From hannes.hauswedell@fu-berlin.de Wed Jan 06 23:10:37 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1aGwHs-000oMk-W1>; Wed, 06 Jan 2016 23:10:37 +0100 Received: from einhorn.in-berlin.de ([192.109.42.8]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1aGwHs-0039ow-UG>; Wed, 06 Jan 2016 23:10:36 +0100 X-Envelope-From: hannes.hauswedell@fu-berlin.de X-Envelope-To: Received: from fbsdmain.soldiner.lan (soulrebel.in-vpn.de [217.197.85.230]) (authenticated bits=0) by einhorn.in-berlin.de (8.14.4/8.14.4/Debian-4) with ESMTP id u06MAZik009068 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Wed, 6 Jan 2016 23:10:35 +0100 To: seqan-dev@lists.fu-berlin.de References: From: Hannes Hauswedell Message-ID: <568D90DB.4050109@fu-berlin.de> Date: Wed, 6 Jan 2016 23:10:35 +0100 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Originating-IP: 192.109.42.8 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1452118236-000A31C7-E59E8416/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.0 required=5.0 tests=RCVD_IN_DNSWL_LOW, SPF_NEUTRAL, T_FILL_THIS_FORM_SHORT X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] GOMP_4.0' not found! 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: Wed, 06 Jan 2016 22:10:37 -0000 On 11.12.2015 22:30, Yifang Tan wrote: > Hello, > When I tried to run mason_smulator, I always got error: > $ ./bin/mason_simulator: > ./bin/mason_simulator: /usr/lib/x86_64-linux-gnu/libgomp.so.1: version > `GOMP_4.0' not found (required by ./bin/mason_simulator) > > But /usr/lib/x86_64-linux-gnu/libgomp.so.1 is there and I am not sure > what I missed. > $ ls -al /usr/lib/x86_64-linux-gnu/libgomp.* > lrwxrwxrwx 1 root root 16 May 14 2015 > /usr/lib/x86_64-linux-gnu/libgomp.so.1 -> libgomp.so.1.0.0 > -rw-r--r-- 1 root root 59872 May 14 2015 > /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 > This means that likely the version is too old. What version of gcc do you have installed? Could you try installing a newer version, e.g. 4.9 or 5.* ? Best regards, -- Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universität Berlin address Institut für Informatik Takustraße 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] From yifangt@gmail.com Thu Jan 07 00:08:27 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1aGxBr-000rjO-4O>; Thu, 07 Jan 2016 00:08:27 +0100 Received: from mail-wm0-f45.google.com ([74.125.82.45]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1aGxBr-003HuQ-1N>; Thu, 07 Jan 2016 00:08:27 +0100 Received: by mail-wm0-f45.google.com with SMTP id u188so77885064wmu.1 for ; Wed, 06 Jan 2016 15:08:25 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=3ibkgBnpo0FsxUuA9tQuaA5fWelqVAM2qnqkR706PAE=; b=Ke7ixW8w+92RJ/s2Sv79S2S2E3iDb/ut/GuWyUUHxELP25suxxBiHGGkG0cOz2hnie /oE+N040P6rm8HhA83haapwnMsyTxvw/qM4mAFSAweNA4o6eK3eDDA1UOrgt5cwTofe9 14GV2rmcgSZtFPgrqizd1QpxKjA9kikftMpdWO50ZdEbpKCg9HVo9OxKf+riNh+xhixX csP6z0/oKO9VoQHz0iwEHOo8KoXLYt48j2vOOeDTaWd3eO2t3+xadqP8KSMVT+76KRyo uHwBnb0J7mBFGeNCyjvtaCLjSKoBo5dVMTjanSVpCp1i+AXo7iaJ+UBS4g2lhFqJe3xb LXEw== MIME-Version: 1.0 X-Received: by 10.28.150.215 with SMTP id y206mr12268577wmd.8.1452121705606; Wed, 06 Jan 2016 15:08:25 -0800 (PST) Received: by 10.194.15.199 with HTTP; Wed, 6 Jan 2016 15:08:25 -0800 (PST) In-Reply-To: <568D90DB.4050109@fu-berlin.de> References: <568D90DB.4050109@fu-berlin.de> Date: Wed, 6 Jan 2016 17:08:25 -0600 Message-ID: From: Yifang Tan To: SeqAn Development Content-Type: multipart/alternative; boundary=001a114b3c686ef6460528b26ec5 X-Originating-IP: 74.125.82.45 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1452121707-000A31C7-D916C83B/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.032905, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.8 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU, FREEMAIL_FROM, HTML_MESSAGE, RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] GOMP_4.0' not found! 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: Wed, 06 Jan 2016 23:08:28 -0000 --001a114b3c686ef6460528b26ec5 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks! I did upgrade gcc-4.9.0 by: sudo apt-get install gcc-4.9 It works now! However, gcc is still the same version as gcc-4.8 as: $ which gcc /usr/bin/gcc -> gcc-4.8 I am trying to understand why. Could you explain a little bit more why this happened? Thanks! Yifang On Wed, Jan 6, 2016 at 4:10 PM, Hannes Hauswedell < hannes.hauswedell@fu-berlin.de> wrote: > On 11.12.2015 22:30, Yifang Tan wrote: > > Hello, > > When I tried to run mason_smulator, I always got error: > > $ ./bin/mason_simulator: > > ./bin/mason_simulator: /usr/lib/x86_64-linux-gnu/libgomp.so.1: version > > `GOMP_4.0' not found (required by ./bin/mason_simulator) > > > > But /usr/lib/x86_64-linux-gnu/libgomp.so.1 is there and I am not sure > > what I missed. > > $ ls -al /usr/lib/x86_64-linux-gnu/libgomp.* > > lrwxrwxrwx 1 root root 16 May 14 2015 > > /usr/lib/x86_64-linux-gnu/libgomp.so.1 -> libgomp.so.1.0.0 > > -rw-r--r-- 1 root root 59872 May 14 2015 > > /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 > > > > > This means that likely the version is too old. What version of gcc do > you have installed? Could you try installing a newer version, e.g. 4.9 > or 5.* ? > > Best regards, > -- > Hannes Hauswedell > > PhD student > Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Berl= in > > address Institut f=C3=BCr Informatik > Takustra=C3=9Fe 9 > Room 019 > 14195 Berlin > telephone +49 (0)30 838-75241 > fax +49 (0)30 838-75218 > e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > --001a114b3c686ef6460528b26ec5 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thanks!
I did upgrade gcc-4.9.0 by:
sudo apt-ge= t install gcc-4.9
It works now!

However, gc= c is still the same version as gcc-4.8 as:
$ which gcc
/usr/bin/gcc -> gcc-4.8

I am trying to unders= tand why. Could you explain a little bit more why this happened?
<= div>Thanks!

Yifang

On Wed, Jan 6, 2016 at 4:10 PM, Hannes H= auswedell <hannes.hauswedell@fu-berlin.de> wrot= e:
On 11.12.2015 22:30, = Yifang Tan wrote:
> Hello,
> When I tried to run mason_smulator, I always got error:
> $ ./bin/mason_simulator:
> ./bin/mason_simulator: /usr/lib/x86_64-linux-gnu/libgomp.so.1: version=
> `GOMP_4.0' not found (required by ./bin/mason_simulator)
>
> But /usr/lib/x86_64-linux-gnu/libgomp.so.1 is there and I am not sure<= br> > what I missed.
> $=C2=A0 ls -al /usr/lib/x86_64-linux-gnu/libgomp.*
> lrwxrwxrwx 1 root root=C2=A0 =C2=A0 16 May 14=C2=A0 2015
> /usr/lib/x86_64-linux-gnu/libgomp.so.1 -> libgomp.so.1.0.0
> -rw-r--r-- 1 root root 59872 May 14=C2=A0 2015
> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>


This means that likely the version is too old. What version of gcc d= o
you have installed? Could you try installing a newer version, e.g. 4.9
or 5.* ?

Best regards,
--
Hannes Hauswedell

PhD student
Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Berlin=

address=C2=A0 =C2=A0 =C2=A0Institut f=C3=BCr Informatik
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Takustra=C3=9Fe 9
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Room 019
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 14195 Berlin
telephone=C2=A0 =C2=A0+49 (0)30 838-75241
fax=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0+49 (0)30 838-75218
e-mail=C2=A0 =C2=A0 =C2=A0 hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]

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

--001a114b3c686ef6460528b26ec5-- From hannes.hauswedell@fu-berlin.de Thu Jan 07 11:05:51 2016 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1aH7S2-001X4T-MD>; Thu, 07 Jan 2016 11:05:50 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1aH7S2-0038Bx-LC>; Thu, 07 Jan 2016 11:05:50 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1aH7S2-003tP7-Fb>; Thu, 07 Jan 2016 11:05:50 +0100 From: Hannes Hauswedell To: SeqAn Development Date: Thu, 07 Jan 2016 11:05:49 +0100 Message-ID: <2658563.U76VCWeKNO@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: References: <568D90DB.4050109@fu-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.111.134 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1452161150-000A31C7-6FB4B8EC/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, RP_MATCHES_RCVD, T_FILL_THIS_FORM_SHORT X-Spam-Checker-Version: SpamAssassin 3.4.1 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] GOMP_4.0' not found! 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, 07 Jan 2016 10:05:51 -0000 Am Mittwoch, 6. Januar 2016, 17:08:25 schrieb Yifang Tan: > Thanks! > I did upgrade gcc-4.9.0 by: > sudo apt-get install gcc-4.9 > It works now! Good to hear! > However, gcc is still the same version as gcc-4.8 as: > $ which gcc > /usr/bin/gcc -> gcc-4.8 > I am trying to understand why. Could you explain a little bit more wh= y this > happened? You now have both gcc-4.8 and gcc-4.9 installed. The default compiler i= s still=20 the old one, but the default libraries are the new ones, because they w= ork=20 with both compilers. You can use the new compiler by specifying gcc-4.9= =20 directly on the command line. Best regards, --=20 Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be= rlin address Institut f=C3=BCr Informatik Takustra=C3=9Fe 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] From yifangt@gmail.com Thu Jan 07 16:20:36 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1aHCMe-001uwl-8V>; Thu, 07 Jan 2016 16:20:36 +0100 Received: from mail-wm0-f43.google.com ([74.125.82.43]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1aHCMe-003HDo-5z>; Thu, 07 Jan 2016 16:20:36 +0100 Received: by mail-wm0-f43.google.com with SMTP id f206so101897780wmf.0 for ; Thu, 07 Jan 2016 07:20:35 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=bR54iamvyipXMYVztTjK2atod7uWuQc9ZN2eGmwdbdA=; b=FYozbKm7Diy6NJ5TIQ41Jzd05ZjeoySXPMt8sVppoohcO44OIE3mUFaX7HnbxApUV1 7B6EiJbGpc1xVj0FtxXrZRR22I054UCMXRChr55vVp9c99kW8u87d8o4G2TI7uq7aRVM T//fy/DZDg4ZpaO4yw7vciAmiv/io2pB8ijogR8Pn1Ir2d2lBmEo0v4VccyD05nIX/S1 zrH9EAIS6oaZIAwWssvDm3Mt0IQ4VAqqpbixWlIGZ+P9qX9hrWiD3ycy9mkipX/KPc0p Qsf7mGxH7dn4w11GeqrMz2TRkoDZACBAo/L2N16TqXnL/QWVqPemtX6vZXD0Rx9XHfO4 DkSw== MIME-Version: 1.0 X-Received: by 10.194.203.228 with SMTP id kt4mr114708715wjc.58.1452180034757; Thu, 07 Jan 2016 07:20:34 -0800 (PST) Received: by 10.194.15.199 with HTTP; Thu, 7 Jan 2016 07:20:34 -0800 (PST) In-Reply-To: <2658563.U76VCWeKNO@celegans.imp.fu-berlin.de> References: <568D90DB.4050109@fu-berlin.de> <2658563.U76VCWeKNO@celegans.imp.fu-berlin.de> Date: Thu, 7 Jan 2016 09:20:34 -0600 Message-ID: From: Yifang Tan To: SeqAn Development Content-Type: multipart/alternative; boundary=047d7bae494a1f2dad0528c003af X-Originating-IP: 74.125.82.43 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1452180036-000A31C7-6A60BA85/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000227, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.8 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU, FREEMAIL_FROM, HTML_MESSAGE, RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] GOMP_4.0' not found! 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, 07 Jan 2016 15:20:36 -0000 --047d7bae494a1f2dad0528c003af Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks! So your mason2 uses part of the libraries, but not the compiler, so that gcc-4.8 still works with the updated libraries. Is that right? I did not see any update with the libs (*.so files under /usr/lib/x86_64-linux-gnu/). Sorry for my naive questions as I do not have CS background. I need your manson2_simulator which coincidently uses seqan libs (I am trying to catch!), so that I want to find out how it works to help my understanding with this example. Thanks again! On Thu, Jan 7, 2016 at 4:05 AM, Hannes Hauswedell < hannes.hauswedell@fu-berlin.de> wrote: > Am Mittwoch, 6. Januar 2016, 17:08:25 schrieb Yifang Tan: > > Thanks! > > I did upgrade gcc-4.9.0 by: > > sudo apt-get install gcc-4.9 > > It works now! > > Good to hear! > > > However, gcc is still the same version as gcc-4.8 as: > > $ which gcc > > /usr/bin/gcc -> gcc-4.8 > > I am trying to understand why. Could you explain a little bit more why > this > > happened? > > You now have both gcc-4.8 and gcc-4.9 installed. The default compiler is > still > the old one, but the default libraries are the new ones, because they wor= k > with both compilers. You can use the new compiler by specifying gcc-4.9 > directly on the command line. > > Best regards, > -- > Hannes Hauswedell > > PhD student > Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Berl= in > > address Institut f=C3=BCr Informatik > Takustra=C3=9Fe 9 > Room 019 > 14195 Berlin > telephone +49 (0)30 838-75241 > fax +49 (0)30 838-75218 > e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > --047d7bae494a1f2dad0528c003af Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thanks!

So your mason2 us= es part of the libraries, but not the compiler, so that gcc-4.8 still works= with the updated libraries. Is that right?
I did not see any upda= te with the libs (*.so files under /usr/lib/x86_64-linux-gnu/).
Sorry= for my naive questions as I do not have CS background. I need your manson2= _simulator which coincidently uses seqan libs (I am trying to catch!), so t= hat I want to find out how it works to help my understanding with this exam= ple.

Thanks again!



On Thu, Jan 7, 2016 at 4:05 AM, = Hannes Hauswedell <hannes.hauswedell@fu-berlin.de> wrote:
Am Mittwoch, = 6. Januar 2016, 17:08:25 schrieb Yifang Tan:
> Thanks!
> I did upgrade gcc-4.9.0 by:
> sudo apt-get install gcc-4.9
> It works now!

Good to hear!

> However, gcc is still the same version as gcc-4.8 as:
> $ which gcc
> /usr/bin/gcc -> gcc-4.8
> I am trying to understand why. Could you explain a little bit more why= this
> happened?

You now have both gcc-4.8 and gcc-4.9 installed. The default compile= r is still
the old one, but the default libraries are the new ones, because they work<= br> with both compilers. You can use the new compiler by specifying gcc-4.9
directly on the command line.

Best regards,
--
Hannes Hauswedell

PhD student
Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Berlin=

address=C2=A0 =C2=A0 =C2=A0Institut f=C3=BCr Informatik
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Takustra=C3=9Fe 9
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Room 019
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 14195 Berlin
telephone=C2=A0 =C2=A0+49 (0)30 838-75241
fax=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0+49 (0)30 838-75218
e-mail=C2=A0 =C2=A0 =C2=A0 hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]

_______________________________________________
seqan-dev mailing list
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--047d7bae494a1f2dad0528c003af-- From bnbowman@gmail.com Thu Jan 21 21:49:50 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1aMMAv-000NQC-WA>; Thu, 21 Jan 2016 21:49:50 +0100 Received: from mail-ob0-f181.google.com ([209.85.214.181]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1aMMAv-001FaA-Qk>; Thu, 21 Jan 2016 21:49:49 +0100 Received: by mail-ob0-f181.google.com with SMTP id is5so45655010obc.0 for ; Thu, 21 Jan 2016 12:49:48 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=KQy2o51eqwL+ohAh00Dp2+CKQ+bByuKV7njA0GOSiDc=; b=BJvv183xmmyRktZq3UmB7xukckrzx0BKoFUxYU9nFrogDamk+2BuP1JWFuR1Z4J9Wf ZEMoQ0yusqp3cq93KAYKbjfzV0n09Q2T38otyPF0utemoAMaIzMiUTEtdqWUe+cWATzK oImA7IZu1fGgOAyHwiQ2CbhudwUna9K4UImRGj5shL6YehxBKX8u8oB+Wdt4fqevZ2cC 4KW5QlyzD2bDJ2VTky3fTtZ2mWQ5Tar2Gg0FiLpP2JgrWPjZwi1Y07PjYVEep1cyR8S9 1ldwT7wIFoGpJM0VqUTt1b+syH3dyjPRz/sVACJ/55flJF1QU1sb68lbh4rgQCV/0MaS OcVA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:date:message-id:subject:from:to :content-type; bh=KQy2o51eqwL+ohAh00Dp2+CKQ+bByuKV7njA0GOSiDc=; b=gPr4Ds0V4FRAA7opWqYjTyntK29eOAvHHd5giaSuOQzGli4UWFv8PZ20ZtSezvdxV9 2Oh2mGtrEz8+28hNwjqhyJii/gz5UAzQA0ErYZ96tggh9jmdnmUQcl/SB1qkUG3rAshZ NjKFW2Yf1n8VU6EDSlVUfX/sH0avsM/1aprO37iQFwIt5eanJpT0WEoICbANMKvRsM7H u+ydODQVOUo8nmbVnqGp+q5eNXygppGR2jQeKwu+IRcoC1lbbSOMXrwcnEnwqH8j+DMj AJgXNrsslduENmnxWn0EzlNpFp1Ns6iFKGrUIJ/BccRTfpdpu2Iuv8jA17/8+yZOGidK l8VQ== X-Gm-Message-State: AG10YOT8YkHScZ9GwRXemqTK9jCrMbfPNGcphggoWXNe2abkpTSytIiZ/UkRR0tYrrfeQ+knuhS4i+CgEC7GBg== MIME-Version: 1.0 X-Received: by 10.60.39.136 with SMTP id p8mr30110104oek.81.1453409387165; Thu, 21 Jan 2016 12:49:47 -0800 (PST) Received: by 10.76.58.212 with HTTP; Thu, 21 Jan 2016 12:49:47 -0800 (PST) Date: Thu, 21 Jan 2016 12:49:47 -0800 Message-ID: From: Brett Bowman To: SeqAn Development Content-Type: multipart/alternative; boundary=089e0160bd103c3ebf0529de3e8f X-Originating-IP: 209.85.214.181 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1453409390-00000D1C-B05E2017/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.359315, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.0 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU, FREEMAIL_FROM, HTML_MESSAGE, RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL,SPF_PASS,UPPERCASE_50_75 X-Spam-Checker-Version: SpamAssassin 3.4.1 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Fatal Crash / Failed Assert in BandedAlignment 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, 21 Jan 2016 20:49:51 -0000 --089e0160bd103c3ebf0529de3e8f Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable I'm using Banded aligner to find potentially low-quality but important spike-in control alignments from single-molecule sequencing data (PacBio, Oxford Nano). When these potential alignments turn out to be junk, bandedAlignment is sometimes either failing on an assert (Debug) or just out-right seg-faulting (Release), instead of getting the expected junk alignment or graceful failure I would expect. As it stands, I've implemented some filters to toss these low-quality seed-chains out before alignment, but it would be preferable if I didn't have to worry about the aligner crashing at all... Sample Error Message: """ /home/UNIXHOME/bbowman/p4/depot/software/smrtanalysis/bioinformatics/third-= party/cpp/seqan-library-2.0.0/include/seqan/seeds/banded_chain_alignment_tr= aceback.h:195 Assertion failed : isGlued =3D=3D true was: 0 !=3D 1 (Fatal error while try= ing to connect trace backs: No glue point available!) """ Sample Test Data/Code: """ #include #include // Type-defs used typedef seqan::Dna TAlphabet; typedef seqan::String TString; typedef seqan::Seed TSeed; typedef seqan::String TSeedChain; typedef seqan::AlignConfig TAlignConfig; typedef seqan::Align TAlign; typedef seqan::Score TScoringScheme; // Variables used const TString query =3D "AAAGAGAGAGAGAGAGAGGGAAAAGAAGGAAAGGGAAAAGGAGAAGGGAGGGAAAAAGAAAGAAAGAAGAAAAG= AGAGGGAAAAGAGGAAGAAGAAAGGGAGGGGAAGAGGAAGAGGGAGAGGAGAGAAGGAGAGGAGGAAGAAAAAAA= AAAGAGAAAAGGGGAGGAGAGGAGAAAGGAAGAAGGGGAAAAGAGGGGAGAGGAAGGAGAAGAGGAAAGAAAAAA= AAGGAGAGAAAGGGAAGGAGAAAAGAGGAAGGAGGAGAGAAGAAAGAAAGAGGAGAAAAGAGAAGGAAAAAGAAA= GGAAGGAGGGAGAGGAGAGAGGAGAAAAGAAAAGGGAAAAGAAAAAGGAAAGAAAAAGAAAGGAAAAAGAAAGAG= AAGAAAAGGAAAAAGAGAAGGGAGGAAAAGAGGAAGAGGAGAAAAAAAAAGGGAGAAAAAAGAGAAAAGGGAGGA= AGAAAAGAAAAAAGGAGGGAGGAGAAAGAAAGAGAAAGAAAGAGGGGAGAAGAAGAGGAAGGAAGGGAGAGAAAG= AGGAAAAAAAGGGAAAGAGGAGAGGAAAGAGGAGAGAAAGAGGAAAGAAGAAAAGAGAAAAAAAAAAAAGAAGAA= GAGAAGAAAAAAAGAAAAAGGGAAAAAGAAGAGGGAAAGGAAAAGAGAAGAGAAAGGGAGAGGAAAAGAGAGAAA= GAGAAAAGAGGAAAAAAAAGAGAGGAAGGAGGAAAAGAAAAAAAGGAA"; const TString ref =3D "AAAGAGAGAGAGAAGGCTGGGCAGGCTATGCACCCTGGTCCAGGTCAAAAGCTGCGGAACCCGCTAGCGGCCAT= CTTGGCCACTAGGGGTCCCGCAGATTCATATTGTCGTCTAGCATGCACAATGCTGCAAACCCAGCTTGCAATGCC= CACAGCAAGCGGCCAATCTTTACGCCACGTTGAATTGTTTATTACCTGTGACTGGCTATGGCTTGCAACGCCACT= CGTAAAACTAGTACTTTGCGGTTAGGGGAAGTAGACAAACCCATTACTCCACTTCCCGGAAGTTCAACTCATTCC= AACACGAAATAAAAGTAAACTCAACACCCCAAGCAGGCTATGTGGGGGGGTGATAGGGGTGGATTCTATTTCCTA= TCCCATCCCCTAGGATCTCAATTAAGTTACTAGCGAGTTAAATGTCTGTAGCGATCCCGTCAGTCCTATCGCGCG= CATCAAGACCTGGTTGGTTGAGCGTGCAGTAGATCATCGATAAGCTGCGAGTTAGGTCATCCCAGACCGCATCTG= GCGCCTAAACGTTCAGTGGTAGCTAAGGCGTCACCTTCGACTGTCTAAAGGCAATATGTCGTCCTTAGCTCCAAG= TCCCTAGCAAGCGTGTCGGGTCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGACCCGACACGCTT= GCTAGGGACTTGGAGCTAAGGACGACATATTGCCTT"; const TScoringScheme scoringScheme =3D TScoringScheme(5, -6, -4, -4, -5, -5= ); const TAlignConfig alignConfig =3D TAlignConfig(); //Seed String of Type: Shift 1 //Seed #1 Seed(1, 1, 13, 13, lower diag =3D 0, upper diag = =3D 0) //Seed #2 Seed(660, 648, 672, 660, lower diag =3D 12, uppe= r diag =3D 12) int main(int argc, char** argv) { // Seed chain TSeedChain chain; seqan::appendValue(chain, TSeed(1, 1, 13)); seqan::appendValue(chain, TSeed(660, 648, 12)); // Alignment TAlign align; seqan::resize(seqan::rows(align), 2); seqan::assignSource(seqan::row(align, 0), query); seqan::assignSource(seqan::row(align, 1), ref); bandedChainAlignment(align, chain, scoringScheme, alignConfig, 15); return 0; } """ Sincerely, Brett --089e0160bd103c3ebf0529de3e8f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I'm using Banded aligner to find potentially low-= quality but important spike-in control alignments from single-molecule sequ= encing data (PacBio, Oxford Nano).=C2=A0 When these potential alignments tu= rn out to be junk, bandedAlignment is sometimes either failing on an assert= (Debug) or just out-right seg-faulting (Release), instead of getting the e= xpected junk alignment or graceful failure I would expect.=C2=A0
=
As it stands, I've implemented some filters to toss= these low-quality seed-chains out before alignment, but it would be prefer= able if I didn't have to worry about the aligner crashing at all...

Sample Error Message:
""&qu= ot;
/home/UNIXHOME/bbowman/p4/depot/software/smrtanalysis/bioinfo= rmatics/third-party/cpp/seqan-library-2.0.0/include/seqan/seeds/banded_chai= n_alignment_traceback.h:195 Assertion failed : isGlued =3D=3D true was: 0 != =3D 1 (Fatal error while trying to connect trace backs: No glue point avail= able!)
"""

Sample Test Da= ta/Code:
"""
#include <seqan/seeds.h&= gt;
#include <seqan/journaled_set/score_biaffine.h>

// Type-defs used
typedef seqan::Dna TAlphabet;=
typedef seqan::String<TAlphabet> TString;
typede= f seqan::Seed<seqan::Simple> TSeed;
typedef seqan::String&l= t;TSeed> TSeedChain;
typedef seqan::AlignConfig<true, true,= true, true> TAlignConfig;
typedef seqan::Align<TString, se= qan::ArrayGaps> TAlign;
typedef seqan::Score<long, seqan::B= iAffine> TScoringScheme;

// Variables used
const TString query =3D "AAAGAGAGAGAGAGAGAGGGAAAAGAAGGAAAGGGAAAA= GGAGAAGGGAGGGAAAAAGAAAGAAAGAAGAAAAGAGAGGGAAAAGAGGAAGAAGAAAGGGAGGGGAAGAGGAAG= AGGGAGAGGAGAGAAGGAGAGGAGGAAGAAAAAAAAAAGAGAAAAGGGGAGGAGAGGAGAAAGGAAGAAGGGGAA= AAGAGGGGAGAGGAAGGAGAAGAGGAAAGAAAAAAAAGGAGAGAAAGGGAAGGAGAAAAGAGGAAGGAGGAGAGA= AGAAAGAAAGAGGAGAAAAGAGAAGGAAAAAGAAAGGAAGGAGGGAGAGGAGAGAGGAGAAAAGAAAAGGGAAAA= GAAAAAGGAAAGAAAAAGAAAGGAAAAAGAAAGAGAAGAAAAGGAAAAAGAGAAGGGAGGAAAAGAGGAAGAGGA= GAAAAAAAAAGGGAGAAAAAAGAGAAAAGGGAGGAAGAAAAGAAAAAAGGAGGGAGGAGAAAGAAAGAGAAAGAA= AGAGGGGAGAAGAAGAGGAAGGAAGGGAGAGAAAGAGGAAAAAAAGGGAAAGAGGAGAGGAAAGAGGAGAGAAAG= AGGAAAGAAGAAAAGAGAAAAAAAAAAAAGAAGAAGAGAAGAAAAAAAGAAAAAGGGAAAAAGAAGAGGGAAAGG= AAAAGAGAAGAGAAAGGGAGAGGAAAAGAGAGAAAGAGAAAAGAGGAAAAAAAAGAGAGGAAGGAGGAAAAGAAA= AAAAGGAA";
const TString ref =C2=A0 =3D "AAAGAGAGAGAGAA= GGCTGGGCAGGCTATGCACCCTGGTCCAGGTCAAAAGCTGCGGAACCCGCTAGCGGCCATCTTGGCCACTAGGGG= TCCCGCAGATTCATATTGTCGTCTAGCATGCACAATGCTGCAAACCCAGCTTGCAATGCCCACAGCAAGCGGCCA= ATCTTTACGCCACGTTGAATTGTTTATTACCTGTGACTGGCTATGGCTTGCAACGCCACTCGTAAAACTAGTACT= TTGCGGTTAGGGGAAGTAGACAAACCCATTACTCCACTTCCCGGAAGTTCAACTCATTCCAACACGAAATAAAAG= TAAACTCAACACCCCAAGCAGGCTATGTGGGGGGGTGATAGGGGTGGATTCTATTTCCTATCCCATCCCCTAGGA= TCTCAATTAAGTTACTAGCGAGTTAAATGTCTGTAGCGATCCCGTCAGTCCTATCGCGCGCATCAAGACCTGGTT= GGTTGAGCGTGCAGTAGATCATCGATAAGCTGCGAGTTAGGTCATCCCAGACCGCATCTGGCGCCTAAACGTTCA= GTGGTAGCTAAGGCGTCACCTTCGACTGTCTAAAGGCAATATGTCGTCCTTAGCTCCAAGTCCCTAGCAAGCGTG= TCGGGTCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGACCCGACACGCTTGCTAGGGACTTGGAG= CTAAGGACGACATATTGCCTT";
const TScoringScheme scoringScheme = =3D TScoringScheme(5, -6, -4, -4, -5, -5);
const TAlignConfig ali= gnConfig =C2=A0 =C2=A0 =3D TAlignConfig();

//Seed = String of Type: Shift 1
//Seed #1 Seed<Simple, TConfig>(1, = 1, 13, 13, lower diag =3D 0, upper diag =3D 0)
//Seed #2 Seed<= Simple, TConfig>(660, 648, 672, 660, lower diag =3D 12, upper diag =3D 1= 2)

int main(int argc, char** argv)
{
=C2=A0 =C2=A0 // Seed chain
=C2=A0 =C2=A0 TSeedChain chain= ;
=C2=A0 =C2=A0 seqan::appendValue(chain, TSeed(1, =C2=A0 =C2=A0 = 1, 13));
=C2=A0 =C2=A0 seqan::appendValue(chain, TSeed(660, 648, = 12));

=C2=A0 =C2=A0 // Alignment
=C2=A0 = =C2=A0 TAlign align;
=C2=A0 =C2=A0 seqan::resize(seqan::rows(alig= n), 2);
=C2=A0 =C2=A0 seqan::assignSource(seqan::row(align, 0), q= uery);
=C2=A0 =C2=A0 seqan::assignSource(seqan::row(align, 1), = =C2=A0 ref);

=C2=A0 =C2=A0 bandedChainAlignment(al= ign, chain, scoringScheme, alignConfig, 15);
=C2=A0 =C2=A0 return= 0;
}
"""

Since= rely,
Brett
--089e0160bd103c3ebf0529de3e8f-- From rene.maerker@fu-berlin.de Fri Jan 22 09:54:57 2016 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1aMXUe-0015ML-MW>; Fri, 22 Jan 2016 09:54:56 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1aMXUe-000GVX-L2>; Fri, 22 Jan 2016 09:54:56 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1aMXUe-0023fg-Df>; Fri, 22 Jan 2016 09:54:56 +0100 Received: from EX03B.campus.fu-berlin.de ([130.133.170.135]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0266.001; Fri, 22 Jan 2016 09:54:55 +0100 From: =?utf-8?B?UmFobiwgUmVuw6k=?= To: SeqAn Development Thread-Topic: [Seqan-dev] Fatal Crash / Failed Assert in BandedAlignment Thread-Index: AQHRVI1NOR+imI154Ui5pIVQXS2dCp8HK0EA Message-ID: <042AA756-E212-4D0A-A874-598E80FD2134@fu-berlin.de> References: In-Reply-To: Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_042AA756E2124D0AA874598E80FD2134fuberlinde_" MIME-Version: 1.0 Date: Fri, 22 Jan 2016 09:54:54 +0100 X-Original-Date: Fri, 22 Jan 2016 08:54:54 +0000 X-Originating-IP: 130.133.170.203 X-Original-X-Originating-IP: [87.77.61.203] X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1453452896-00000D1C-27DEC8D3/0/0 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,HTML_MESSAGE, RP_MATCHES_RCVD X-Spam-Checker-Version: SpamAssassin 3.4.1 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Fatal Crash / Failed Assert in BandedAlignment 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(envelope-from ) id <1aMfjW-001ezO-Cx>; Fri, 22 Jan 2016 18:42:50 +0100 Received: from ironport2.embl.de ([194.94.44.228]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1aMfjW-000Yjo-AY>; Fri, 22 Jan 2016 18:42:50 +0100 X-IronPort-AV: E=Sophos; i="5.22,332,1449529200"; d="scan'208,217"; a="23883090" Received: from lxmail01-vm.embl.de (HELO mail.embl.de) ([10.11.5.101]) by ironport2.embl.de with ESMTP; 22 Jan 2016 18:42:49 +0100 Received: (qmail 28342 invoked by uid 107); 22 Jan 2016 17:42:48 -0000 Received: from unknown (HELO DESKTOPRJUHAET) (10.11.18.176) by lxmail01-vm.embl.de with SMTP; 22 Jan 2016 17:42:48 -0000 From: "Ivan Protsyuk" To: Date: Fri, 22 Jan 2016 18:42:48 +0100 Message-ID: <003901d1553c$4eeb3090$ecc191b0$@embl.de> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_003A_01D15544.B0AFE6B0" X-Mailer: Microsoft Outlook 15.0 Thread-Index: AdFVO2t8DjChi3qSTSStn/IIUrTIuQ== Content-Language: en-us X-Originating-IP: 194.94.44.228 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1453484570-00000D1C-C21DECB2/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.020202, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=HTML_MESSAGE, RCVD_IN_DNSWL_NONE,RP_MATCHES_RCVD X-Spam-Checker-Version: SpamAssassin 3.4.1 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Problem with KNIME "Input Files" node 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: Fri, 22 Jan 2016 17:42:50 -0000 This is a multipart message in MIME format. ------=_NextPart_000_003A_01D15544.B0AFE6B0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi everyone, I'm wondering if it's possible anyhow to use "Input Files" node (from GenericKnimeNodes) with no input files. In my workflow, I use several of nodes of this kind, and the logic of the workflow implies that some input datasets can be empty. However, "Input files" seems to be not usable if I don't select any file. Are there any alternatives to this? My current workaround is giving a stub-file with a predefined name that stands for an empty dataset. However, it's rather non-intuitive for other people when I share workflows with them. Kind regards, Ivan Protsyuk Bioinfomatician EMBL, Heidelberg ------=_NextPart_000_003A_01D15544.B0AFE6B0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi everyone,

 

I'm = wondering if it's possible anyhow to use "Input Files" node = (from GenericKnimeNodes) with no input files. In my workflow, I use = several of nodes of this kind, and the logic of the workflow implies = that some input datasets can be empty. However, "Input files" = seems to be not usable if I don't select any file. Are there any = alternatives to this?

 

My current = workaround is giving a stub-file with a predefined name that stands for = an empty dataset. However, it’s rather non-intuitive for other = people when I share workflows with them.

 

Kind = regards,

Ivan = Protsyuk

 

Bioinfomatician

EMBL, Heidelberg

 

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