[EMBOSS] emboss 2.10 'marscan' now silently fails on Mac OS X 10.4

[Marc Logghe]

Hi Chris,
Do you see any particularities when you compare the working sequence
with the non working ones in debug mode ?
Cheers,
Marc


> Thanks for all the advice but I've still got marscan failing 
> silently on me with Emboss 2.10 on OS X.
> 
> The given EMBOSS test sequence hsbhh.fasta works perfectly fine.
> 
> My other test case containing sequence given to me still 
> generates zero size output files with no content.
> 
> The 'failing' input is a normal fasta-formatted DNA sequence 
> roughly 2000 bp with no special or odd characters or alphabet members.
> 
> So far all file twiddling efforts via BBedit and emacs have had no
> effect:
> 
>   - changing from upper to lower case
>   - adding/removing the fasta naming line
>   - adding/removing line breaks
>   - changing line wrapping from 0 to 72 and 50 chars
>   - DOS linebreaks
>   - Unix linebreaks
>   - Mac linebreaks
>   - Windows Latin 1 encoding
>   - Mac Roman encoding
> 
> I'm stumped. Either something really simple is wrong with my 
> query or perhaps marscan is just not writing any output if it 
> does not find anything?
> 
> I'm going to see if its OK to post the query sequence in this forum.
> 
> Regards,
> Chris
> 
> 
> 
> 
> On Jan 19, 2006, at 7:05 AM, pmr at ebi.ac.uk wrote:
> 
> > Alan writes,
> >
> >> There used to be a problem with the old Mac end-of-line characters 
> >> but I believe that was solved before 2.10.0. It may be 
> worth checking 
> >> precisely what format your fasta file is in though: EMBOSS 
> has always 
> >> been OK with just standard UNIX <LF> terminators.
> >
> > Yup, that would be something that could cause an empty 
> sequence - if 
> > EMBOSS fails to find some kind of end-of-line character then the 
> > seqeunce becomes just part of the description in FASTA format.
> >
> > Does editing the input file make a difference?
> >
> > Does seqret like the same input sequence?
> >
> > Hope that helps,
> >
> > Peter
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at emboss.open-bio.org
> http://newportal.open-bio.org/mailman/listinfo/emboss
>