Velvet maximum element with 32bit error

thh32 · 11-17-2014, 03:59 AM

So I have been running velvet on a metagenomic dataset (35Gb flash joined) using 51 Kmer and it failed with the error:

[888200.245154] >>> Reached maximum elements addressable with 32 bits
/cm/local/apps/sge/current/spool/node001/job_scripts/791542: line 15: 9081 Aborted (core dumped) velvetg out-dir -exp_cov auto

Has anyone had a similar error and if so how do I get around it?

GenoMax · 11-17-2014, 04:41 AM

Are you using (32-bit OS, 32-bit compiler) anywhere on your system (I doubt it, since you seem to be using SGE, but never hurts to ask)?

There was a past thread on this topic with no apparent resolution:http://seqanswers.com/forums/showthread.php?t=10855

thh32 · 11-17-2014, 06:10 AM

No we dont from what I know and thanks, I had a google around before posting and saw a few others have had the same issue and as you say with that thread, no resolution had been found.

GenoMax · 11-17-2014, 06:39 AM

Using Metavelvet is probably more appropriate in your case: http://metavelvet.dna.bio.keio.ac.jp/ (not clear if you are using plain velvet).

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11-17-2014, 03:59 AM	#1
thh32 Member Location: UK Join Date: Feb 2014 Posts: 60	Velvet maximum element with 32bit error So I have been running velvet on a metagenomic dataset (35Gb flash joined) using 51 Kmer and it failed with the error: [888200.245154] >>> Reached maximum elements addressable with 32 bits /cm/local/apps/sge/current/spool/node001/job_scripts/791542: line 15: 9081 Aborted (core dumped) velvetg out-dir -exp_cov auto Has anyone had a similar error and if so how do I get around it?

11-17-2014, 04:41 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	Are you using (32-bit OS, 32-bit compiler) anywhere on your system (I doubt it, since you seem to be using SGE, but never hurts to ask)? There was a past thread on this topic with no apparent resolution:http://seqanswers.com/forums/showthread.php?t=10855

11-17-2014, 06:10 AM	#3
thh32 Member Location: UK Join Date: Feb 2014 Posts: 60	No we dont from what I know and thanks, I had a google around before posting and saw a few others have had the same issue and as you say with that thread, no resolution had been found.

11-17-2014, 06:39 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	Using Metavelvet is probably more appropriate in your case: http://metavelvet.dna.bio.keio.ac.jp/ (not clear if you are using plain velvet).