Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Agalma pipeline only using a single thread for RAxML

    Hello all,

    I've been playing with the Agalma transcriptomics pipeline.

    I'm attempting to run the genetree step in the pipeline, which involves running raxml on a large set of homologs clustered by mcl. Agalma then takes the individual gene trees and 'prunes' out paralogs.

    Here's the problem: the genetree script works, but instead of executing multiple runs simultaneously, raxml is being run on one homolog at a time and only using a single thread despite having access to more. This isn't a huge issue on small datasets with few taxa, but it quickly becomes an insurmountable bottleneck.

    I'd assumed there was a simple fix (Agalma is just calling raxml with bash) or some setting I'd overlooked, but after considerable exertion, I've yet to make any progress. The only thing I can think of doing is running raxml externally on all 7000+ homologs and inserting the trees back into Agalma, but I've got a feeling the SQL database won't like that.

    Has anyone encountered this issue, or have any suggestions on solutions? Thanks!

    I'm using a mac pro running Mavericks, and I get the same issue with a Ubuntu Linux 14.04 virtual machine.

Latest Articles

Collapse

  • seqadmin
    Genetic Variation in Immunogenetics and Antibody Diversity
    by seqadmin



    The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
    11-06-2024, 07:24 PM
  • seqadmin
    Choosing Between NGS and qPCR
    by seqadmin



    Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
    10-18-2024, 07:11 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 11:09 AM
0 responses
22 views
0 likes
Last Post seqadmin  
Started by seqadmin, Today, 06:13 AM
0 responses
20 views
0 likes
Last Post seqadmin  
Started by seqadmin, 11-01-2024, 06:09 AM
0 responses
30 views
0 likes
Last Post seqadmin  
Started by seqadmin, 10-30-2024, 05:31 AM
0 responses
21 views
0 likes
Last Post seqadmin  
Working...
X