<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">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 class="h5"><br>
<br>
On 09/18/2014 03:19 AM, Sammy Desilva wrote:<br>
</div></div></div>
<blockquote type="cite"><div><div class="h5">
<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>
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