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From: Apurv P. <apu...@gm...> - 2009-10-18 22:28:27
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Hi, I've been having some problems using the promer and nucmer options of the mummer program. The following error keeps popping up when I use Promer and Nucmer. Promer ERROR: prepro -r returned non-zero Nucmer ERROR: prenuc -r returned non-zero The scripts in aux_bin seem to not work. I am not sure if it is the query or reference files that keep producing these errors. I am absolutely sure I am using fasta format files. Any help is appreciated. ------------------------------------------------------------ Apurv Puri University of Illinois at Urbana-Champaign Chemical & Biomolecular Engineering apu...@gm... 814 490 7971 |
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From: Bossers, A. <Ale...@wu...> - 2009-10-20 08:38:55
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I am not sure if this is your problem but when I notice non zero errors its usually because I migrate files between unix and windows which use different line-endings. Convert your fasta files to unix format (various ustils but Notepad++ is a free good solution on windows). This usually resolves it for me. Alex From: Apurv Puri [mailto:apu...@gm...] Sent: Monday, October 19, 2009 12:28 AM To: mum...@li... Subject: [MUMmer-help] MUMmer: Promer Nucmer errors Hi, I've been having some problems using the promer and nucmer options of the mummer program. The following error keeps popping up when I use Promer and Nucmer. Promer ERROR: prepro -r returned non-zero Nucmer ERROR: prenuc -r returned non-zero The scripts in aux_bin seem to not work. I am not sure if it is the query or reference files that keep producing these errors. I am absolutely sure I am using fasta format files. Any help is appreciated. ------------------------------------------------------------ Apurv Puri University of Illinois at Urbana-Champaign Chemical & Biomolecular Engineering apu...@gm... 814 490 7971 |
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From: Apurv P. <apu...@gm...> - 2009-10-27 03:32:20
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Alex, I tried the file conversion but still no luck. To make sure, lets say I converted test.fasta to UNIX format. What does the new file name look like? I want to make sure I followed the procedure to the tee. Thanks for your help. ------------------------------------------------------------ Apurv Puri University of Illinois at Urbana-Champaign Chemical & Biomolecular Engineering apu...@gm... 814 490 7971 On Tue, Oct 20, 2009 at 2:07 PM, Bossers, Alex <Ale...@wu...> wrote: > I am not sure if this is your problem but when I notice non zero errors > its usually because I migrate files between unix and windows which use > different line-endings. Convert your fasta files to unix format (various > ustils but Notepad++ is a free good solution on windows). > > This usually resolves it for me. > > Alex > > > > > > *From:* Apurv Puri [mailto:apu...@gm...] > *Sent:* Monday, October 19, 2009 12:28 AM > *To:* mum...@li... > *Subject:* [MUMmer-help] MUMmer: Promer Nucmer errors > > > > Hi, > I've been having some problems using the promer and nucmer options of the > mummer program. The following error keeps popping up when I use Promer and > Nucmer. > > Promer > ERROR: prepro -r returned non-zero > > Nucmer > ERROR: prenuc -r returned non-zero > > The scripts in aux_bin seem to not work. I am not sure if it is the query > or reference files that keep producing these errors. I am absolutely sure I > am using fasta format files. Any help is appreciated. > ------------------------------------------------------------ > Apurv Puri > University of Illinois at Urbana-Champaign > Chemical & Biomolecular Engineering > apu...@gm... > 814 490 7971 > > > |
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From: Adam P. <aph...@gm...> - 2009-10-27 15:31:06
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Hi Apurv, Sorry that didn't work. Another idea, are there any spaces in the system path to the mummer directory? There is a known bug in Nucmer that prevents it from properly handling spaces in either the input file names or the system path of the mummer directory (or any of the parent directories). Best, -Adam On Mon, Oct 26, 2009 at 11:32 PM, Apurv Puri <apu...@gm...> wrote: > Alex, > I tried the file conversion but still no luck. To make sure, lets say I > converted test.fasta to UNIX format. What does the new file name look like? > I want to make sure I followed the procedure to the tee. Thanks for your > help. > > ------------------------------------------------------------ > Apurv Puri > University of Illinois at Urbana-Champaign > Chemical & Biomolecular Engineering > apu...@gm... > 814 490 7971 > > > > On Tue, Oct 20, 2009 at 2:07 PM, Bossers, Alex <Ale...@wu...>wrote: > >> I am not sure if this is your problem but when I notice non zero errors >> its usually because I migrate files between unix and windows which use >> different line-endings. Convert your fasta files to unix format (various >> ustils but Notepad++ is a free good solution on windows). >> >> This usually resolves it for me. >> >> Alex >> >> >> >> >> >> *From:* Apurv Puri [mailto:apu...@gm...] >> *Sent:* Monday, October 19, 2009 12:28 AM >> *To:* mum...@li... >> *Subject:* [MUMmer-help] MUMmer: Promer Nucmer errors >> >> >> >> Hi, >> I've been having some problems using the promer and nucmer options of the >> mummer program. The following error keeps popping up when I use Promer and >> Nucmer. >> >> Promer >> ERROR: prepro -r returned non-zero >> >> Nucmer >> ERROR: prenuc -r returned non-zero >> >> The scripts in aux_bin seem to not work. I am not sure if it is the query >> or reference files that keep producing these errors. I am absolutely sure I >> am using fasta format files. Any help is appreciated. >> ------------------------------------------------------------ >> Apurv Puri >> University of Illinois at Urbana-Champaign >> Chemical & Biomolecular Engineering >> apu...@gm... >> 814 490 7971 >> >> >> > > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > > |
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From: Apurv P. <apu...@gm...> - 2009-10-28 02:46:40
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Hi Adam, what you suggested was precisely my next guess. After looking at some of the sample files, I realized there could be spaces somewhere that would cause this problem. I installed MUMmer this time from the synaptic package manager instead of on my own and then creating symbolic links. So I looked at my files again, the input names have no spaces, only underscores, and the path to the mummer directory has no spaces either. Then I wondered if the spaces within the files themselves could cause this problem. So if a .fasta file looked like this: >Organism name, blah blah blah ACTGCTAGGGTTCGTAAA.... I changed it to look like this: >organism_name ACTACTGCTAGGGTTCGTAAA.... But so far still no luck. The thing that I don't understand is only the prenuc prepro scripts are creating problems. I have used exact-tandems, repeat-match, etc. with no hitches. Maybe this will give you some aha! moments. ------------------------------------------------------------ Apurv Puri University of Illinois at Urbana-Champaign Chemical & Biomolecular Engineering apu...@gm... 814 490 7971 On Tue, Oct 27, 2009 at 9:00 PM, Adam Phillippy <aph...@gm...>wrote: > Hi Apurv, > Sorry that didn't work. Another idea, are there any spaces in the system > path to the mummer directory? There is a known bug in Nucmer that prevents > it from properly handling spaces in either the input file names or the > system path of the mummer directory (or any of the parent directories). > > Best, > -Adam > > On Mon, Oct 26, 2009 at 11:32 PM, Apurv Puri <apu...@gm...> wrote: > >> Alex, >> I tried the file conversion but still no luck. To make sure, lets say I >> converted test.fasta to UNIX format. What does the new file name look like? >> I want to make sure I followed the procedure to the tee. Thanks for your >> help. >> >> ------------------------------------------------------------ >> Apurv Puri >> University of Illinois at Urbana-Champaign >> Chemical & Biomolecular Engineering >> apu...@gm... >> 814 490 7971 >> >> >> >> On Tue, Oct 20, 2009 at 2:07 PM, Bossers, Alex <Ale...@wu...>wrote: >> >>> I am not sure if this is your problem but when I notice non zero errors >>> its usually because I migrate files between unix and windows which use >>> different line-endings. Convert your fasta files to unix format (various >>> ustils but Notepad++ is a free good solution on windows). >>> >>> This usually resolves it for me. >>> >>> Alex >>> >>> >>> >>> >>> >>> *From:* Apurv Puri [mailto:apu...@gm...] >>> *Sent:* Monday, October 19, 2009 12:28 AM >>> *To:* mum...@li... >>> *Subject:* [MUMmer-help] MUMmer: Promer Nucmer errors >>> >>> >>> >>> Hi, >>> I've been having some problems using the promer and nucmer options of the >>> mummer program. The following error keeps popping up when I use Promer and >>> Nucmer. >>> >>> Promer >>> ERROR: prepro -r returned non-zero >>> >>> Nucmer >>> ERROR: prenuc -r returned non-zero >>> >>> The scripts in aux_bin seem to not work. I am not sure if it is the query >>> or reference files that keep producing these errors. I am absolutely sure I >>> am using fasta format files. Any help is appreciated. >>> ------------------------------------------------------------ >>> Apurv Puri >>> University of Illinois at Urbana-Champaign >>> Chemical & Biomolecular Engineering >>> apu...@gm... >>> 814 490 7971 >>> >>> >>> >> >> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! >> http://p.sf.net/sfu/devconference >> _______________________________________________ >> MUMmer-help mailing list >> MUM...@li... >> https://lists.sourceforge.net/lists/listinfo/mummer-help >> >> > |
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From: Adam P. <aph...@gm...> - 2009-10-22 19:38:33
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Hi Apurv, Did you move the mummer directory after building the source? The package has a very basic Makefile, and moving the programs (especially the location of aux_bin) after building the source can cause the pipelines, such as nucmer and promer, to fail. Best, -Adam On Sun, Oct 18, 2009 at 6:28 PM, Apurv Puri <apu...@gm...> wrote: > Hi, > I've been having some problems using the promer and nucmer options of the > mummer program. The following error keeps popping up when I use Promer and > Nucmer. > > Promer > ERROR: prepro -r returned non-zero > > Nucmer > ERROR: prenuc -r returned non-zero > > The scripts in aux_bin seem to not work. I am not sure if it is the query > or reference files that keep producing these errors. I am absolutely sure I > am using fasta format files. Any help is appreciated. > ------------------------------------------------------------ > Apurv Puri > University of Illinois at Urbana-Champaign > Chemical & Biomolecular Engineering > apu...@gm... > 814 490 7971 > > > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > > |
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