytest: 4.4.2 - PySocks: 1.6.8 - pyrsistent: 0.15.1 - pyparsing: 2.3.0 - pyOpenSSL: 19.0.0 - Pygments: 2.4.0 - pycparser: '2.19' - py: 1.8.0 - ptyprocess: 0.6.0 - psutil: 5.6.2 - prompt-toolkit: 2.0.9 - prometheus-client: 0.6.0 - pluggy: 0.11.0 - pip: 19.1.1 - Pillow: 6.0.0 - pickleshare: 0.7.5 - pexpect: 4.7.0 - patsy: 0.5.1 - parso: 0.4.0 - pandocfilters: 1.4.2 - pandas: 0.24.2 - packaging: '19.0' - olefile: '0.46' - numpy: 1.16.2 - notebook: 5.7.8 - nose: 1.3.7 - networkx: '2.3' - nbformat: 4.4.0 - nbconvert: 5.5.0 - natsort: 6.0.0 - msgpack: 0.6.1 - more-itertools: 4.3.0 - mistune: 0.8.4 - matplotlib: 3.0.3 - MarkupSafe: 1.1.1 - lockfile: 0.12.2 - kiwisolver: 1.1.0 - jupyter-core: 4.4.0 - jupyter-client: 5.2.4 - jsonschema: 3.0.1 - Jinja2: 2.10.1 - jedi: 0.13.3 - ipywidgets: 7.4.2 - ipython: 7.5.0 - ipython-genutils: 0.2.0 - ipykernel: 5.1.0 - ijson: '2.3' - idna: '2.8' - hdmedians: '0.13' - h5py: 2.9.0 - gneiss: 0.4.4 - future: 0.17.1 - fastcluster: 1.1.25 - entrypoints: '0.3' - emperor: 1.0.0b19 - dnaio: '0.3' - defusedxml: 0.5.0 - decorator: 4.4.0 - deblur: 1.1.0 - cycler: 0.10.0 - cutadapt: '2.3' - cryptography: 2.6.1 - Click: '7.0' - chardet: 3.0.4 - cffi: 1.12.3 - certifi: 2019.3.9 - CacheControl: 0.12.5 - bz2file: '0.98' - bokeh: 1.1.0 - bleach: 3.1.0 - biom-format: 2.1.7 - bibtexparser: 1.1.0 - backcall: 0.1.0 - attrs: 19.1.0 - atomicwrites: 1.3.0 - asn1crypto: 0.24.0 diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/metadata.yaml deleted file mode 100644 index 4de7c5c..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/artifacts/ffbbd0dd-d70b-460d-8e62-9e2393cd0edf/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: ffbbd0dd-d70b-460d-8e62-9e2393cd0edf -type: SampleData[PairedEndSequencesWithQuality] -format: SingleLanePerSamplePairedEndFastqDirFmt diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/citations.bib b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/citations.bib deleted file mode 100644 index 3ddfe2a..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/citations.bib +++ /dev/null @@ -1,13 +0,0 @@ -@article{framework|qiime2:2019.4.0|0, - author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory}, - doi = {10.7287/peerj.preprints.27295v1}, - issn = {2167-9843}, - journal = {PeerJ Preprints}, - month = {oct}, - pages = {e27295v1}, - title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}, - url = {https://doi.org/10.7287/peerj.preprints.27295v1}, - volume = {6}, - year = {2018} -} - diff --git a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/metadata.yaml b/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/metadata.yaml deleted file mode 100644 index cfefc8e..0000000 --- a/data/qiime_qza/tmpExtract/0dc9056e-4a2f-46da-b816-d5b6182f7dcd/provenance/metadata.yaml +++ /dev/null @@ -1,3 +0,0 @@ -uuid: 0dc9056e-4a2f-46da-b816-d5b6182f7dcd -type: Phylogeny[Rooted] -format: NewickDirectoryFormat