These are chat archives for dereneaton/ipyrad

15th
Dec 2018
tle003
@tle003
Dec 15 2018 01:26
@isaacovercast - that fixed the problem immediately. I was under the impression that conda install ipyrad - c ipyrad always installed the latest version. I made it past that step and then got another error with the sra.run function in the Pedicularis jupyter notebook tutorial : "exception in run() - index 29 is out of bounds for axis 0 with size 1". Since I first got the error, I moved everything from my /home directory and created a new, larger instance and now am working out of the /mnt directory as instructed by the support staff for the server I am using. I now am only using 10% of the space available in that directory, so I don't think it is a space issue. However, I tried again and am still getting the same error.
Isaac Overcast
@isaacovercast
Dec 15 2018 03:07
@tle003 did you install all the dependencies? including entrez-direct from bioconda?
Isaac Overcast
@isaacovercast
Dec 15 2018 03:12
conda install ipyrad -c ipyrad
conda install toytree -c eaton-lab
conda install sra-tools -c bioconda
conda install entrez-direct -c bioconda
ipyclient = ipp.Client()
ipyclient.ids
sra = ipa.sratools(accession="SRP021469", workdir="fastqs-Ped")
sra.run(force=True, ipyclient=ipyclient)
[####################] 100%  Downloading fastq files | 0:03:12 |  
13 fastq files downloaded to /home/isaac/tmp/fastqs-Ped
Works for me on a clean install.
tle003
@tle003
Dec 15 2018 12:26
Yes those are the instructions I am following, including installing sra-tools and entrez-direct. It's a new install that I just did last night using the latest version of ipyrad and toytree-0.1.16. In addition, all 20 cores seem to be up and running.
Isaac Overcast
@isaacovercast
Dec 15 2018 18:17
Can you show me the commands you're running and the exact error output?