mummer4 - multithreaded examples?

[MikeEHMatson]

Hello, I am trying to run analysis with mummer/nucmer 4 using a multithreaded approach.

I first ran nucmer/mummer3.23 via:

nucmer -maxmatch -l 100 -c 500 $ref $query -prefix out

Which works. However, the complexity of our organism means this will probably run for a day or so (currently unknown, the .delta output is being populated and has been running for at least 3 hours by now).

To speed things up, I tried mummer 4.0 via:

nucmer --maxmatch -l 100 -c 500 -t 32 $ref $query -prefix out32

Yet nothing happens other than the file "out32.delta" appearing in the directory. out32.delta is of size zero, and the stdout from the widow running the command is also blank. This is in contrast to running the command in mummer 3.23, which produced and wrote to the expected .ntref, .mgaps, and .delta files.

Several users have discussed using mummer 4.0 in a multithreaded format, but I can't seem to find any submission examples so I am not sure if there is a simple syntax error or if other issues are at play.

• Genome size is ~240 Mb
• $ref is 15 scaffolds containing 218 Mb and several hundred contigs of 28Mb
• $query is nearly 5000 scaffolds, none larger than 6.9 Mb

[ViriatoII]

I am also using nucmer -t 20 but it appears that it is only using one core! Did you find this out?

[zhiyongli1995]

I have the same problem and look forward to the author's reply. The nucmer seems only use one CPU core.

[lzy@localhost ~]$ nucmer -V
4.0.0rc1
nucmer --maxmatch -c 100 -b 500 -l 50 -t 12 $refgenome $qrygenome -p mumer4

[zhidaobuzhidao]

Has anyone solved this problem?Nucmer has no output for one day.

[jianshu93]

Any update for multi-threads? Thanks

Jianshu