Assembly using ALLPATHS-LG: error MergeNeighborhoods2 step
Dear all,
I am trying to perform a de novo assembly of a mammal genome (~2.7 GB) in ALLPATHS An error message appears always in the same step:
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# Step: MergeNeighborhoods2:
wo jan 21 19:26:39 2015 (MN2): skipped overlaps 1707
Call to new failed, memory usage before call = 311673076k.
Here is the output of top:
Aborting
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It looks like a memory issue... I'm running it within a linux server, node of 64 cores and 1TB RAM. The test dataset of ALLPATHS runs perfectly and other smaller genomes ran smoothly in the past.
I would be very thankful if you could you help me to solve it.
Regards,
Juan Manuel
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jmherrero •
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jmherrero •
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Hi, i encounter this problem too. my genome size is about 2 GB. Have you resolve it ?
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chenllianfu •
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Very quick but dirty answer... just re-run your command. Allpaths is build to continue at the last possible completed part.
Hi, thanks for your answer. I'm aware of that, but it has stopped twice at the same step... I will try again anyway! Meanwhile, any insight is very welcome
Indeed, I have run the program three times and always stops at the same step.