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pml()
segfault: memory not mapped
#144
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Dear @iferres, with this data set it is a case that it runs out of memory. More that one cannot allocate enough memory.
Where 153762 is the number of site pattern, 664 number of sequences and 4 bytes for an integer.
Where 153762 is the number of site pattern, 664 number of sequences and 8 rate classes, 4 states and 8 bytes for an double. So maybe iqtree or RAxML can handle your data set. Maybe we can discuss offline and brainstorm how to handle such data sets. Kind regards, |
Thank you very much for your quick response, Klaus! I see. However, I ran it on a my desktop which has 64Gb of RAM, and then on a server with 1Tb of RAM. It fails in both of them. (The funny thing is that this is actually a 1/5 subset of my real dataset, which is a core genome concatenated alignment of 664 organisms and about 1000 genes 😅 ). I'm a user-level phylogenetist, not sure if I could help with this, but I'm open to try to improve it. Regards, |
Hi, I'm having this issue with
pml()
:I'm send you the files through wetransfer to reproduce the error (https://we.tl/t-SrejR8GFvG). The
phydat.RDS
is quite big (about 41 Mb). If I subset it before computingpml
, the error disappears.The text was updated successfully, but these errors were encountered: