--ERROR: MAX_N_PID exceded -- Recompile changing the value of MAX_N_PID

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jlmat...@gmail.com

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Apr 30, 2020, 4:55:17 PM4/30/20
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Hello,
I'm using the last t_coffee from conda

PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)

And i'm getting this error:
--ERROR: MAX_N_PID exceded -- Recompile changing the value of MAX_N_PID (current: 260000 Requested: 267175)


conda is using this recipe from bioconda, which uses the bin installer version.

I found this script from homebrew and you can see they fix this PID limitation because they compile:


inreplace "io_lib_header.h", "define MAX_N_PID 260000", "define MAX_N_PID 520000"
inreplace
"define_header.h", "define MAX_N_PID 260000", "define MAX_N_PID 520000"

Is it possible for the `t_coffee` team produce binaries without this limitation?

Best regards

Jose Luis

Cedric Notredame

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Apr 30, 2020, 5:00:56 PM4/30/20
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Hello Jose

I will take a look and we can hopefully implement it soon

Cheers 

Cedric 

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Notredame's lab - Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
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Centre de Regulació Genòmica (CRG)
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ORC-ID: 0000-0003-1461-0988
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On 30 Apr 2020, at 22:55, jlmat...@gmail.com wrote:


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jlmat...@gmail.com

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May 1, 2020, 11:02:23 AM5/1/20
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Thank you Cedric

Cedric Notredame

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May 1, 2020, 11:59:21 AM5/1/20
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Hi Jose Luis,

I have just posted a new beta where the MAX_N_PID value can be changed using the MAX_N_PID_4_TCOFFEE environment variable. Hope it does the trick. On may side it seems to work fine and pass the tests. Do not hesitate to let me know if you have any issue

Thanks for pointing out this limitation,

Cheers,


Cedric


Le 1/5/20 à 17:02, jlmat...@gmail.com a écrit :
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Dr Cedric Notredame, PhD
Group Leader
Notredame's lab - Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
Room 440.03

Centre de Regulació Genòmica (CRG)
Dr. Aiguader, 88
08003 Barcelona
Spain

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ORC-ID: 0000-0003-1461-0988
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jlmat...@gmail.com

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May 4, 2020, 12:39:56 PM5/4/20
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It's working for me too. Thanks!


On Thursday, April 30, 2020 at 4:55:17 PM UTC-4, jlmat...@gmail.com wrote:

modoc...@gmail.com

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May 8, 2020, 10:48:50 PM5/8/20
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Since your still providing support for tcoffee why can't you answer my post "problems installing sara on vagrant"???


On Friday, May 1, 2020 at 11:59:21 AM UTC-4, cedric....@gmail.com wrote:

Hi Jose Luis,

I have just posted a new beta where the MAX_N_PID value can be changed using the MAX_N_PID_4_TCOFFEE environment variable. Hope it does the trick. On may side it seems to work fine and pass the tests. Do not hesitate to let me know if you have any issue

Thanks for pointing out this limitation,

Cheers,


Cedric


Le 1/5/20 à 17:02, jlmat...@gmail.com a écrit :
Thank you Cedric

On Thursday, April 30, 2020 at 4:55:17 PM UTC-4, jlmat...@gmail.com wrote:
Hello,
I'm using the last t_coffee from conda

PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)

And i'm getting this error:
--ERROR: MAX_N_PID exceded -- Recompile changing the value of MAX_N_PID (current: 260000 Requested: 267175)


conda is using this recipe from bioconda, which uses the bin installer version.

I found this script from homebrew and you can see they fix this PID limitation because they compile:



inreplace "io_lib_header.h", "define MAX_N_PID 260000", "define MAX_N_PID 520000"
inreplace
"define_header.h", "define MAX_N_PID 260000", "define MAX_N_PID 520000"

Is it possible for the `t_coffee` team produce binaries without this limitation?

Best regards

Jose Luis
--
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##########################################
Dr Cedric Notredame, PhD
Group Leader
Notredame's lab - Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
Room 440.03

Centre de Regulació Genòmica (CRG)
Dr. Aiguader, 88
08003 Barcelona
Spain

Ph#     + 34 93 316 02 71
Fax#    + 34 93 316 00 99
Mobile# + 34 66 250 47 82

email   cedric....@crg.eu

Cedric Notredame

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May 9, 2020, 5:33:03 AM5/9/20
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Hello,

Sara is a third party software that we have interfaced with T-Coffee for 3D structured based RNA molecule alignments. Unfortunately, SARA has many dependencies and it turned out to be very difficult to maintain a stable sara-Coffee. We tried with Vagrant but it breaks every once in a while. We have no intention to maintain the vagrant port of SARA, and if you need it, I encourage you to reach out to the original authors of SARA.

As an alternative, for anyone unable to install the SARA RNA 3D aligner, we are now providing the rsapcoffee mode (-mode=srapcoffee), in which the sap protein structure aligner is used instead of SARA. The idea is very simple and draws on the observation by the SARA authors that the best RNA superpositions are achieved using the the C3PRIME carbon atom on the ribose. In the rsapcoffee mode, the RNA 3D structures are therefore superposed by SAP using the C3PRIME carbon instead of the CALPHA. We ztested these things on the original SARA datasets - sorry I did not keep any record of that - and found it to be only slightly inferior to SARA RMSDd-wise but quite acceptable, and very clearly superior to sequence or secondary structure based alignments.

This procedure is actually supported by all the protein 3D aligners supported by T-Coffee (TMalign, sap, mustang). It takes place automatically when the provided structures are RNA molecules

Best,


Cedric


Le 9/5/20 à 04:48, modoc...@gmail.com a écrit :
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-- 
##########################################
Dr Cedric Notredame, PhD
Group Leader
Notredame's lab - Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
Room 440.03

Centre de Regulació Genòmica (CRG)
Dr. Aiguader, 88
08003 Barcelona
Spain

Ph#     + 34 93 316 02 71
Fax#    + 34 93 316 00 99
Mobile# + 34 66 250 47 82

email   cedric.n...@crg.eu

Barry Kesner

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May 9, 2020, 6:53:37 PM5/9/20
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Thanks,  
  I was able to install docker and SARA that way.   
   If I attained RNA structures from some repository how would i incorporate them into SARA or any of your tools?

Thanks again,

Barry  

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Cedric Notredame

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May 9, 2020, 7:25:38 PM5/9/20
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Hello Barry

The use of SARA-Coffee is documented in http://www.tcoffee.org/Projects/tcoffee/documentation/index.html#aligning-rna-sequences

Basically, you simply need a file that looks like a FASTA file and declares the binding between your FASTA identifiers (FASTA names) and your PDB file. One per line

>fastaname1 _P_ <pdbfile>

etc....

(_P_ declares the template to be a PDB file)

You can then run sara or rsap coffee 

T-Coffee can to some extend re-conciliate FASTA sequences with the PDB in cases when there are discrpencies between ATOM, SEQRES and FASTA but the best is to have a perfect match between the sequences as deduced in the ATOM of PDB and the FASTA


Le 10/5/20 à 00:53, Barry Kesner a écrit :

Barry Kesner

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May 9, 2020, 7:37:52 PM5/9/20
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Awesome, thanks! 
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