mahulchak
commented
4 years ago Hi, the lastz support is experimental and is not integrated well yet. I have updated the code. So, you can update the package at your end. Also, the new version works with delta files created with nucmer WITHOUT maxmatch so you can recreate the delta file and try to run svmu. Rest of the command stays the same. You don't need a lastz file. Just add a blank file there.
I use the command "~/software/svmu/svmu test.delta 140001.fas 140028.fas h sam_lastz.txt test", it return "segmentation fault (core dumped) " and produce 3 empty files: cm.test.txt, cnv_all.test.txt and cords.test.txt. I have tried in three sever, it showed the same problem. Maybe the problem is sam_lastz.txt? There are 8 coloums rather than 6 (in the mannual) in this file. If I replace sam_lastz.txt by a nonexist file name like "sam_txt", it seems fine and produce 6 files as below:
drwxrwxr-x 2 bac bac 4096 1月 24 00:50 ./ drwxrwxrwx 26 bac bac 4096 1月 23 23:48 ../ -rw------- 1 bac bac 38016751 1月 23 21:00 140001.fas -rw------- 1 bac bac 37523890 1月 23 21:01 140028.fas -rw-rw-r-- 1 bac bac 169630 1月 24 00:50 cm.test.txt -rw-rw-r-- 1 bac bac 644808 1月 24 00:50 cnv_all.test.txt -rw-rw-r-- 1 bac bac 1014481 1月 24 00:50 cords.test.txt -rw-rw-r-- 1 bac bac 4196598 1月 23 21:49 sam_lastz.txt -rw-rw-r-- 1 bac bac 0 1月 24 00:50 small.test.txt -rw-rw-r-- 1 bac bac 289469 1月 24 00:50 sv.test.txt -rw-rw-r-- 1 bac bac 1050793 1月 23 21:04 test.delta