[maker-devel] Problems with failed contigs

[Carson Holt]

First make sure you are using the most current version (3.01.02).

If you are providing a GFF3 issue, it may be an issue with one or more of the features you are giving. Finally, there is a possibility this is a BLAST report issue, as there is a BLAST truncation bug that appears to be fixed in NCBI BLAST 2.7.1+

—Carson

> On Mar 6, 2018, at 2:30 AM, p sz <seoanezonjic at hotmail.com> wrote:
> 
> Hi
> Currently i'm annotating a fish genome using the Maker 3 version and the execution don't finish properly. I execute Maker in a shared cluster trough MPI, asking for 96 cores (in order to not block the maker manager nor the file system) in 6 nodes of 16 cores each one. The work run 3 or 4 days and the output suddenly stops. The work remains 3 days more, but the index datastore is not modified and the only files that their attributes change are the lock files. When the job exceed the working time (7 days) it is cancelled. Then, I inspect the datastore index and count the uniq started and finished tags for each scaffold. The results are:
> STARTED:3890
> FINISHED:3378
> So, there are about 500 scaffolds in which the analysis fails. When I inspect the STDERR maker output I see this error line repeated ~2000 times, at differents sites:
> substr outside of string at /mnt/home/users/pab_001_uma/pedro/software/maker/bin/../lib/PhatHit_utils.pm line 850
> and near this line, the following:
> ERROR: Failed while annotating transcripts
> My questions are, what can I do to annotate the failed scaffolds? and in addition, is the great amount of failed analysis the reason of the job freeze? 
> Thanks in advance
> 
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <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/20180315/cfdb76f6/attachment-0003.html>