[Inparanoid] Analyzing 17 proteome orthology with Inparanoid

[Sammy Desilva]

Dear all,

So finally I canceled the computations. Can you please check the error log
file (attached) and let me know
what exactly is the problem?


*Thanks*
*Sammy*

On Tue, Sep 29, 2015 at 4:53 PM, Verena Haunschmid <veroamilbe at gmail.com>
wrote:

> Dear Sammy,
>
> I once did comparisons of several organisms and had the same problem as
>  you. To speed it up a little bit I precomputed the blast files since that
> is the most time consuming step as far as I remember.
>
> And if you do comparisons A-B, A-C, B-C, ... you would need to compute the
> blast output for A-A, B-B, C-C several times and that's half of the
> computation time for each pairwise comparison. Just compute all blast files
> for each organism with itself and uncomment those lines in the perl script.
> (might be that I still have these script, I will check later...)
>
> Best regards,
> Verena
>
>
>
> On Tue, Sep 29, 2015 at 4:46 PM Sammy Desilva <sammy.ich17 at gmail.com>
> wrote:
>
>> Dear all,
>>
>> I am again starting this thread here again. At that time I finally
>> shifted to normal PC instead of cluster. Now, I am analyzing 29 proteome
>> for orthology with multiparanoid. I used  the above script with sbatch seq
>> array in slurm but it  is still not finished in 15 days. Is there any
>> alternative way exist for doing this computations/
>>
>> Thnaks
>>
>> On Tue, Oct 7, 2014 at 1:39 PM, mateusz.kaduk at gmail.com <
>> mateusz.kaduk at gmail.com> wrote:
>>
>>> Dear Sammy,
>>>
>>> There is no script with inparanoid to automate pairwise runs, but I am
>>> using the following code to run all n(n-1)/2 pairwise comparisons without
>>> outgroup, it's just few lines of code, but maybe you will find it useful.
>>>
>>> #!/usr/bin/perl
>>> use strict;
>>> use warnings;
>>>
>>> # Here is the list of fasta files in the same directory as inparanoid.pl
>>> my @species = ("c_albicans-2011-04i.fa",
>>>                "c_neoformans-2011-04i.fa",
>>>                "s_cerevisiae-2011-04i.fa",
>>>                "s_pombe-2011-04i.fa",
>>>                "y_lipolytica-2011-04i.fa");
>>>
>>> my $numberOfspecies = @species;
>>>
>>> # Run all n(n-1)/2 combinations without outgroup
>>> for (my $i = 0; $i < $numberOfspecies-1; $i++) {
>>>     for(my $j = $i+1; $j < $numberOfspecies; $j++) {
>>>     print "Staring inparanoid for: ".
>>> $species[$i]."\t".$species[$j]."\n";
>>>     system ("./inparanoid.pl ".$species[$i]."\t".$species[$j]."\n");
>>>     }
>>> }
>>>
>>> Regards,
>>> Mateusz
>>>
>>>
>>>
>>> On Tue, Oct 7, 2014 at 1:27 PM, Sammy Desilva <sammy.ich17 at gmail.com>
>>> wrote:
>>>
>>>> Dear Prof. Sonnhammer,
>>>>
>>>> I understand in case of 17 proteome I have to use multiparanoid for
>>>> clustering after computing 17*16/2 = 136 pairs with InParanoid. I wonder is
>>>> any script already available to automate the computations of multiple pairs
>>>> (here 136) with InParanoid for getting input for MultiParanoid?
>>>>
>>>> Regads
>>>> Sammy
>>>>
>>>>
>>>> On Mon, Sep 22, 2014 at 2:33 PM, Erik Sonnhammer <
>>>> erik.sonnhammer at scilifelab.se> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> If you want ortholog groups that include all 17 species, InParanoid
>>>>> won't work. But if you only need pairwise relationships (which is usually
>>>>> the case) then it will.  Then you have to run InParanoid for all 17*16/2
>>>>> pairs.
>>>>>
>>>>> Erik Sonnhammer
>>>>>
>>>>> On 09/20/2014 11:32 AM, Sammy Desilva wrote:
>>>>>
>>>>> Hi, I want to assign orthology relationship among 17 proteomes. Could
>>>>> someone please suggest me how to do it offline in Inparanoid? The running
>>>>> command for such cases? I guess putting 3 organism it treats third as
>>>>> outgroup.
>>>>> Thanks
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> InParanoid mailing listInParanoid at lists.su.sehttps://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>>>>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> InParanoid mailing list
>>>> InParanoid at lists.su.se
>>>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>>>
>>>>
>>>
>> _______________________________________________
>> InParanoid mailing list
>> InParanoid at lists.su.se
>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.su.se/pipermail/inparanoid-at-sbc.su.se/attachments/20151001/f542a2d1/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: error1.tar.gz
Type: application/x-gzip
Size: 7726 bytes
Desc: not available
URL: <http://lists.su.se/pipermail/inparanoid-at-sbc.su.se/attachments/20151001/f542a2d1/attachment.bin>