[Inparanoid] Problem with Inparanoid groups

Thu Sep 18 11:12:28 CEST 2014

Well clearly you can't expect more than 71 orthologs if that's how many 
homologs Blast finds.

My guess is that your sequences are not read properly by Blast.

Erik

On 09/18/2014 10:45 AM, Sammy Desilva wrote:
> This is my truncated output:
>
> 18651 sequences in file int1.fasta
> 9630 sequences in file afum.fasta
> 143 sequences int1.fasta have homologs in dataset afum.fasta
> 71 sequences afum.fasta have homologs in dataset int1.fasta
> 184 int1.fasta-int1.fasta matches
> 101 afum.fasta-afum.fasta matches
> ###################################
> 66 groups of orthologs
> 87 in-paralogs from int1.fasta
> 77 in-paralogs from afum.fasta
> Grey zone 0 bits
> Score cutoff 40 bits
> In-paralogs with confidence less than 0.05 not shown
> Sequence overlap cutoff 0.5
> Group merging cutoff 0.5
> Scoring matrix BLOSUM62
> ###################################
> ___________________________________________________________________________________
> Group of orthologs #1. Best score 122 bits
> Score difference with first non-orthologous sequence - int1.fasta:3   
> afum.fasta:122
> int1|P04914             100.00%        afum|XP_752748.1     100.00%
>                                        afum|XP_755719.2     85.71%
> Bootstrap support for int1|P04914 as seed ortholog is 100%.
> Bootstrap support for afum|XP_752748.1 as seed ortholog is 100%.
> ..
> Score difference with first non-orthologous sequence - int1.fasta:41   
> afum.fasta:41
> int1|Q9VTE5             100.00%        afum|XP_750133.1     100.00%
> Bootstrap support for int1|Q9VTE5 as seed ortholog is 100%.
> Bootstrap support for afum|XP_750133.1 as seed ortholog is 100%.
>
> This is the Screen LOG for other analysis with similar problem:
>
> sam28 at wbbi180:~/opt/inparanoid/int2_afum$ perl inparanoid.pl 
> <http://inparanoid.pl> int2.fasta afum.fasta
> 18486 sequences in file int2.fasta
> 9096 sequences in file afum.fasta
> Trying to run BLAST now - this may take several hours ... or days in 
> worst case!
> Formatting BLAST databases
> Done formatting
> Starting BLAST searches...
>
> Starting first BLAST pass for int2.fasta - int2.fasta on Wed Sep 17 
> 18:12:38 CEST 2014
> [blastall] WARNING: the -C 3 argument is currently experimental
>
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
>
>
> Starting second BLAST pass for int2.fasta - int2.fasta on Wed Sep 17 
> 20:05:44 CEST 2014
> do_ypcall: clnt_call: RPC: Timed out
>
> Starting first BLAST pass for int2.fasta - afum.fasta on Wed Sep 17 
> 20:22:59 CEST 2014
> [blastall] WARNING: the -C 3 argument is currently experimental
>
>
> Starting second BLAST pass for int2.fasta - afum.fasta on Wed Sep 17 
> 21:03:38 CEST 2014
>
> Starting first BLAST pass for afum.fasta - int2.fasta on Wed Sep 17 
> 21:11:10 CEST 2014
> [blastall] WARNING: the -C 3 argument is currently experimental
>
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
> Selenocysteine (U) at position 37 replaced by X
>
> Starting second BLAST pass for afum.fasta - int2.fasta on Wed Sep 17 
> 21:52:14 CEST 2014
>
> Starting first BLAST pass for afum.fasta - afum.fasta on Wed Sep 17 
> 21:56:03 CEST 2014
> [blastall] WARNING: the -C 3 argument is currently experimental
>
>
> Starting second BLAST pass for afum.fasta - afum.fasta on Wed Sep 17 
> 22:18:41 CEST 2014
> do_ypcall: clnt_call: RPC: Timed out
> Done BLAST searches. Starting ortholog detection...
> Output saved to file Output.int2.fasta-afum.fasta
> HTML output saved to orthologs.int2.fasta-afum.fasta.html
> Table output saved to table.int2.fasta-afum.fasta
> mysql output saved to sqltable.int2.fasta-afum.fasta
> sam28 at wbbi180:~/opt/inparanoid/int2_afum$
>
>
> 2014-09-18 10:24 GMT+02:00 Erik Sonnhammer 
> <erik.sonnhammer at scilifelab.se <mailto:erik.sonnhammer at scilifelab.se>>:
>
>     Hi, probably something went wrong with Blast.
>
>     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.
>
>     Erik Sonnhammer
>
>
>     On 09/18/2014 03:19 AM, Sammy Desilva wrote:
>>     Hello,
>>
>>     I downloaded the latest version of Inparanoid8 on my Ubuntu 12.1
>>     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.
>>     Please let me know what i am doing wrong?
>>
>>     Thanks
>>     Sam
>>
>>
>>     _______________________________________________
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>
>

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