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<div class="moz-cite-prefix">Looks ok, but I don't know what that
warning means.<br>
<br>
/Erik<br>
<br>
On 11/10/2014 05:36 PM, Sammy Desilva wrote:<br>
</div>
<blockquote
cite="mid:CAJXH_1MaNm+2d3YR_jhme605eJhCYCGt1=wwY_4H_Un4h3h2Gg@mail.gmail.com"
type="cite">
<div dir="ltr">Thanks, please have a look whether the format of
file-AA is correct for input<br>
<br>
aml_g1t1 aml_g1t1 880.6 423 423 423 423
423 423 q:1-423 h:1-423 <br>
aml_g1t1 aml_g10385t1 150.6 423 301 210 248
210 248 q:1-210 h:39-286 <br>
aml_g1t1 aml_g15430t1 98.6 423 162 139 137
139 137 q:1-139 h:3-139 <br>
aml_g1t1 aml_g10384t1 89.0 423 620 132 128
132 128 q:266-397 h:15-142 <br>
aml_g1t1 aml_g15143t1 85.5 423 246 108 107
108 107 q:301-408 h:16-122 <br>
aml_g1t1 aml_g13567t1 81.3 423 376 112 104
112 104 q:306-417 h:181-284 <br>
aml_g1t1 aml_g15245t1 67.0 423 153 95 94
95 94 q:313-407 h:33-126<br>
<br>
Parser Warning<br>
<br>
junk after document element at line 1, column 6899908, byte
6899908 at <a moz-do-not-send="true"
href="http://blast_parser.pl">blast_parser.pl</a> line 105<br>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Nov 10, 2014 at 1:49 PM, Erik
Sonnhammer <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:erik.sonnhammer@scilifelab.se"
target="_blank">erik.sonnhammer@scilifelab.se</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><span class="">
<div>On 11/10/2014 12:27 PM, Sammy Desilva wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>As mentioned in <a moz-do-not-send="true"
href="http://inparanoid.pl" target="_blank">inparanoid.pl</a>
$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)? </div>
</div>
</div>
</blockquote>
</span> Hi, simply use the same parameters ;)<br>
<br>
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.<span class=""><br>
<br>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>Next, when setting $run_blast = 0 the
blastall results should already be parsed?<br>
</div>
</div>
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</blockquote>
</span> Yes.<br>
<br>
/Erik<br>
<blockquote type="cite">
<div dir="ltr">
<div>
<div><br>
</div>
Thanks.<br>
</div>
Sammy<br>
</div>
<br>
<fieldset></fieldset>
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