[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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