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Old 03-28-2014, 04:56 AM   #3
Location: USA

Join Date: Mar 2014
Posts: 13

Originally Posted by Hyunmin View Post
This is my lastz command
$ lastz hg19/chrAll.fa[multiple] merged.fsa
FAILURE: in load_fasta_sequence for hg19/chrAll.fa, sequence length 2,084,766,314+115,169,878 exceeds maximum (2,147,483,637)
The short answer is you need to use lastz_32 instead of lastz.

The long answer… the default lastz build can only handle a target up to 2Gbp combined length. This was a conscious design choice (circa 2004), as there is some efficiency gain from limiting the variables that track sequence positions to 31 bits. The lastz_32 build relaxes that constraint so that it can handle a target up to 4Gbp combined length.

The efficiency gain was more important on machines 10 years ago than it is now, but for backward compatibility I am keeping that as the default behavior. I'll (probably) change this error report on future releases so that it tells the user to consider using lastz_32.

The issue is discussed in the readme file here:

Bob H
(lastz author)
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