[maker-devel] failed contigs

[Carson Holt]

Do you have STDERR log stored somewhere?  Could you send it to me?
Sometimes the error causing the failure is upstream in the log and then
cascades into other errors.  Also if it is the repeatrunner step failing,
the log will have the command to run the BLAST step outside of MAKER (is
helpful for debugging).  If you don't have the captured STDERR, could you
run again and send it to me.

Thanks,
Carson

On 12-08-04 7:51 AM, "Michael Thon" <mike.thon at gmail.com> wrote:

>running maker 2.26 some contigs seem to consistently fail to run,
>according to XXX_master_datastore_index.log
>
>Here are the last few lines of run.log for one of the failed contigs:
>
>CTL_OPTIONS     run
>LOGCHILD        
>/home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1
>.6/theVoid.supercont1.6/run.log.child.0
>LOGCHILD        
>/home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1
>.6/theVoid.supercont1.6/run.log.child.0
>LOGCHILD        
>/home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1
>.6/theVoid.supercont1.6/run.log.child.0
>LOGCHILD        
>/home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1
>.6/theVoid.supercont1.6/run.log.child.1
>LOGCHILD        
>/home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1
>.6/theVoid.supercont1.6/run.log.child.1
>LOGCHILD        
>/home/mike/projects/cg_maker/cgram.maker.output/cgram_datastore/supercont1
>.6/theVoid.supercont1.6/run.log.child.1
>DIED    RANK    0
>DIED    COUNT   1
>
>
>the contents of run.log.child.1 for the same contig:
>STARTED 
>cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/super
>cont1%2E6.1.Repeat_Type_Elements%2Efasta.specific.out
>FINISHED        
>cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/super
>cont1%2E6.1.Repeat_Type_Elements%2Efasta.specific.out
>STARTED 
>cgram.maker.output/cgram_datastore/supercont1.6/theVoid.supercont1.6/super
>cont1%2E6.1.te_proteins%2Efasta.repeatrunner
>DIED    RANK    0:2:0:1
>DIED    COUNT   1
>
>So perhaps its a problem with the repeat masking step.  I already have
>annotated repeats using RepeatMasker and I have the gff2 file produced by
>RepeatMasker.  Do I need to convert this to gff3 before adding to to my
>maker_opts file?  Better yet, does anyone know why these contigs are
>failing and how to fix it?
>Mike
>
>
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