News and Announcements » – Parallel merge BIOM tables


This script works like the script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.

Usage: [options]

Input Arguments:



-i, --input_fps
The otu tables in biom format (comma-separated)
-o, --output_dir
The output otu table directory path


-C, --cluster
Submit to a torque cluster
-Z, --seconds_to_sleep
Number of seconds to sleep between checks for run completion when polling runs [default: 1]
-X, --job_prefix
Job prefix [default: descriptive prefix + random chars]


The output consists of many files (i.e. merged_table.biom, merged_table.log and all intermediate merge tables). The .biom file contains the result of merging the individual BIOM tables. The resulting .log file contains a list of parameters passed to this script along with the output location of the resulting .txt file, the dependency hierarchy and runtime information for each individual merge.


Merge the OTU tables $PWD/t1.biom,$PWD/t2.biom,$PWD/t3.biom,$PWD/t4.biom and write the resulting output table to the $PWD/merged/ directory. -i $PWD/t1.biom,$PWD/t2.biom,$PWD/t3.biom,$PWD/t4.biom -o $PWD/merged/

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