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Old 08-29-2013, 02:57 PM   #1
huzefa_mehta
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Default STAR core dump

I havent been able to run STAR successfully yet. It exits with a core dump message. Any clues?



Aug 29 20:52:35 ..... Started STAR run
Aug 29 20:52:35 ... Starting to generate Genome files

terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
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Old 08-29-2013, 05:42 PM   #2
GenoMax
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What OS is this? Did you compile STAR on this machine or download the binaries?
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Old 08-30-2013, 12:06 AM   #3
dpryan
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In addition to what GenoMax wrote, how much RAM does the computer you're using have?
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Old 08-30-2013, 10:42 AM   #4
huzefa_mehta
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I compiled the libraries myself

I have about 0.5G of RAM, however have about 12G of swap virtual memory.
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Old 08-30-2013, 10:47 AM   #5
dpryan
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That's unlikely to be enough, unless you work on bacteria or something like that. You'll need to use a bigger computer.
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Old 08-30-2013, 03:01 PM   #6
GenoMax
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Defining large amounts of swap does not help with lack of real memory. I concur with Devon about finding alternate hardware.

If you are working with NGS data then 512 MB of RAM (I really hope 0.5G is a typo) is not going to get you anywhere with any program.

STAR major memory requirements posted by Alex in a thread on STAR on the google group:
1. Genome + SA: ~9*GenomeLength bytes
2. SAindex: ~6*4^(--genomeSAindexNbases). By default --genomeSAindexNbases 14 and it takes 1.5GB of RAM.

Last edited by GenoMax; 08-30-2013 at 03:19 PM.
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Old 09-02-2013, 08:43 PM   #7
ymc
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With so little RAM, it doesn't make sense to use rna-star
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