Assembly using ALLPATHS-LG: error MergeNeighborhoods2 step

Question

[jmherrero]

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:

########################
# 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
########################

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

[Coryza]

Very quick but dirty answer... just re-run your command. Allpaths is build to continue at the last possible completed part.

[jmherrero]

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

[jmherrero]

Indeed, I have run the program three times and always stops at the same step.

Answer 1

[chenllianfu]

Hi, i encounter this problem too. my genome size is about 2 GB. Have you resolve it ?