temporary directory

[leulmi selma]

Hi,

is there a way to set a specific temporary directory when using methylKit ? I am trying to read a large dataset, but I am bumping into errors, which I think might be related to the use of a temporary directory, which hasn't enough space.

example errors:

Error in fread.gzipped(filepath = filename, header = header, skip = skip, : ERROR: File /tmp/RtmpLiC4da/T2_trimmed_bismark_bt2.bismark.cov is empty.

In writeBin(bfr, con = out, size = 1L) : problem writing to connection

I would be grateful if you could let me to how how to work around this issue.

All the best,

Selma.

[Altuna Akalin]

Did you try unzipping the file and reading unzipped version? The problem is probably that decompression is using the temp directory, if the file is decompressed you may avoid this problem 

Sent from mobile, excuse the brevity

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