These are chat archives for dereneaton/ipyrad
-fflag to force overwrite a corrupted .json file. Like this:
ipyrad -p params.txt -s 1 -f
-dflag to enable debugging and then email me the ipyrad_log.txt file? I'll pm you my email
I'm having a couple of issues. First, when trying to upgrade from 0.6.25 to 0.6.26, my conda install command just hangs, no output (not sure if you can help with that). I'm also getting an error during step 6 "KeyError("Unable to open object (Object 'ichrom' doesn't exist)")". My ipyrad_log.txt is quite large and filled with a lot of "Unable to read from file " errors e.g. "Unable to read from file (/dev/shm/oberonS1_SML142p2-occidentalis_paired_contig_309160:1380-1484-R2)" I'm using a reference genome and have ~180 ddRAD samples, some with very few reads.
Thanks for any help!