These are chat archives for dereneaton/ipyrad

20th
Dec 2016
danielyao12
@danielyao12
Dec 20 2016 03:58
Hi @dereneaton and @isaacovercast , I encountered a problem today when I run the ipyrad analysis. The error message is following:

ipyrad [v.0.5.13]

Interactive assembly and analysis of RAD-seq data

New Assembly: sy_1220
establishing parallel connection with hosts...
host compute node: [40 cores] on smp02.local

Step 1: Loading sorted fastq data to Samples
[####################] 100% loading reads | 0:00:14
ERROR:ipyrad.core.assembly:IOError(CRC check failed 0xce294bac != 0x16bd63c7L)

Encountered an unexpected error (see ./ipyrad_log.txt)
Error message is below -------------------------------
IOError(CRC check failed 0xce294bac != 0x16bd63c7L)

do you know how should I do to solve this problem?
James Clugston
@Cycadales_twitter
Dec 20 2016 10:18
@dereneaton @isaacovercast Hi guys I have a few questions about getting data from ipyrad into structure and adegenet. I asked a question the structure of the ipyrad structure of ipyrad as I do not understand why we have two rows per samples, as from my understanding a structure file has one row per sample. Any ideas and I am having a problem getting this data to work so far.
MINQICAI
@MINQICAI
Dec 20 2016 12:02
Hi, @James Clugston I think the two rows per sample due to the species is diploid.
Isaac Overcast
@isaacovercast
Dec 20 2016 18:02
@danielyao12 I've seen that problem before, it normally comes from malformed raw data files. Doublecheck that all your fastq files are intact and complete.
James Clugston
@Cycadales_twitter
Dec 20 2016 22:17
@MINQICAI thanks for that it helped loads