These are chat archives for dereneaton/ipyrad

2nd
Jan 2019
tle003
@tle003
Jan 02 20:07
Hi - I have been trying to run analyze my own data with Tetrad, but am getting a similar error when I do the tet(run) command to which I had been getting using the practice data:
inferring 3321960 quartet tree sets
host compute node: [20 cores] on practice2
[####################] 100% generating q-sets | 0:00:07 |
[ ] 0% initial tree | 0:00:39 |
Unknown exception encountered: EngineError(Engine 'dc7457d1-2e1662c82011331d0b5a312a' died while running task u'e01a6187-785d59ab8c99ee95f152ef93')
warning: error during shutdown:
[Errno 3] No such process
After reading the online links that you have provided on your additional help page, I added the following to my .bash in my home directory: ## sudo nano .bashrc
export QT_QPA_PLATFORM=offscreen
I continue to get the same EngineError message though. I know that the .bashrc file is located and to be altered from your home directory, but I am running the analyses from my /mnt directory. I am not sure if that will make a difference.
tle003
@tle003
Jan 02 20:13
Regarding the sra error that I had earlier. I did as suggested above and installed conda install -c bioconda perl-net-ssleay; however, I still get the same error as I did before. My work around was to download the files manually, which, for the most part, did the job.
LinaValencia85
@LinaValencia85
Jan 02 22:37
Hi, I am trying to run s67 and for some reason in s6 ipyrad stops (with no apparent error) in the indexing step. Nonetheless an output files folder is created and a stats file as well as .loci, .alleles.loci and .hdf5 files are created. However, none of the other output files are created. I tried then running s7 only and get the following error "ImportError: libhdf5.so.10: cannot open shared object file: No such file or directory". I am currently running it in a cluster using -c 1 -t 1. NOt sure if there is a memory error.