[maker-devel] Private message regarding: MAKER run error

[Carson Holt]

The issue is with Berkley DB. BioPerl is using perl’s DB_File module to index the fastas. 

1. Make sure you do not have an extremely large number of reads in the fasta files (i.e. mRNA-seq data which cannot be used directly as input to MAKER, you must assemble it first into transcriptome contigs)
2. Reinstall perl and compile against the newly installed BerkleyDB libraries.
3. Remove the brew installed BerkleyDB and use perl’s precompiled DB_File module.

You can count reads in your fasta input using this command (replace file.fasta)

grep -c “>” file.fasta

If your counts are really high (i.e. higher than a few hundred thousand maximum), then you have a data issue. You are either giving too much data or the wrong data as input.

—Carson



> On Apr 11, 2018, at 11:39 AM, ohon Kin <ohon.kin at gmail.com> wrote:
> 
> 
> hello ; Carson 
> 
> i really would appreciate your help im kind of having same issue 
> i get this Error when i run maker i assumed that it required big memory space  
> 
> 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
> Filesize limit exceeded: 25
> 
> while working 1T of my Hard-disc capacity seems not enough for maker annotation
> i think something wrong in my input data or the dependencies 
>  would you please advice on the matter and elaborate solutions please 
> 
> i have install BerkleyDB using brew 
> 
> The input giving to Maker as followed :
> Genome , EST , Protein. all in Fasta format, downloaded from NCBI ---> then added it directly to maker for annotation
> 
>  do i have to apply these data pre-process before it applied to maker 
> 
> 
> 
> 
> 
> 
> 
> 
> On Thursday, 7 December 2017 19:00:52 UTC+3, Carson Holt wrote:
> 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 <sc...@ <>scottcain.net <http://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 <tagi...@ <>ualberta.ca <http://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
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