Error: A link must have two entries - a start and an end

[曾雋恩]

Dear Martin,

I hope this message finds you well.

I am currently using Circos version "0.69-8" (15 Jun 2019) with Perl "5.026003". When attempting to draw a circos plot using the command "circos -conf circos.conf", I encountered an error.

To address this, I checked my link file, "circos.segdup_filter.txt". This file was derived from "circos.segdup.txt" by extracting, deleting, and reordering some links to start from "block_000". Upon review, the file appears to be correctly formatted, with two numbers indicating the start and ending position of each sequence. I'm puzzled about the source of the problem.

I've attached the file for your reference. Your assistance in resolving this issue would be greatly appreciated.

Thank you for your time and consideration.

Best regards,

David Tseng

The error message:

links in "circos.conf":

circos.highlights.txt:

circos.segdup.txt:

circos.segdup_filter.txt:

circos.sequences.txt:

[Martin]

There are two link file formats. The one you're using which is

LINK_ID chr1 start1 end1 [options]

LINK_ID chr2 start2 end2 [options}

and

chr1 start1 end1 chr2 start2 end2 [options]

e.g.

seq1 100 200 seq5 500 700 color=chr1

The error you're seeing is due to -- for some reason -- only one of the ends of a link with a given ID (e.g. block_000) being found. Which is weird, because I see both in the file. 

I suggest that you reformat your file to the single-line format -- it's a lot easier to manage and you don't need to create a unique ID for a link anymore.

If you want me to follow up on the error with the two-line format, email me your data, karyotype and conf files (mar...@bcgsc.ca).

m