These are chat archives for dereneaton/ipyrad

17th
Oct 2016
mtcthome
@mtcthome
Oct 17 2016 12:13

Hi there! Not sure how this works yet. I have just finished demultiplexing samples separately per library, but when I try running step two I get Error: Steps >1 (234567) requested but no current assembly found - /Users/Pleurodema/ipyrad/Rhi/raw/c90d8m192. So I tried running step one first, and I'm getting this: ipyrad [v.0.4.4]

Interactive assembly and analysis of RAD-seq data

New Assembly: c90d8m192
local compute node: [4 cores] on pleurodema.rc.unesp.br

Step 1: Loading sorted fastq data to Samples
[####################] 100% loading reads | 0:11:56

Encountered an unexpected error (see ./ipyrad_log.txt)
Error message is below -------------------------------
IOError(CRC check failed 0xa791c986 != 0x94386a38L)

mtcthome
@mtcthome
Oct 17 2016 12:29
Ops, issue solved: ipyrad loaded the fastq and is now filtering reads. I just had to run steps 1 and 2 together (-s12).
Jay Dimond
@jldimond
Oct 17 2016 15:36
Hello,
I am creating a branch with a subset of samples and was wondering which steps need to be run again. In other words, at which step should I start the new branch with the subset of samples? Thanks.
Jay Dimond
@jldimond
Oct 17 2016 15:46
Based on some earlier posts it looks like step 4 is the place to start - let me know if this is not correct. Thanks.
Edgardo M. Ortiz
@edgardomortiz
Oct 17 2016 16:10
It depends on the parameters you want to change in your branch, what are you trying to accomplish?
Jay Dimond
@jldimond
Oct 17 2016 21:16
I don't want to change any parameters, just use a subset of the original samples. I tried doing this and just rerunning step 7, but some of the output files were empty (e.g., .str file).
Edgardo M. Ortiz
@edgardomortiz
Oct 17 2016 21:18
I would do the branching with the subset and then run ipyrad with -f -s67
Jay Dimond
@jldimond
Oct 17 2016 21:37
OK thanks - I was thinking maybe steps 6 and 7 would do it but I did see some earlier posts where others suggested starting from step 4, although maybe these instances involved more changes to the params file. Anything that will avoid another couple days of waiting sounds good to me!
Jay Dimond
@jldimond
Oct 17 2016 22:44
I have another question about .vcf files. I am very interested in read depth per locus per sample. This information appears to be in the the .vcf file output from ipyrad in the form of: ##FORMAT=<ID=CATG,Number=1,Type=String,Description="Base Counts (CATG)">
However, VCF tools apparently cannot sumarize this info. It needs read depth in a format more like this: ##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">
Is there a way I can get ipyrad to give me such a file?
Or does anyone know of a way to summarize the "Base Counts" data?