News and Announcements » – This script submits a FASTA file to MG-RAST


This script takes a split-library FASTA file and generates individual FASTA files for each sample, then submits each sample FASTA file to MG-RAST, given the user provides an MG-RAST web-services authorization key and Project ID. To get a web-services authorization key, the user should have an account on MG-RAST. Once logged in, the user can go to their Account Management page and under Preferences they should click ‘here’, where they will see a Web Services section where they can click on the ‘generate new key’ if they have not already been provided one.

Usage: [options]

Input Arguments:



-i, --input_fasta_fp
Path to the input fasta file
-w, --web_key_auth
The web services authorization key from MG-RAST
-p, --project_id
The title to be used for the project
-o, --output_dir
Path to the output directory


The resulting directory will contain all of the sample-separated FASTA files, along with a log html file, which informs the user of the jobs started on MG-RAST


The user can submit a post-split-library FASTA file, which will be loaded and processed into MG-RAST under the users account (‘-w’) and project (‘-p’), as follows: -i split_lib_seqs.fna -w user_mgrast_auth_key -p qiime_test_dataset -o ./output_dir

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