From eik.dahms@gmail.com Thu Nov 05 13:18:10 2015 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 <1ZuJUX-000vIi-G2>; Thu, 05 Nov 2015 13:18:09 +0100 Received: from mail-ob0-f178.google.com ([209.85.214.178]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1ZuJUX-004A4p-AH>; Thu, 05 Nov 2015 13:18:09 +0100 Received: by obbww6 with SMTP id ww6so37984791obb.0 for ; Thu, 05 Nov 2015 04:18:06 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :content-type; bh=fswTQu9DPY9mbInu3EGZYaNY4VOZjMkuoWUORl9fYJU=; b=mNZOQtGx1By0SN5ECBH2jJFSKFgpQ6Bjfds3WElf9mqzstlq+byiBU+IcjF/vtuIxJ t7jywDnasF05EbiNz85l6G3QR1TD+Ote2d3zi0slOghYnE328KiNG0P02+HTHtaLCIAM dRRGw05Gi43Iahy69V4DQtala3cNodkcxUTfzz9bASgamM+uT2W8Da9Q1lNHheaw9o5O z56qbYNjXG3BGOKK7/4umGlZmcH4aid2glGxNZWKk30FSBcqFUSsoGTXOzVv2QkxvdyS 5qjLxlcUTJ8rya/5lHB1FnzcMFIbCl6scipZ3coSL9IHshlZq6L8JamXLXUK2eO+NOSO NxbA== X-Received: by 10.60.155.33 with SMTP id vt1mr4444865oeb.27.1446725886542; Thu, 05 Nov 2015 04:18:06 -0800 (PST) MIME-Version: 1.0 References: <56336749.1080604@ed.univ-lille1.fr> In-Reply-To: <56336749.1080604@ed.univ-lille1.fr> From: Eik Dahms Date: Thu, 05 Nov 2015 12:17:57 +0000 Message-ID: To: Christophe VROLAND , SeqAn Development Content-Type: multipart/alternative; boundary=047d7bd6b1648e1aff0523ca1e6d X-Originating-IP: 209.85.214.178 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1446725889-00000D05-785A83F8/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, 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] bug report readSequence() 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, 05 Nov 2015 12:18:10 -0000 --047d7bd6b1648e1aff0523ca1e6d Content-Type: text/plain; charset=UTF-8 Hello, my sequence alphabet uses strictly "ACTG". This seems not to be causing this allocation error. Also it shouldn't work on any system then. Cordially Eik Dahms Christophe VROLAND schrieb am Fr., 30. Okt. 2015 um 13:49 Uhr: > On 30/10/2015 13:21, Eik Dahms wrote: > > Dear all, > > i recently upgraded sequan from 1.4.0 to 2.0.0. I did not change my code. > > When i now try to run the program i get the following allocation error > when i try to read a sequence via readSequence() from a FaiIndex: > > /seqan/basic/basic_exception.h:368 FAILED! (Uncaught exception of type > std::bad_alloc: std::bad_alloc) > > This error occurs only on my laptop with 4GB RAM. When i run the program > on a Server with 500GB RAM - it works. > > It seems that the memory that is allocated, for the string that the > sequence is read in, is to high. > > I appended the stacktrace from gnu debugger. > > Thanks in advance ! > Eik > > > > > _______________________________________________ > seqan-dev mailing listseqan-dev@lists.fu-berlin.dehttps://lists.fu-berlin.de/listinfo/seqan-dev > > Hello, > I have ever got this problem when my sequence alphabet used in the code > doesn't include all the alphabet of the sequence I try to read. > You use a Dna5 alphabet, maybe, there's an other letter than "ACGTN" in > your sequence (a "X" ?). > > Cordially > > > -- > Christophe VROLAND > > --047d7bd6b1648e1aff0523ca1e6d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello,
my sequence alphabet uses strictly "ACTG&q= uot;. This seems not to be causing this allocation error. Also it shouldn&#= 39;t work on any system then.

Cordially
Eik Dahms

Christophe VROLAND &= lt;christophe.vrola= nd@ed.univ-lille1.fr> schrieb am Fr., 30. Okt. 2015 um 13:49=C2=A0Uh= r:
On 30/10/2015 13:21, Eik Dahms wrote:
Dear all,

i recently upgraded sequan from 1.4.0 to 2.0.0. I did not change my code.=C2=A0

When i now try to run the program =C2=A0i get the following allocation error when i try to read a sequence via readSequence() from a FaiIndex:

/seqan/basic/basic_exception.h:368 FAILED! =C2=A0(Uncaught exception of type std::bad_alloc: std::bad_alloc)

This error occurs only on my laptop with 4GB RAM. When i run the program on a Server with 500GB RAM - it works.

It seems that the memory that is allocated, for the string that the sequence is read in, is to high.

I appended the stacktrace from gnu debugger. =C2=A0

Thanks in advance !
Eik




______________=
_________________________________
seqan-dev mailing list
seqan-dev=
@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev
Hello,
I have ever got this problem when my sequence alphabet used in the code doesn't include all the alphabet of the sequence I try to read= .
You use a Dna5 alphabet, maybe, there's an other letter than "= ACGTN" in your sequence (a "X" ?).

Cordially


--=20
Christophe VROLAND
--047d7bd6b1648e1aff0523ca1e6d-- From Enrico.Siragusa@fu-berlin.de Thu Nov 05 14:06:57 2015 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 <1ZuKFl-000zfd-Av>; Thu, 05 Nov 2015 14:06:57 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) with esmtp (envelope-from ) id <1ZuKFl-001UB8-8c>; Thu, 05 Nov 2015 14:06:57 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.85) with esmtps (envelope-from ) id <1ZuKFk-000307-UL>; Thu, 05 Nov 2015 14:06:57 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0248.002; Thu, 5 Nov 2015 14:04:06 +0100 From: "Siragusa, Enrico" To: SeqAn Development Thread-Topic: [Seqan-dev] bug report readSequence() Thread-Index: AQHREw2PuYZJb9zNBkWmw3ntWNQpt56NYh5J///7vwA= Message-ID: <021F074D-9DEE-4117-99F5-43508015D54F@fu-berlin.de> References: <56336749.1080604@ed.univ-lille1.fr> In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-ID: <76FF73F374773B42A59F9A272941E827@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Thu, 05 Nov 2015 14:04:05 +0100 X-Original-Date: Thu, 5 Nov 2015 13:04:05 +0000 X-Originating-IP: 130.133.170.203 X-Original-X-Originating-IP: [160.45.43.67] X-ZEDAT-Hint: X X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1446728817-00000D05-B9BB714A/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, T_RP_MATCHES_RCVD X-Spam-Checker-Version: SpamAssassin 3.4.1 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] bug report readSequence() 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, 05 Nov 2015 13:06:57 -0000 Hello, Could you please create a GitHub issue (https://github.com/seqan/seqan/issu= es/new) including a small example to reproduce your problem? Thanks, Enrico On 05 Nov 2015, at 13:17, Eik Dahms wrote: > Hello, > my sequence alphabet uses strictly "ACTG". This seems not to be causing t= his allocation error. Also it shouldn't work on any system then. >=20 > Cordially > Eik Dahms >=20 > Christophe VROLAND schrieb am Fr.,= 30. Okt. 2015 um 13:49 Uhr: > On 30/10/2015 13:21, Eik Dahms wrote: >> Dear all, >>=20 >> i recently upgraded sequan from 1.4.0 to 2.0.0. I did not change my code= .=20 >>=20 >> When i now try to run the program i get the following allocation error = when i try to read a sequence via readSequence() from a FaiIndex: >>=20 >> /seqan/basic/basic_exception.h:368 FAILED! (Uncaught exception of type = std::bad_alloc: std::bad_alloc) >>=20 >> This error occurs only on my laptop with 4GB RAM. When i run the program= on a Server with 500GB RAM - it works. >>=20 >> It seems that the memory that is allocated, for the string that the sequ= ence is read in, is to high. >>=20 >> I appended the stacktrace from gnu debugger. =20 >>=20 >> Thanks in advance ! >> Eik >>=20 >>=20 >>=20 >>=20 >> _______________________________________________ >> seqan-dev mailing list >>=20 >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > Hello, > I have ever got this problem when my sequence alphabet used in the code d= oesn't include all the alphabet of the sequence I try to read. > You use a Dna5 alphabet, maybe, there's an other letter than "ACGTN" in y= our sequence (a "X" ?). >=20 > Cordially >=20 >=20 > --=20 > Christophe VROLAND >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev