From christosmatzoros@gmail.com Sat May 08 20:43:22 2021 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.94) for seqan-dev@lists.fu-berlin.de with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (envelope-from ) id 1lfRv4-002Bg0-8X; Sat, 08 May 2021 20:43:18 +0200 Received: from mail-ej1-f51.google.com ([209.85.218.51]) by relay1.zedat.fu-berlin.de (Exim 4.94) for seqan-dev@lists.fu-berlin.de with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256 (envelope-from ) id 1lfRv4-000461-4W; Sat, 08 May 2021 20:43:18 +0200 Received: by mail-ej1-f51.google.com with SMTP id s20so13044775ejr.9 for ; Sat, 08 May 2021 11:43:01 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=ZA5IwW/zFdtYjZNjXLyk83hSOtSddSZkKESE6Xlc5gU=; b=j2NQNGBZKNAot3o18s/RL4g3Eh3nIzHyi5QSsHKWbdpSLKt9Aj16j6P93J9FEC2QgU OjrB1/yN3EiFA92Yo0XkIDNmtfdB69BNYw7ccroqgTN3vvf9U4hRTnatyuapQn056SqZ PrwH3Zk7RkjJXx9epkwU5hbxjmkeNOh2PA+o1PD3E7+SsrelyNhwPViBrSZgdtkRSMpa mUpR4e5E+HCaJSOzpOq3tyioVPSXBXho6ECoFrkvniYVCY9UpxWTrh+AWmi3qekGPq8B jAjuZUXSMfztQsKPGQxGiKXLlgT3+76F0ef7pkdijYY4K7TkjB/0JoCqCFchbvcX2MWQ 4IUg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=ZA5IwW/zFdtYjZNjXLyk83hSOtSddSZkKESE6Xlc5gU=; b=KhI0gCvMb84RCR3H7yBs3bjjcpE+iS8B3RZOaLOTCfEtMoyR3wQIDpWRyR0NE3p/qX J09QWQgBzQreHZX73mKlfq11+T//NyRIZc3tIOBAZZRjd5EWsI325xM63n2jyrGbR69L 7ksXnGGlrSqU+/JUKoN9mEiu3J3hPELX0MZ/1pOAbXXVtoFSYtYRCewvl0Xk+6fiaq9M BE5WBHRskSNXOk+ASdsuwtM251m/4Q4F+OsNMrByAkM8mauw/1CsC7tSd0bDDYa60p7c Q9QEp99zsZgsqMD8he/sOp+vSqio4quoTVk4qLN32aRLqTw+6DN+QAlGq9uMO90xW7FY zS9g== X-Gm-Message-State: AOAM531WYWiLVRaJAhxYR++QUZ1Mam3WNrJJXi0lX8HTrUi9uSV/Gg3C vtjWvqn0Ucw+nn80czJMil/sMHXVgScHGSA2v7o7Wl6gokcEEg== X-Google-Smtp-Source: ABdhPJx07OBEWGdd3AImK1LqZ0zruUqlX5d+Jl+BMWV+fIfIMP9orC6DJSGOVGwCPAqQVicXflaDRrdpPYeme6XMYnQ= X-Received: by 2002:a17:906:5ad5:: with SMTP id x21mr16967253ejs.422.1620499380638; Sat, 08 May 2021 11:43:00 -0700 (PDT) MIME-Version: 1.0 From: Christos Matzoros Date: Sat, 8 May 2021 20:42:50 +0200 Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary="000000000000f1173805c1d5e9c9" X-Originating-IP: 209.85.218.51 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1620499398-000004C0-BABEBEFA/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.461288, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.2 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_NONE,SPF_PASS, T_FORGED_RELAY_MUA_TO_MX X-Spam-Checker-Version: SpamAssassin 3.4.6 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Mason2 exception error X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.29 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 08 May 2021 18:43:22 -0000 --000000000000f1173805c1d5e9c9 Content-Type: text/plain; charset="UTF-8" Hello, I use mason2 to create paired-end reads as shown bellow: ./mason_simulator -ir /home/chris/Desktop/GRCh38_latest_genomic.fa --num-threads 12 -n 1000000 --illumina-read-length 150 --input-vcf /home/chris/mason_output/variation/hg_out.vcf --out /home/chris/mason_output/simulator_output/pair_end_left_reads.fq --out-right /home/chris/mason_output/simulator_output/pair_end_right_reads.fq and I get the following error: MASON SIMULATOR =============== ____INITIALIZING______________________________________________________________ Opening reference and variants file ... OK Initializing fragment-to-contig distribution ... OK Initializing simulation threads ... OK Opening output file /home/chris/mason_output/simulator_output/pair_end_left_reads.fq ... OK Opening output file /home/chris/mason_output/simulator_output/pair_end_right_reads.fq .../home/osboxes/seqan/include/seqan/basic/basic_exception.h:363 FAILED! (Uncaught exception of type MasonIOException: Could not open right/single-end output file.) stack trace: 0 [0x4c401d] 1 [0x4c96a6] 2 [0x4c96f1] 3 [0x4d4c38] 4 [0x467abf] 5 [0x468312] 6 [0x400b42] 7 [0x53c62b] 8 [0x405f51] Aborted (core dumped) I really don't know where is the problem. Any advice would be very helpful. Thank you, Chris --000000000000f1173805c1d5e9c9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hello, I use mason2 to create paired-e= nd reads as shown bellow:

./mason_simulator -ir /home/chris/D= esktop/GRCh38_latest_genomic.fa --num-threads 12 -n 1000000 --illumina-read= -length 150 --input-vcf /home/chris/mason_output/variation/hg_out.vcf --out= /home/chris/mason_output/simulator_output/pair_end_left_reads.fq --out-rig= ht /home/chris/mason_output/simulator_output/pair_end_right_reads.fq
<= /blockquote>


and I get the following erro= r:


MASON SIMULAT= OR
=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D

____INITIALIZING_____________= _________________________________________________

O= pening reference and variants file ... OK
Initializing fragment-to-contig distribution ... OK
Initializing simulation threads ... O= K
Opening output file /home/= chris/mason_output/simulator_output/pair_end_left_reads.fq ... OK
Opening output file /home/chris/mason= _output/simulator_output/pair_end_right_reads.fq .../home/osboxes/seqan/inc= lude/seqan/basic/basic_exception.h:363 FAILED! =C2=A0(Uncaught exception of= type MasonIOException: Could not open right/single-end output file.)

stack trace:
=C2=A0 0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0[0x4c401d]
= =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0[0x4c96a6]
=C2=A0 = 2 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0[0x4c96f1]
=C2=A0 3 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0= x4d4c38]
=C2=A0 4 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x467abf= ]
=C2=A0 5 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x468312]
=C2=A0 6 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x400b42]
=
=C2=A0 7 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x53c62b]
=C2=A0 8 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x405f51]

Ab= orted (core dumped)


=
I really don't know where is the problem.
Any advice wou= ld be very helpful.=C2=A0

Thank you,
Chr= is

--000000000000f1173805c1d5e9c9-- From marehr@zedat.fu-berlin.de Mon May 10 00:05:14 2021 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.94) for seqan-dev@lists.fu-berlin.de with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (envelope-from ) id 1lfrXy-0005Z0-QT; Mon, 10 May 2021 00:05:11 +0200 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.94) for seqan-dev@lists.fu-berlin.de with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (envelope-from ) id 1lfrXy-0034sx-NW; Mon, 10 May 2021 00:05:10 +0200 Received: from ip5b400097.dynamic.kabel-deutschland.de ([91.64.0.151] helo=[192.168.1.173]) by inpost2.zedat.fu-berlin.de (Exim 4.94) for seqan-dev@lists.fu-berlin.de with esmtpsa (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256 (envelope-from ) id 1lfrXy-002LzX-Ds; Mon, 10 May 2021 00:05:10 +0200 To: seqan-dev@lists.fu-berlin.de References: From: Marcel Ehrhardt Message-ID: <39579658-9159-1a99-0871-53c32088431c@zedat.fu-berlin.de> Date: Mon, 10 May 2021 00:05:10 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.10.1 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------3A4F299C9D23C3A040350BEF" Content-Language: en-US X-Original-Sender: marehr2@zedat.fu-berlin.de X-Originating-IP: 91.64.0.151 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1620597910-000004C8-3AE8A963/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.153790, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE, NICE_REPLY_A X-Spam-Checker-Version: SpamAssassin 3.4.6 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Mason2 exception error X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.29 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 09 May 2021 22:05:15 -0000 This is a multi-part message in MIME format. --------------3A4F299C9D23C3A040350BEF Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hi Christos, this seems like a bug, can you open a bug ticket at https://github.com/seqan/seqan/issues? Could you also provide links to the used files? Thank you! On 5/8/21 8:42 PM, Christos Matzoros wrote: > > Hello, I use mason2 to create paired-end reads as shown bellow: > > ./mason_simulator -ir /home/chris/Desktop/GRCh38_latest_genomic.fa > --num-threads 12 -n 1000000 --illumina-read-length 150 --input-vcf > /home/chris/mason_output/variation/hg_out.vcf --out > /home/chris/mason_output/simulator_output/pair_end_left_reads.fq > --out-right > /home/chris/mason_output/simulator_output/pair_end_right_reads.fq > > > > and I get the following error: > > > MASON SIMULATOR > =============== > > ____INITIALIZING______________________________________________________________ > > Opening reference and variants file ... OK > Initializing fragment-to-contig distribution ... OK > Initializing simulation threads ... OK > Opening output file > /home/chris/mason_output/simulator_output/pair_end_left_reads.fq > ... OK > Opening output file > /home/chris/mason_output/simulator_output/pair_end_right_reads.fq > .../home/osboxes/seqan/include/seqan/basic/basic_exception.h:363 > FAILED!  (Uncaught exception of type MasonIOException: Could not > open right/single-end output file.) > > stack trace: >   0  [0x4c401d] >   1  [0x4c96a6] >   2  [0x4c96f1] >   3  [0x4d4c38] >   4  [0x467abf] >   5  [0x468312] >   6  [0x400b42] >   7  [0x53c62b] >   8  [0x405f51] > > Aborted (core dumped) > > > > I really don't know where is the problem. > Any advice would be very helpful. > > Thank you, > Chris > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --------------3A4F299C9D23C3A040350BEF Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit

Hi Christos,

this seems like a bug, can you open a bug ticket at https://github.com/seqan/seqan/issues?

Could you also provide links to the used files?

Thank you!

On 5/8/21 8:42 PM, Christos Matzoros wrote:

Hello, I use mason2 to create paired-end reads as shown bellow:

./mason_simulator -ir /home/chris/Desktop/GRCh38_latest_genomic.fa --num-threads 12 -n 1000000 --illumina-read-length 150 --input-vcf /home/chris/mason_output/variation/hg_out.vcf --out /home/chris/mason_output/simulator_output/pair_end_left_reads.fq --out-right /home/chris/mason_output/simulator_output/pair_end_right_reads.fq


and I get the following error:


MASON SIMULATOR
===============

____INITIALIZING______________________________________________________________

Opening reference and variants file ... OK
Initializing fragment-to-contig distribution ... OK
Initializing simulation threads ... OK
Opening output file /home/chris/mason_output/simulator_output/pair_end_left_reads.fq ... OK
Opening output file /home/chris/mason_output/simulator_output/pair_end_right_reads.fq .../home/osboxes/seqan/include/seqan/basic/basic_exception.h:363 FAILED!  (Uncaught exception of type MasonIOException: Could not open right/single-end output file.)

stack trace:
  0                      [0x4c401d]
  1                      [0x4c96a6]
  2                      [0x4c96f1]
  3                      [0x4d4c38]
  4                      [0x467abf]
  5                      [0x468312]
  6                      [0x400b42]
  7                      [0x53c62b]
  8                      [0x405f51]

Aborted (core dumped)


I really don't know where is the problem.
Any advice would be very helpful. 

Thank you,
Chris


_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev
--------------3A4F299C9D23C3A040350BEF-- From christosmatzoros@gmail.com Mon May 10 11:39:20 2021 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.94) for seqan-dev@lists.fu-berlin.de with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (envelope-from ) id 1lg2Ng-001FmE-US; Mon, 10 May 2021 11:39:17 +0200 Received: from mail-ed1-f46.google.com ([209.85.208.46]) by relay1.zedat.fu-berlin.de (Exim 4.94) for seqan-dev@lists.fu-berlin.de with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256 (envelope-from ) id 1lg2Ng-000h5N-QY; Mon, 10 May 2021 11:39:16 +0200 Received: by mail-ed1-f46.google.com with SMTP id s6so17901128edu.10 for ; Mon, 10 May 2021 02:38:59 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to; bh=8lAi6U/himWcPo2+C6nwJebBChRXGc0PRXmR8GrfjvU=; b=Pts1cyxEhwO1aHchkxzhbDYCVZrdNNDxVBMs292TFV0S+Q7DOGfQhJnQU2qZhBoRT1 Y5i+4z/UCyqeUb9AbTaCJj8J1E9EHzvfmltnaCpXblE1xQbRtp4s0E3+6Xu4QIp7tSJe rdBT6EiR8440JN2KbL0LooPIpCpopcQ1pC/wGJJT1BHLq3Orn8Vz3QC9RsgpNlT+07Lg hKOLdcuinXZTLQwPrjNNk6XeJ1Qcfbx9o2JroFzjzzQXwJ2C7ymTbKIHoRuVaSFlD6l1 b3vxpyGlUhoPGkFVJjdD9diVavrgu+cenga5ejNktbvjr++Wx3pJeDm7GTlNftAgDn2z Nk3A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=8lAi6U/himWcPo2+C6nwJebBChRXGc0PRXmR8GrfjvU=; b=AJNXQ+oTKDmiSwkfMd4y1w4dYHXWVmRLx5MOel6G06gUyZnxuw2C7FFIEuIuRmvHqJ AZkw/0KXUKrzLM4LS2XxnRXqZdLBONNoK+/JqePiMewyLNupkgJ9syPxEjiR+1iYgLmJ kV2OvRVBJeXdC/mXGHoXrRuGQQHPSXwb9lvA5J5wqVUHW9uh3EsJ2NPP2NegrZvKuSyc 9A3JJ3Dk+vboaeXp2OSK4g7SfxsVmOF+x3b0lygrGXUSmAn3iEEGOgmxyGycW94JD8ed fY9dCACP4Xru2hcQUkHHUdFaxq9RDOBh9IjCMb3FndeORSphB0QbbKR/q1f4YLFeT8jJ jOjA== X-Gm-Message-State: AOAM530rzY4rDMyP+v7VPg8hWqpSR/hS9yXGx0zRrPCkNG7qYHRko/lw Agkl60Twv2ccZEyAf0lns2ytdQItyEviQT0WGlCX2PbLq0M= X-Google-Smtp-Source: ABdhPJwxteczZ3u1iR2MJKE7QzmyZCccpq1VUnQqT/6dpipTAZTibN2qTGDJ6m1ROPDitJYlby+F4+Ba2f8UmkwL5jg= X-Received: by 2002:aa7:c495:: with SMTP id m21mr28203418edq.123.1620639539399; Mon, 10 May 2021 02:38:59 -0700 (PDT) MIME-Version: 1.0 References: <39579658-9159-1a99-0871-53c32088431c@zedat.fu-berlin.de> In-Reply-To: <39579658-9159-1a99-0871-53c32088431c@zedat.fu-berlin.de> From: Christos Matzoros Date: Mon, 10 May 2021 11:38:47 +0200 Message-ID: To: SeqAn Development Content-Type: multipart/alternative; boundary="0000000000000e0d4c05c1f68c29" X-Originating-IP: 209.85.208.46 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1620639556-000004AD-E2823976/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.307789, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.2 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_MSPIKE_H2,SPF_HELO_NONE,SPF_PASS,T_FORGED_RELAY_MUA_TO_MX X-Spam-Checker-Version: SpamAssassin 3.4.6 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Mason2 exception error X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.29 Precedence: list List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 10 May 2021 09:39:20 -0000 --0000000000000e0d4c05c1f68c29 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Thank you Marcel. I just submitted my issue. =CE=A3=CF=84=CE=B9=CF=82 =CE=94=CE=B5=CF=85, 10 =CE=9C=CE=B1=CE=90 2021, 12= :06 =CF=80.=CE=BC. =CE=BF =CF=87=CF=81=CE=AE=CF=83=CF=84=CE=B7=CF=82 Marcel= Ehrhardt < marehr2@zedat.fu-berlin.de> =CE=AD=CE=B3=CF=81=CE=B1=CF=88=CE=B5: > Hi Christos, > > this seems like a bug, can you open a bug ticket at > https://github.com/seqan/seqan/issues? > > Could you also provide links to the used files? > > Thank you! > On 5/8/21 8:42 PM, Christos Matzoros wrote: > > > Hello, I use mason2 to create paired-end reads as shown bellow: > > ./mason_simulator -ir /home/chris/Desktop/GRCh38_latest_genomic.fa > --num-threads 12 -n 1000000 --illumina-read-length 150 --input-vcf > /home/chris/mason_output/variation/hg_out.vcf --out > /home/chris/mason_output/simulator_output/pair_end_left_reads.fq > --out-right > /home/chris/mason_output/simulator_output/pair_end_right_reads.fq > > > > and I get the following error: > > > MASON SIMULATOR > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > > ____INITIALIZING_________________________________________________________= _____ > > Opening reference and variants file ... OK > Initializing fragment-to-contig distribution ... OK > Initializing simulation threads ... OK > Opening output file > /home/chris/mason_output/simulator_output/pair_end_left_reads.fq ... OK > Opening output file > /home/chris/mason_output/simulator_output/pair_end_right_reads.fq > .../home/osboxes/seqan/include/seqan/basic/basic_exception.h:363 FAILED! > (Uncaught exception of type MasonIOException: Could not open > right/single-end output file.) > > stack trace: > 0 [0x4c401d] > 1 [0x4c96a6] > 2 [0x4c96f1] > 3 [0x4d4c38] > 4 [0x467abf] > 5 [0x468312] > 6 [0x400b42] > 7 [0x53c62b] > 8 [0x405f51] > > Aborted (core dumped) > > > > I really don't know where is the problem. > Any advice would be very helpful. > > Thank you, > Chris > > > _______________________________________________ > seqan-dev mailing listseqan-dev@lists.fu-berlin.dehttps://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 > --0000000000000e0d4c05c1f68c29 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thank you Marcel. I just submitted my issue.


=CE=A3=CF=84=CE=B9=CF=82 =CE=94=CE=B5=CF=85, 10 = =CE=9C=CE=B1=CE=90 2021, 12:06 =CF=80.=CE=BC. =CE=BF =CF=87=CF=81=CE=AE=CF= =83=CF=84=CE=B7=CF=82 Marcel Ehrhardt <marehr2@zedat.fu-berlin.de> =CE=AD=CE=B3=CF=81=CE=B1=CF= =88=CE=B5:
=20 =20 =20

Hi Christos,

this seems like a bug, can you open a bug ticket at https://github.com/seqan/seqan/issues?

Could you also provide links to the used files?

Thank you!

On 5/8/21 8:42 PM, Christos Matzoros wrote:
=20

Hello, I use mason2 to create paired-end reads as shown bellow:

./mason_simulator -ir /home/chris/Desktop/GRCh38_latest_genomic.fa --num-threads 12 -n 1000000 --illumina-read-length 150 --input-vcf /home/chris/mason_output/variation/hg_out.vcf --out /home/chris/mason_output/simulator_output/pair_end_left_reads.f= q --out-right /home/chris/mason_output/simulator_output/pair_end_right_reads.= fq


and I get the following error:


MASON SIMULATOR
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D

____INITIALIZING______________= ________________________________________________

Opening reference and variants file ... OK
Initializing fragment-to-contig distribution ... OK
Initializing simulation threads ... OK
Opening output file /home/chris/mason_output/simulator_output/pair_end_left_reads= .fq ... OK
Opening output file /home/chris/mason_output/simulator_output/pair_end_right_read= s.fq .../home/osboxes/seqan/include/seqan/basic/basic_exception.h:363 FAILED! =C2=A0(Uncaught exception of type MasonIOException: Could not open right/single-end output file.)

stack trace:
=C2=A0 0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x4c401d]
=C2=A0 1 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x4c96a6]
=C2=A0 2 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x4c96f1]
=C2=A0 3 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x4d4c38]
=C2=A0 4 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x467abf]
=C2=A0 5 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x468312]
=C2=A0 6 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x400b42]
=C2=A0 7 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x53c62b]
=C2=A0 8 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0[0x405f51]

Aborted (core dumped)


I really don't know where is the problem.
Any advice would be very helpful.=C2=A0

Thank you,
Chris


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