These are chat archives for dereneaton/ipyrad

May 2018
Anna Page
May 02 2018 14:20
@isaacovercast Yes, I restarted the notebook after updating and then to double check I ran "print ipyrad.__version__"in the notebook and it printed 0.7.23
Jenna Dorey
May 02 2018 19:58

Hi all,

I've been getting the following error message:
"Encountered an unexpected error (see ./ipyrad_log.txt)
Error message is below -------------------------------
writelines() argument must be a sequence of strings"

At first I ignored the error because all of the steps were still working, the only problem was that the stats files (s1, s2, s3, s4, s5, stats files) were only tracking the stats for the first half of my samples. The ipyrad -p params -r command still showed me the summary results for all of my samples, so I knew the steps were working just fine, so I continued without investigating the source of the error. However, when I got to step 7 the error prevented ipyrad from writing any kind of output format other than .loci. All of the filtering during step 7 worked, but I couldn't get ipyrad to write Phylip or Nexus or any other file formats. I finally went searching for the source of the error, and found that one of my sample names has the special character รถ. I find it puzzling that I was able to make it all the way to the end of the analysis pipeline, only to have the last step fail because of a special character that was present since the first step. I have a question and a comment about this.

First: I don't want to restart the analysis if possible. What are all of the files that I need to access to rename that character? If I rename that sample in the raw_fastq, sorted_fastq, edits, consensus, across, and cluster_0.85 folders should that be enough? Do I need to mess with the .json file?

Second: It could be helpful in a future release if ipyrad were to search the names of the raw_fastq.gz and/or sorted_fastq.gz files during step 1 for special characters and then return an error that prevents step 1 from occurring and tells the user to rename the offending file if it finds one.