From: Florent A. <flo...@gm...> - 2010-07-11 06:17:16
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The command I ran was: AMOScmp -D TGT=contig12.afg -D REF=../quality_trimmed_sequences/BIXY.fna mapping contig12.afg contains a single long target sequence (49kb) while BIXY.fna contains ~16,000 Sanger reference reads (a large fraction but not all of them are expected to map on the target sequence). You are entirely right, I have inverted "target" and "reference" files and I should have run: AMOScmp -D TGT=../quality_trimmed_sequences/BIXY.afg -D REF=contig12.fa mapping Now it works! I thought that the AMOScmp documentation was quite confusing concerning what are the "target" and "reference" sequences. Hence, I changed it in the CVS repository so that future users don't get burnt by this mistake like I did. Thanks for your input Adam, Florent On 10/07/10 05:10, Adam Phillippy wrote: > Hi Florent, > That's strange. Conflict file should look something like this: > > >> gi|89255449|ref|NC_007880.1| >> > ? 1 0 0 2 N.0 Y.32 > S: -5185 -15220 -33404 -40799 -84048 -84990 -118301 -196214 -273479 -286208 > -31 > D: > > - 116 0 0 2 N.33 Y.1 > S: -13283 > D: -5185 -15220 +21842 -33404 -40799 +62800 -84048 -84990 -118301 +154082 > +1751 > > - 947 0 0 2 N.48 Y.10 > S: -24032 -33941 -41264 -66024 -78564 -83967 -86371 -261088 -389302 -603285 > > D: +3335 +21984 -39813 +40310 +46224 +51204 +55802 +62911 +69969 +73111 > +93396 > > ... > > > Where there '>' character indicates the reference sequence being mapped to > and is followed by positions where the read alignment disagree with the > reference. In your file, it looks like just a bunch of read names and > nothing else. How did you invoke the assembler? Is it possible that you > accidentally swapped the reference and read files? > > -Adam > > > > > On Wed, Jul 7, 2010 at 8:10 PM, Florent Angly<flo...@gm...>wrote: > > >> Thanks Adam, that's what my conflict file looks like. >> Florent >> >> >> >> On 08/07/10 00:10, Adam Phillippy wrote: >> >> Hi Florent, >> Can you post the .conflict file, or a portion of it if the whole thing is >> too big? I should be able to tell from that. It's possible it could be a >> trimming problem. >> >> Thanks, >> -Adam >> >> >> >> On Wed, Jul 7, 2010 at 1:05 AM, Florent Angly<flo...@gm...>wrote: >> >> >>> Hi all, >>> >>> I have Sanger sequences that I try to map on a reference consensus >>> sequence assembled using an external assembler. I am using AMOScmp for >>> the mapping I am encountering problems. AMOScmp runs without crashing >>> but the desired output files are empty. >>> >>> The nucmer step of AMOScmp produces>2000 entries in the .delta file. I >>> think that the problem is at the next step, casm-layout, that seem to >>> generate a .conflict file with as many entries as iDelivered-To: flo...@gm... >>> > Received: by 10.229.189.20 with SMTP id dc20cs80706qcb; > Fri, 9 Jul 2010 12:10:31 -0700 (PDT) > Return-Path:<aph...@gm...> > Received-SPF: pass (google.com: domain of aph...@gm... designates 10.42.9.29 as permitted sender) client-ip=10.42.9.29; > Authentication-Results: mr.google.com; spf=pass (google.com: domain of aph...@gm... designates 10.42.9.29 as permitted sender) smtp.mail=aph...@gm...; dkim=pass header.i=aph...@gm... > Received: from mr.google.com ([10.42.9.29]) > by 10.42.9.29 with SMTP id k29mr4297485ick.90.1278702631222 (num_hops = 1); > Fri, 09 Jul 2010 12:10:31 -0700 (PDT) > DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; > d=gmail.com; s=gamma; > h=domainkey-signature:mime-version:received:received:in-reply-to > :references:date:message-id:subject:from:to:cc:content-type; > bh=8RbVW3At3dN0ROX9v5z+pyQaLlfym40RikwXOR0a1pM=; > b=GxinXL54QT6ReGi/8DnWy3e/zhuHDrk/16VKSuDgbPpIGqQrJi93QhfayEVswO0DDg > MKu2qACz/sNpeC1ok2vcqrJCLME8rju5QJF/v4gp9dWCDGtFlMbfyACPuOxkw/unwv2Y > Cy9VWDQ3vxrIRz5bjR8KUOs0zLL3KDXugYsiM= > DomainKey-Signature: a=rsa-sha1; c=nofws; > d=gmail.com; s=gamma; > h=mime-version:in-reply-to:references:date:message-id:subject:from:to > :cc:content-type; > b=apD9fsx1y2iTFk3A+LUk/rkB8NsRdPZcnA7AhXVxRlFLX7oFvYSuUnc+QJ91ytUDXO > yYQ2HJ/KfHxAGP6jiyLsyrdt2MEeywFySXEmSxbv/3jesJLrpsnt7L/0tlXrH7bqEUQi > J8+V/s5pW4pmKhwbaUc9KPIwbw7jWCbmoLjP0= > MIME-Version: 1.0 > Received: by 10.42.9.29 with SMTP id k29mr3324439ick.90.1278702631173; Fri, 09 > Jul 2010 12:10:31 -0700 (PDT) > Received: by 10.231.15.140 with HTTP; Fri, 9 Jul 2010 12:10:31 -0700 (PDT) > In-Reply-To:<4C3...@gm...> > References:<4C3...@gm...> > <AAN...@ma...> > <4C3...@gm...> > Date: Fri, 9 Jul 2010 15:10:31 -0400 > Message-ID:<AAN...@ma...> > Subject: Re: [AMOS-help] AMOScmp and empty output > From: Adam Phillippy<aph...@gm...> > To: Florent Angly<flo...@gm...> > Cc: "amo...@li..."<amo...@li...> > Content-Type: multipart/alternative; boundary=0016e6d279021abfe9048af9282b > > --0016e6d279021abfe9048af9282b > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Florent, > That's strange. Conflict file should look something like this: > > >> gi|89255449|ref|NC_007880.1| >> > ? 1 0 0 2 N.0 Y.32 > S: -5185 -15220 -33404 -40799 -84048 -84990 -118301 -196214 -273479 -286208 > -31 > D: > > - 116 0 0 2 N.33 Y.1 > S: -13283 > D: -5185 -15220 +21842 -33404 -40799 +62800 -84048 -84990 -118301 +154082 > +1751 > > - 947 0 0 2 N.48 Y.10 > S: -24032 -33941 -41264 -66024 -78564 -83967 -86371 -261088 -389302 -603285 > > D: +3335 +21984 -39813 +40310 +46224 +51204 +55802 +62911 +69969 +73111 > +93396 > > ... > > > Where there '>' character indicates the reference sequence being mapped to > and is followed by positions where the read alignment disagree with the > reference. In your file, it looks like just a bunch of read names and > nothing else. How did you invoke the assembler? Is it possible that you > accidentally swapped the reference and read files? > > -Adam > > > > > On Wed, Jul 7, 2010 at 8:10 PM, Florent Angly<flo...@gm...>wrote: > > >> Thanks Adam, that's what my conflict file looks like. >> Florent >> >> >> >> On 08/07/10 00:10, Adam Phillippy wrote: >> >> Hi Florent, >> Can you post the .conflict file, or a portion of it if the whole thing is >> too big? I should be able to tell from that. It's possible it could be a >> trimming problem. >> >> Thanks, >> -Adam >> >> >> >> On Wed, Jul 7, 2010 at 1:05 AM, Florent Angly<flo...@gm...>wrote: >> >> >>> Hi all, >>> >>> I have Sanger sequences that I try to map on a reference consensus >>> sequence assembled using an external assembler. I am using AMOScmp for >>> the mapping I am encountering problems. AMOScmp runs without crashing >>> but the desired output files are empty. >>> >>> The nucmer step of AMOScmp produces>2000 entries in the .delta file. I >>> think that the problem is at the next step, casm-layout, that seem to >>> generate a .conflict file with as many entries as in the .delta file. It >>> also generates a .layout file that is empty. >>> >>> Any idea what is wrong and how to fix it? >>> >>> Thanks, >>> >>> Florent >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.net email is sponsored by Sprint >>> What will you do first with EVO, the first 4G phone? >>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >>> _______________________________________________ >>> AMOS-help mailing list >>> AMO...@li... >>> https://lists.sourceforge.net/lists/listinfo/amos-help >>> >>> >> >> >> > --0016e6d279021abfe9048af9282b > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Hi Florent,<br>That's strange. Conflict file should look something like= > this:<br><br>>gi|89255449|ref|NC_007880.1|<br>?=A0 1=A0=A0=A0 0=A0=A0= > =A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=A0=A0=A0 N.0=A0=A0=A0=A0 Y.32= > =A0=A0=A0<br>=A0S: -5185 -15220 -33404 -40799 -84048 -84990 -118301 -19621= > 4 -273479 -286208 -31<br> > =A0D:<br><br>-=A0 116=A0 0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0 2=A0=A0= > =A0=A0=A0=A0 N.33=A0=A0=A0 Y.1=A0=A0=A0=A0<br>=A0S: -13283<br>=A0D: -5185= > -15220 +21842 -33404 -40799 +62800 -84048 -84990 -118301 +154082 +1751<br>= > <br>-=A0 947=A0 0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=A0=A0=A0= > N.48=A0=A0=A0 Y.10=A0=A0=A0<br>=A0S: -24032 -33941 -41264 -66024 -78564 -= > 83967 -86371 -261088 -389302 -603285<br> > =A0D: +3335 +21984 -39813 +40310 +46224 +51204 +55802 +62911 +69969 +73111 = > +93396<br><br>...<br><br><br>Where there'>' character indicate= > s the reference sequence being mapped to and is followed by positions where= > the read alignment disagree with the reference. In your file, it looks lik= > e just a bunch of read names and nothing else. How did you invoke the assem= > bler? Is it possible that you accidentally swapped the reference and read f= > iles?<br> > <br>-Adam<br><br><br><br><br><div class=3D"gmail_quote">On Wed, Jul 7, 2010= > at 8:10 PM, Florent Angly<span dir=3D"ltr"><<a href=3D"mailto:florent.= > an...@gm...">flo...@gm...</a>></span> wrote:<br><blockquo= > te class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; border-left: 1= > px solid rgb(204, 204, 204); padding-left: 1ex;"> > > > > =20 > > <div bgcolor=3D"#ffffff" text=3D"#000000"> > Thanks Adam, that's what my conflict file looks like.<br><font color=3D= > "#888888"> > Florent</font><div><div></div><div class=3D"h5"><br> > <br> > <br> > On 08/07/10 00:10, Adam Phillippy wrote: > <blockquote type=3D"cite">Hi Florent,<br> > Can you post the .conflict file, or a portion of it if the whole thing > is too big? I should be able to tell from that. It's possible it could > be a trimming problem.<br> > <br> > Thanks,<br> > -Adam<br> > <br> > <br> > <br> > <div class=3D"gmail_quote">On Wed, Jul 7, 2010 at 1:05 AM, Florent > Angly<span dir=3D"ltr"><<a href=3D"mailto:flo...@gm..." targ= > et=3D"_blank">flo...@gm...</a>></span> > wrote:<br> > <blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204= > , 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi > all,<br> > <br> > I have Sanger sequences that I try to map on a reference consensus<br> > sequence assembled using an external assembler. I am using AMOScmp for<br> > the mapping I am encountering problems. AMOScmp runs without crashing<br> > but the desired output files are empty.<br> > <br> > The nucmer step of AMOScmp produces>2000 entries in the .delta > file. I<br> > think that the problem is at the next step, casm-layout, that seem to<br> > generate a .conflict file with as many entries as in the .delta file. It<br= > >> > also generates a .layout file that is empty.<br> > <br> > Any idea what is wrong and how to fix it?<br> > <br> > Thanks,<br> > <br> > Florent<br> > <br> > <br> > <br> > ---------------------------------------------------------------------------= > ---<br> > This SF.net email is sponsored by Sprint<br> > What will you do first with EVO, the first 4G phone?<br> > Visit<a href=3D"http://sprint.com/first" target=3D"_blank">sprint.com/firs= > t</a> -- <a href=3D"http://p.sf.net/sfu/sprint-com-first" target=3D"_blank"= > >> http://p.sf.net/sfu/sprint-com-first</a><br> >> > _______________________________________________<br> > AMOS-help mailing list<br> > <a href=3D"mailto:AMO...@li..." target=3D"_blank">AM= > OS...@li...</a><br> > <a href=3D"https://lists.sourceforge.net/lists/listinfo/amos-help" targ= > et=3D"_blank">https://lists.sourceforge.net/lists/listinfo/amos-help</a><br= > >> > </blockquote> > </div> > <br> > </blockquote> > <br> > </div></div></div> > > </blockquote></div><br> > > --0016e6d279021abfe9048af9282b-- > |