Sequence size error

[onbio]

Hi,
I am trying to run AliTV for three plant genomes (same species but different sub-species). the genomes have been assembled using HifiAsm. As they are from the same species the sequences have long stretches of similar sequence. the genome size is about 1Gb.

Can you suggest a remedy for the below error? It seems that the long matching sequence is causing the LastZ program to break. One possible fix I can think of now is masking repeats, but it would be great if you could suggest a remedy.

INFO - Created temporary folder at '/tmp/dB3SQ7kwnl'
INFO - Starting alignment generation... (820 alignments required)
FAILURE: in add_segment()
table size (4,869,542,152 for 101,448,794 segments) exceeds allocation limit of 4,294,967,279;
consider raising scoring threshold (--hspthresh or --exact) or breaking your target sequence into smaller pieces
"/bin/lastz" unexpectedly returned exit value 1 at /AliTV-perl-interface/bin/../lib/AliTV/Alignment/lastz.pm line 107.

Thank you for your assistance

[onbio]

I did try running for just the first sequence/chromosome, but I still got the same error message.

[iimog]

This is a problem with lastz on large and very similar genomes. In addition to the suggestion in the message

consider raising scoring threshold (--hspthresh or --exact) or breaking your target sequence into smaller pieces

the discussion in lastz/lastz#53 might be helpful.

You can add lastz options to AliTV in the yml file, see the documentation