287.6 M reads processed, 0 read-pairs mapped

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) hic_R1R2FullMap

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

Thanks again for the great tool, Solenne

sanger-tol / PretextMap

287.6 M reads processed, 0 read-pairs mapped #7