Annotation panel is empty

[AswinSSoman]

Hi,

I have been trying to view some optical mapping data (omd files) in OMViewer (OMTools Version 1.4a) but the annotation panel remains blank.

System info :
Architecture : x86_64
OS : Ubuntu 18.04.3 LTS
java : openjdk version "11.0.11" 2021-04-20
OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.18.04)

Steps performed:

1. Alignment of optical mapping data

java -jar OMTools.jar OMBlastMapper --refmapin file.ref --optmapin file.bnx --optresout file.omd --filtermode 1 --alignmentjoinmode 1 --overlapmergemode 2 --writeunmap false --thread 32

2. Loaded the files in the following order :

• reference : file.ref
• alignment result : file.omd
• annotation : file.gff / file.bed

3. Different file formats tried for annotation:

Bed file (left), GFF version 1 (right)

GFF version 2

4. Visualize in OMViewer

Albeit trying different annotation formats in PCs, the annotation panels stay blank. This issue is observed even in the example dataset Ecoli.gff.

Can you please look into this matter?

Thanks in advance,
Aswin