These are chat archives for dereneaton/ipyrad

8th
Jun 2018
qqsl
@qqsl
Jun 08 2018 11:05
Hello all!
qqsl
@qqsl
Jun 08 2018 11:37

I'm using ipyrad to analyze some 2bRAD data but I'm stuck at the very beginning since I want to do the demultiplexing but I don't know how to set the restriction_overhang parameter correctly. Digestion was made with BsaXI which has this recognition site pattern:
N{12}ACN{5}CTCCN{10} --> 33bp
Reads are adapter free, just 5'insert+barcode3' (33+8=41bp long)
After running step 1, I get plenty of cut_found but barely any bar_matched. Barcodes's file is present and consist of name(TAB)sequence with one barcode per line, as expected.

Any suggestion on how to correctly enter the overhang pattern?

Thanks a lot!
PS: I've read you are after some more 2bRAD testing so I'll be glad to try anything you suggest or provide feedback.

jianlizhao
@jianlizhao
Jun 08 2018 14:22

Hi all,

When the ipyrad is running step 7, errors occurred as follows. ipyrad was executed by a subbranch params file.

Do you have any suggestion to resolve it?

Thank you.
Jianli

ipyrad [v.0.7.24]

Interactive assembly and analysis of RAD-seq data


Begin run: 2018-06-08 00:45

Using args {'preview': False, 'force': True, 'threads': 2, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': None, 'cores': 40, 'p

Platform info: ('Linux', 'service01', '3.10.0-862.2.3.el7.x86_64', '#1 SMP Wed May 9 18:05:47 UTC 2018', 'x86_64')2018-06-08 00:52:04,513

2018-06-08 00:52:04,980 pid=65792 [assembly.py] ERROR IPyradWarningExit: error in filter_stacks on chunk 36894: EngineError(En

2018-06-08 00:52:06,174 pid=65792 [assembly.py] ERROR shutdown warning: [Errno 3] No such process

Isaac Overcast
@isaacovercast
Jun 08 2018 16:27
@jianlizhao The error message is truncated so I can't tell what it actually says. 90% of the time EngineErrors are a result of resource exhaustion, so make sure you have enough RAM allocated (at least 4GB per core).