The running time of searching unique sequence for potentially allelic read pairs

[xiaolon...@gmail.com]

Hi, Mike:

I running the AfteRAD.pl on the Server for 18 individuals. The paramter was 'perl AftrRAD.PY re-TGCAG maxProcesses-10 dplexedData-1'. In the step of  searching unique sequence for potentially allelic read pairs likely running very slow. After running three days, the software likely only finished about 1/20 search (below fig). Where is wrong or this phenomenon is normal?

Thank you~

[Mike Sovic]

Hi,

This is probably normal.  The good news is that this step will speed up somewhat as it runs - especially as it gets toward the end it will likely get much faster.  This is one part of the program that I haven't written to run in parallel yet - still trying to come up with a good way to do that.  This length of this step is dependent almost entirely on the number of loci in the dataset (actually, the number of unique reads, but that is likely related to the number of loci), and probably won't be affected much by the number of samples.  The only thing I can suggest at this point is to make sure you have a working version of ACANA and it's associated dnaMatrix file in the directory.  This is one of the next steps in the script, and I've made the mistake of copying a Linux version of ACANA onto my Mac or vice-versa, and then having the program crash at that step.  This type of thing would be very unfortunate when you have such a long analysis, so just worth a double check. 

A couple of other possible issues/explanations for this step being very long...
1.) There is a lot of error in the sequencing.  Any error reads that pass through the initial quality filtering will be treated as unique reads and analyzed.
2.) Having reads of different lengths.  Two reads from the same allele that have different lengths (likely from different sequencing runs) will be treated as unique reads.

Good luck!

            Mike