Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • Yanda
    Junior Member
    • Oct 2012
    • 1

    #1

    Seqclean indexing problem

    I downloaded Seqcleanx86_64. I want to remove contaminants from a powdery mildew DNA sequence data using databases I created using makeblast. I use Mac operating system. I tried running the following command line:

    $ Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A

    The terminal output recorded the following error:

    Process terminated with an error!
    seqclean (LA_Run18_R1.fa) encountered an error.
    Working directory was /Volumes/Data_2/Sandile/raw_data
    seqclean (LA_Run18_R1.fa) encountered an error.
    Working directory was /Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
    * Using screening files:

    /Volumes/Data_2/Sandile/raw_data/cont_db/bgh
    seqclean running options:
    seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
    Standard log file: seqcl_LA_Run18_R1.fa.log
    Error log file: err_seqcl_LA_Run18_R1.fa.log
    Using 1 CPUs for cleaning
    -= Rebuilding LA_Run18_R1.fa cdb index =-
    Error at cdbfasta LA_Run18_R1.fa -o LA_Run18_R1.fa.cidx

    Process terminated with an error!
    seqclean (LA_Run18_R1.fa) encountered an error.
    Working directory was /Volumes/Data_2/Sandile/raw_data
    seqclean (LA_Run18_R1.fa) encountered an error.
    Working directory was /Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A

    I am beginner level at bioinformatics, hence may not have phrased my question properly. Please advise on the probable cause of this error and ways to overcome it.
  • asperjelly
    Member
    • Jan 2013
    • 11

    #2
    I've had the same problem. It's unclear to me if SeqClean can actually run on a Mac - does anybody know this? Since the download appears to be already compiled - I'm assuming it is compiled for Linux and not Mac - hence I've run into the same problems and can't seem to get it to work on my Mac.

    Comment

    Latest Articles

    Collapse

    • kinpict.com
      Reply to 16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
      by kinpict.com
      The part about this topic feels surprisingly grounded, and the details on the page is the bit that made me slow down. I’d keep <a href="https://kinpict.com/">ai family photo generator</a> bookmarked for later.
      Today, 06:37 PM
    • SEQadmin2
      16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
      by SEQadmin2





      NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...
      10-30-2026, 06:46 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by SEQadmin2, 11-12-2026, 07:59 AM
    0 responses
    26 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 11-05-2026, 09:25 AM
    0 responses
    35 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 11-03-2026, 11:54 AM
    2 responses
    56 views
    0 reactions
    Last Post kinpict.com  
    Started by SEQadmin2, 10-28-2026, 09:57 AM
    0 responses
    175 views
    0 reactions
    Last Post SEQadmin2  
    Working...