Hi @antgonza,
Thanks for the quick reply!
Darn, I was hoping the error wasn’t unique!
To answer your questions,
Regards,
Jon
That makes 2 of us! 
Anyway, could you post your rep-seqs-dada2.qza so I can take a closer look?
Thanks!
This was one of the files I tried. https://docs.qiime2.org/2018.6/data/tutorials/moving-pictures/rep-seqs-dada2.qza
It was in a reply from Stefan Janssen to another user about a similar issue. But the rep seq file seemed to work fine for Stefan.
Thanks!
Sorry for the delay. I have tested with that artifact and everything seems fine. Took ~20min:
07:24:42 Downloads$ qiime fragment-insertion sepp --i-representative-sequences rep-seqs-dada2.qza --o-tree rep-seqs-dada2-tree.qza --o-placements rep-seqs-dada2=placements.qza
Saved Phylogeny[Rooted] to: rep-seqs-dada2-tree.qza
Saved Placements to: rep-seqs-dada2=placements.qza
07:47:13 Downloads$
Note that I used the latest version and this might be the source of the issue, you are using an older version. This is what I have:
$ conda list | grep frag
fragment-insertion 4.3.5 py35_0 biocore
q2-fragment-insertion 2018.11.0 py35_0 qiime2-staging/label/r2018.11
$ pip freeze | grep frag
q2-fragment-insertion==2018.11.0
Would you mind updating your qiime2 to the latest version and see if you still have the same issue? If you still have it, could it be possible that you are running out of space in /tmp?
Hope this helps.
No worries at all!
I will try updating soon, but when I installed the plugin for picrust2 that was the version of q2-fragment-insertion. Where can I get the latest version? Is it contained with the november qiime2 update?
Also, I have tried running the plugins in the latest qiime virtualbox (which uses version 2018.8) and it was successful using the tutorial files. I am currently testing our own sequencing data now.
To me this would indicate a problem related to the ubuntu shell on windows, but I have no idea why it would not work when qiime2 works fine…
Any thoughts on that?
I will update asap and let you know if that works. Thanks again!
That right, fragment insertion is now part of the qiime2 official release 
!!
Windows not playing nice: who knew?! Anyway, not really sure but it’s good to know and I’ll keep an eye open for this. BTW did you try your data in the VM, it will be interesting to figure out if it’s the install or your qza … but things are pointing to the install.
Hi Antonio,
That is great news! I will try using the plugin on the new qiime2 release!
Haha. Yeah, I would like to work in native Linux… another day perhaps.
But in other news, I tested everything in the virtual box (qiime 2018.8 image), and its working fine! So it’s definitely something to do with Windows not playing nice with the Ubuntu shell. It would be excellent to find a solution and then everything would be working great on this setup with qiime.
I will let you know if the new qiime2 release helps solve the issue. Cheers!
Hi Antonio,
I am getting the same error message running the command qiime fragment-insertion sepp. I checked the version and I have the lastest version but I am still getting this error message. I also have enough memory. Do you have any suggestion, please? thank you
Dear all,
I just run the following command:
qiime fragment-insertion sepp \
--i-representative-sequences rep-seqs.qza
--o-tree insertion-tree.qza
--o-placements insertion-placements.qza
And I got the following error:
Plugin error from fragment-insertion:
Command '['run-sepp.sh', '/home/ubuntu/linaqiimefiles/HealthyD/qiime2-archive-x43sce73/baad438c-4bca-4720-92b4-d43bb1ce65b6/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000']' returned non-zero exit status 1
Debug info has been saved to /home/ubuntu/linaqiimefiles/HealthyD/qiime2-q2cli-err-8oiauqwd.log
Could you tell what this error means, please? What can I do for making the command works? Thank you for all your suggestions
Can you share your input file with us? Thanks!
Hi Antonio,
Yes, of course. Please find attached the file of representative sequences. Thank you so much for your help
rep-seqsA.qza (187.3 KB)
Sorry for the delay, your file ran without issues on my laptop. I used the command: qiime fragment-insertion sepp --i-representative-sequences rep-seqsA.qza --o-tree rep-seqsA.tree --o-placements insertion-placements.qza and the generated three is: rep-seqsA.tree.qza (2.4 MB); not adding the insertion-placements.qza file cause it's ~5M.
Anyway, would you mind trying again and checking the log files? My guess is that you are running out of memory or space.