These are chat archives for dereneaton/ipyrad

6th
Nov 2017
Wind-ant
@Wind-ant
Nov 06 2017 14:32
Hello everyone,I want to do the D-test,however,when I input "import ipyrad.analysis as ipa" and "import toytree" as the tutorial put into the ipython terminal,the terminal return "Could not find a version that satisfies the requirement ipyrad.analysis (from versions: ) No matching distribution found for ipyrad.analysis". I don't know how to fix it,any ideas about it?
Akanksha Pandey
@aakanksha12
Nov 06 2017 17:09
Hello, I'm currently running a ddRAD assembly. It works till step 2 and then I'm getting this error in step 3. Here are the last two lines from the ipyrad.log
Platform info: ('Linux', 'c28a-s36.ufhpc', '2.6.32-642.6.2.el6.x86_64', '#1 SMP Mon Oct 24 10:22:33 EDT 2016', 'x86_64')2017-11-04 12:36:31,396 pid=31773 [assembly.py] ERROR IndexError(list index out of range)
2017-11-04 12:36:32,648 pid=31773 [assembly.py] ERROR shutdown warning: [Errno 3] No such process
Can anyone suggest what is going wrong ? @isaacovercast @dereneaton
JStarrett
@JStarrett
Nov 06 2017 17:46
@isaacovercast The source of the error (2017-11-02 10:22:08,736 pid=9857 [rawedit.py] ERROR error in run_cutadapt(): AttributeError('NoneType' object has no attribute 'replace') is that in the json file after step 1 both barcodes are not read when I use sorted fastqs, only the first barcode is read in the barcode list: "barcodes":{
"MY4221":"CTGCAACT", and for each sample the barcode reads null: "name":"MY4221",
"barcode":null, I manually added the correct barcode pair and was able to successfully run step2. This problem did not occur when ipyrad was used to demulitplex, only when sorted fastqs were used. I'm using v.0.7.17.
Isaac Overcast
@isaacovercast
Nov 06 2017 18:21
@JStarrett Yeah, that's exactly what I figured. When i implemented the 3rad pipeline I forgot to account for this case. I made a ticket to fix this #280.
@aakanksha12 Can you rerun ipyrad and include the -d flag? This will put more verbose debugging to the ipyrad_log.txt file.