I'm trying lastz-1.03.73 from here: http://www.bx.psu.edu/~rsharris/lastz/newer/
But I don't see lastz_32... Is this now the default behaviour?
I just tried 'make lastz_32' and it appeared :-D
Thanks,
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sorry, my late thread..Originally posted by Bob-Harris View PostThe 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)
I solve the problem with upper.
Thanks!Leave a comment:
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The short answer is you need to use lastz_32 instead of lastz.Originally posted by Hyunmin View Post
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)Leave a comment:
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Have you tried to do the comparison choosing a smaller set of chromosomes from hg19 at a time and checking if that works?Leave a comment:
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Using lastz (FAILURE: in load_fasta_sequence)
This is my lastz command
$ lastz hg19/chrAll.fa[multiple] merged.fsa
Error
FAILURE: in load_fasta_sequence for hg19/chrAll.fa, sequence length 2,084,766,314+115,169,878 exceeds maximum (2,147,483,637)
I got the error in above.
What's wrong thing?
Thanks,
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