Roger Volden

What about when it gets to the index error? What's the last printed splitLine? Try ```python3 splitLine = line[1:].split('_') if len(splitLine) != 2: print(splitLine) root, seed = splitLine[0], splitLine[1] ```

But what's the header that it prints right before it errors out?

Yeah that's a quality line, something's going wrong with the parser. Can you email me ([email protected]) so I can send you a modified version of C3POa.py? I'm going to add...

It looks like your config file isn't tab delimited, but is delimited with a space instead. I think changing the spaces to tabs will fix your issue.

[configf.txt](https://github.com/rvolden/C3POa/files/2958280/configf.txt) I have added tabs to your file, this should work

Check your blat file to make sure it's executable

Median distance is calculated on a per read basis, so it would be the median of a1 and b1. You would usually set this as the smallest length of your...

Reads without splint sequences are removed during preprocessing. Reads with one splint sequence are usually okay.

If there's one splint sequence, it won't calculate the median distance, but it will try to make it into a zero repeat read. If there's a partial splint sequence, it...

If you try to execute the gonk binary outside of the script, do you get a message telling you to enter sequences?