Hello Team Picrust,
I am new to Picrust and trying to run the example data set following the commands on
https://github.com/picrust/picrust2/wiki/Swapping-in-SEPP-for-read-placement-with-q2-picrust2, but when I run the command - " qiime fragment-insertion sepp --i-representative-sequences mammal_seqs.qza --i-reference-database picrust2_default_sepp_ref.qza --output-dir tutorial_placed_out --p-threads 1 "
This error pops up:
Plugin error from fragment-insertion:
Command ‘[‘run-sepp.sh’, ‘/tmp/qiime2-archive-j0r63x6r/38a5d748-739e-44d1-b547-a35c0c8b8f29/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/tmp/qiime2-archive-dge6cgsp/2028ee20-c65b-470e-9cf5-80e2b4e28d0d/data/aligned-dna-sequences.fasta’, ‘-t’, ‘/tmp/qiime2-archive-dge6cgsp/2028ee20-c65b-470e-9cf5-80e2b4e28d0d/data/tree.nwk’, ‘-r’, ‘/tmp/qiime2-archive-dge6cgsp/2028ee20-c65b-470e-9cf5-80e2b4e28d0d/data/raxml-info.txt’]’ returned non-zero exit status 1.
What I have been missing? Is it the memory constraint? I am trying to run it on 8GB RAM as QIIME2 pluggin.
Note: I have changed the title since this is really a SEPP error, and an error you are getting from QIIME 2, not from PICRUST itself, per se.
I am pinging
@gmdouglas since these are tutorial files causing this error, in case he wants to take a look.
Given that these are tutorial files, I agree with you that this is
probably a memory error, but you can follow the debugging steps in this forum topic (note the
verbose flags) to get more diagnostic details:
I encountered a similar error.
qiime version 2019.10
My input file size is 815KB. I also tried another with 794KB but had the same issues. I am using Imac with 32GB memory.
What could be the problem?
qiime fragment-insertion sepp --i-representative-sequences “my_rep_seq.qza” --i-reference-database “Silva 128 SEPP reference from qiime2 data resources” --output-dir “my folder”
–p-threads 3 # I used the default as well
My log 1:
let us know what you find!
Thank you for your prompt reply
I tried with what is mentioned in the post you indicated, but I could not see what the actual problem is because I am using the example dataset in this link “ https://github.com/picrust/picrust2/wiki/Swapping-in-SEPP-for-read-placement-with-q2-picrust2”.
I will try running it on a system with higher specifications and will get back to you soon.
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