Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Need help with Genemark-ES

    I am working on a fungal genome (454-data) and want to run Genemark-ES, but am having a lot of problems getting it to work. Usually I get the error-message "St9bad_alloc", but I have on one occassion actually managed to get it to spit out a mod-file. However, when I try to use that mod-file together with gmhmm3 to extract the protein sequences, I get the "St9bad_alloc" error again. The thing is that, as far as I know, I am running the program in the same way, but am getting different error messages, and as mentioned I have even managed to get it to work (sort of) once. It seems unstable. The logfile also reports "warning, error in input file format" on occassion.

    I have assembled the genome with Mira into roughly 4000 contigs and a number of singles, and have all the sequences in a fasta file. I have tried keeping the contig-names in the fasta-file as well as removing them, but no difference. If the problem lies in the contig-file, I just can't understand what it might be.

    I am running the 64-bit Linux version and have tried both Ubuntu 64bit and Scientific Linux 64-bit. I run the program using the gm_es.pl script as I want the program to train itself on the genome.


    Any help would be much appreciated. Just now I don't know if the problem is with my indata or with the program, so all ideas are welcome.

  • #2
    Managed to resolve the issue myself. Turns out that St9bad_alloc is a memoryrelated problem, and by running on a machine with more memory, the error message disappeared.

    Comment


    • #3
      Originally posted by Hobbe View Post
      Managed to resolve the issue myself. Turns out that St9bad_alloc is a memoryrelated problem, and by running on a machine with more memory, the error message disappeared.
      Yep - it means the C++ call to "new" to allocate some memory for an array (or something) failed, and the exception was not caught by the programmer... naughty.

      Comment

      Latest Articles

      Collapse

      • 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
      • seqadmin
        Multiomics Techniques Advancing Disease Research
        by seqadmin


        New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

        A major leap in the field has
        ...
        02-08-2024, 06:33 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 02-28-2024, 06:12 AM
      0 responses
      28 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-23-2024, 04:11 PM
      0 responses
      74 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-21-2024, 08:52 AM
      0 responses
      85 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-20-2024, 08:57 AM
      0 responses
      70 views
      0 likes
      Last Post seqadmin  
      Working...
      X