[Inparanoid] Analyzing 17 proteome orthology with Inparanoid

[Sammy Desilva]

Could someone face this same "SeqPortNew blast error" before which is
affecting my computations? How can I solve this?

On 10/1/15, Sammy Desilva <sammy.ich17 at gmail.com> wrote:
> 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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>>
>>>>>>
>>>>>
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>>>>
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