These are chat archives for dereneaton/ipyrad

13th
Dec 2018
Jamie Hudson
@Jamie_Bio_twitter
Dec 13 2018 12:50
Hi there, I am running ipyrad 0.7.28 on a HPC cluster and am getting the following error at Step 7 after filtering the loci:
[write_outfiles.py] ERROR error in filter_stacks on chunk 123300: ValueError(zero-size array to reduction operation minimum which has no identity)
2018-12-13 00:08:50,284 pid=4838 [assembly.py] ERROR IPyradWarningExit: error in filter_stacks on chunk 123300: ValueError(zero-size array to reduction operation minimum which has no identity).
I have seen online a similar error with filter_stacks providing an IndexError, but this appears to be when a pop file is being used (I am not including a pop file). As I am new to bioinformatics, I have left the params file with the default parameters for now, and I am analysing gbs data. Has anyone come across this error message before? Apologies if there is a simple solution- Jamie
Isaac Overcast
@isaacovercast
Dec 13 2018 21:11
@Jamie_Bio_twitter Can you rerun step 7 and include the -d flag to generate debug output. Then email me the ipyrad_log.txt file.