These are chat archives for dereneaton/ipyrad

5th
Jun 2017
Isaac Overcast
@isaacovercast
Jun 05 2017 00:20
@mav1234 You need to add the -f flag to force overwrite a corrupted .json file. Like this: ipyrad -p params.txt -s 1 -f
@cwessinger Great!
mav1234
@mav1234
Jun 05 2017 01:32
@isaacovercast That's got it running! Thanks!
mav1234
@mav1234
Jun 05 2017 01:52
It seems that I am hitting that error for every step, so I have to run all of them at once with -f... which is fine for the tutorial, but would be a bit annoying for real data. Do you know what might be corrupting the .json file after every run?
mav1234
@mav1234
Jun 05 2017 02:03
Heh! I found what was causing my problem. At some point I had accidentally created an empty file with the same name as the name I gave to the project and had not noticed it until I went poking around closer. If I didn't use -f (and include step 1), then for some reason there was the above JSON error. But once I removed the file, all was fine, and no error. Sorry about all this!
Lily Roberta Lewis
@LilyRobertLewis_twitter
Jun 05 2017 15:20
Good morning, i'm running ipyrad v.0.6.25. and have been getting the following error message: 2017-06-02 17:57:18,989 pid=14982 [assembly.py] ERROR array([ 0.01806668]) is not JSON serializable. Have others encountered this with ipyrad? Thank you for your help!
Also, this error about JSON not being serializable is happening during step 4.
Isaac Overcast
@isaacovercast
Jun 05 2017 15:59
@LilyRobertLewis_twitter Can you run step 4 and include the -d flag to enable debugging and then email me the ipyrad_log.txt file? I'll pm you my email
Lily Roberta Lewis
@LilyRobertLewis_twitter
Jun 05 2017 17:08
thank you @isaacovercast , I just started that, and will send the log file shortly. Before I saw your reply, I had just restarted the run at step 4, and it ran all the way through step 7 to completion, but no loci were recovered between samples. In the outfiles directory, the stats.txt file indicates that all the loci were filtered out by min sample (which is set to 4, and I have 44 samples). The output files for s4 and s5 however, looked fine. I should have the log file in shortly. Thank you for your help
Isaac Overcast
@isaacovercast
Jun 05 2017 17:10
If you can send me the params file and also the _clust_085/s3.txt file that'd be helpful.
Lily Roberta Lewis
@LilyRobertLewis_twitter
Jun 05 2017 17:10
okay, thank you!
Shea Lambert
@SheaML
Jun 05 2017 18:27

Hi guys,
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!

Shea Lambert
@SheaML
Jun 05 2017 18:33
Sorry, conda is now working. I'll try again with the new version.
Shea Lambert
@SheaML
Jun 05 2017 19:07
Still getting the "Object 'ichrom' doesn't exist" after upgrading to 0.6.27 and re-running step 6. Should I re-run from the beginning using the new version? Mapping took quite a long time (2 days 11 hours using 28 cores).
Isaac Overcast
@isaacovercast
Jun 05 2017 19:39
@SheaML You have to re-run from at least step 5, but I would re-run from step 3 because there were a couple changes to reference mapping that you'll probably want.
Shea Lambert
@SheaML
Jun 05 2017 19:41
@isaacovercast Thanks. Does that sound about right for step 3 performance? It's PE ddRAD data, 180 individuals. Also, is there a way to restrict ipyrad to a subset of individuals (other than manually moving files)?
Isaac Overcast
@isaacovercast
Jun 05 2017 19:44
This is what branching is for. You can create a new branch with just a subset of the samples and run just those samples. Here's the example of branching from the documentation: http://ipyrad.readthedocs.io/tutorial_advanced_cli.html?highlight=branching#branching-example
Shea Lambert
@SheaML
Jun 05 2017 19:50
I see - thanks Isaac. I thought I remembered seeing this before -- however, the link to the "advanced tutorial" here (http://ipyrad.readthedocs.io/userguide.html) appears to be broken (leads to introductory tutorial), so I was having trouble finding it!
Isaac Overcast
@isaacovercast
Jun 05 2017 20:20
Oops, i'll fix that, thanks..