[maker-devel] retrying the FAILED scaffolds

[Carson Holt]

Is there any way to re-try maker pipeline on just Failed scaffolds
separately?

> Yes. The failed contig fasta will be in the maker.output subdirectory for that
> contig.  Alternatively use the fasta_tool script to extract them from the
> genome file.  You can then run them in a separate directory, or use the
> '-base' command line flag to force it to use the base name of the current
> results directory.  Use the ­g option to override the genome file without
> having to edit the control files
> 
> Example:
> 
> maker -g failed.fasta ­base maize_assemby
> 
> Output will end up here --> maize_assemby.maker.output


And do I have to manually erase for the failed directories named as
../theVoid.scaffold_#/?
> No.  You can let MAKER just retry them as is (let maker handle what to delete
> and keep) or set clean_try=1 to force full deletion before rerunning


 

And how can I track down the reason why only those 20 out of around 3000
scaffolds?
> Search for the tag "ERROR" in the standard output of your run. What MAKER
> version are you using?  I can take a look at the STDERR as wel if you want.
> If it's too big for e-mail, you can share it via dropbox.



Thanks,
Carson


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