[maker-devel] MAKER run error

[Carson Holt]

The FASTA file gets indexed by BioPerl using BerkleyDB. I’m guessing there is something odd about your input file and the database has run out of HASHes for indexing. You can google if there is a setting you can configure in BerkleyDB on Mac. But I suspect you are doing something like giving the raw reads from an mRNA-seq experiment or DNA sequencing to MAKER (resulting in billions of entrires to be indexed), which would be incorrect. MAKER can’t handle raw data. You must first assemble it using using like Trinity for example for mRNA.

Thanks,
Carson

> On Dec 7, 2017, at 8:53 AM, Scott Cain <scott at scottcain.net> wrote:
> 
> Hi Guinara,
> 
> I don't know (though my guess would be that you're running out of memory).  I'm cc'ing the MAKER developer's mailing list to see if anybody on that list knows.
> 
> Scott
> 
> 
> On Wed, Dec 6, 2017 at 8:36 PM, Gulnara Tagirdzhanova <tagirdzh at ualberta.ca <mailto:tagirdzh at ualberta.ca>> wrote:
> Hello,
> 
> I got this error running maker on mac:
> 
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> HASH: Out of overflow pages. Increase page size
> Filesize limit exceeded: 25
> 
> Is there anything that could solve it?
> 
> Thank you,
> Gulnara
> 
> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20171207/c0572ac5/attachment-0003.html>