Table 1 Elastic Map Reduce commands

--stream

Activates the "streaming" module

N/A

--input

File(s) to be processed by EMR

hdfs:///home/hadoop/blast_runner hdfs:///home/hadoop/ortho_runner

--mapper

Name of mapper file

s3n://rsd_bucket/blast_mapper.py s3n://rsd_bucket/ortho_mapper.py

--reducer

None required, reduction done within RSD algorithm

N/A

--cache-archive

Individual symlinks to the executables, genomes,

s3n://rsd_bucket/executables.tar.gz #executables,#genomes, #RSD_standalone,#blastinput,#results

--output

hdfs:///home/hadoop/outl

-- jobconf mapred.map.tasks

Number of blast and ortholog calculation processes

= N

-- jobconf mapred.tasktracker.map.tasks.maximum

Total number of task trackers

= 8

--jobconf mapred. task, timeout

Time at which a process was considered a failure and restarted

= 86400000 ms

--jobconf mapred.tasktracker.expiry.interval

Time at which an instance was declared dead.

3600000 (set to be large to avoid instance shut down with long running jobs)

--jobconf mapred.map.tasks.speculative.execution

If true, EMR will speculate that a job is running slow and run the same job in parallel

False (because the time for each genome-vs-genome run varied widely, we elected to set this argument to False to ensure maximal availability of the cluster)