Re: [MUMmer-help] MUMmer: Promer Nucmer errors

[Adam P. <aph...@gm...>]

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
>>
>>
>>
>
>
>
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