[Inparanoid] offline blast parameters when setting run_blast = 0

Erik Sonnhammer erik.sonnhammer at scilifelab.se
Mon Nov 10 17:43:40 CET 2014


Looks ok, but I don't know what that warning means.

/Erik

On 11/10/2014 05:36 PM, Sammy Desilva wrote:
> Thanks, please have a look whether the format of file-AA is correct  
> for input
>
> aml_g1t1    aml_g1t1    880.6    423    423    423    423 423    
> 423    q:1-423 h:1-423
> aml_g1t1    aml_g10385t1    150.6    423    301    210    248 210    
> 248    q:1-210 h:39-286
> aml_g1t1    aml_g15430t1    98.6    423    162    139    137 139    
> 137    q:1-139 h:3-139
> aml_g1t1    aml_g10384t1    89.0    423    620    132    128 132    
> 128    q:266-397 h:15-142
> aml_g1t1    aml_g15143t1    85.5    423    246    108    107 108    
> 107    q:301-408 h:16-122
> aml_g1t1    aml_g13567t1    81.3    423    376    112    104 112    
> 104    q:306-417 h:181-284
> aml_g1t1    aml_g15245t1    67.0    423    153    95    94 95    94    
> q:313-407 h:33-126
>
> Parser Warning
>
> junk after document element at line 1, column 6899908, byte 6899908 at 
> blast_parser.pl <http://blast_parser.pl> line 105
>
> On Mon, Nov 10, 2014 at 1:49 PM, Erik Sonnhammer 
> <erik.sonnhammer at scilifelab.se <mailto:erik.sonnhammer at scilifelab.se>> 
> wrote:
>
>     On 11/10/2014 12:27 PM, Sammy Desilva wrote:
>>     As mentioned in inparanoid.pl <http://inparanoid.pl> $run_blast
>>     could be set 0 if we have the blast files. For the pairwise
>>     comparison of a big dataset I want to run the blastall on
>>     cluster. Could you tell me which parameter-set of blastall I
>>     should use so that there will be no difference in results (when
>>     $run_blast is 1)?
>     Hi, simply use the same parameters ;)
>
>     You can save compute time by running the "A-A" comparisons only
>     once. If you run the script for each species comparisons, A-A and
>     B-B will be rerun every time, so you almost save half the compute
>     if you just do it once for the whole batch.
>
>>     Next, when setting $run_blast = 0 the blastall results should
>>     already be parsed?
>     Yes.
>
>     /Erik
>>
>>     Thanks.
>>     Sammy
>>
>>
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>
>

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