HiCKRy.py KeyError: '0' about fithic HOT 5 CLOSED

My guess would be that you have some chr-midpoint combinations in your contact count file that are not there in the fragment mappability or a chromosome/contig with all fragments filtered out due to mappability or bias filters. KeyError: '0' suggests you may have an entry with 0 as midpoint or as chr, not sure

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Hi Thanks, Indeed I do have chr entries in the contact counts file that are 0. What could be causing it? Should I just filter it out?

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Filtering is an option but you might want to understand what causes it before doing so.

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I looked at my input pairs file, and there were extraneous lines in the beginning that were not giving information about valid pairs.
I removed those lines and remade the contact counts file. using this and the fragments file, the HiCKRy was running. However, it's still not working and giving me a new message:

Creating sparse matrix...
Sparse matrix creation took 659.9486513137817 seconds
Removing 0.05 percent of most sparse bins
... corresponds to 27310 total rows
... corresponds to all bins with less than or equal to 0.0 total interactions
Killed

I have now idea why it's getting killed. please advise

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oh i realized it's cause the memory was not enough. i increased the memory and the HiCKRy is working now. thanks!

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