lastz error

[jigaoxiang]

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]

Hi, lastz is not needed to run SVMU. Just run nucmer as shown in the Readme and run svmu on the delta file. If you encounter an issue, let me know.

On Mon, Aug 10, 2020 at 4:51 AM jigaoxiang [email protected] wrote:

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!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/mahulchak/svmu/issues/17, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZQH2GPLK55WEFV5Y7PKKTR77NIJANCNFSM4PZ37OFA .

-- Mahul Chakraborty Department of Ecology and Evolutionary Biology University of California-Irvine Phone: 949 824 9559 Fax: 949 824 9559 Website: https://mahulchakraborty.wordpress.com/ Github: https://github.com/mahulchak

[jigaoxiang]

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]

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]

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。