[Inparanoid] Problem with Inparanoid groups

Sammy Desilva sammy.ich17 at gmail.com
Thu Sep 18 10:45:02 CEST 2014


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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