These are chat archives for dereneaton/ipyrad
Hello @dereneaton @isaacovercast, I have had multiple runs of ipyrad end with errors in step 6. I was hoping that some changes to my settings and use of new versions of ipyrad would fix it, but the last run failed as well (using v.0.5.9). Perhaps you have some advice?
2016-12-12 20:38:21,255 pid=36133 [cluster_across.py] ERROR error in singlecat (Qw_HPR10M) IOError(Driver write request failed (File write failed: time = mon dec 12 20:38:20 2016
, filename = '/panfs/pfs.acf.ku.edu/scratch/jkarch/cam/ch1/m04c90_consens/qw_hpr10m.tmp.h5', file descriptor = 61, errno = 5, error message = 'input/output error', buf = 0x7fff1b00b910, total write size = 96, bytes this sub-write = 96, bytes actually written = 18446744073709551615, offset = 0))
2016-12-12 20:38:22,104 pid=36133 [assembly.py] ERROR tuple index out of range
Some of my settings:
ipyrad -p params-m04c90.txt -s 67 -c 64
running as pairedgbs, 288 accessions
I saw some advice above about using fewer cores. Am I using way too many? I am unfortunately almost out of space on our cluster and so I can't just try running several different iterations to see what works. Thanks for all your work on ipyrad!
@dereneaton @isaacovercast Hi guys I am wondering if you can help me. I am trying to get some data into the R package Adegenet and I was wondering if can offer me some pointers to some of the questions it asks. I know @isaacovercast mentioned before I am better using the mydata.u.stu rather then mydata.stu. When I bring the file into the package is asks me a number of questions.
How many genotypes are there? (am assuming this is just the number of samples e.g. 74)
Which column contains labels for genotypes ('0' if absent)?
Which column contains the population factor ('0' if absent)?
Which other optional columns should be read (press 'return' when done)?
Which row contains the marker names ('0' if absent)?
Are genotypes coded by a single row (y/n)?
Can you guys offer any advice or anyone? also when are you going to be supporting fineradstrcuture package?