[mira_talk] Re: 0.5TB not enough space?
- From: Robert Bruccoleri <bruc@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Aug 2011 13:29:10 -0400
Dear Iddo,
The run failed because the log files are being written to an NFS
mounted filesystem. NFS filesystem do slow things down, so Bastien made
Mira stop unless you specifically tell it to continue on NFS.
Please add -MI:sonfs=no to the COMMON_SETTINGS section and try again.
Regards,
Bob
Iddo Friedberg wrote:
Hi,
I have 9582196 mate-paired Solexa seqeunces, 100bp long. The genome I
am assembling is somewhere between 700KB and 1.5MB (Mycoplasma).
Anyhow, It seems like I rant out of my 500GB local space for the log
files. Is that reasonable? I can increase local scratch space, I just
want to make sure that I am not doing something wrong. Seems like
quite a bit of space to be used for such an assembly.
Parameters I used:
--project=CCGTCC COMMON_SETTINGS
-DI:trt=/localscratch/friedbi/mira_logs
--job=denovo,genome,accurate,solexa SOLEXA_SETTINGS
-GE:tismin=150:tismax=350
The entire logfile is available here, if someone is interested in more
information: http://db.tt/6VxJ8sW
Thanks in advance for any help!
Iddo
--
Iddo Friedberg
http://iddo-friedberg.net/contact.html
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