mahulchak/svmu

lastz error

Opened this issue · 4 comments

jigaoxiang commented

Hello professor:
When I use the lastz to get *_lastz.txt file using
lastz *.genomic.fa[multiple] *.genomic.fa[multiple] --chain --format=general:name1,strand1,start1,end1,name2,strand2,start2,end2 > *_lastz.txt
some problem like below happen:
"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"
look like "raising scoring threshold" will working? the default of "--hspthresh" is 3000 ,so how many can set ？ could you give me some advice! Thank you very much!

mahulchak commented
jigaoxiang commented

Thanks for your response!
but this is another error when i use directly the outputfile of nucmer to run svmu
Segmentation fault (core dumped)
the code what I use svmu *_numcer.delta ref.genomic.fa sample.genomic.fa samvsref”svmu *_numcer.delta ref.genomic.fa sample.genomic.fa samvsref

CAShuangchao commented

Thanks for your response!
but this is another error when i use directly the outputfile of nucmer to run svmu
Segmentation fault (core dumped)
the code what I use svmu *_numcer.delta ref.genomic.fa sample.genomic.fa samvsref”svmu *_numcer.delta ref.genomic.fa sample.genomic.fa samvsref

Hi,
Have you solved this problem?I have encountered the same error as yours.

jigaoxiang commented

Thanks for your response!
but this is another error when i use directly the outputfile of nucmer to run svmu
Segmentation fault (core dumped)
the code what I use svmu *_numcer.delta ref.genomic.fa sample.genomic.fa samvsref”svmu *_numcer.delta ref.genomic.fa sample.genomic.fa samvsref

Hi,
Have you solved this problem?I have encountered the same error as yours.

没有呢，一直没得到作者的回复，也没解决掉。