Empty cool and mcool files

[laracolombo]

Empty cool and mcool files

[laracolombo]

Hello, thank you for your replies!
I was able to find out what the issue was: I must have compromised the index file that is needed to compute the cool matrices but not the hic matrix.

[clarabakker]

Hi Lara,
Hm, it's tough to say what is happening. Can you see any logs or output from the singularity command that could help identify the issue?

One particular issue that we've seen is that the chromsizes file needs to exist in the same directory. If you haven't, you can try copying the chromsizes over just before you run that step (as simple as cp /path/to/chrsize_file ./tmpchrsize). You can see slightly more context in our cwl for that step, which I'm guessing you've already seen.

[nvictus]

If you are having issues with the pairix loader, you can also try cload pairs which doesn't require the index file.