No link data

[SergejN]

Dear authors,

I'm trying to scaffold a huge genome (~32Gbp). We produced about 2 billion valid Hi-C reads. LACHESIS runs through, and generates 14 clusters that totally make sense (judging by contig IDs, because I also have other linkage information available, therefore, I know which contigs might be on the same chromosome. Not all of them, though, but a few is enough for that kind of test). However, at the last stage LACHESIS does not generate any scaffolds and gives me the following error messages

TESTME: /projects/scaffolding/HiC/lachesis/scaffolds_run01/cached_data/group13.CLM
: ChromLinkMatrix::ReadFile <- /projects/scaffolding/HiC/lachesis/scaffolds_run01/cached_data/group13.CLM N contigs = 423
WARNING: ChromLinkMatrix::ReadFile: CLM file '/projects/scaffolding/HiC/lachesis/scaffolds_run01/cached_data/group13.CLM' has multiple contigs but no link data
Loading contig RE lengths for use in normalization <- /projects/scaffolding/HiC/lachesis/scaffolds_run01/cached_data/group13.CLM.RE_sites
MakeTrunkOrder!
MakeFullOrder!

I would be very thankful for any advice

With the test dataset it runs through beautifully and produces a meaningful result. Therefore, I suspect that either something is wrong with my dataset or the program just runs out of memory (huge genome!), but doesn't really report that.
At the end of the day, it manages to report 14 clusters. Therefore, I believe that the HiC data are at least not garbage. But why does it fail to find links? Are there any specific options I must set in the INI file? Does anyone have any experience with scaffolding large genomes?

Thank you!

[zhusheng303]

I have the same problem. My bam are drived from HicExplorer.
Could you give some advices?
Thanks.

[zhusheng303]

I solve the problem. samtools sort -n -o in.n.bam i n.bam