Hello - I am attempting to use the
q2-picrust2 plug in for my dataset. Download and activation of the plugin seemed to go fine, no errors thrown.
Per the tutorial the plugin needs a tree created by
q2-fragment-insertion I did this with the following commands per the q2-fragment-insertion documentation :
(qiime2-2018.6) wsb255bioimac27:AllPrimerAnalysis_071118 mel_local$ qiime fragment-insertion sepp --i-representative-sequences allPrimers-rep-seqs.qza --o-tree insertion-tree.qza --o-placements insertion-placements.qza --p-threads 4
Filtered my feature table to ensure only those features found in the tree were in the table:
(qiime2-2018.6) wsb255bioimac27:AllPrimerAnalysis_071118 mel_local$ qiime fragment-insertion filter-features --i-table allPrimers-dada2-table.qza --i-tree insertion-tree.qza --o-filtered-table allPrimers_filtered-insertion-table.qza --o-removed-table allPrimers_removed-insertion-table.qza --verbose
I further filtered my feature-table as I was only interested in the output pertaining to two of the three primer sets I was working with:
qiime feature-table filter-samples --i-table allPrimers_filtered-insertion-table.qza --m-metadata-file Pro_V4_keep.tsv --o-filtered-table table_V4-Pro.qza
Another filter step to only keep those samples pertaining to the 2 fermenters (rather than also including initial manure and food samples)
(qiime2-2018.8) wsb255bioimac27:Issue_0037_Bacteria mel_local$ qiime feature-table filter-samples --i-table table_V4-Pro.qza --m-metadata-file sample_metadata_110718.tsv --o-filtered-table table_V4-Pro-F12.qza --p-where "Subject IN ('Fermenter1', 'Fermenter2')" Saved FeatureTable[Frequency] to: table_V4-Pro-F12.qza
So now I have:
- SEPP tree - insertion-tree.qza
I ran the q2-picrust2 plugin per the tutorial with the suggested parameters just to see if I could get it working:
(qiime2-2018.8) wsb255bioimac27:Issue_0037_Bacteria mel_local$ qiime picrust2 custom-tree-pipeline --i-table table_V4-Pro-F12.qza --i-tree insertion-tree.qza --output-dir q2-picrust2-output --p-threads 1 --p-hsp-method pic --p-max-nsti 2
I got the following error:
Error running this command: hsp.py -i 16S -t /var/folders/12/2j8hq03s52lbnstw5wh008k80000gq/T/tmp0356q166/placed_seqs.tre -p 1 -n -o /var/folders/12/2j8hq03s52lbnstw5wh008k80000gq/T/tmp0356q166/picrust2_out/16S_predicted -m pic
I was unable to open the directory path to the tmp files to figure out what might have happened? The error is not informative…at least not intuitive in terms of what might have went wrong?
I would appreciate any suggestions… files attached.