I am trying to use the fragment insertion plugin with Silva132 as a reference phylogeny. I understand that you need three additional input files:
Reference alignment- I generated this by inputing the aligned 97% identity fasta file from Silva as type FeatureData[AlignedSequence]
Reference phylogeny- I generated this by inputing the 97% identity tree (.tre) file from Silva as type Phylogeny[Rooted]
Reference info- This is where I ran into problems. I tried generating the RAxMLinfo file by inputing the fasta file from (1) into a RAxML GUI here http://www.phylo.org/sub_sections/portal/ with no success.
Any recommendations for generating this file? Also, do 1 and 2 appear to be correct?
you are doing the right things in principle. However, the branch length of the original reference phylogeny need to be reestimated to be in sync with the alignment distances. This is not necessarily guaranteed by Silva. SEPP’s developer explains what to do in detail in the file “sepp-package/buildref/README.md” of this archive: https://github.com/smirarab/sepp-refs/blob/master/gg/sepp-package.tar.bz?raw=true
I went ahead and used the pre-compiled 12.8 files for the time being. While I don’t think it will change anything given my dataset, I will give a go at compiling the Silva 13.2 files later this week when I get a chance, as I think it would be a good exercise. I’ll let you know if anything comes up.
sorry for the late response. Unfortunately, SEPP is very silent if it runs into errors. This is caused by the bash script itself which is engineered to NOT leave temporary files across several compute nodes when failing.
You might want to change this behaviour. Take a look into this post: Run-sepp.sh returned non-zero exit status 1 But make sure you personalize this path to your needs /Users/mish0397/miniconda3/envs/qiime2-2018.4/bin/run-sepp.sh
No worries, thanks for getting back. I did what you suggested and got back the same error message as before. I've attached the associated log file as .txt file if it is of any help... qiime2-q2cli-err-ljhx5s2z.txt (1.9 KB)