Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • megahit failing without an error message in (x)ubuntu virtual machine

    Hi.

    I can get megahit (v1.1) to work as expected (either by compiling it myself or using precompiled binaries) on our cluster with CentOS (6.8).

    The same version of megahit initially appears to run on Ubuntu (14.04) but no contigs are assembled and there are no errors displayed. The command I am using for testing purposes is:

    Code:
    megahit -t 1 -m 1000000000 --verbose -r /home/input/readsInterleaved3.fa -o /home/output/assembly
    On Ubuntu, the screen only displays:

    Code:
    MEGAHIT v1.1.1
    --- [Wed Jan 18 15:32:08 2017] Start assembly. Number of CPU threads 1 ---
    --- [Wed Jan 18 15:32:08 2017] Available memory: 2099187712, used: 1000000000
    ..and the resulting assembly folder is empty.

    If I execute the same command line instructions as above on Centos (on our cluster) the screen displays:

    Code:
    MEGAHIT v1.1.1
    --- [Wed Jan 18 15:45:15 2017] Start assembly. Number of CPU threads 1 ---
    --- [Wed Jan 18 15:45:15 2017] Available memory: 126861316096, used: 1000000000
    --- [Wed Jan 18 15:45:15 2017] Converting reads to binaries ---
    ...and lots more output as the program correctly executes and assembles the contigs.


    I'm guessing that perhaps megahit is coded to abort if there is not a minimum amount of memory available on the machine??

    Usually I like to construct pipelines etc on my small virtual machine before porting them over to the cluster, hence my attempts to get them to work on this low memory machine.

    Have I come to the correct conclusion or is there some other possibility (and associated fix) that exists?
    Last edited by quokka; 01-17-2017, 11:11 PM.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X