These are chat archives for dereneaton/ipyrad

23rd
May 2016
Isaac Overcast
@isaacovercast
May 23 2016 15:28
@roneytan Got it. Thanks ron. I'll check it out.
roneytan
@roneytan
May 23 2016 16:54
@isaacovercast Hi Isaac, I actually just got dinged with the same error using a param file without the modified phredq. I'm not sure what's happening. Some runs are working, and some are returning the "[assembly.py] ERROR sequence item 0: expected string, Sample found" error.
The run is hanging on "aligning". It reads 100% complete, but does not move on to "concatenating" right away, although there are still python processes running and using CPUs
When it fails and quits out, it looks like "concatenating" was going on for a while, although it never showed that it was actually doing it.
Deren Eaton
@dereneaton
May 23 2016 17:16
It looks like it is failing when trying to print the errors, and so it's not printing the actual error. Also, the appearance of hanging between progressbars may sometimes just be that we haven't fully refined the progress tracking. Those intermediate times should be very short tho.
Isaac Overcast
@isaacovercast
May 23 2016 17:59
@roneytan Mm, it's good to know it's not the phredq score, that would have been weird, but it's bad that it happens intermittently... I'm looking at it now.
Isaac Overcast
@isaacovercast
May 23 2016 18:21
Ok, i realized that the code to handle the error properly was in my local repo, so i pushed it up and created new mac and linux conda installs for v 0.2.9
I think Deren is right, in that it was crashing on error reporting, but not actually showing us the real error, so 0.2.9 will fix a problem, but not the problem, i'm betting. I'm still testing on yr data tho.