It gets stuck while running step 0.3 hcr

[wjq1981]

Hello, when I use cphasing 0.3.0 to process Hi-C data, it always gets stuck at the point shown in the figure. Even after running it multiple times, it still hangs there, but locally it shows that the run has already finished. How can I solve this? Thank you!

2026-06-14T02:28:30 [INFO] - Load input.pairs.pqs/_contigsizes
2026-06-14T02:28:50 [INFO] - Calculating the depth of each contig
2026-06-14T02:28:59 [INFO] - Successful output depth file input.10000.depth

[wangyibin]

Hi,

We sincerely apologize for the very late reply.

We have tried to address this issue in the latest version, v0.3.1.r311. Could you please download and install the latest version, then rerun the analysis to see whether the problem is resolved?

If the issue still persists, please share the full log file so we can investigate further.

Best,
Yibin

[wjq1981]

I'll give it a try.