These are chat archives for dereneaton/ipyrad

22nd
Nov 2016
draheem
@draheem
Nov 22 2016 13:59
Just switched to ipyrad from pyrad - am working with ipyrad v. 5.3 and have a couple of questions.
1) I ran the introductory single-end rad-seq tutorial and the tutorial with the Eaton + Ree (2013) dataset (ran both tutorials twice with the same parameter settings). All steps ran fine, but the numbers in the final stats output (e.g. number of filtered reads, loci recovered for each sample, distribution of snps across loci etc. ) are similar but not identical to the numbers actually shown in the documentation for the tutorials. Ditto for the content of the output files (e.g. length of concatenation in the phy file differs between my runs and the the documentation). This is to be expected isn't (i.e. results should be approximately the same not precisely the same)?
2) The output files do not include the nexus, .geno and .u.geno files, and the vcf file has the fomat vcf (not vcf.gz). Is there a simple fix for this? E.g. can I list all the different file formats individually in the params file?
Deren Eaton
@dereneaton
Nov 22 2016 18:11
@draheem Hey, those differences just reflect recent changes we've made that have not yet been updated in the tutorial. The geno and nexus outputs will be available in an upcoming release very soon. The vcf output is no longer gzipped. Cheers.
joqb
@joqb
Nov 22 2016 18:48
@dereneaton I also realized that the .allele file disappeared, that was pretty nice to work with polyploids. Any particular reason why it was omitted in ipyrad? Any hope to see it coming back?
I am trying to convert vcf or str into geno format but it doesn't always work and there are things I don't understand. I would expect that str have only 0 1 2 -9 but my file also contains 3. What does 3 code for in .str? Is it for ambiguities, but then why the two lines per individuals?
draheem
@draheem
Nov 22 2016 19:35
@dereneaton Many thanks. Is there any way I can modify the number of threads/cores - the default is set at 24 cores on the server I am using. How would one reduce this number? It would be really handy to be able to change this with each run/step as was possible with the pyrad params file.
Deren Eaton
@dereneaton
Nov 22 2016 19:51
Hi @draheem , you can use the -c argument to the ipyrad command line. For example, ipyrad -p params-test.txt -s 2 -c 20 would use 20 cores to run step 2. Take a look at the -h help screen to see more command line options.
draheem
@draheem
Nov 22 2016 19:57
Cheers @dereneaton . Will do.