Memory Setting Error about megahit HOT 4 CLOSED

Hi Josh,

I guess that you are using a rather old version which does not support parsing float value like 60e9 for the “-m” option. What’s the version you are using? (if you use checked it out from github, use "git describe” in the directory)

Cheers,
Dinghua

On 13 Mar, 2015, at 10:31 pm, Josh Herr [email protected] wrote:

Hi, I've searched all over the issues and online and I can't find a reference to this, perhaps you can help.

When I try this command:

megahit --cpu-only -m 60e9 -max_read_len 250 -r input.fastq
I get this error message:

Traceback (most recent call last):
File "/opt/software/megahit/20141001--GCC-4.4.5/bin/megahit", line 584, in
sys.exit(main())
File "/opt/software/megahit/20141001--GCC-4.4.5/bin/megahit", line 513, in main
host_mem = long(value)
ValueError: invalid literal for long() with base 10: '60e9'
Could I have compiled incorrectly or do I need to adjust the memory? Memory should not be an issue as I am on a shared server. I don't know what the error is with the '60e9' string.

Thanks so much for your time!

—
Reply to this email directly or view it on GitHub #28.

from megahit.

Thank you very much for the quick reply Dinghua...

I'm using megahit on a shared high performance cluster, the version is stated as:

megahit:
  ---------------------------------------------------------------------------------
     Versions:
        megahit/20141001

Looks like this is an older version -- I should ask to have the sysadmin recompile a newer version. Should that fix the problem?

from megahit.

Yes, it should. Please checkout the head of the master branch.

On 13 Mar, 2015, at 10:47 pm, Josh Herr [email protected] wrote:

Thank you very much for the quick reply Dinghua...

I'm using megahit on a shared high performance cluster, the version is stated as:

megahit:

---

 Versions:
    megahit/20141001

Looks like this is an older version -- I should ask to have the sysadmin recompile a newer version. Should that fix the problem?

—
Reply to this email directly or view it on GitHub #28 (comment).

from megahit.

Thank you -- I will have the module updated. Cheers!

UPDATE: Everything worked great when I had our sysadmin update megahit. Thanks for the help!

from megahit.