Using lastz (FAILURE: in load_fasta_sequence)

[Hyunmin]

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,

[GenoMax]

Have you tried to do the comparison choosing a smaller set of chromosomes from hg19 at a time and checking if that works?

[Bob-Harris]

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:

http://www.bx.psu.edu/~rsharris/lastz/newer/README.lastz-1.03.54.html#adv_whole_genome

Bob H
(lastz author)

[Hyunmin]

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:

http://www.bx.psu.edu/~rsharris/lastz/newer/README.lastz-1.03.54.html#adv_whole_genome

Bob H
(lastz author)

sorry, my late thread..

I solve the problem with upper.
Thanks!

[dan]

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,