Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • some error message from BFAST match

    hi,

    I got some error message when I use BFAST for solid data mapping:

    error 1:

    In function "RGMatchPrint": Fatal Error[WriteFileError]. Message: Could not write m->readLength, m->qualLength, m->read, m->qual, m->maxReached, and m->numEntries.
    The file stream error was:: No space left on device
    ***** Exiting due to errors *****

    Does it mean I don't have enough memory or space to run it? But I run it on a cluster, it should have enough memory or space.

    error 2:

    In function "RGMatchPrint": Fatal Error[WriteFileError]. Message: Could not write masks[i].
    The file stream error was:: No space left on device
    ***** Exiting due to errors *****

    error 3:

    ************************************************************
    Searching for main indexes...
    ************************************************************

    In function "GetIndexFileNames": Fatal Error[OutOfRange]. Variable/Value: /icgc/lsdf/mb/analysis_final/reference/bfastCS/hg19.fa.cs.
    Message: Could not find any indexes with the given prefix.
    ***** Exiting due to errors *****

    For this error, I do have indexes there. Sometimes it can find them, sometimes it reports this error. So I don't understand why.

  • #2
    You need more disk space: "No space left on device".

    Comment


    • #3
      Hi,
      II am new using bfast, I have a question: How can I define the mask values??, in index option.

      Thanks

      Comment


      • #4
        Originally posted by fenciso View Post
        Hi,
        II am new using bfast, I have a question: How can I define the mask values??, in index option.

        Thanks
        Welcome! In general, if you have a new question, post to a new thread. Use the "-m" option, and see the appendix in the bfast manual for the recommended settings.

        Comment


        • #5
          ok, it works.

          Thanks

          Comment


          • #6
            had similar error too, like the following:


            In function "AlignedEndRead": Fatal Error[ReadFileError]. Variable/Value: a->reads, a->qual, and a->numEntries.
            Message: Could not read from file.
            The file stream error was:: Success
            ***** Exiting due to errors *****

            Comment


            • #7
              found a solution for my problem.
              bfast gives error when align reads contains non a t c g n base.

              Comment

              Latest Articles

              Collapse

              • 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
              • seqadmin
                The Impact of AI in Genomic Medicine
                by seqadmin



                Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                02-26-2024, 02:07 PM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 03-14-2024, 06:13 AM
              0 responses
              32 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-08-2024, 08:03 AM
              0 responses
              71 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-07-2024, 08:13 AM
              0 responses
              80 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-06-2024, 09:51 AM
              0 responses
              68 views
              0 likes
              Last Post seqadmin  
              Working...
              X