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Old 08-30-2010, 12:08 AM   #1
Hobbe
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Location: Uppsala, Sweden

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Default 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.
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Old 08-30-2010, 11:58 PM   #2
Hobbe
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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.
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Old 09-21-2010, 01:22 AM   #3
Torst
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Quote:
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.
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