[maker-devel] PARALLELIZED DE NOVO GENOME ANNOTATION WITHOUT MPI

[Quanwei Zhang]

Hello:

I am doing genome annotation using Maker on our high performance
computational cluster (HPC). Due to some issues of MPI, I submitted the
Maker jobs several times under the same directory to HPC. Followed by the
example in the protocol (as shown below), when I submit the jobs I make
them as background processes by "&" except the first one. Is this necessary
when I submit a job to a HPC? I found it costed much much longer time than
I expected (according to a testing on a smaller data set). I am not sure
whether setting the process as background process lead to this issue?

The example in the protocol
% maker 2> maker1.error
% maker 2> maker2.error &
% maker 2> maker3.error &
......

BTW, will the annotation on shorter contig (e.g., 500bp) cost ~ 1/100 of
the time that cost for annotation a 50000bp contig? I am using SNAP for an
inito and RNA-seq assembly and protein sequences as evidence. I have more
than half contigs shorter than 300bp (whose total length is only about 5%
of the total length of all contigs), I want to know whether I can save
about half (or only about 5%) of the time if I ignore those short contigs.

 Thanks

Best
Quanwei
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