<div dir="ltr">I got the error.. It was do_ypcall: clnt_call:RPC: Timed out<br></div><div class="gmail_extra"><br><div class="gmail_quote">2014-09-18 11:12 GMT+02:00 Erik Sonnhammer <span dir="ltr"><<a href="mailto:erik.sonnhammer@scilifelab.se" target="_blank">erik.sonnhammer@scilifelab.se</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Well clearly you can't expect more than
71 orthologs if that's how many homologs Blast finds.<br>
<br>
My guess is that your sequences are not read properly by Blast.<span class="HOEnZb"><font color="#888888"><br>
<br>
Erik</font></span><div><div class="h5"><br>
<br>
On 09/18/2014 10:45 AM, Sammy Desilva wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">
<div>This is my truncated output:<br>
<br>
<font size="1">18651 sequences in file int1.fasta<br>
9630 sequences in file afum.fasta<br>
143 sequences int1.fasta have homologs in dataset afum.fasta<br>
71 sequences afum.fasta have homologs in dataset int1.fasta<br>
184 int1.fasta-int1.fasta matches<br>
101 afum.fasta-afum.fasta matches<br>
###################################<br>
66 groups of orthologs<br>
87 in-paralogs from int1.fasta<br>
77 in-paralogs from afum.fasta<br>
Grey zone 0 bits<br>
Score cutoff 40 bits<br>
In-paralogs with confidence less than 0.05 not shown<br>
Sequence overlap cutoff 0.5<br>
Group merging cutoff 0.5<br>
Scoring matrix BLOSUM62<br>
###################################<br>
___________________________________________________________________________________<br>
Group of orthologs #1. Best score 122 bits<br>
Score difference with first non-orthologous sequence -
int1.fasta:3 afum.fasta:122<br>
int1|P04914 100.00% afum|XP_752748.1
100.00%<br>
afum|XP_755719.2
85.71%<br>
Bootstrap support for int1|P04914 as seed ortholog is 100%.<br>
Bootstrap support for afum|XP_752748.1 as seed ortholog is
100%.<br>
..<br>
Score difference with first non-orthologous sequence -
int1.fasta:41 afum.fasta:41<br>
int1|Q9VTE5 100.00% afum|XP_750133.1
100.00%<br>
Bootstrap support for int1|Q9VTE5 as seed ortholog is 100%.<br>
Bootstrap support for afum|XP_750133.1 as seed ortholog is
100%.</font><br>
<br>
</div>
This is the Screen LOG for other analysis with similar problem:<br>
<br>
<font size="1">sam28@wbbi180:~/opt/inparanoid/int2_afum$ perl <a href="http://inparanoid.pl" target="_blank">inparanoid.pl</a>
int2.fasta afum.fasta<br>
18486 sequences in file int2.fasta<br>
9096 sequences in file afum.fasta<br>
Trying to run BLAST now - this may take several hours ... or
days in worst case!<br>
Formatting BLAST databases<br>
Done formatting<br>
Starting BLAST searches...<br>
<br>
Starting first BLAST pass for int2.fasta - int2.fasta on Wed
Sep 17 18:12:38 CEST 2014<br>
[blastall] WARNING: the -C 3 argument is currently
experimental<br>
<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
<br>
<br>
Starting second BLAST pass for int2.fasta - int2.fasta on Wed
Sep 17 20:05:44 CEST 2014<br>
do_ypcall: clnt_call: RPC: Timed out<br>
<br>
Starting first BLAST pass for int2.fasta - afum.fasta on Wed
Sep 17 20:22:59 CEST 2014<br>
[blastall] WARNING: the -C 3 argument is currently
experimental<br>
<br>
<br>
Starting second BLAST pass for int2.fasta - afum.fasta on Wed
Sep 17 21:03:38 CEST 2014<br>
<br>
Starting first BLAST pass for afum.fasta - int2.fasta on Wed
Sep 17 21:11:10 CEST 2014<br>
[blastall] WARNING: the -C 3 argument is currently
experimental<br>
<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
Selenocysteine (U) at position 37 replaced by X<br>
<br>
Starting second BLAST pass for afum.fasta - int2.fasta on Wed
Sep 17 21:52:14 CEST 2014<br>
<br>
Starting first BLAST pass for afum.fasta - afum.fasta on Wed
Sep 17 21:56:03 CEST 2014<br>
[blastall] WARNING: the -C 3 argument is currently
experimental<br>
<br>
<br>
Starting second BLAST pass for afum.fasta - afum.fasta on Wed
Sep 17 22:18:41 CEST 2014<br>
do_ypcall: clnt_call: RPC: Timed out<br>
Done BLAST searches. Starting ortholog detection...<br>
Output saved to file Output.int2.fasta-afum.fasta<br>
HTML output saved to orthologs.int2.fasta-afum.fasta.html<br>
Table output saved to table.int2.fasta-afum.fasta<br>
mysql output saved to sqltable.int2.fasta-afum.fasta<br>
sam28@wbbi180:~/opt/inparanoid/int2_afum$ <br>
</font>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2014-09-18 10:24 GMT+02:00 Erik
Sonnhammer <span dir="ltr"><<a href="mailto:erik.sonnhammer@scilifelab.se" target="_blank">erik.sonnhammer@scilifelab.se</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi, probably something went wrong with Blast.<br>
<br>
In the beginning of the output file Output.xxx you can
see how many homologs were detected by Blast, that will
probably tell you what went wrong.<br>
<br>
Erik Sonnhammer
<div>
<div><br>
<br>
On 09/18/2014 03:19 AM, Sammy Desilva wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>Hello,<br>
</div>
<div><br>
</div>
I downloaded the latest version of
Inparanoid8 on my Ubuntu 12.1 </div>
and ran Inparanoid on 2 big proteome. On the
default paramete the algorithm resulted only
70 groups while when I used orthomcl on same
dataset it resulted around 3000 groups. <br>
</div>
Please let me know what i am doing wrong?<br>
<br>
</div>
Thanks<br>
</div>
Sam<br>
</div>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
<pre>_______________________________________________
InParanoid mailing list
<a href="mailto:InParanoid@lists.su.se" target="_blank">InParanoid@lists.su.se</a>
<a href="https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se" target="_blank">https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se</a>
</pre>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
</div></div></div>
</blockquote></div><br></div>