These are chat archives for dereneaton/ipyrad

20th
Feb 2017
Bohao Fang
@fangbohao_twitter
Feb 20 2017 14:36
@isaacovercast Now have run all step 1-7 by using old version iPyrad. If I want to know the CHR/POS infomation, which step should I restart (setting a branch)?
Should I restart form the scratch?
Thank you!
Bohao Fang
@fangbohao_twitter
Feb 20 2017 14:45
Restarting from the ZERO hurts ☺
Deren Eaton
@dereneaton
Feb 20 2017 15:05
Hi @fangbohao_twitter, it depends how hold your version was. If you were using 0.5+ then you should only have to rerun steps 6 and 7.
Bohao Fang
@fangbohao_twitter
Feb 20 2017 15:33
@dereneaton OK thanks!
vieves
@vieves
Feb 20 2017 19:59

@dereneaton @isaacovercast I have been running into a problem with step 7 of the assembly. At first, ipyrad was getting stuck on the vcf file, because of the input array dimensions that other people had mentioned on this feed. Step 7: Filter and write output files for 93 Samples
[####################] 100% filtering loci | 0:01:03
[####################] 100% building loci/stats | 0:00:24
[####################] 100% building vcf file | 0:04:00

Encountered an error, see ./ipyrad_log.txt.
error in vcf build chunk 54275: ValueError(all the input arrays must have same number of dimensions)

And I saw you mentioned that version 0.5.15 should fix that
I updated to version 0.6.4-1, and tried to run step 7 agian. Now I get this error.

Step 7: Filter and write output files for 93 Samples
ERROR:ipyrad.core.assembly:'A'

Encountered an unexpected error (see ./ipyrad_log.txt)
Error message is below -------------------------------
'A'

Alexander McKelvy
@SnakeEvolution_twitter
Feb 20 2017 21:19
@isaacovercast thanks! and tell her hi back! With the update, so far I'm unable to replicate the problem
Deren Eaton
@dereneaton
Feb 20 2017 21:20
@vieves @isaacovercast We're trying our best to maintain backwards compatibility between versions while also adding lots of improvements and new features. I think in this case that the new version is incompatible with your step6 state. I would recommend running it from step 6 again with the force flag. If that doesn't fix it, let us know and we can take a look at your JSON file and maybe figure it out.