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.. _parallel_merge_otu_tables:
.. index:: parallel_merge_otu_tables.py
*parallel_merge_otu_tables.py* -- Parallel merge BIOM tables
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script works like the `merge_otu_tables.py <./merge_otu_tables.html>`_ script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.
**Usage:** :file:`parallel_merge_otu_tables.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_fps
The otu tables in biom format (comma-separated)
-o, `-`-output_dir
The output otu table directory path
**[OPTIONAL]**
-C, `-`-cluster
Submit to a torque cluster
-N, `-`-merge_otus_fp
Full path to scripts/`merge_otu_tables.py <./merge_otu_tables.html>`_ [default: /Users/caporaso/code/Qiime/scripts/`merge_otu_tables.py <./merge_otu_tables.html>`_]
-Y, `-`-python_exe_fp
Full path to python executable [default: python]
-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]
**Output:**
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.
**Example:**
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.
::
parallel_merge_otu_tables.py -i $PWD/t1.biom,$PWD/t2.biom,$PWD/t3.biom,$PWD/t4.biom -o $PWD/merged/
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