Hi all,
I'm curious as to how the pipeline for aligning two chromosomes has changed
with the replacement of blastz with lastz. I notice lastz has quite a bit
more functionality than blastz, such as the ability to perform chaining. Are
there additional tools you recommend for filtering the output of lastz?
When using lastz for whole genome alignments, can you intuitively estimate
the expected memory usage for running the following command on a query of
184,000 sequences with each sequence having an average size of ~1000 bases
and a target of 1,200 sequences with each sequence having an average length
of 845,000 bases (expected % identity ~95)?
lastz query.fasta[multiple] target.fasta --chain --gapped --ambiguous=n
--format=sam --output=query-target_aligned.sam
Upon running, I get this message after some time:
FAILURE: call to realloc failed to allocate 135051136 bytes, for
add_segment
I am running this on a 32bit Linux virtual machine which has 3.5GB of memory
allocated to it. Are there different recommended parameters when dealing
with whole genome alignment vs. interspecies chromosomal alignment?
Thanks,
--
Bremen Braun
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
