[Inparanoid] Problem with Inparanoid groups

[Sammy Desilva]

I got the error.. It was do_ypcall: clnt_call:RPC: Timed out

2014-09-18 11:12 GMT+02:00 Erik Sonnhammer <erik.sonnhammer at scilifelab.se>:

>  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 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>
> :
>
>>  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
>>
>>
>>  _______________________________________________
>> InParanoid mailing listInParanoid at lists.su.sehttps://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>
>>
>>
>
>
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