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

[Chris Dagdigian]

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