These are chat archives for dereneaton/ipyrad

Apr 2018
Apr 10 2018 01:50
@isaacovercast Thanks! I tried vdb-config -p that seems print out configuration information about softwares under my account . I also tried to call some commands in the sratools without its full path and got right response, which means the sratolls folder has been in my default path file. Then, I check the sratools installed under anaconda again and ensured that sratools has been there in the conda list. Is it possible because of the file system of the hpc cluster I used? Like my last problem about hdf5 error. The sratools worked right in my local computer with bio-linux system but it will cost a lot of time because my computer isn't as powerful as the public hpc cluster in my institute.
Isaac Overcast
Apr 10 2018 15:34
@danielyao12 It really feels like an issue with the cluster (like the hdf5 error) , often times the environment on the head node can be quite different from the environment on the compute nodes. Can you verify sratools works right on the compute nodes? You can test this by submitting an interactive job and then testing sratools at the command line on the compute nodes.
Amanda Haponski
Apr 10 2018 17:08
Hi @dereneaton and @isaacovercast, I have what I hope is a quick and easy question. I am doing paired end ddRAD and using EcoRI (rare) and MspI (common) as my two enzymes. For parameter 8 I should enter AATTC, CGG? Thanks in advance!!
Isaac Overcast
Apr 10 2018 18:36
@ahaponski_twitter Yep, that's right.