These are chat archives for dereneaton/ipyrad

19th
Jan 2018
markusruhsam
@markusruhsam
Jan 19 2018 08:44

@dereneaton @isaacovercast Hello, I run into the following error during step 7 (command used ipyrad -p params-Araucaria_min3.txt -s 7 -c 35 --MPI). Any ideas what the problem is? Thank you!
ipyrad [v.0.7.17]

Interactive assembly and analysis of RAD-seq data

loading Assembly: Araucaria_min3
from saved path: /mirror/5tb/markus/Araucaria/Araucaria_min3.json
establishing parallel connection:
host compute node: [5 cores] on hpc5
host compute node: [5 cores] on hpc4
host compute node: [5 cores] on hpc6
host compute node: [5 cores] on hpc1
host compute node: [5 cores] on hpc0
host compute node: [5 cores] on hpc3
host compute node: [5 cores] on hpc2

Step 7: Filter and write output files for 41 Samples

[####################] 100% filtering loci | 0:00:58
[####################] 100% building loci/stats | 0:00:49
[####################] 100% building vcf file | 0:00:48
[####################] 100% writing vcf file | 0:00:00
ERROR:ipyrad.core.assembly:All chunk dimensions must be positive (All chunk dimensions must be positive)
ERROR:ipyrad.core.assembly:shutdown warning: [Errno 3] No such process

Encountered an unexpected error (see ./ipyrad_log.txt)
Error message is below -------------------------------
All chunk dimensions must be positive (All chunk dimensions must be positive)
warning: error during shutdown:
[Errno 3] No such process

Isaac Overcast
@isaacovercast
Jan 19 2018 17:23
@markusruhsam Mmm, it's hard to say exactly without seeing the data, but it could be something goofy is happening during the vcf creation preprocessing step. This error is coming from hdf5, and it's coming from inside one of the parallel threads. If I had to guess I'd say the large number of parallel cores with respect to the number of samples is causing the chunking process to try to pull a slice of data with some dimension equal to 0. You might try reducing the number of cores you're running, just try with 5 cores on one node, and see how that goes. This is just a guess.