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We will update the system on Monday September 20th, 2020. No new jobs will start from 6am the day before until the new version is deployed. Please plan accordingly.

Available Software

Here you will find our current processing recommendations.
Plugin Commands
ID 3: Target Gene type, 0.1.0
Command Name Resource Allocation
ID 6: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 7: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 8: Visualization types, 0.1.0
Command Name Resource Allocation
ID 40: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 41: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 11: QIIMEq2, 1.9.1
Command Name Resource Allocation
ID 60: Split libraries FASTQ -q qiita -l nodes=1:ppn=1 -l mem=60gb -l walltime=400:00:00
ID 59: Split libraries -q qiita -l nodes=1:ppn=1 -l mem=60gb -l walltime=25:00:00
ID 57: Trimming -q qiita -l nodes=1:ppn=1 -l mem={input_size}+(4*(2**30)) -l walltime=240:00:00
ID 58: Pick closed-reference OTUs -q qiita -l nodes=1:ppn=5 -l mem=120gb -l walltime=160:00:00
ID 15: BIOM type, 2.1.4 - Qiime2
Command Name Resource Allocation
ID 106: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 107: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 20: deblur, 1.1.0
Command Name Resource Allocation
ID 134: Deblur -q qiita -l nodes=1:ppn=5 -l mem=({input_size}*3)+(13*(2**30)) -l walltime=400:00:00
ID 24: Diversity types, 0.1.1
Command Name Resource Allocation
ID 185: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 186: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 29: qiime2, 2020.6.0
Command Name Resource Allocation
ID 330: Collapse features by their taxonomy at the specified level [collapse] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 338: Remove features from table if they're not present in tree. [filter_table] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 346: Filter features from table [filter_features] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 354: Core diversity metrics (phylogenetic and non-phylogenetic) [core_metrics_phylogenetic] -q qiita -l nodes=1:ppn=5 -l mem=40gb -l walltime=35:00:00
ID 362: Compute first differences or difference from baseline between sequential states [first_differences] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 370: Beta diversity group significance [beta_group_significance] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 378: Alpha diversity correlation [alpha_correlation] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 331: Visualize taxonomy with an interactive bar plot [barplot] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 339: Identify core features in table [core_features] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 347: Convert to relative frequencies [relative_frequency] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 355: Beta diversity (phylogenetic) [beta_phylogenetic] -q qiita -l nodes=1:ppn=5 -l mem=8gb -l walltime=35:00:00
ID 363: Paired difference testing and boxplots [pairwise_differences] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 371: Beta diversity correlation [beta_correlation] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 379: Pre-fitted sklearn-based taxonomy classifier [classify_sklearn] -q qiita -l nodes=1:ppn=5 -l mem=84gb -l walltime=150:00:00
ID 332: Taxonomy-based feature table filter. [filter_table] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 340: Convert to presence/absence [presence_absence] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 348: Renames sample or feature ids in a table [rename_ids] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 356: Beta diversity [beta] -q qiita -l nodes=1:ppn=5 -l mem=16gb -l walltime=35:00:00
ID 364: Generate interactive volatility plot [volatility] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 372: bioenv [bioenv] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 333: Generate heatmap of important features. [heatmap] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 341: Filter samples from table [filter_samples] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 349: Transpose a feature table. [transpose] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 357: Core diversity metrics (non-phylogenetic) [core_metrics] -q qiita -l nodes=1:ppn=5 -l mem=16gb -l walltime=35:00:00
ID 365: Linear mixed effects modeling [linear_mixed_effects] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 373: Filter samples from a distance matrix. [filter_distance_matrix] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 334: Nested cross-validated supervised learning regressor. [regress_samples_ncv] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 342: Rarefy table [rarefy] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 350: Alpha diversity (phylogenetic) - alternative implementation [alpha_phylogenetic_alt] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 358: Alpha rarefaction curves [alpha_rarefaction] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 366: Plot longitudinal feature volatility and importances [plot_feature_volatility] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 374: adonis PERMANOVA test for beta group significance [adonis] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 335: Nested cross-validated supervised learning classifier. [classify_samples_ncv] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 343: Summarize table [summarize] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 351: Alpha diversity [alpha] -q qiita -l nodes=1:ppn=1 -l mem=16gb -l walltime=3:00:00
ID 359: Alpha diversity (phylogenetic) [alpha_phylogenetic_old] -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=10:00:00
ID 367: Run k-nearest-neighbors on a labeled distance matrix. [classify_samples_from_dist] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 375: Principal Coordinate Analysis [pcoa] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 336: Split a feature table into training and testing sets. [split_table] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 344: Subsample table [subsample] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 352: Beta diversity rarefaction [beta_rarefaction] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 360: Add pseudocount to table [add_pseudocount] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 368: Paired pairwise distance testing and boxplots [pairwise_distances] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 376: Visualize and Interact with Principal Coordinates Analysis Plots [plot] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 337: Convert (and merge) positive numeric metadata (in)to feature table. [metatable] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 345: Generate a heatmap representation of a feature table [heatmap] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 353: Alpha diversity (phylogenetic) [alpha_phylogenetic] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 361: Nonparametric microbial interdependence test [nmit] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 369: Compute first distances or distance from baseline between sequential states [first_distances] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 377: Alpha diversity comparisons [alpha_group_significance] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 30: qp-shogun, 072020
Command Name Resource Allocation
ID 380: Atropos v1.1.24 -q qiita -l nodes=1:ppn=15 -l mem=30gb -l walltime=1000:00:00
ID 383: Sortmerna v2.1b -q qiita -l nodes=1:ppn=10 -l mem=40gb -l walltime=500:00:00
ID 381: QC_Filter -q qiita -l nodes=1:ppn=5 -l mem=16gb -l walltime=310:00:00
ID 382: Shogun v1.0.8 -q qiita -l nodes=1:ppn=15 -l mem=90gb -l walltime=400:00:00