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<div>Good morning,</div>
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<div>I am a Phd student woking on plant genomics and I am stuggling with an issue regarding LastZ.</div>
<div>I choose to use LastZ because it was used for plant genome alignments in Ensembl Plants, so I hope that someone who succesfully used it before can help me with this. </div>
<div> </div>
<div>I am trying to align two references genomes from very close species: I have two FASTA files, </div>
<div>representing the same chromosome in the two species, each around 800Mb long, with at least one long repetitive region. </div>
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<div>the command I am using: </div>
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<div>lastz target.fasta query.fasta --notransition --step=20 --maxwordcount=70 ‑‑exact=20 --chain --gapped --ambiguous=iupac --rdotplot=plot --format=differences > alignment.differences</div>
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<div>I always get the same error:</div>
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<div>FAILURE: in add_segment()</div>
<div>table size (4,869,542,152 for 101,448,794 segments) exceeds allocation limit of 4,294,967,279;</div>
<div>consider raising scoring threshold (--hspthresh or --exact) or breaking your target sequence into smaller pieces.</div>
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<div>I tried several strategies to overcome this issue:</div>
<div>increasing values of exact up to 100</div>
<div>using values of hspthresh up to 10 000</div>
<div>adding --seed=match12</div>
<div>dividing my target sequence in two (one multiFASTA file)</div>
<div>working with just half chromosome (400Mb)</div>
<div>set the parameters as they were set to align <i>T. aestivum</i> and <i>A. tauschii</i> (<a href="https://plants.ensembl.org/mlss.html?mlss=9814" style="font-size: 10pt;">https://plants.ensembl.org/mlss.html?mlss=9814</a><span style="font-size: 10pt;">)</span></div>
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<div>Still, I get the same error.</div>
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<div>Just a few times I was able to get an output (e.g. when exact=100), but it is always more than 700Gb big, thus, even if the file is generated, I run out of memory and I can not work on it. </div>
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<div>I also used LastZ_32 but the process gets killed without giving me any info.</div>
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<div>I was wondering if you can help me with this issue, maybe I am not using properly some of the options, or give me some advice on how to proberly deal with this alignment. </div>
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<div>Thank you.</div>
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<div><span>Alice Iob<br>
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<div><span>PhD student <br>
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<div><span>Plant and Animal Genomics Program<br>
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CRAG, Centre for Research in Agricultural Genomics<br>
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<div><span></span><span>Campus UAB - CRAG Building | 08193 Cerdanyola | BARCELONA</span>
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<div>Office: 3.01</div>
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<div><span></span><span></span><span></span><span></span><span>Tel. +34 935636600 ext 3351
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