287.6 M reads processed, 0 read-pairs mapped

[scorreard]

Hi team,

Thanks for the great tool!

I get pretext to work, I use it for manual curation, this is great.
However, once I am done with the manual curation and I am trying to re-generate the HiC map with the curated assembly, I run into an issue.

This is the steps I do :

• Map the HiC reads against the curated assembly using chromap. It outputs a bam file, which looks fine.
• Then I run the pretext map command line

samtools \
        view \
        -h \
        hic_R1R2_sorted.bam | PretextMap \
	-o hic_R1R2.pretext

Unfortunately, I get this output in the log :

[PretextMap status] :: Mapping to 218 sequences, sorted by length, descending. Filtering by minimum mapping quality 10
[PretextMap status] :: 287.6 M reads processed, 0  read-pairs mapped            
[PretextMap status] :: Creating MipMaps...
[PretextMap status] :: Equalising contrast...
[PretextMap status] :: Compressing textures...
[PretextMap status] :: 528/528 (100.00%) texture blocks written to disk

and the snapshot is empty. It detects the scaffolds, but does not put any heat map in it (attached)

What do you think? Have you run into the same issue for other bam files?

Thanks again for the great tool,
Solenne