Usage: qiime tools import [OPTIONS] Import data to create a new QIIME 2 Artifact. See https://docs.qiime2.org/ for usage examples and details on the file types and associated semantic types that can be imported. Options: --type TEXT The semantic type of the artifact that will be created upon importing. Use --show-importable-types to see what importable semantic types are available in the current deployment. [required] --input-path PATH Path to file or directory that should be imported. [required] --output-path ARTIFACT Path where output artifact should be written. [required] --input-format TEXT The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type. --show-importable-types Show the semantic types that can be supplied to --type to import data into an artifact. --show-importable-formats Show formats that can be supplied to --input-format to import data into an artifact. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': Path 'PR_MCB_Files/PR_MCB_11/out_dir//manifest.txt' does not exist. Usage: qiime vsearch dereplicate-sequences [OPTIONS] Dereplicate sequence data and create a feature table and feature representative sequences. Feature identifiers in the resulting artifacts will be the sha1 hash of the sequence defining each feature. If clustering of features into OTUs is desired, the resulting artifacts can be passed to the cluster_features_* methods in this plugin. Inputs: --i-sequences ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated. [required] Parameters: --p-derep-prefix / --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False] Outputs: --o-dereplicated-table ARTIFACT FeatureTable[Frequency] The table of dereplicated sequences. [required] --o-dereplicated-sequences ARTIFACT FeatureData[Sequence] The dereplicated sequences. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-sequences': 'sequences.qza' is not a valid filepath Usage: qiime vsearch cluster-features-de-novo [OPTIONS] Given a feature table and the associated feature sequences, cluster the features based on user-specified percent identity threshold of their sequences. This is not a general-purpose de novo clustering method, but rather is intended to be used for clustering the results of quality- filtering/dereplication methods, such as DADA2, or for re-clustering a FeatureTable at a lower percent identity than it was originally clustered at. When a group of features in the input table are clustered into a single feature, the frequency of that single feature in a given sample is the sum of the frequencies of the features that were clustered in that sample. Feature identifiers and sequences will be inherited from the centroid feature of each cluster. See the vsearch documentation for details on how sequence clustering is performed. Inputs: --i-sequences ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required] --i-table ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required] Parameters: --p-perc-identity PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required] --p-threads INTEGER Range(0, 256, inclusive_end=True) The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1] Outputs: --o-clustered-table ARTIFACT FeatureTable[Frequency] The table following clustering of features. [required] --o-clustered-sequences ARTIFACT FeatureData[Sequence] Sequences representing clustered features. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-sequences': 'rep-seqs_tmp.qza' is not a valid filepath (2/2) Invalid value for '--i-table': 'table_tmp.qza' is not a valid filepath rm: cannot remove 'table_tmp.qza': No such file or directory rm: cannot remove 'rep-seqs_tmp.qza': No such file or directory Usage: qiime demux summarize [OPTIONS] Summarize counts per sample for all samples, and generate interactive positional quality plots based on `n` randomly selected sequences. Inputs: --i-data ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be summarized. [required] Parameters: --p-n INTEGER The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences. [default: 10000] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-data': 'sequences.qza' is not a valid filepath Usage: qiime feature-table summarize [OPTIONS] Generate visual and tabular summaries of a feature table. Inputs: --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required] Parameters: --m-sample-metadata-file METADATA... (multiple The sample metadata. arguments will be merged) [optional] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table.qza' is not a valid filepath Usage: qiime feature-table tabulate-seqs [OPTIONS] Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database. Inputs: --i-data ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-data': 'rep-seqs.qza' is not a valid filepath Usage: qiime feature-classifier classify-consensus-vsearch [OPTIONS] Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global alignment between query and reference_reads, then assigns consensus taxonomy to each query sequence from among maxaccepts top hits, min_consensus of which share that taxonomic assignment. Unlike classify- consensus-blast, this method searches the entire reference database before choosing the top N hits, not the first N hits. Inputs: --i-query ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required] --i-reference-reads ARTIFACT FeatureData[Sequence] reference sequences. [required] --i-reference-taxonomy ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required] Parameters: --p-maxaccepts VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to keep for each query. Set to "all" to keep all hits > perc-identity similarity. Note that if strand=both, maxaccepts will keep N hits for each direction (if searches in the opposite direction yield results that exceed the minimum perc-identity). In those cases use maxhits to control the total number of hits returned. This option works in pair with maxrejects. The search process sorts target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if the first target sequence passes the acceptation criteria, it is accepted as best hit and the search process stops for that query. If maxaccepts is set to a higher value, more hits are accepted. If maxaccepts and maxrejects are both set to "all", the complete database is searched. [default: 10] --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. [default: 0.8] --p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8] --p-strand TEXT Choices('both', 'plus') Align against reference sequences in forward ("plus") or both directions ("both"). [default: 'both'] --p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. [default: 0.51] --p-unassignable-label TEXT [default: 'Unassigned'] --p-search-exact / --p-no-search-exact Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity and query-cov settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False] --p-top-hits-only / --p-no-top-hits-only Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False] --p-maxhits VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to show once the search is terminated. [default: 'all'] --p-maxrejects VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of non-matching target sequences to consider before stopping the search. This option works in pair with maxaccepts (see maxaccepts description for details). [default: 'all'] --p-output-no-hits / --p-no-output-no-hits Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. [default: True] --p-weak-id PROPORTION Range(0.0, 1.0, inclusive_end=True) Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0] --p-threads INTEGER Number of threads to use for job parallelization. Range(1, None) [default: 1] Outputs: --o-classification ARTIFACT FeatureData[Taxonomy] The resulting taxonomy classifications. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-query': 'rep-seqs.qza' is not a valid filepath There was an issue with loading the file taxonomy.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): taxonomy.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime taxa barplot [OPTIONS] This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be merged) [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa filter-table [OPTIONS] This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored. [required] Parameters: --p-include TEXT One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional] --p-exclude TEXT One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional] --p-query-delimiter TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ','] --p-mode TEXT Choices('exact', 'contains') Mode for determining if a search term matches a taxonomic annotation. "contains" requires that the annotation has the term as a substring; "exact" requires that the annotation is a perfect match to a search term. [default: 'contains'] Outputs: --o-filtered-table ARTIFACT FeatureTable[Frequency] The taxonomy-filtered feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa barplot [OPTIONS] This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be merged) [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table-no-Unassigned.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level1.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level1.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level1.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level1.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level1.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level1.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level1.biom' does not exist. cat: feature-table_absfreq_level1.tsv: No such file or directory cat: feature-table_absfreq_level1.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level2.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level2.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level2.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level2.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level2.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level2.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level2.biom' does not exist. cat: feature-table_absfreq_level2.tsv: No such file or directory cat: feature-table_absfreq_level2.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level3.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level3.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level3.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level3.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level3.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level3.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level3.biom' does not exist. cat: feature-table_absfreq_level3.tsv: No such file or directory cat: feature-table_absfreq_level3.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level4.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level4.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level4.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level4.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level4.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level4.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level4.biom' does not exist. cat: feature-table_absfreq_level4.tsv: No such file or directory cat: feature-table_absfreq_level4.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level5.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level5.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level5.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level5.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level5.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level5.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level5.biom' does not exist. cat: feature-table_absfreq_level5.tsv: No such file or directory cat: feature-table_absfreq_level5.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level6.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level6.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level6.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level6.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level6.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level6.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level6.biom' does not exist. cat: feature-table_absfreq_level6.tsv: No such file or directory cat: feature-table_absfreq_level6.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level7.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level7.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level7.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level7.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level7.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level7.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level7.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.11/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level7.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level7.biom' does not exist. cat: feature-table_absfreq_level7.tsv: No such file or directory cat: feature-table_absfreq_level7.tsv: No such file or directory mkdir: cannot create directory ‘collapsed_feature_tables’: File exists mv: cannot stat 'table_collapsed*': No such file or directory mv: cannot stat 'feature-table_*freq_level*.biom': No such file or directory