[maker-devel] Status check?

[Barry Moore]

Xavier,

In the ouput directory there will be a file with a name something like  
fasta_name_master_datastore_index.log where "fasta_name" is the base  
name of your input genomic fasta file.  BTW, your output directory  
will be located in the working directory where started your MAKER run  
- will also be named after the genomic input file - something like  
fasta_name.maker.output.  Have a look at that  
master_datastore_index.log - it will have entries in it something like  
this:

v31.001000	smed_assembly_v31_datastore/BB/AC/v31.001000/	STARTED
v31.000600	smed_assembly_v31_datastore/E9/82/v31.000600/	FINISHED
v31.001200	smed_assembly_v31_datastore/37/15/v31.001200/	STARTED
v31.000800	smed_assembly_v31_datastore/42/28/v31.000800/	FINISHED

There may also be entries with tags like DIED or DIED_PERMANENTLY.

A command line like the following will give you a count of all of the  
tags in this file from which you can deduce how many contigs have  
started, finished and/or died.

Barry

On Oct 21, 2009, at 3:21 AM, Xavier Watkins wrote:

> Hi,
> I'm currently doing a test run of Maker on the D. mel genome and I  
> would like to estimate the time it takes to run on our system (it  
> has now been running for 2 weeks on 5 processors).
> Is there a way to know how many processes are left to run when  
> running MAKER, or to know which contigs (chromosomes in my case)  
> have finished running? From what I see it chops up the contigs into  
> slices when running RepeatMasker (currently on .151) is there a way  
> to know the total number of slices?
>
> Apologies if I've missed this info in the documentation, I couldn't  
> find it.
>
> All the best,
> Xavier
>
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