[maker-devel] Maker failing a number of contigs when running tblastx or blastn

[Carson Holt]

Hi Srividya,

First make sure you are using the most recent version of MAKER (currently 2.31.8).  Some of your error log information suggests that you have an older version. After installing the newest version, delete the mpi_blastdb directory from you current run before retrying.

The errors suggest there are issues either with the sequence you are using, or perhaps with the /tmp directory becoming full on one of your nodes during the run.  The current version of MAKER may give you a little more info if it is a sequence file content error.

Thanks,
Carson



> On Jun 23, 2015, at 7:52 AM, Srividya Ramakrishnan <srividya.ramki at gmail.com> wrote:
> 
> ​
>  error.log.gz <https://drive.google.com/file/d/0BxTwS_7TqV3GUVVYSTFPM3M0TDQ/edit?usp=drive_web>​Hi ,
> 
> I am trying to run maker on a rice genome assembly. The assembly has about 1074 contigs and maker successfully runs on about 655 contigs and fails on the rest of them. I ran a few times on the failed contigs changing the number of tries , clean try option set to true and also increasing the memory.  None of these options worked. Please help me figure  out the problem with my maker run. I have attached the error file with this mail
> 
> 
> Thanks 
> 
> Srividya Ramakrishnan
> Computational Science Analyst,
> Cold Spring Harbor Laboratory,
> 1 Bungtown Rd,
> Cold Spring Harbor , NY 11743​​
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