SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
orthomcl error zxl124 Bioinformatics 7 11-10-2015 08:29 PM
Fasta with one entry per chromosome (for methylation analysis and others) mixter Epigenetics 0 06-28-2011 01:52 AM
Orthomcl Installation Canadian_philosophy Bioinformatics 0 07-29-2010 07:36 AM
MosaikBuild entry point missing ursaan Bioinformatics 0 04-23-2010 06:08 AM
How to estimate error rate for short-reads and base-calling duplicate? zchou Illumina/Solexa 10 01-20-2010 08:13 AM

Reply
 
Thread Tools
Old 09-05-2011, 05:49 PM   #1
flipwell
Member
 
Location: Queensland

Join Date: Feb 2011
Posts: 14
Default OrthoMCL duplicate entry error

I have made it up to step 10 of the orthomcl process, finding protein pairs, but have become stuck with a duplicate entry error:

Duplicate entry '5206|CNAG_00003-5206|CNE00390' for key 'better_hit_ix' at /data/ngs/apps/orthomclSoftware/bin/orthomclPairs line 693, <F> line 14

I thought maybe it was something to do with the way I ran BLAST so I reran with parameters recommended but still get an error, although a different one:

Duplicate entry '5206|CNAG_00006-5206--181-0-5206-5206|CNAG_00006' for key 'ss_qtaxexp_ix' at /data/ngs/apps/orthomclSoftware/bin/orthomclPairs line 693, <F> line 14

Has anyone had a similar issue?

Thanks for your help
flipwell is offline   Reply With Quote
Old 05-09-2012, 04:11 PM   #2
jollymrt
Junior Member
 
Location: los angeles

Join Date: May 2012
Posts: 3
Default

the duplicate entry error can be removed by selecting only the distinct rows in the similarSequence table
jollymrt is offline   Reply With Quote
Old 01-07-2013, 02:11 AM   #3
guyleonard
Junior Member
 
Location: London

Join Date: Mar 2012
Posts: 6
Default

Quote:
Originally Posted by jollymrt View Post
the duplicate entry error can be removed by selecting only the distinct rows in the similarSequence table
Never mind. There was a duplicate or two that I had missed. Sorting and using the tool 'uniq' works but you have to use the command -w and a number (I used 40) to limit the match to just the accession - sometimes the duplicates had different score values and so were effectively unique... Phew.

Quote:
Any chance you could expand on that?

I have the same error as the OP, my file is 6.5GB.

I've gone through the file and removed duplicates...or at least I thought I had.

I managed to find a list of duplicate accessions and so removed them from similarsequences with AWK. I then also sorted the file on the first column and performed a uniq removal of any next neighbour duplicates...

Every time the same error:
Duplicate entry 'didi|DDB_G0279353-didi|DDB_G0283451' for key 'better_hit_ix' at /home/cs02gl/programs/orthomclSoftware-v2.0.3/bin/orthomclPairs line 693, <F> line 14.

Looking at those accessions in the file (using grep) reveals no duplicates for that matching.

Last edited by guyleonard; 01-07-2013 at 02:39 AM.
guyleonard is offline   Reply With Quote
Old 01-07-2013, 09:37 AM   #4
jollymrt
Junior Member
 
Location: los angeles

Join Date: May 2012
Posts: 3
Default

to check if you have duplicate entries use the following command

select * from similarSequences group by query_id,subject_id having count(*)>1;

this command will give you the rows that are duplicated.

Then you can create a new table that will have only distinct rows.

create table holdup as select distinct * from similarSequences;
jollymrt is offline   Reply With Quote
Old 09-24-2013, 01:20 AM   #5
robinvvelzen
Junior Member
 
Location: Wageningen

Join Date: Jan 2013
Posts: 6
Default

I am also having the same errors as the OP.

Apart from trying ways to fix it I am wondering what causes the duplicate error in the orthoMCL pipeline. Given that duplicates are to be expected after an all-vs-all blast I would expect that the orthoMCL scripts would appropriately deal with them.

Is this a matter of orthomclBlastParser, orthomclLoadBlast or orthomclPairs not doing a proper job?

Quote:
Originally Posted by jollymrt View Post
to check if you have duplicate entries use the following command

select * from similarSequences group by query_id,subject_id having count(*)>1;

this command will give you the rows that are duplicated.

Then you can create a new table that will have only distinct rows.

create table holdup as select distinct * from similarSequences;
Thanks for the help but I have a few questions:
1. Looking at those commands I assume these are to be executed within mysql, is that correct?
2. Will they simply replace the similarSequences table with itself with duplicates removed, or do I need to do more to be able to continue the analysis?
3. Will this (changing the table somewhere midway the orthoMCL pipeline) not compromise the analysis?

Thanks again!
robinvvelzen is offline   Reply With Quote
Old 09-24-2013, 06:42 AM   #6
jollymrt
Junior Member
 
Location: los angeles

Join Date: May 2012
Posts: 3
Default

Yes, the commands have to be executed on mysql.
first you need to select distinct rows in a different table(holdup table), delete all the rows in similarSequence table and then insert the rows from the holdup table. I hope this clears it
jollymrt is offline   Reply With Quote
Old 09-24-2013, 06:48 AM   #7
robinvvelzen
Junior Member
 
Location: Wageningen

Join Date: Jan 2013
Posts: 6
Default

Quote:
Originally Posted by jollymrt View Post
Yes, the commands have to be executed on mysql.
first you need to select distinct rows in a different table(holdup table), delete all the rows in similarSequence table and then insert the rows from the holdup table. I hope this clears it
Yes, it does. Thanks very much!

In the meantime I had redone the whole orthoMCL pipeline and for some reason got no more duplicate errors . Possibly, some table entries were accidentally copied the last time. This just to inform others that may run into the same problems..
robinvvelzen is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:26 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO