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 defaultassign_taxonomy_reference_seqs_fp
: reference database to use with assign_taxonomy.py (and parallel versions), if you prefer to not use the defaultblastmat_dir
: directory where BLAST substitution matrices are storedblastall_fp
: path toblastall
executablecluster_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 runsjobs_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 defaultpynast_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 forpynast_template_alignment_fp
pynast_template_alignment_fp
: template alignment to use with PyNAST as a fasta file, if you prefer to not use the defaultsc_queue
: default queue to submit jobs to when running parallel QIIME on StarCluster-based Amazon Web Services clustersseconds_to_sleep
: number of seconds to wait when checking whether parallel jobs have completedslurm_memory
: amount of memory in megabytes to request per CPU, when usingstart_parallel_jobs_slurm.py
; will default to slurm’s defaultslurm_queue
: queue to submit jobs to, when usingstart_parallel_jobs_slurm.py
; will default to slurm’s defaulttemp_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 installedtorque_queue
: default queue to submit jobs to when usingstart_parallel_jobs_torque.py
slurm_time
: default runtime limit for jobs when usingstart_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.)