#42 trouble with contig coordinates in the backbone file

[Cristina]

Hi everyone,

My 2 inquiries is about the coordinates' correctness and respectively, the genomic code corresponding to intervals in the backbone file:

-- I recently ran progressiveMauve on several CoGe DB inputs and to my surprise I found among the output contigs, genomic regions coded with the character X (times many). Is this due to an error in my param settings? e.g.:

Sb_650296980_650297512|strand|-
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

-- among the output contig coordinates I also get lines like the ones below; I denoe coordinate values as s-small, B-big preceded by the "-" for the strandedness:

WARNING 2015-05-12 15:42:20,252 ++ sequence length of [segment -700243823:-700243822] is -1 in line:
7691835(s) 7691966(B) -85715547 -85715547 0 0 0 0 349474437 349474583 -700243823(-B) -700243822(-s) 0 0
WARNING 2015-05-12 15:42:20,344 ++ sequence length of [segment -775957157:-775957156] is -1 in line:
-111590704(-s) -111590848(-B) 0 0 0 0 0 0 0 0 -775957157(-B) -775957156(-s) 0 0
W

The confusion comes from having in the same run coordinate pairs (-B : -s) and (-s : -B) for independent contigs of the same genomes.

How should I handle this phenomena? (I compare 7 genomes btw)

Thank you very much!

Best,
Cristina