From samuelfloresc@gmail.com Mon Feb 17 00:32:39 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WFBCQ-002M2e-HB>; Mon, 17 Feb 2014 00:32:38 +0100 Received: from mail-pb0-f51.google.com ([209.85.160.51]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1WFBCQ-0029bN-9s>; Mon, 17 Feb 2014 00:32:38 +0100 Received: by mail-pb0-f51.google.com with SMTP id un15so14599227pbc.10 for ; Sun, 16 Feb 2014 15:32:35 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=from:content-type:content-transfer-encoding:subject:message-id:date :to:mime-version; bh=a2DqZSZAuLXlfRcSNMtA7EqTp67SbJVg7/57IWAzMHs=; b=K8xnmLoLP4T11sE/q0yz59GJCXJGhme1sFKtUvPNY8ks/yqH4CZy3TxEkaEusA1Oun r+bGu1L7pEuiTcSeSRQdClzQbC8hjaePztSMItawpv5y4m9uXFsYUtw0H9Io9TVgSZqF ZoS2uu2PFLHID4GVqvsg5MZyQtRDjCRR9aGajumpjyOFicxspm0hfAHjjaN56CHcloT9 svIGJc1tTMAfosdgPOu1OrMHynn/nnoOCNfOaK9tKF/sR+hLlYfcZgOduoNv+6ojg3mR hZ5zeeMVs22+Rkv1NP1U9QFul0NY+KAp292KnJa+xVp4YLGqkKQ4px9oCWcHalm1aYl6 w7IQ== X-Received: by 10.66.251.42 with SMTP id zh10mr23184850pac.84.1392593555026; Sun, 16 Feb 2014 15:32:35 -0800 (PST) Received: from [10.42.1.121] ([199.115.243.185]) by mx.google.com with ESMTPSA id ac5sm39391301pbc.37.2014.02.16.15.32.32 for (version=TLSv1 cipher=ECDHE-RSA-RC4-SHA bits=128/128); Sun, 16 Feb 2014 15:32:33 -0800 (PST) From: Samuel Flores Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Message-Id: <5B6BD84A-6E19-45AA-832C-0706D5333613@gmail.com> Date: Sun, 16 Feb 2014 15:32:26 -0800 To: seqan-dev@lists.fu-berlin.de Mime-Version: 1.0 (Mac OS X Mail 6.6 \(1510\)) X-Mailer: Apple Mail (2.1510) X-Originating-IP: 209.85.160.51 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1392593558-0000CD40-C9A6EF39/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.003320, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM, RCVD_IN_DNSWL_LOW,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] scoring schemes X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 16 Feb 2014 23:32:40 -0000 Guys, I can't seem to get globalAlignment to use any scoring scheme otehr than = seqan::Simple: TAlign align; seqan::resize(rows(align), 2); assignSource(row(align,0),seqA); assignSource(row(align,1),seqB); int score =3D globalAlignment(align, = seqan::Score(0,-1,-1,gapOpenPenalty)); I tried changing the last line to just: int score =3D globalAlignment(align, = seqan::Score(0,-1,-1,gapOpenPenalty)); and every conceivable variant thereof. None seem to be recognized, = e.g.: /Users/Sam/svn/RNAToolbox/trunk/src/ParameterReader.cpp:1000:65: error: = use of undeclared identifier 'Pam' Can someone tell me how to switch to Blossum, PAM, or some other? Thanks Sam= From rene.maerker@fu-berlin.de Mon Feb 17 10:48:54 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WFKon-003F3P-2A>; Mon, 17 Feb 2014 10:48:53 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WFKom-000dZj-W8>; Mon, 17 Feb 2014 10:48:53 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1WFKom-002ppA-Kx>; Mon, 17 Feb 2014 10:48:52 +0100 Received: from EX03A.campus.fu-berlin.de ([130.133.170.134]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0174.001; Mon, 17 Feb 2014 10:48:51 +0100 From: =?iso-8859-1?Q?Rahn=2C_Ren=E9?= To: SeqAn Development Thread-Topic: [Seqan-dev] scoring schemes Thread-Index: AQHPK29myw7ZcjDrm0md5hlkd26ipZq5I0yA Message-ID: References: <5B6BD84A-6E19-45AA-832C-0706D5333613@gmail.com> In-Reply-To: <5B6BD84A-6E19-45AA-832C-0706D5333613@gmail.com> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_B441F9DD72C841F9A4140DFF5CB73011fuberlinde_" MIME-Version: 1.0 Date: Mon, 17 Feb 2014 10:48:50 +0100 X-Original-Date: Mon, 17 Feb 2014 09:48:50 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1392630533-0000CD40-D646D5D7/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-49.7 required=5.0 tests=ALL_TRUSTED, HTML_FONT_FACE_BAD,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] scoring schemes X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 17 Feb 2014 09:48:54 -0000 --_000_B441F9DD72C841F9A4140DFF5CB73011fuberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hey Sam, if you want to use scoring matrices you need to use a different specializat= ion of our Score class. To use scoring schemes like the Pam or Blosum matri= ces you need to use the following code: Score > scorePam120(gap, gapOpen); You can also use our shortcuts to make the code look nicer. You can find a = list of all available shortcuts here: http://docs.seqan.de/seqan/1.4.1/SPEC= _Score+_Matrix.html. For the example above this would look like: Pam120 scorePam120(gap, gapOpen); I hope that will solve your problem! Kind regards, Ren=E9 Rahn On Feb 17, 2014, at 12:32 AM, Samuel Flores > wrote: Guys, I can't seem to get globalAlignment to use any scoring scheme otehr than se= qan::Simple: TAlign align; seqan::resize(rows(align), 2); assignSource(row(align,0),seqA); assignSource(row(align,1),seqB); int score =3D globalAlignment(align, seqan::Score(0,-1,-1,gapOpenPenalty)); I tried changing the last line to just: int score =3D globalAlignment(align, seqan::Score(0,-1,= -1,gapOpenPenalty)); and every conceivable variant thereof. None seem to be recognized, e.g.: /Users/Sam/svn/RNAToolbox/trunk/src/ParameterReader.cpp:1000:65: error: use= of undeclared identifier 'Pam' Can someone tell me how to switch to Blossum, PAM, or some other? Thanks Sam _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --- Ren=E9 Rahn Ph.D. Student --------------------------------- Mail: rene.rahn@fu-berlin.de Phone: +49 (0)30 838 75 277 --------------------------------- Algorithmic Bioinformatics (ABI) Department of Computer Science Room 018 --------------------------------- Freie Universit=E4t Berlin Takustra=DFe 9 14195 Berlin --------------------------------- --_000_B441F9DD72C841F9A4140DFF5CB73011fuberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-ID: Content-Transfer-Encoding: quoted-printable Hey Sam, 

if you want to use scoring matrices you need to use a different specia= lization of our Score class. To use scoring schemes like the Pam or Blosum = matrices you need to use the following code: 

Score<int, Scor= eMatrix<AminoAcid, Pam120_> > scorePam120(gap, gapOpen);

You can also use our shortcuts to make the code look nicer. You can fi= nd a list of all available shortcuts here: http://docs.seqan.de/seqan/1.= 4.1/SPEC_Score+_Matrix.html.
For the example above this would look like:

Pam120 scorePam120= (gap, gapOpen);

I hope that will solve your problem!

Kind regards,

Ren=E9 Rahn


On Feb 17, 2014, at 12:32 AM, Samuel Flores <samuelfloresc@gmail.com> wrote:

Guys,

I can't seem to get globalAlignment to use any scoring scheme otehr than se= qan::Simple:

           TAlign al= ign;
           seqan::re= size(rows(align), 2);
           assignSou= rce(row(align,0),seqA);
           assignSou= rce(row(align,1),seqB);
           int score= =3D globalAlignment(align, seqan::Score<int,seqan::Simple>(0,-1,-1,g= apOpenPenalty));

I tried changing the last line to just:

           int score= =3D globalAlignment(align, seqan::Score<int,Pam>(0,-1,-1,gapOpenPena= lty));

and every conceivable variant thereof.  None seem to be recognized, e.= g.:


/Users/Sam/svn/RNAToolbox/trunk/src/ParameterReader.cpp:1000:65: error: use= of undeclared identifier 'Pam'


Can someone tell me how to switch to Blossum, PAM, or some other?

Thanks

Sam
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev


---

Ren=E9 Rahn
Ph.D. Student<= /font>
--------------= -------------------
Mail:  rene.rahn@fu-berlin.de
Phone: +49= (0)30 838 75 277
--------------= -------------------
Algorithmic Bi= oinformatics (ABI)
Department of = Computer Science 
Room  018
--------------= -------------------
Freie Universi= t=E4t Berlin
Takustra=DFe 9=  
14195 Berlin
--------------= -------------------

--_000_B441F9DD72C841F9A4140DFF5CB73011fuberlinde_-- From samuelfloresc@gmail.com Mon Feb 17 15:41:29 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WFPNv-0005rT-9V>; Mon, 17 Feb 2014 15:41:27 +0100 Received: from mail-pd0-f179.google.com ([209.85.192.179]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1WFPNu-000utk-Mq>; Mon, 17 Feb 2014 15:41:27 +0100 Received: by mail-pd0-f179.google.com with SMTP id fp1so14644730pdb.10 for ; Mon, 17 Feb 2014 06:41:23 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=from:content-type:message-id:mime-version:subject:date:references :to:in-reply-to; bh=pdTazfPOwLvp7lyxoOnhyCivthQlpmWiJB3DbZclMjs=; b=NxQgf6UVhvr1plqBw0JLtjXPlPlzaqURGZo6qILzvkK8cCcvPUFGhH8e9GOUj8rWNt wpZgPHt3VvkdwQBZ0y4gXPefhNU0hY4p7z7+0/W2CinBAVtTPKbF8Q39eGz6D9z3Xu79 8fs1jh7ZhaPiFWxyhfNDjhUu6JiuKbZukVUspMGa3TCEun4yJUQp+rQISz+bHh9uTajF FrgF2WzQigkMcspM7PMu4c0iGPWEKxmK26VQQQur9Do52ZXfBCjfhNQ3hNnYmRQCPPYC 8USfxSOIZ1klOf4YZB9Ey6IumRaUC52el1oK2LQ5I44+/z0f1LeMIkXba2m7GOmEntDO Xqeg== X-Received: by 10.67.14.231 with SMTP id fj7mr26313802pad.115.1392648083010; Mon, 17 Feb 2014 06:41:23 -0800 (PST) Received: from [10.199.32.169] (71.4.138.3.ptr.us.xo.net. [71.4.138.3]) by mx.google.com with ESMTPSA id xf3sm3388154pbc.30.2014.02.17.06.41.19 for (version=TLSv1 cipher=ECDHE-RSA-RC4-SHA bits=128/128); Mon, 17 Feb 2014 06:41:21 -0800 (PST) From: Samuel Flores Content-Type: multipart/alternative; boundary="Apple-Mail=_AE4A7B00-0C96-496D-9059-DDFFA56333A9" Message-Id: <7C142372-CE91-4474-BC8E-489AC90D5535@gmail.com> Mime-Version: 1.0 (Mac OS X Mail 6.6 \(1510\)) Date: Mon, 17 Feb 2014 06:41:19 -0800 References: <5B6BD84A-6E19-45AA-832C-0706D5333613@gmail.com> To: SeqAn Development In-Reply-To: X-Mailer: Apple Mail (2.1510) X-Originating-IP: 209.85.192.179 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1392648087-0000CD40-D8F7E69B/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.005678, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=1.4 required=5.0 tests=FREEMAIL_FROM, HTML_FONT_FACE_BAD, HTML_MESSAGE, RCVD_IN_DNSWL_NONE, TRACKER_ID, T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: x Subject: Re: [Seqan-dev] scoring schemes X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 17 Feb 2014 14:41:29 -0000 --Apple-Mail=_AE4A7B00-0C96-496D-9059-DDFFA56333A9 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Thanks for your help! However the alignment is not right. The second = sequence lines up about 100 residues from where it should, whereas the = "Simple" scoring scheme works reasonably. See the "LMIS", which should = line up at residue 251 on the first sequence. I'm using -1 for both gap = and gapOpen: 200 . : . : . : . : . :=20 NVAHPASSTKVDKKIEPRGPTIKPCPPCKCPAPNLLGGPSVFIFPPKIKD =20 -------------------------------------------------- 250 . : . : . : . : . :=20 VLMISLSPIVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHREDYNST =20 -------------------------------------------------- 300 . : . : . : . : . :=20 LRVVSALPIQHQDWMSGKEFKCKVNNKDLPAPIERTISKPKGSVRAPQVY | | =20 ---------------------------------PELLGGPSVFLFPPKPK 350 . : . : . : . : . :=20 VLPPPEEEMTKKQVTLTCMVTDFMPEDIYVEWTNNGKTELNYKNTEPVLD | | | =20 DTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNS 400 . : . : . : . : =20 SDGSYFMYSKLRVEKKNWVERNSYSCSVVHEGLHNHHTTKSFSR | | | | =20 TYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQ Here's the code snippet: 1002 seqan::Score > scorePam120(gap,gapOpenPenalty); 1003 int score =3D globalAlignment(align, scorePam120 ); Maybe I need to specify the algorithm as well? Also, how can I retrieve the aligned residue numbers? Right now I'm = just retrieving the two aligned sequences and assuming they are aligned = if neither character is a '-':=20 1022 if ((String(seqan::row (align,0)[i]).compare("-") = !=3D 0 ) && 1023 (String(seqan::row (align,1)[i]).compare("-") = !=3D 0 )) { /* aligned residues*/ } This works well enough for very simple, high sequence identity = alignments. However I'd really like to know which residues are = positively aligned ( "|" in the above alignment). Thanks Sam > Hey Sam,=20 >=20 > if you want to use scoring matrices you need to use a different = specialization of our Score class. To use scoring schemes like the Pam = or Blosum matrices you need to use the following code:=20 >=20 > Score > scorePam120(gap, > gapOpen);=20 >=20 >=20 > You can also use our shortcuts to make the code look nicer. You can = find a list of all available shortcuts here: = http://docs.seqan.de/seqan/1.4.1/SPEC_Score+_Matrix.html. > For the example above this would look like: >=20 > Pam120 scorePam120(gap, gapOpen); >=20 > I hope that will solve your problem! >=20 > Kind regards, >=20 > Ren=E9 Rahn >=20 >=20 > On Feb 17, 2014, at 12:32 AM, Samuel Flores = wrote: >=20 >> Guys, >>=20 >> I can't seem to get globalAlignment to use any scoring scheme otehr = than seqan::Simple: >>=20 >> TAlign align; >> seqan::resize(rows(align), 2); >> assignSource(row(align,0),seqA); >> assignSource(row(align,1),seqB); >> int score =3D globalAlignment(align, = seqan::Score(0,-1,-1,gapOpenPenalty)); >>=20 >> I tried changing the last line to just: >>=20 >> int score =3D globalAlignment(align, = seqan::Score(0,-1,-1,gapOpenPenalty)); >>=20 >> and every conceivable variant thereof. None seem to be recognized, = e.g.: >>=20 >>=20 >> /Users/Sam/svn/RNAToolbox/trunk/src/ParameterReader.cpp:1000:65: = error: use of undeclared identifier 'Pam' >>=20 >>=20 >> Can someone tell me how to switch to Blossum, PAM, or some other? >>=20 >> Thanks >>=20 >> Sam >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >=20 >=20 > --- >=20 > Ren=E9 Rahn > Ph.D. Student > --------------------------------- > Mail: rene.rahn@fu-berlin.de > Phone: +49 (0)30 838 75 277 > --------------------------------- > Algorithmic Bioinformatics (ABI) > Department of Computer Science=20 > Room 018 > --------------------------------- > Freie Universit=E4t Berlin > Takustra=DFe 9=20 > 14195 Berlin > --------------------------------- >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_AE4A7B00-0C96-496D-9059-DDFFA56333A9 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1


    200     .    :   =  .    :    .    :    . =    :    .   =  : 
    =     = NVAHPASSTKVDKKIEPRGPTIKPCPPCKCPAPNLLGGPSVFIFPPKIKD
                =                     =                     =   
    =     = --------------------------------------------------

  =   250     .    :    .    : =    .    :    .    :   =  .    : 
        = VLMISLSPIVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHREDYNST
                =                     =                     =   
    =     = --------------------------------------------------

  =   300     .    :    .    : =    .    :    .    :   =  .    : 
        = LRVVSALPIQHQDWMSGKEFKCKVNNKDLPAPIERTISKPKGSVRAPQVY
                =                     =            |      | =   
    =     = ---------------------------------PELLGGPSVFLFPPKPK

  =   350     .    :    .    : =    .    :    .    :   =  .    : 
        = VLPPPEEEMTKKQVTLTCMVTDFMPEDIYVEWTNNGKTELNYKNTEPVLD
                =      |       |         =               |   =  
      =   = DTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNS

  =   400     .    :    .    : =    .    :    .    :   =   
    =     = SDGSYFMYSKLRVEKKNWVERNSYSCSVVHEGLHNHHTTKSFSR
                =   |     |  |           =         |    
        = TYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQ


Here's the code snippet:
1002 =             seqan::Score<int, = seqan::ScoreMatrix<seqan::AminoAcid, seqan::Pam120_> > = scorePam120(gap,gapOpenPenalty);
1003       =       int score =3D globalAlignment(align, scorePam120 = );

Maybe I need to specify the algorithm = as well?

Also, how can I retrieve the aligned = residue numbers?  Right now I'm just retrieving the two aligned = sequences and assuming they are aligned if neither character is a = '-': 

1022       =           if ((String(seqan::row = (align,0)[i]).compare("-")  !=3D 0  ) =  &&
1023           =           (String(seqan::row = (align,1)[i]).compare("-")  !=3D 0  )) { /* aligned residues*/ = }


This works well = enough for very simple, high sequence identity alignments.  However = I'd really like to know which residues are positively aligned ( "|" in the above = alignment).

Thanks

Sam


Hey Sam, 

if you want to use scoring matrices you need to use a different = specialization of our Score class. To use scoring schemes like the Pam = or Blosum matrices you need to use the following code: 

http://d= ocs.seqan.de/seqan/1.4.1/SPEC_Score+_Matrix.html.
For the example above this would look like:

samuelfloresc@gmail.com> = wrote:

Guys,

I can't seem to get globalAlignment to use any scoring scheme otehr than = seqan::Simple:

           TAlign = align;
=            seqan::r= esize(rows(align), 2);
=            assignSo= urce(row(align,0),seqA);
=            assignSo= urce(row(align,1),seqB);
           int = score =3D globalAlignment(align, = seqan::Score<int,seqan::Simple>(0,-1,-1,gapOpenPenalty));

I tried changing the last line to just:

           int = score =3D globalAlignment(align, = seqan::Score<int,Pam>(0,-1,-1,gapOpenPenalty));

and every conceivable variant thereof.  None seem to be recognized, = e.g.:


/Users/Sam/svn/RNAToolbox/trunk/src/ParameterReader.cpp:1000:65: error: = use of undeclared identifier 'Pam'


Can someone tell me how to switch to Blossum, PAM, or some other?

Thanks

Sam
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de<= /a>
https://lists.fu-be= rlin.de/listinfo/seqan-dev


---

Ren=E9 = Rahn
Ph.D. = Student
---------------------------------
Mail: =  rene.rahn@fu-berlin.de
Phone: +49 = (0)30 838 75 277
---------------------------------
Algorithmic = Bioinformatics (ABI)
Department = of Computer Science 
Room  018
---------------------------------
Freie = Universit=E4t Berlin
Takustra=DFe = 9 
14195 = Berlin
---------------------------------

_______________________________________________
seqan-dev mailing = list
seqan-dev@lists.fu-berlin.de<= /a>
https://lists.fu-berlin.de/listinfo/seqan-dev

= --Apple-Mail=_AE4A7B00-0C96-496D-9059-DDFFA56333A9-- From rene.maerker@fu-berlin.de Mon Feb 17 18:23:14 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WFRuS-000JfC-O2>; Mon, 17 Feb 2014 18:23:12 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WFRuS-003gq4-LT>; Mon, 17 Feb 2014 18:23:12 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1WFRuS-004056-7b>; Mon, 17 Feb 2014 18:23:12 +0100 Received: from EX03A.campus.fu-berlin.de ([130.133.170.134]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0174.001; Mon, 17 Feb 2014 18:23:11 +0100 From: =?iso-8859-1?Q?Rahn=2C_Ren=E9?= To: SeqAn Development Thread-Topic: [Seqan-dev] scoring schemes Thread-Index: AQHPK29myw7ZcjDrm0md5hlkd26ipZq5I0yAgABRtYCAAC04AA== Message-ID: <24D0AA30-418D-4C02-A484-EF6B83370B5F@fu-berlin.de> References: <5B6BD84A-6E19-45AA-832C-0706D5333613@gmail.com> <7C142372-CE91-4474-BC8E-489AC90D5535@gmail.com> In-Reply-To: <7C142372-CE91-4474-BC8E-489AC90D5535@gmail.com> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_24D0AA30418D4C02A484EF6B83370B5Ffuberlinde_" MIME-Version: 1.0 Date: Mon, 17 Feb 2014 18:23:10 +0100 X-Original-Date: Mon, 17 Feb 2014 17:23:10 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1392657792-0000CD40-9B34ADC2/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-48.6 required=5.0 tests=ALL_TRUSTED, HTML_FONT_FACE_BAD,HTML_MESSAGE,TRACKER_ID X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] scoring schemes X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 17 Feb 2014 17:23:14 -0000 --_000_24D0AA30418D4C02A484EF6B83370B5Ffuberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hey Sam, On Feb 17, 2014, at 3:41 PM, Samuel Flores > wrote: Thanks for your help! However the alignment is not right. The second seque= nce lines up about 100 residues from where it should, whereas the "Simple" = scoring scheme works reasonably. See the "LMIS", which should line up at r= esidue 251 on the first sequence. I'm using -1 for both gap and gapOpen: 200 . : . : . : . : . : NVAHPASSTKVDKKIEPRGPTIKPCPPCKCPAPNLLGGPSVFIFPPKIKD -------------------------------------------------- 250 . : . : . : . : . : VLMISLSPIVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHREDYNST -------------------------------------------------- 300 . : . : . : . : . : LRVVSALPIQHQDWMSGKEFKCKVNNKDLPAPIERTISKPKGSVRAPQVY | | ---------------------------------PELLGGPSVFLFPPKPK 350 . : . : . : . : . : VLPPPEEEMTKKQVTLTCMVTDFMPEDIYVEWTNNGKTELNYKNTEPVLD | | | DTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNS 400 . : . : . : . : SDGSYFMYSKLRVEKKNWVERNSYSCSVVHEGLHNHHTTKSFSR | | | | TYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQ Here's the code snippet: 1002 seqan::Score > scorePam120(gap,gapOpenPenalty); 1003 int score =3D globalAlignment(align, scorePam120 ); It is really hard to tell what went wrong without a proper code example. Co= uld you please provide all the code associated with the alignment computati= on? Maybe I need to specify the algorithm as well? Also, how can I retrieve the aligned residue numbers? Right now I'm just r= etrieving the two aligned sequences and assuming they are aligned if neithe= r character is a '-': 1022 if ((String(seqan::row (align,0)[i]).compare("-") != =3D 0 ) && 1023 (String(seqan::row (align,1)[i]).compare("-") != =3D 0 )) { /* aligned residues*/ } At the moment we don't store any state of the alignment. Thus it is not pos= sible to receive such information. However, we have the function isGap(gaps= , viewPosition) or isGap(GapsIterator). In this case the code could look li= ke this, avoiding the string comparisons: typedef Row >::Type TRow; typedef Iterator::Type TRowIterator; TRowIterator itRow0 =3D begin(row(align, 0), Standard()); TRowIterator itRow0End =3D end(row(align, 0), Standard()); TRowIterator itRow1 =3D begin(row(align, 1), Standard()); for (; itRow0 !=3D itRow0End; ++itRow0, ++itRow1) { if (!isGap(itRow0) && !isGap(itRow1)) // Count aligned residues. } Since this is only a linear scan over the aligned sequences, this won't add= much to the overall runtime considering the quadratic runtime for the alig= nments you have to do before. You can also have a glance at our alignment tutorials at http://trac.seqan.= de/wiki/Tutorial/PairwiseSequenceAlignment. Here you can find all informati= on about the pairwise sequence alignments in SeqAn. Kind regards, Ren=E9 Rahn This works well enough for very simple, high sequence identity alignments. = However I'd really like to know which residues are positively aligned ( "|= " in the above alignment). Thanks Sam Hey Sam, if you want to use scoring matrices you need to use a different specializat= ion of our Score class. To use scoring schemes like the Pam or Blosum matri= ces you need to use the following code: Score > scorePam120(gap, gapOpen); You can also use our shortcuts to make the code look nicer. You can find a = list of all available shortcuts here: http://docs.seqan.de/seqan/1.4.1/SPEC= _Score+_Matrix.html. For the example above this would look like: Pam120 scorePam120(gap, gapOpen); I hope that will solve your problem! Kind regards, Ren=E9 Rahn On Feb 17, 2014, at 12:32 AM, Samuel Flores > wrote: Guys, I can't seem to get globalAlignment to use any scoring scheme otehr than se= qan::Simple: TAlign align; seqan::resize(rows(align), 2); assignSource(row(align,0),seqA); assignSource(row(align,1),seqB); int score =3D globalAlignment(align, seqan::Score(0,-1,-1,gapOpenPenalty)); I tried changing the last line to just: int score =3D globalAlignment(align, seqan::Score(0,-1,= -1,gapOpenPenalty)); and every conceivable variant thereof. None seem to be recognized, e.g.: /Users/Sam/svn/RNAToolbox/trunk/src/ParameterReader.cpp:1000:65: error: use= of undeclared identifier 'Pam' Can someone tell me how to switch to Blossum, PAM, or some other? Thanks Sam _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --- Ren=E9 Rahn Ph.D. Student --------------------------------- Mail: rene.rahn@fu-berlin.de Phone: +49 (0)30 838 75 277 --------------------------------- Algorithmic Bioinformatics (ABI) Department of Computer Science Room 018 --------------------------------- Freie Universit=E4t Berlin Takustra=DFe 9 14195 Berlin --------------------------------- _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --- Ren=E9 Rahn Ph.D. Student --------------------------------- Mail: rene.rahn@fu-berlin.de Phone: +49 (0)30 838 75 277 --------------------------------- Algorithmic Bioinformatics (ABI) Department of Computer Science Room 018 --------------------------------- Freie Universit=E4t Berlin Takustra=DFe 9 14195 Berlin --------------------------------- --_000_24D0AA30418D4C02A484EF6B83370B5Ffuberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-ID: <91EFB46A19B89E4EBE9EC18047980223@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable Hey Sam,


 wrote:

Thanks for your help! However the alignment is not right.  The second = sequence lines up about 100 residues from where it should, whereas the &quo= t;Simple" scoring scheme works reasonably.  See the "LMIS&qu= ot;, which should line up at residue 251 on the first sequence.  I'm using -1 for both gap and gapOpen:



    200     .    = :    .    :    .    :    = .    :    .    : 
        NVAHPASSTKVDKKIEPRG= PTIKPCPPCKCPAPNLLGGPSVFIFPPKIKD
             = ;                     &nb= sp;                     &= nbsp; 
        -------------------= -------------------------------

    250     .    = :    .    :    .    :    = .    :    .    : 
        VLMISLSPIVTCVVVDVSE= DDPDVQISWFVNNVEVHTAQTQTHREDYNST
             = ;                     &nb= sp;                     &= nbsp; 
        -------------------= -------------------------------

    300     .    = :    .    :    .    :    = .    :    .    : 
        LRVVSALPIQHQDWMSGKE= FKCKVNNKDLPAPIERTISKPKGSVRAPQVY
             = ;                     &nb= sp;            |      |  =  
        -------------------= --------------PELLGGPSVFLFPPKPK

    350     .    = :    .    :    .    :    = .    :    .    : 
        VLPPPEEEMTKKQVTLTCM= VTDFMPEDIYVEWTNNGKTELNYKNTEPVLD
             = ;        |       |       =                 |    
        DTLMISRTPEVTCVVVDVS= HEDPEVKFNWYVDGVEVHNAKTKPREEQYNS

    400     .    = :    .    :    .    :    = .    :     
        SDGSYFMYSKLRVEKKNWV= ERNSYSCSVVHEGLHNHHTTKSFSR
             = ;     |     |  |          = ;         |    
        TYRVVSVLTVLHQDWLNGK= EYKCKVSNKALPAPIEKTISKAKGQ


Here's the code snippet:
1002             seqan::Score<int, se= qan::ScoreMatrix<seqan::AminoAcid, seqan::Pam120_> > scorePam120(g= ap,gapOpenPenalty);
1003             int score =3D globalAli= gnment(align, scorePam120 );

It is really hard to tell what went wrong without a proper code example. Co= uld you please provide all the code associated with the alignment computati= on?


Maybe I need to specify the algorithm as well?

Also, how can I retrieve the aligned residue numbers?  Right now = I'm just retrieving the two aligned sequences and assuming they are aligned= if neither character is a '-': 

1022                 if ((Stri= ng(seqan::row (align,0)[i]).compare("-")  !=3D 0  ) &nb= sp;&&
1023                   &n= bsp; (String(seqan::row (align,1)[i]).compare("-")  !=3D 0 &= nbsp;)) { /* aligned residues*/ }

At the moment we don't store any state of the alignment. Thus it is not pos= sible to receive such information. However, we have the function isGap(gaps= , viewPosition) or isGap(GapsIterator). In this case the code could look li= ke this, avoiding the string comparisons:

typedef Row<Align<DnaString> >::Type TRow;
typedef Iterator<TRow, Standard>::Type TRowIterator;

TRowIterator itRow0 =3D begin(row(align, 0), Standard());
TRowIterator itRow0End =3D end(row(align, 0), Standard());
TRowIterator itRow1 =3D begin(row(align, 1), Standard());

for (; itRow0 !=3D itRow0End; ++itRow0, ++itRow1)
{
if (!i= sGap(itRow0) && !isGap(itRow1))
// Cou= nt aligned residues.
}

Since this is only a linear scan over the aligned sequences, this won'= t add much to the overall runtime considering the quadratic runtime for the= alignments you have to do before.

You can also have a glance at our alignment tutorials at http://trac.seqan.de/wiki/Tutorial/PairwiseSequenceAlignment. Here you = can find all information about the pairwise sequence alignments in SeqAn.

Kind regards,

Ren=E9 Rahn




This works well enough for very simple, high sequence identity alignme= nts.  However I'd really like to know which residues are positively al= igned ( "|" in the above a= lignment).

Thanks

Sam


Hey Sam, 

if you want to use scoring matrices you need to use a different specia= lization of our Score class. To use scoring schemes like the Pam or Blosum = matrices you need to use the following code: 

Score<int, Scor= eMatrix<AminoAcid, Pam120_> > scorePam120(gap, gapOpen);

You can also use our shortcuts to make the code look nicer. You can fi= nd a list of all available shortcuts here: http://docs.seqan.de/seqan/1.= 4.1/SPEC_Score+_Matrix.html.
For the example above this would look like:

Pam120 scorePam120= (gap, gapOpen);

I hope that will solve your problem!

Kind regards,

Ren=E9 Rahn


On Feb 17, 2014, at 12:32 AM, Samuel Flores <samuelfloresc@gmail.com> wrote:

Guys,

I can't seem to get globalAlignment to use any scoring scheme otehr than se= qan::Simple:

           TAlign al= ign;
           seqan::re= size(rows(align), 2);
           assignSou= rce(row(align,0),seqA);
           assignSou= rce(row(align,1),seqB);
           int score= =3D globalAlignment(align, seqan::Score<int,seqan::Simple>(0,-1,-1,g= apOpenPenalty));

I tried changing the last line to just:

           int score= =3D globalAlignment(align, seqan::Score<int,Pam>(0,-1,-1,gapOpenPena= lty));

and every conceivable variant thereof.  None seem to be recognized, e.= g.:


/Users/Sam/svn/RNAToolbox/trunk/src/ParameterReader.cpp:1000:65: error: use= of undeclared identifier 'Pam'


Can someone tell me how to switch to Blossum, PAM, or some other?

Thanks

Sam
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-= berlin.de/listinfo/seqan-dev


---

Ren=E9 Rahn
Ph.D. Student<= /font>
--------------= -------------------
Mail:  rene.rahn@fu-berlin.de
Phone: +49= (0)30 838 75 277
--------------= -------------------
Algorithmic Bi= oinformatics (ABI)
Department of = Computer Science 
Room  018
--------------= -------------------
Freie Universi= t=E4t Berlin
Takustra=DFe 9=  
14195 Berlin
--------------= -------------------

_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-= berlin.de/listinfo/seqan-dev

_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev


---

Ren=E9 Rahn
Ph.D. Student<= /font>
--------------= -------------------
Mail:  rene.rahn@fu-berlin.de
Phone: +49= (0)30 838 75 277
--------------= -------------------
Algorithmic Bi= oinformatics (ABI)
Department of = Computer Science 
Room  018
--------------= -------------------
Freie Universi= t=E4t Berlin
Takustra=DFe 9=  
14195 Berlin
--------------= -------------------

--_000_24D0AA30418D4C02A484EF6B83370B5Ffuberlinde_-- From NHTran@ntu.edu.sg Thu Feb 27 06:24:32 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WItSQ-0038S7-DY>; Thu, 27 Feb 2014 06:24:30 +0100 Received: from smtp3.ntu.edu.sg ([155.69.5.81]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WItSP-0042o1-Tm>; Thu, 27 Feb 2014 06:24:30 +0100 X-AuditID: 9b450551-b7b4bae000003fc4-ab-530ecc0a504c Received: from EXSMTP6.staff.main.ntu.edu.sg (exsmtp6.ntu.edu.sg [155.69.5.101]) by SMTP3.ntu.edu.sg (Symantec Messaging Gateway) with SMTP id E9.46.16324.A0CCE035; Thu, 27 Feb 2014 13:24:26 +0800 (MYT) Received: from EXCHHUB14.staff.main.ntu.edu.sg (155.69.25.17) by EXSMTP6.staff.main.ntu.edu.sg (155.69.5.101) with Microsoft SMTP Server (TLS) id 14.3.123.3; Thu, 27 Feb 2014 13:24:11 +0800 Received: from EXCHMBOX33.staff.main.ntu.edu.sg ([169.254.3.167]) by EXCHHUB14.staff.main.ntu.edu.sg ([155.69.25.17]) with mapi id 14.03.0123.003; Thu, 27 Feb 2014 13:23:21 +0800 From: "Tran Ngoc Hieu (Dr)" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: RazerS 3 compilation issue Thread-Index: Ac8zfAdmU0kq6xZITbSzIcuYzO2mqw== Date: Thu, 27 Feb 2014 05:23:21 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_DA28F38A7BD3CF4799A3B54A9986CAFFBF54EXCHMBOX33staffmain_" MIME-Version: 1.0 X-Brightmail-Tracker: H4sIAAAAAAAAA+NgFtrCKsWRmVeSWpSXmKPExsUy25U1VZfrDF+wwfz5chbb361md2D02LRj L1sAYxSXTUpqTmZZapG+XQJXxptfHawF68IrZt/8ydzA2OLfxcjJISFgInHk5BJ2CFtM4sK9 9WxdjFwcQgJnGCWuvl3MAuEcZJT42fgVytnGKLG65S4jSAubgL7Ev5/3wWwRAUeJvp42oHYO DmEBZYnmgwIQYQ2JxVPnQZXoScw7PZ0JxGYRUJXoOrOQBcTmFQiW6Ht5EcxmBLri+6k1YDXM AuISt57MZ4K4TkBiyZ7zzBC2qMTLx/9YQVZJCChIvPvrDFGeL3G7YQ/USEGJkzOfgNlCAnIS d543MU1gFJmFZOosJC2zkLRAxPUkbkydwgZha0ssW/iaGcLWlZjx7xALsvgCRvZVjALBviEB xnp5JaV6qSmlesXpmxghkRO4g/HqH71DjAIcjEo8vKF7+YKFWBPLiitzDzFKcjApifL+2Q8U 4kvKT6nMSCzOiC8qzUktPsQowcGsJMJ7yAUox5uSWFmVWpQPk5LmYFES59WcxRssJJCeWJKa nZpakFoEk5Xh4FCS4F1+CqhRsCg1PbUiLTOnBCHNxMEJMpwHaHg/SA1vcUFibnFmOkT+FKOi lDjvHpCEAEgiozQPrheU2Or/////ilEc6BVh3j6QKh5gUoTrfgU0mAlo8FFpHpDBJYkIKakG xpDrDLOc/hwJbf50KnaCxy0lp1iVxpeJYTVbHxo7rJ3vZy2rsmN2z9OJE7UT7q6+YXBPU9L8 7oZTy+6HR8oKvTtTfnfKnwBBkdmPvs58tK7ihLDo+htJ5y69kz25MVZzjkpcHectI+1PE98d KGVTsLpo+tiW26dVUrhBSPiCws3eqioNthU695RYijMSDbWYi4oTAW5Oh5xHAwAA X-Originating-IP: 155.69.5.81 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1393478670-0000CD40-B22732BB/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.500000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-2.3 required=5.0 tests=HTML_MESSAGE, RCVD_IN_DNSWL_MED,RCVD_IN_MSPIKE_H2 X-Spam-Checker-Version: SpamAssassin 3.4.0 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] RazerS 3 compilation issue X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 27 Feb 2014 05:24:32 -0000 --_000_DA28F38A7BD3CF4799A3B54A9986CAFFBF54EXCHMBOX33staffmain_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All, I encountered the following errors when trying to compile RazerS 3 (everyth= ing was fine when I tried other tools such as Mason, Masai). Could anyone p= lease help with some advice? Thank you very much! $ make razers3 [ 0%] Built target seqan_extras [ 0%] Built target seqan_core [100%] Building CXX object extras/apps/razers3/CMakeFiles/razers3.dir/razer= s.cpp.o /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/basic/test_system.h:73: w= arning: =E2class seqan::Test=E2 has virtual functions but non-virtual destr= uctor /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:197:= warning: =E2class seqan::ToolDocPrinter_=E2 has virtual functions but non-= virtual destructor /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:210:= warning: =E2class seqan::ManToolDocPrinter_=E2 has virtual functions but n= on-virtual destructor /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:223:= warning: =E2class seqan::HtmlToolDocPrinter_=E2 has virtual functions but = non-virtual destructor /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:318:= warning: =E2class seqan::TextToolDocPrinter_=E2 has virtual functions but = non-virtual destructor /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_paralle= l.h: In function =E2void seqan::initializeThreadLocalStoragesPaired(TThread= LocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [wi= th TThreadLocalStorages =3D seqan::String, seqan::= Alloc >, seqan::FragmentStore >, seqan::Finder, seqan::Alloc >, seqan::Swift > > >, seqan::Finder, seqan::Alloc = >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc >, seqan::InfixSegment>, seqan::Owner > >, s= eqan::IndexQGram= , seqan::UngappedShape<0u> >, seqan::Tag > >, seqan= ::Swift > > >, seqan::Shape, seqan::UngappedShape<0u> >, seqan:= :RazerSOptions >, seqan::String >, seqan::Alloc >, seqan::R= azerSMode > >, seqan::Alloc >, TFragmentStore =3D seqan::Fr= agmentStore >, TSplitters =3D seqan::String >, TShap= e =3D const seqan::Shape, seq= an::UngappedShape<0u> >, TOptions =3D seqan::RazerSOptions >]=E2: /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_paralle= l.h:338: internal compiler error: in single_succ_edge, at basic-block.h:620 Please submit a full bug report, with preprocessed source if appropriate. See for instructions. Preprocessed source stored into /tmp/ccHRTako.out file, please attach this = to your bugreport. make[3]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o] Erro= r 1 make[2]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/all] Error 2 make[1]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/rule] Error 2 make: *** [razers3] Error 2 ________________________________ CONFIDENTIALITY:This email is intended solely for the person(s) named and m= ay be confidential and/or privileged.If you are not the intended recipient,= please delete it,notify us and do not copy,use,or disclose its contents. Towards a sustainable earth:Print only when necessary.Thank you. --_000_DA28F38A7BD3CF4799A3B54A9986CAFFBF54EXCHMBOX33staffmain_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear All,

 

I encountered the following errors when trying to co= mpile RazerS 3 (everything was fine when I tried other tools such as Mason,= Masai). Could anyone please help with some advice? Thank you very much!

 

$ make razers3

[  0%] Built target seqan_extras

[  0%] Built target seqan_core

 

[100%] Building CXX object extras/apps/razers3/CM= akeFiles/razers3.dir/razers.cpp.o

/home/nhtran/SeqAn/seqan-trunk/core/include/seqan= /basic/test_system.h:73: warning: =E2class seqan::Test=E2 has virtual funct= ions but non-virtual destructor

/home/nhtran/SeqAn/seqan-trunk/core/include/seqan= /arg_parse/tool_doc.h:197: warning: =E2class seqan::ToolDocPrinter_=E2 has = virtual functions but non-virtual destructor

/home/nhtran/SeqAn/seqan-trunk/core/include/seqan= /arg_parse/tool_doc.h:210: warning: =E2class seqan::ManToolDocPrinter_=E2 h= as virtual functions but non-virtual destructor

/home/nhtran/SeqAn/seqan-trunk/core/include/seqan= /arg_parse/tool_doc.h:223: warning: =E2class seqan::HtmlToolDocPrinter_=E2 = has virtual functions but non-virtual destructor

/home/nhtran/SeqAn/seqan-trunk/core/include/seqan= /arg_parse/tool_doc.h:318: warning: =E2class seqan::TextToolDocPrinter_=E2 = has virtual functions but non-virtual destructor

 

/home/nhtran/SeqAn/seqan-trunk/extras/apps/razers= 3/razers_matepairs_parallel.h: In function =E2void seqan::initializeThreadL= ocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TS= plitters&, TShape&, TOptions&) [with TThreadLocalStorages =3D seqan::String<seqan::ThreadLocalStorage<seqan::MapPairedReads<= ;seqan::String<seqan::MatchRecord<long unsigned int>, seqan::Alloc= <void> >, seqan::FragmentStore<MyFragStoreConfig, seqan::Fragme= ntStoreConfig<MyFragStoreConfig> >, seqan::Finder<seqan::String= <seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Swift<se= qan::Tag<seqan::SwiftSemiGlobal_<void> > > >, seqan::Find= er<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char= , seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>= , seqan::Swift<seqan::Tag<seqan::SwiftSemiGlobal_<void> > > >, seqan::Pattern<seqan::Index<seqan::StringSet<seqa= n::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::D= na5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::O= wner<seqan::Tag<seqan::Default_> > >, seqan::IndexQGram<s= eqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, seqan::Tag<= seqan::OpenAddressing_> > >, seqan::Swift<seqan::Tag<seqan::= SwiftSemiGlobal_<void> > > >, seqan::Shape<seqan::SimpleT= ype<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >,= seqan::RazerSOptions<seqan::RazerSSpec<false, false> >, seqan::String<seqan::String<short unsigned int, seqa= n::Alloc<void> >, seqan::Alloc<void> >, seqan::RazerSMode= <seqan::RazerSGlobal, seqan::RazerSGapped, seqan::RazerSErrors, seqan::N= MatchesNone_> > >, seqan::Alloc<void> >, TFragmentStore = =3D seqan::FragmentStore<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig> >, TSplitters =3D s= eqan::String<unsigned int, seqan::Alloc<void> >, TShape =3D con= st seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seq= an::UngappedShape<0u> >, TOptions =3D seqan::RazerSOptions<seqa= n::RazerSSpec<false, false> >]=E2:

 

/home/nhtran/SeqAn/seqan-trunk/extras/apps/razers= 3/razers_matepairs_parallel.h:338: internal compiler error: in single_succ_= edge, at basic-block.h:620

Please submit a full bug report,

with preprocessed source if appropriate.

See <URL:http://bugzilla.redhat.com/bugzilla&g= t; for instructions.

Preprocessed source stored into /tmp/ccHRTako.out= file, please attach this to your bugreport.

make[3]: *** [extras/apps/razers3/CMakeFiles/raze= rs3.dir/razers.cpp.o] Error 1

make[2]: *** [extras/apps/razers3/CMakeFiles/raze= rs3.dir/all] Error 2

make[1]: *** [extras/apps/razers3/CMakeFiles/raze= rs3.dir/rule] Error 2

make: *** [razers3] Error 2



CONFIDENTIALITY:This email is intended solely for the person(s) named and m= ay be confidential and/or privileged.If you are not the intended recipient,= please delete it,notify us and do not copy,use,or disclose its contents.
Towards a sustainable earth:Print only when necessary.Thank you.
 --_000_DA28F38A7BD3CF4799A3B54A9986CAFFBF54EXCHMBOX33staffmain_-- From weese@campus.fu-berlin.de Thu Feb 27 09:23:16 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WIwFO-003OFW-Nu>; Thu, 27 Feb 2014 09:23:14 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WIwFO-003Rgm-Ls>; Thu, 27 Feb 2014 09:23:14 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1WIwFO-000HTX-9T>; Thu, 27 Feb 2014 09:23:14 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0174.001; Thu, 27 Feb 2014 09:23:13 +0100 From: "Weese, David" To: SeqAn Development Thread-Topic: [Seqan-dev] RazerS 3 compilation issue Thread-Index: Ac8zfAdmU0kq6xZITbSzIcuYzO2mqwAEL4oA Message-ID: <9D8A5A9D-9EF0-4803-9206-1B0E3EEA57AA@fu-berlin.de> References: In-Reply-To: Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Content-Type: multipart/signed; boundary="Apple-Mail=_EE437486-4036-48A7-BD01-AF8815B3C6B8"; protocol="application/pkcs7-signature"; micalg=sha1 MIME-Version: 1.0 Date: Thu, 27 Feb 2014 09:23:12 +0100 X-Original-Date: Thu, 27 Feb 2014 08:23:12 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1393489394-0000CD40-45292677/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.4.0 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] RazerS 3 compilation issue X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 27 Feb 2014 08:23:16 -0000 --Apple-Mail=_EE437486-4036-48A7-BD01-AF8815B3C6B8 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Hi, the "internal compiler error" in correlation with the heavy templating = in RazerS3 is usually an indicator for insufficient memory of your build = machine. If you compile using the gcc make sure you have at least 4GB of = free memory available. Cheers, David -- David Weese, Ph.D. david.weese@fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75137 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 020 Am 27.02.2014 um 06:23 schrieb Tran Ngoc Hieu (Dr) : > Dear All, > =20 > I encountered the following errors when trying to compile RazerS 3 = (everything was fine when I tried other tools such as Mason, Masai). = Could anyone please help with some advice? Thank you very much! > =20 > $ make razers3 > [ 0%] Built target seqan_extras > [ 0%] Built target seqan_core > =20 > [100%] Building CXX object = extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o > = /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/basic/test_system.h:73: = warning: =E2class seqan::Test=E2 has virtual functions but non-virtual = destructor > = /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:197= : warning: =E2class seqan::ToolDocPrinter_=E2 has virtual functions but = non-virtual destructor > = /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:210= : warning: =E2class seqan::ManToolDocPrinter_=E2 has virtual functions = but non-virtual destructor > = /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:223= : warning: =E2class seqan::HtmlToolDocPrinter_=E2 has virtual functions = but non-virtual destructor > = /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h:318= : warning: =E2class seqan::TextToolDocPrinter_=E2 has virtual functions = but non-virtual destructor > =20 > = /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_parall= el.h: In function =E2void = seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, = TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with = TThreadLocalStorages =3D = seqan::String, seqan::Alloc >, = seqan::FragmentStore >, = seqan::Finder, seqan::Alloc >, = seqan::Swift > > >, = seqan::Finder, seqan::Alloc >, seqan::InfixSegment>, = seqan::Swift > > >, = seqan::Pattern, seqan::Alloc >, = seqan::InfixSegment>, seqan::Owner > >, = seqan::IndexQGram, seqan::UngappedShape<0u> >, = seqan::Tag > >, = seqan::Swift > > >, = seqan::Shape, = seqan::UngappedShape<0u> >, = seqan::RazerSOptions >, = seqan::String >, = seqan::Alloc >, seqan::RazerSMode > >, = seqan::Alloc >, TFragmentStore =3D = seqan::FragmentStore >, TSplitters =3D = seqan::String >, TShape =3D const = seqan::Shape, = seqan::UngappedShape<0u> >, TOptions =3D = seqan::RazerSOptions >]=E2: > =20 > = /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_parall= el.h:338: internal compiler error: in single_succ_edge, at = basic-block.h:620 > Please submit a full bug report, > with preprocessed source if appropriate. > See for instructions. > Preprocessed source stored into /tmp/ccHRTako.out file, please attach = this to your bugreport. > make[3]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o] = Error 1 > make[2]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/all] Error 2 > make[1]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/rule] Error 2 > make: *** [razers3] Error 2 >=20 >=20 > CONFIDENTIALITY:This email is intended solely for the person(s) named = and may be confidential and/or privileged.If you are not the intended = recipient,please delete it,notify us and do not copy,use,or disclose its = contents. >=20 > Towards a sustainable earth:Print only when necessary.Thank you. > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_EE437486-4036-48A7-BD01-AF8815B3C6B8 Content-Disposition: attachment; filename="smime.p7s" Content-Type: application/pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 MIAGCSqGSIb3DQEHAqCAMIACAQExCzAJBgUrDgMCGgUAMIAGCSqGSIb3DQEHAQAAoIIPZjCCBCEw ggMJoAMCAQICAgDHMA0GCSqGSIb3DQEBBQUAMHExCzAJBgNVBAYTAkRFMRwwGgYDVQQKExNEZXV0 c2NoZSBUZWxla29tIEFHMR8wHQYDVQQLExZULVRlbGVTZWMgVHJ1c3QgQ2VudGVyMSMwIQYDVQQD ExpEZXV0c2NoZSBUZWxla29tIFJvb3QgQ0EgMjAeFw0wNjEyMTkxMDI5MDBaFw0xOTA2MzAyMzU5 MDBaMFoxCzAJBgNVBAYTAkRFMRMwEQYDVQQKEwpERk4tVmVyZWluMRAwDgYDVQQLEwdERk4tUEtJ MSQwIgYDVQQDExtERk4tVmVyZWluIFBDQSBHbG9iYWwgLSBHMDEwggEiMA0GCSqGSIb3DQEBAQUA A4IBDwAwggEKAoIBAQDpm8NnhfkNrvWNVMOWUDU9YuluTO2U1wBblSJ01CDrNI/W7MAxBAuZgeKm FNJSoCgjhIt0iQReW+DieMF4yxbLKDU5ey2QRdDtoAB6fL9KDhsAw4bpXCsxEXsM84IkQ4wcOItq 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EXSMTP6.staff.main.ntu.edu.sg (155.69.5.101) with Microsoft SMTP Server (TLS) id 14.3.123.3; Thu, 27 Feb 2014 17:25:18 +0800 Received: from EXCHMBOX33.staff.main.ntu.edu.sg ([169.254.3.167]) by EXCHHUB14.staff.main.ntu.edu.sg ([155.69.25.17]) with mapi id 14.03.0123.003; Thu, 27 Feb 2014 17:25:33 +0800 From: "Tran Ngoc Hieu (Dr)" To: SeqAn Development Thread-Topic: [Seqan-dev] RazerS 3 compilation issue Thread-Index: Ac8zfAdmU0kq6xZITbSzIcuYzO2mqwAEL4oAAAQphMA= Date: Thu, 27 Feb 2014 09:25:32 +0000 Message-ID: References: <9D8A5A9D-9EF0-4803-9206-1B0E3EEA57AA@fu-berlin.de> In-Reply-To: <9D8A5A9D-9EF0-4803-9206-1B0E3EEA57AA@fu-berlin.de> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Brightmail-Tracker: H4sIAAAAAAAAA+NgFtrGKsWRmVeSWpSXmKPExsUy25U1VbeXhT/Y4OR5c4vt71azOzB6bNqx 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151147::1393493137-0000CD40-C9E13D22/2/13074394677 X-Bogosity: Ham, tests=bogofilter, spamicity=0.495896, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-1.3 required=5.0 tests=FU_XPURGATE_SUSP, RCVD_IN_DNSWL_MED,RCVD_IN_MSPIKE_H2 X-Spam-Checker-Version: SpamAssassin 3.4.0 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] RazerS 3 compilation issue X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 27 Feb 2014 09:25:39 -0000 Dear David, Thank you for your prompt reply. I run on a Linux server with more than 20G= B free memory available. Is there any other possible reasons? Any requireme= nt about gcc version? Cheers, Hieu -----Original Message----- From: Weese, David [mailto:weese@campus.fu-berlin.de]=20 Sent: Thursday, 27 February, 2014 4:23 PM To: SeqAn Development Subject: Re: [Seqan-dev] RazerS 3 compilation issue Hi, the "internal compiler error" in correlation with the heavy templating in R= azerS3 is usually an indicator for insufficient memory of your build machin= e. If you compile using the gcc make sure you have at least 4GB of free mem= ory available. Cheers, David -- David Weese, Ph.D. david.weese@fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75137 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 020 Am 27.02.2014 um 06:23 schrieb Tran Ngoc Hieu (Dr) : > Dear All, > =20 > I encountered the following errors when trying to compile RazerS 3 (every= thing was fine when I tried other tools such as Mason, Masai). Could anyone= please help with some advice? Thank you very much! > =20 > $ make razers3 > [ 0%] Built target seqan_extras > [ 0%] Built target seqan_core > =20 > [100%] Building CXX object=20 > extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o > /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/basic/test_system.h: > 73: warning: =E2class seqan::Test=E2 has virtual functions but non-virtua= l=20 > destructor > /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h > :197: warning: =E2class seqan::ToolDocPrinter_=E2 has virtual functions=20 > but non-virtual destructor > /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h > :210: warning: =E2class seqan::ManToolDocPrinter_=E2 has virtual function= s=20 > but non-virtual destructor > /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h > :223: warning: =E2class seqan::HtmlToolDocPrinter_=E2 has virtual=20 > functions but non-virtual destructor > /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h > :318: warning: =E2class seqan::TextToolDocPrinter_=E2 has virtual=20 > functions but non-virtual destructor > =20 > /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_paral= lel.h: In function =E2void seqan::initializeThreadLocalStoragesPaired(TThre= adLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [= with TThreadLocalStorages =3D seqan::String, seqan= ::Alloc >, seqan::FragmentStore >, seqan::Finder, seqan::Alloc >, seqan::Swift > > >, seqan::Finder, seqan::Alloc >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc >, seqan::InfixSegment>, seqan::Owner > >,= seqan::IndexQGram, seqan::UngappedShape<0u> >, seqan::Tag > >, seq= an::Swift > > >, seqan::Shape, seqan::UngappedShape<0u> >, seqa= n::RazerSOptions >, seqan::String >, seqan::Alloc >, seqan:= :RazerSMode > >, seqan::Alloc >, TFragmentStore =3D seqan::= FragmentStore >, TSplitters =3D seqan::String >, TSh= ape =3D const seqan::Shape, s= eqan::UngappedShape<0u> >, TOptions =3D seqan::RazerSOptions >]=E2: > =20 > /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_pa > rallel.h:338: internal compiler error: in single_succ_edge, at=20 > basic-block.h:620 Please submit a full bug report, with preprocessed sour= ce if appropriate. > See for instructions. > Preprocessed source stored into /tmp/ccHRTako.out file, please attach thi= s to your bugreport. > make[3]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o]=20 > Error 1 > make[2]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/all] Error 2 > make[1]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/rule] Error 2 > make: *** [razers3] Error 2 >=20 >=20 > CONFIDENTIALITY:This email is intended solely for the person(s) named and= may be confidential and/or privileged.If you are not the intended recipien= t,please delete it,notify us and do not copy,use,or disclose its contents. >=20 > Towards a sustainable earth:Print only when necessary.Thank you. > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From weese@campus.fu-berlin.de Thu Feb 27 13:50:41 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WJ0QB-003kW7-LP>; Thu, 27 Feb 2014 13:50:39 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1WJ0QB-001LV6-JC>; Thu, 27 Feb 2014 13:50:39 +0100 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1WJ0QB-000weO-54>; Thu, 27 Feb 2014 13:50:39 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.03.0174.001; Thu, 27 Feb 2014 13:50:38 +0100 From: "Weese, David" To: SeqAn Development Thread-Topic: [Seqan-dev] RazerS 3 compilation issue Thread-Index: Ac8zfAdmU0kq6xZITbSzIcuYzO2mqwAEL4oAAAQphMAABS06AA== Message-ID: References: <9D8A5A9D-9EF0-4803-9206-1B0E3EEA57AA@fu-berlin.de> In-Reply-To: Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Content-Type: multipart/signed; boundary="Apple-Mail=_20D2954F-CBB9-451B-AAC3-94F0895DB6E6"; protocol="application/pkcs7-signature"; micalg=sha1 MIME-Version: 1.0 Date: Thu, 27 Feb 2014 13:50:36 +0100 X-Original-Date: Thu, 27 Feb 2014 12:50:36 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1393505439-0000CD40-023F3602/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.4.0 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] RazerS 3 compilation issue X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 27 Feb 2014 12:50:41 -0000 --Apple-Mail=_20D2954F-CBB9-451B-AAC3-94F0895DB6E6 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Mmh. Difficult to say. You could check that there are no limitations to = the amount of memory your processes are allowed to allocate (see ulimit) = or try to use cmake with another compiler "CXX=3Dg++-4.7 cmake ...". Cheers Dave -- David Weese, Ph.D. david.weese@fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75137 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 020 Am 27.02.2014 um 10:25 schrieb Tran Ngoc Hieu (Dr) : > Dear David, >=20 > Thank you for your prompt reply. I run on a Linux server with more = than 20GB free memory available. Is there any other possible reasons? = Any requirement about gcc version? >=20 > Cheers, > Hieu >=20 > -----Original Message----- > From: Weese, David [mailto:weese@campus.fu-berlin.de]=20 > Sent: Thursday, 27 February, 2014 4:23 PM > To: SeqAn Development > Subject: Re: [Seqan-dev] RazerS 3 compilation issue >=20 > Hi, >=20 > the "internal compiler error" in correlation with the heavy templating = in RazerS3 is usually an indicator for insufficient memory of your build = machine. If you compile using the gcc make sure you have at least 4GB of = free memory available. >=20 > Cheers, > David >=20 > -- > David Weese, Ph.D. david.weese@fu-berlin.de > Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ > Institut f=FCr Informatik Phone: +49 30 838 75137 > Takustra=DFe 9 Algorithmic Bioinformatics > 14195 Berlin Room 020 >=20 > Am 27.02.2014 um 06:23 schrieb Tran Ngoc Hieu (Dr) = : >=20 >> Dear All, >>=20 >> I encountered the following errors when trying to compile RazerS 3 = (everything was fine when I tried other tools such as Mason, Masai). = Could anyone please help with some advice? Thank you very much! >>=20 >> $ make razers3 >> [ 0%] Built target seqan_extras >> [ 0%] Built target seqan_core >>=20 >> [100%] Building CXX object=20 >> extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o >> = /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/basic/test_system.h: >> 73: warning: =E2class seqan::Test=E2 has virtual functions but = non-virtual=20 >> destructor >> = /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h >> :197: warning: =E2class seqan::ToolDocPrinter_=E2 has virtual = functions=20 >> but non-virtual destructor >> = /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h >> :210: warning: =E2class seqan::ManToolDocPrinter_=E2 has virtual = functions=20 >> but non-virtual destructor >> = /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h >> :223: warning: =E2class seqan::HtmlToolDocPrinter_=E2 has virtual=20 >> functions but non-virtual destructor >> = /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h >> :318: warning: =E2class seqan::TextToolDocPrinter_=E2 has virtual=20 >> functions but non-virtual destructor >>=20 >> = /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_parall= el.h: In function =E2void = seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, = TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with = TThreadLocalStorages =3D = seqan::String, seqan::Alloc >, = seqan::FragmentStore >, = seqan::Finder, seqan::Alloc >, = seqan::Swift > > >, = seqan::Finder, seqan::Alloc >, seqan::InfixSegment>, = seqan::Swift > > >, = seqan::Pattern, seqan::Alloc >, = seqan::InfixSegment>, seqan::Owner > >, = seqan::IndexQGram, seqan::UngappedShape<0u> >, = seqan::Tag > >, = seqan::Swift > > >, = seqan::Shape, = seqan::UngappedShape<0u> >, = seqan::RazerSOptions >, = seqan::String >, = seqan::Alloc >, seqan::RazerSMode > >, = seqan::Alloc >, TFragmentStore =3D = seqan::FragmentStore >, TSplitters =3D = seqan::String >, TShape =3D const = seqan::Shape, = seqan::UngappedShape<0u> >, TOptions =3D = seqan::RazerSOptions >]=E2: >>=20 >> = /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_pa >> rallel.h:338: internal compiler error: in single_succ_edge, at=20 >> basic-block.h:620 Please submit a full bug report, with preprocessed = source if appropriate. >> See for instructions. >> Preprocessed source stored into /tmp/ccHRTako.out file, please attach = this to your bugreport. >> make[3]: *** = [extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o]=20 >> Error 1 >> make[2]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/all] Error 2 >> make[1]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/rule] Error = 2 >> make: *** [razers3] Error 2 >>=20 >>=20 >> CONFIDENTIALITY:This email is intended solely for the person(s) named = and may be confidential and/or privileged.If you are not the intended = recipient,please delete it,notify us and do not copy,use,or disclose its = contents. >>=20 >> Towards a sustainable earth:Print only when necessary.Thank you. >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_20D2954F-CBB9-451B-AAC3-94F0895DB6E6 Content-Disposition: attachment; filename="smime.p7s" Content-Type: application/pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 MIAGCSqGSIb3DQEHAqCAMIACAQExCzAJBgUrDgMCGgUAMIAGCSqGSIb3DQEHAQAAoIIPZjCCBCEw ggMJoAMCAQICAgDHMA0GCSqGSIb3DQEBBQUAMHExCzAJBgNVBAYTAkRFMRwwGgYDVQQKExNEZXV0 c2NoZSBUZWxla29tIEFHMR8wHQYDVQQLExZULVRlbGVTZWMgVHJ1c3QgQ2VudGVyMSMwIQYDVQQD ExpEZXV0c2NoZSBUZWxla29tIFJvb3QgQ0EgMjAeFw0wNjEyMTkxMDI5MDBaFw0xOTA2MzAyMzU5 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