[maker-devel] ncRNA support in maker

[Mikael Brandström Durling]

Hi Carson,

it’s nice to see all these new features in maker.

I gave the trnascan option a try by enabling it in the config file for one of my fungal genomes. It failed though, with this error message:

ERROR: You found a tRNA with an intron! This should not happen
--> rank=12, hostname=my-mgrid6
ERROR: Failed while gathering ab-init output files
ERROR: Chunk failed at level:1, tier_type:2
FAILED CONTIG:scf_013

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:scf_013

I checked the trnascan output (scf_013.abinit_nomask.0.eukaryotic.trnascan) in theVoid for that contig, and the output seems valid to me:

scf_013         1       189339  189410  Thr     AGT     0       0       82.83
scf_013         2       510381  510462  Ser     AGA     0       0       67.09
scf_013         3       586886  587000  Leu     CAA     586924  586956  57.97
scf_013         4       942166  942069  Leu     AAG     942128  942113  57.48
scf_013         5       169102  168993  Leu     TAA     169065  169037  56.49


Hope this can be of some help while debugging. I’ll leave trnascan off for now.

thanks,

Mikael


10 jan 2014 kl. 22:03 skrev Carson Holt <carsonhh at gmail.com>:

> Hi Mikael,
> 
> The options are part of the new MAKER-P integration
> (http://www.plantphysiol.org/content/early/2013/12/06/pp.113.230144.abstrac
> t).  Additional documentation/tutorials will be forthcoming - probably in
> a nice wiki page as part of the upcoming GMOD Malaysia courses in February
> or alternatively with the annual GMOD summer school. The tRNA option is
> easy enough to turn on (just set trna=1 in the maker_opts.ctl file).
> 
> Thanks,
> Carson
> 
> 
> 
> On 1/10/14, 2:48 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
> wrote:
> 
>> Hi Carson and other maker developers,
>> 
>> I was reading the source code of the latest maker release and noted
>> several references to ncRNAs, snoscan and trnascan. Can these be
>> incorporated into the normal annotation workflow? If so, are there any
>> instructions available for that?
>> 
>> best regards,
>> Mikael Durling
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> 
>