Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • doublealice
    Member
    • Feb 2011
    • 24

    #1

    MEGAN5 license and command line

    Hello,

    I recently installed MEGAN5 to my linux server to analyze my NGS data. I have some questions about the license and file input/output.

    I got license file from email and saved it as "MEGAN5-academic-license.txt" under ~/megan. But I am not sure how I can active the license via option -L in command line. Below are commands I tried:

    Code:
    $ MEGAN -g -E -L ~/megan/MEGAN5-academic-license.txt
    MEGAN fatal error:
    java.awt.HeadlessException:
    No X11 DISPLAY variable was set, but this program performed an operation which requires it.

    No X11 DISPLAY variable was set, but this program performed an operation which requires it.

    Code:
    $xvfb-run --auto-servernum --server-num=1 MEGAN -g false -L ~/megan/MEGAN5-academic-license.txt
    No output

    Would you please help to correct the command? And, should I involve the license file every time I use MEGAN5 or it has a way to active only once?

    Another question is, I have a 2G blastn output file which generated from a illumina sequencing. I tried to import it and get a rma file. But my command have no output after 26 hours running. I guess there must be something wrong with the command. Here are two files I used:

    commands.txt
    -----------------

    load treeFile='/home/megan/class/resources/ncbi.map';
    load treeFile='/home/megan/class/resources/ncbi.tre';
    load taxGIFile='/home/megan/gi_taxid-March2015X.bin';
    import blastfile='/home/blast/blast_map/blastn_veroall_tab7' fastaFile='/home/blast/blast_map/Veroall.fasta' meganfile='veroal.rma' blastFormat=BlastTAB;
    quit;

    job_megan
    -------------

    #!/bin/bash
    #PBS -l nodes=1pn=12
    #PBS -l mem=20gb
    #PBS -l walltime=30:00:00
    #PBS -m abe
    #PBS -q default
    #PBS -N megan
    cd ${PBS_O_WORKDIR}
    xvfb-run --auto-servernum --server-num=1 MEGAN -g false -v tree -L /home/megan/MEGAN5-academic-license.txt -c commands.txt

    I use qsub system to submit the job, but no feedback.

    Would you please help to correct it? I appreciate your help.

Latest Articles

Collapse

  • SEQadmin2
    Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool
    by SEQadmin2



    CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

    Despite this, “CRISPR helped turn genome editing from a specialized technique into
    ...
    07-31-2026, 11:01 AM
  • SEQadmin2
    Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications
    by SEQadmin2


    Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

    The systematic characterization of the human proteome has
    ...
    07-20-2026, 11:48 AM
  • SEQadmin2
    Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
    by SEQadmin2



    Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
    ...
    07-09-2026, 11:10 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 08-06-2026, 07:41 AM
0 responses
13 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 08-03-2026, 10:13 AM
0 responses
31 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 07-31-2026, 02:55 AM
0 responses
40 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 07-24-2026, 12:17 PM
0 responses
26 views
0 reactions
Last Post SEQadmin2  
Working...