Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bcftools installed via Cygwin plugin error

    Hi! I am trying to look at several genomes of different individuals of the same species and call the SNPs for each genome using bcftools. I installed bcftools via Cygwin terminal on Windows 10, but I keep receiving the following error when I am trying to use the plugins (count, etc.):

    Code:
    No functional bcftools plugins were found in
            BCFTOOLS_PLUGINS="/usr/local/libexec".
    
    - Is the plugin path correct?
    
    - Run "bcftools plugin -l" or "bcftools plugin -lvv" for a list of available plugins.
    When I run "bcftools plugin -l" I get the same message. The original bcftools installation folder is in a different place compared to the installed bcftools that are in usr/local/libexec (the actual program is in usr/local/bin), so I tried to export the path to the plugins to the plugin folder in the original bcftools directory which didn't help. I also tried to leave the plugins path to "/usr/local/libexec" and manually copy-paste the plugins folder in there, but that issued again the error above. The plugins folder is in the path mentioned, but it is either not recognized or doesn't contain functional plugins. When I try to ask why does the count plugin specifically not work, I get the following message:

    Code:
    $ bcftools plugin count -vv
    plugin directory /usr/local/libexec .. ok
    /usr/local/libexec/count.cygdll:
            dlopen   .. No such file or directory
    count:
            dlopen   .. No such file or directory
    
    The bcftools plugin "count" was not found or is not functional in
            BCFTOOLS_PLUGINS="/usr/local/libexec".
    
    - Is the plugin path correct?
    
    - Run "bcftools plugin -l" or "bcftools plugin -lvv" for a list of available plugins.
    
    Could not load "count".
    The count.cygdll and count.c files do exist though in the plugins directory so I am confused of why the plugins are not recognized. I would deeply appreciate any input!

    Furthermore, I would also appreciate any separate advice about how to align whole-genome assemblies to one reference genome in order to generate the required aligned .SAM file as input for bcftools. I know how to align short sequences, but I don't know for sure how to employ that for an entire genome.

    Thank you very much!

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
33 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
37 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
31 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Working...
X