These are chat archives for dereneaton/ipyrad

Nov 2016
Nov 25 2016 11:52

Nice :)
I have a problem with running ipyrad... I keep receiving the message
"Encountered an error, see ./ipyrad_log.txt.
No ipcluster instance found. This may be a problem with your installation
setup. I would recommend that you contact the ipyrad developers."

When struggling with running step1 I read the thread on the google groups, I tried what suggested there (ipcluster start --n 48 --profile=ipyrad --daemonize sleep 60)
but it did not help. I contacted the IT guy responsible for the installations of ipyrad on our servers and he found out that was a problem with the installation so suddenly Step1 started working. Now when trying to run step 2 or 3 I get again exactly the same problem and I don't understand why.

On top of this I also am having problems if I try to run step 3 starting from data that have been already quality filtered and demultiplexed. Even if I refer to the location of the files in the params file argument ## [4] [sorted_fastq_path]: Location of demultiplexed/sorted fastq files, the program crushes saying "no assebly found".

So all in all I can't step forward in either step12 nor in step3...
Any help would be really precious. I am working on European time so there is a time delay in exchanging messages.

Thank you very much already from now!

Nov 25 2016 12:01
Just for clarification: I refer to two independent problems using two independent sets of data - 1) running step123 on raw data from illumina (non demultiplexed and non quality filtered); 2) running step3 starting directly from data that are already demultiplexed and cleaned.
Deren Eaton
Nov 25 2016 17:57
Hi @ViviSette, after step 1 when the data is demultiplexed all following steps 2-7 will work exactly the same whether the data was from the raw_fastq_path or sorted_fastq_path.
@ViviSette do you know what the installation problem was? Did you install ipyrad yourself following the instructions in the documentation? It is recommended that you install ipyrad into your own local home directory, rather than having your IT administrator install it system-wide (assuming you are working on a HPC cluster). This is because when you install it locally you can update it when ever you want, and we are currently producing frequent updates.
@ViviSette For your step 3 problem, it sounds like you may have changed the assembly_name or project_dir parameters in your params file. If you do that then ipyrad will no longer be able to find your Assembly.
Edgardo M. Ortiz
Nov 25 2016 19:16
@ViviSette or maybe you tried starting from step 3 directly, even if your fastqs are demultiplexed and cleaned you have to start from step 1 in ipyrad. That happened to me :)