These are chat archives for dereneaton/ipyrad

May 2018
Francisco Pina-Martins
May 29 2018 09:48 UTC
@isaacovercast Found the problem! I forgot to do the export PYTHONNOUSERSITE=True in the session I was running the analysis.
I have to report that when I do this, I can use a single file, as well as the glob pattern
I will still check, just out of curiosity if the .tar.gz also works
Francisco Pina-Martins
May 29 2018 10:09 UTC
Yes, I can confirm, that using file.tar.gz also works
Katherine Silliman
May 29 2018 15:10 UTC
@isaacovercast Ok played around with it a little, and I'm pretty sure the problem is when you load an Assembly object (where Steps 1-7 had previously been done) from a .json file into a notebook, it does not populate the Assembly with the .stats_dfs.s7_filters info. This kind of makes sense, because whenever I do Assembly.stats, I only ever see the stats through Step 6. Is there another way to read in a saved Assembly where it will still have the Step 7 results, or should I just rerun Step 7 if I have to load an Assembly?
Isaac Overcast
May 29 2018 17:59 UTC
@StuntsPT This is what I suspected. The raw_fastq_path must be a directory. The directory optionally can contain ungzipped fastq files or gzipped fastq files, but it must be a directory that contains these. I think there was a little confusion about what deren had suggested. Is Qsuber.fastq.gz the raw data? If so you can 'mkdir raws' then 'mv Qsuber.fastq.gz raws/Qsuber_R1_.fastq.gz' then use './raws/*.fastq.gz' for this parameter.
Haha, whoa this is weirdly wrong. Must have been a long day yesterday.
@StuntsPT Glad you got it figured out.
Isaac Overcast
May 29 2018 18:08 UTC
@ksil91 Hmm, yeah, that's interesting, i didn't realize it's not saving the more extensive s7 stats. I'll look into it, but yeah for now, re-running step 7 will be the most straightforward get you going. Sorry for the hassle!
@ksil91 #297
May 29 2018 20:47 UTC
Hi. New to Ipyrad. I want to run ipyrad to filter and de novo assembly for SNP's based on paired-end ddRAD sequences. I received demultiplexed samples from the sequencing facility. They ran process_radtags to separate samples based on a barcode file. However, they did not do any filtering. I received a set of fastq files (2 per sample). I want to run ipyrad to filter and de novo assembly for SNP's. This is a new species without a reference genome. My specific questions are: (1) can I start the pipeline at step 2? (2) Should I test for the presence of Ilumina adapters? and if so, how should modify the param file to test for sequence adapters?
Francisco Pina-Martins
May 29 2018 20:56 UTC
@isaacovercast No sweat. I'll be bugging you again soon, when I dig deeper into the reference mapping mode. xD
And of course, thank you for your input. Dev help is always appreciated. =-)