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

[Quanwei Zhang]

Hi Carson:

I split my contigs into 50 files and annotated them parallelized. After
annotation finish, I used "gff3_merge -d"  and "fasta_merge -d" to get the
gff and fasta files for each of the 50 files. Now I am trying to merge
those gff files into one gff. But I found behind the annotation
information, the contig sequences are attached into the gff files. So I
think I can not simply merge them using the command "cat file1.gff
file2.gff ...file50.gff > merged.gff". So I am considering to merge those
files in two ways, would you please give me a suggestion (which works)?
(1) If the contigs sequences will not be useful for downstream functional
annotation, then I want to remove all the contig sequences from those gff,
and then merge gff file with only annotation information using "cat"
command.
(2) Merge the annotation part and the contig sequences part (from those 50
gff files) separately, then merge the two file (i.e., the file including
all annotation information, and the file including all the contigs
sequences) by adding the contig sequence to the end of annotation
information.

Thanks



2017-03-01 16:10 GMT-05:00 Carson Holt <carsonhh at gmail.com>:

> That will work.
>
> —Carson
>
> On Mar 1, 2017, at 2:09 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
> Thank you. I have submit my jobs to our server. What I plan to do is like
> this: (1) split contigs into 50 files; (2) for each contig file, I
> collected the annotation into gff and protein sequences into fasta format;
> (3) manually merge the 50 gff files and protein sequences files. Is what I
> am doing also correct?
>
> Best
> Quanwei
>
> 2017-03-01 15:54 GMT-05:00 Carson Holt <carsonhh at gmail.com>:
>
>> If you split into separate files, you can use the -g option to select the
>> input file together with the -base option so all output goes to the same
>> directory. Because they technically have different input files, this will
>> avoid file locking issues. You have to use the -dsindex option at the end
>> to rebuild the datastore index, so it looks like a single job. But that is
>> one way to get around the issue.
>>
>> —Carson
>>
>>
>>
>> On Mar 1, 2017, at 1:52 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>>
>> Thank you. But I met some problems  with MPI on our server. So now I
>> split my contigs into several files and annotate those files separately.
>> After I finish the annotation on each file, I will merge the results.
>>
>> Thank you for your explanation!
>>
>> Best
>> Quanwei
>>
>> 2017-03-01 15:36 GMT-05:00 Carson Holt <carsonhh at gmail.com>:
>>
>>> If you submit too many simultaneous, MAKER run then file locks will
>>> start to collide and one run will slow down the others. You should submit
>>> fewer simultaneous jobs and instead use MPI (maker must be configured and
>>> compiled to use MPI).
>>>
>>> An example MPI launch command for running on 200 CPUs on a cluster —>
>>> mpiexec -n 200 maker 2> maker_mpi1.error
>>>
>>> —Carson
>>>
>>>
>>>
>>> > On Feb 27, 2017, at 8:25 AM, Quanwei Zhang <qwzhang0601 at gmail.com>
>>> wrote:
>>> >
>>> > 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
>>> > _______________________________________________
>>> > maker-devel mailing list
>>> > maker-devel at box290.bluehost.com
>>> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yand
>>> ell-lab.org
>>>
>>>
>>
>>
>
>
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