Plugin error from fragment-insertion


(aji) #1

Hi Qiime2

Just wondering if this topic Run-sepp.sh returned non-zero exit status 1 is resolved or not. I am facing similar issues and upon looking at the forum it seems no solutions have been discussed.

Best
Aji


(Justine) #2

Maybe not helpful, I’m also running into the same issue. I’m currently trying the solution to decrease my number of threads. Its particularly weird, because this worked two weeks ago on almost the same dataset, and now I’m having failures as well.


(Michael Shaffer) #3

The issue I ended up having was that I was trying to make a tree on closed reference OTUs and therefore there were redundant names between my sequences and the reference tree. The solution was to change the names of the closed reference OTUs in the input sequence qza. I have a script to do this if this is your problem.

Mike


(aji) #4

Thanks @jwdebelius . I tried decreasing the threads but the error is persistent.


(aji) #5

Thanks Mike. If you can post the script here or send me email at [email protected] that would be helpful. It is worth checking if that is why i have this error.

Aji


(Michael Shaffer) #6

@ajiwahyu

I have attached it here. As long as you don’t have any OTU ids which are all numbers that are not greengenes OTUs. Those shouldn’t exist as long as you are using the standard qiime2 pipelines.

Here is an example command:
python change_names_for_sepp.py --input your_seqs.qza --output your_seqs.mod.qza

And then use your_seqs.mod.qza as the input to fragment insertion.

change_names_for_sepp.py (1.0 KB)


(aji) #7

Thanks for the script Mike!


(Justine) #8

@ajiwahyu,

Has the script worked? Sorry, I’m still trying to deblug by switching enviroments. If there’s something else major, it would be helpful.

Out of curiosity, do you have the PICRUSt plugin? I built a tree okay about a month ago, and then put in PICRUSt, and now… no luck?


(Justine) #9

As my update to this, I switched to my QIIME2-2018.11 vanilla environment, with no PICRUSt (compared to my 2018 8 enviroment where I added PICRUSt.) My tree build in this environment (or at least, I got one out), along with a lovely informative error log.


(Matthew Ryan Dillon) #10

An off-topic reply has been split into a new topic: Q2-picrust2 error

Please keep replies on-topic in the future.