Failed to create index

[wu123tj]

hi, thanks for your tools

I got an error as follows when I tried to run a 20G genome :
ERROR Failed to create index of assembly.index. mapper.py:326

what can I do if I run big gonome ?

[wangyibin]

Hi,

Thanks for using C-Phasing.

For a very large genome, this error is likely caused by the Chromap index construction step. If the total length of your input genome is larger than 8 Gb, please try increasing the k-mer and window sizes for the Hi-C mapper:

--hic-mapper-k 27 --hic-mapper-w 14

This should help prevent the "Failed to create index" error from Chromap when running on large genomes.

Alternatively, you can also try using BWA-MEM2 instead of Chromap for Hi-C alignment:

--hic-aligner bwa-mem2

If the issue persists, please provide the complete log file so we can investigate further.

Best,
Yibin