Setting up your qiime config file

Your QIIME installation can be customized using a qiime config file.

You have two options of where your qiime config file can be stored, and you can use either or both of these options. First, you can place a file called .qiime_config in your home directory (i.e., $HOME/.qiime_config). Second, you can put the qiime config file in a location of your choice, and define an environment variable called QIIME_CONFIG_FP whose value is the absolute path to the qiime config file. If you use both of these options, the settings that are defined in $HOME/.qiime_config will take precedence over the settings that are defined in $QIIME_CONFIG_FP.

The values that you can set in your qiime config file are listed below. Defining any of these is optional. QIIME will use built-in defaults for any of these values that you don’t set.

• assign_taxonomy_id_to_taxonomy_fp : id-to-taxonomy map to use with assign_taxonomy.py (and parallel versions), if you prefer to not use the default
• assign_taxonomy_reference_seqs_fp : reference database to use with assign_taxonomy.py (and parallel versions), if you prefer to not use the default
• blastmat_dir : directory where BLAST substitution matrices are stored
• blastall_fp : path to blastall executable
• cluster_jobs_fp : path to your cluster jobs file. This file is described in detail in Using parallel QIIME.
• denoiser_min_per_core : minimum number of flowgrams to denoise per core in parallel denoiser runs
• jobs_to_start : default number of jobs to start when running QIIME in parallel. This value is described in detail in Using parallel QIIME.
• pick_otus_reference_seqs_fp : reference database to use with all OTU picking scripts and workflows, if you prefer to not use the default
• pynast_template_alignment_blastdb : template alignment to use with PyNAST as a pre-formatted BLAST database, if you prefer to not have a BLAST database constructed from the fasta filepath provided for pynast_template_alignment_fp
• pynast_template_alignment_fp : template alignment to use with PyNAST as a fasta file, if you prefer to not use the default
• sc_queue : default queue to submit jobs to when running parallel QIIME on StarCluster-based Amazon Web Services clusters
• seconds_to_sleep : number of seconds to wait when checking whether parallel jobs have completed
• slurm_memory : amount of memory in megabytes to request per CPU, when using start_parallel_jobs_slurm.py; will default to slurm’s default
• slurm_queue : queue to submit jobs to, when using start_parallel_jobs_slurm.py; will default to slurm’s default
• temp_dir : directory for storing temporary files created by QIIME scripts. When a script completes successfully, any temporary files that it created are cleaned up. If you’re working in a cluster environment, this directory must be shared across all of the worker nodes that QIIME jobs may be running on. This directory is described in detail in Using parallel QIIME.
• topiaryexplorer_project_dir : directory where TopiaryExplorer is installed
• torque_queue : default queue to submit jobs to when using start_parallel_jobs_torque.py
• slurm_time : default runtime limit for jobs when using start_parallel_jobs_slurm.py

Viewing and testing your qiime_config settings

To see the qiime_config values as read by QIIME, run:

print_qiime_config.py -t

We refer to the output of this command as the print_qiime_config.py output.

If you have added some of the above settings to a qiime config file, and you do not see those settings associated with the values in your print_qiime_config.py output, that means that QIIME did not find your qiime config file. Check that it is in one of the two allowed locations described above.

Default reference files

Several of the above settings will fall back to default files if not overwritten. These are:

• assign_taxonomy_id_to_taxonomy_fp
• assign_taxonomy_reference_seqs_fp
• pick_otus_reference_seqs_fp
• pynast_template_alignment_fp

In the QIIME default reference information section of the print_qiime_config.py output, you’ll be presented with a link to a page that describes what files are used as the defaults for each of these. These files come from the qiime-default-reference project, one of QIIME’s core dependencies. (We don’t describe those here as the defaults may differ based on how recent your QIIME installation is.)