I am trying to work on Picrust 2 via the QIIME2 plugin, but I am stuck on the first step which uses the plugin q2-fragment insertion.
I have looked through the forums but cannot not seem to find a definitive answer. I was hoping someone could help me out!
Disclaimer: I’m using QIIME2-2018.8, running via Ubuntu for Windows10. We successfully used QIIME2-2018.6 using this method. But we wanted to work with picrust2 and there was also an update to QIIME2 so it happened all together - hopefully not confounding the issues…
I followed the picrust2 installation protocol as outlined here:
and for q2-fragment-insertion here:
Everything seemed to install correctly, but I am getting errors right from the start with the tutorials (using fragment-insertion). I thought that the reference alignment and phylogeny files might have been an issue so I also tried the default settings as outlined in the fragment-insertion tutorial. But still the same errors.
I have tried my own rep-seqs.qza, mammal_seqs.qza (from picrust2 tutorial), and the sequences from the dada2 moving pictures tutorial. Same errors.
Error log states
“CalledProcessError: Command ‘[‘run-sepp.sh’, ‘/tmp/qiime2-archive-d0fhf34c/38a5d748-739e-44d1-b547-a35c0c8b8f29/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’]’ returned non-zero exit status 1”
I found a suggestion from Stefan Janssen (here) to run the following command on the moving pictures data:
qiime fragment-insertion sepp --i-representative-sequences rep-seqs-dada2.qza --o-tree i-tree.qza --o-placements insertion-placements.qza --p-debug --verbose 2> err.txt > out.txt
- Errors again
- see attached files
I ran the command as outlined here to get the version number
conda list | grep frag
fragment-insertion 4.3.5 py35_0 biocore
q2-fragment-insertion 2018.6.17 py35_1 biocore
Any help would be greatly appreciated. Thank you!