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segfault when uniting large methylrawlistDB object #269
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HI @ethan-shealy, Thanks for reporting this issue. Unfortunately, these kinds of errors are rather hard to debug without the actual data at hand. Is this error actually reproducible and happens repeatedly? Would you be able to generate a minimal, reproducible example? Also, are you running the latest package versions of Related to the fix of your previous error, it seems that the use of Best, |
Hi @alexg9010, this error does occur consistently on the |
Hi, I am having an issue where a my analysis is proceeding normally, then a crash happens which terminates the process. I am working with a large methylation dataset from a whole-genome bisulfite experiment, so have something like 10 million CpGs over 40 samples. The first "unite" function I tried worked fine,
but since I want to utilize two different filtering steps I used the 'reorganize' function and tried to unite again. Upon doing this, I received this recursive error and the process crashed.
I only utilized ~50% of my allocated memory, so I do not think this is the issue. I previously ran into a segfault error using methylkit's "as" command to extract methylbase data to a matrix. I had to use
methylation.matrix <- methylKit:::fread.gzipped(methFrame.total@dbpath, stringsAsFactors = FALSE, data.table = FALSE,skipDecompress=FALSE)
to resolve that issue and avoid the segfault error. Is this issue arising from something similar? Thanks for your help.
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