View source for Lastz DEF file parameters

Adjusting SEQ_LAP, SEQ_CHUNK and SEQ_LIMIT parameters for the lastz/chain/net
pipeline.

The goal of adjusting these parameters is to obtain a reasonable
number of cluster jobs.

* SEQ1_LAP is always 10000
* SEQ2_LAP is always 0

This sets the amount of overlapping sequence in the resulting
partitioned sequences.  The overlap of 10,000 for SEQ1 will help
prevent artifical breaks in alignments due to boundary issues.

Typical CHUNK sizes are 10000000 or 20000000
for both SEQ1_CHUNK and SEQ2_CHUNK.  This sets the limit
of total sequence size allowed in one alignment.
The typical run-time of one alignment and your cluster
characteristics will help determine how much sequence you
want in one alignment.  cluster efficiency wants to have
run-time of one alignment be short enough to allow jobs to
cycle through the cluster at a reasonable rate to allow
appropriate cluster sharing with other users.  If CHUNK
size of 20000000 makes a run-time too long, use the smaller
size of 10000000.

The LIMIT is the adjustment that determines the number of chunks.
This is related to the number of contigs in your assembly.
The LIMIT means, when placing multiple sequences into one alignment,
before the CHUNK size limit is reached for the total sum of
sequences, how many individual sequences should be placed in
one CHUNK.  Very high contig count assemblies could use LIMITS
up to 1000, low contig count assemblies could use LIMITS as
low as 5.  Again, this is a trade off for run-time of one
alignment and cluster efficiency.  If both genome assemblies
are high contig counts, this will require a high LIMIT for both,
and will take an extra amount of cluster time.

To see the effect of CHUNK size and LIMIT, use the option
to the command: '''-stop=partition''' which will stop the process
after chopping up both genome sequences.  Save the output
of that procedure into a log file, it will contain the statement:
  cluster batch jobList size: 95567 = 227 * 421
where the 227 is the number of lines in run.blastz/target.lst
and the 421 is the number of lines in run.blastz/query.lst

In general, a cluster batch jobList size of something less
than 100000 is reasonable for a cluster of 500 to 1000 CPUs/cores.

To experiment repeatedly with this partition step, remove the run.blastz
directory to start over.

[[Category:Cluster FAQ]]
[[Category:Technical FAQ]]