Dada2 plugin error return code error 1

[HIMANI_KHURANA]

Dear Sir,

I have two samples as both dada2 and deblur failed, I opted for vsearch in order to get feature table as table.qza and feature sequences as rep-seq.qza. I operated both samples individually.
For one sample, I tried to cluster the sequences at 99% getting rep-seqs-dn-99.qza.
The size of the rep-seqs.qza is 2.2 GB and of rep-seqs-dn-99.qza is 794.1 Mb.
I have been running qiime2 fragment insertion as an alternative as mafft failed to process more than million sequences.
But it has been almost two weeks that it is running using rep-seqs.qza using 60 threads, and yesterday only I started operating the same on rep-seqs-dn-99.qza.
My questions are

Is it okay to process samples independently as I do not have metadata file and my ultimate aim is diversity analysis?
I do not know whether to work on rep-seqs.qza or rep-seqs-dn-99.qza?
What is the next step after clustering otus at 99
How to get the otu network map from this information?
If for example, I want to see the relationship of one OTU with other using Pearson correlation, is it possible and how?
I have been struggling with this since past one month for now, please help me at the earliest.
Should I stop because fragment insertion step as it is taking a lot of time and no other work am I able to do because of the server being occupied.

Thank you very much

[thermokarst]

@HIMANI_KHURANA

I have been running qiime2 fragment insertion as an alternative as mafft failed to process more than million sequences

If you want to use mafft with more than a million seqs you can use the --p-parttree flag.

@HIMANI_KHURANA

Is it okay to process samples independently as I do not have metadata file and my ultimate aim is diversity analysis?

What do you mean by "process"? What steps or actions are you asking about specifically?

@HIMANI_KHURANA

I do not know whether to work on rep-seqs.qza or rep-seqs-dn-99.qza?

I suggest trying both and comparing the results. 99% clustering is pretty common, too.

@HIMANI_KHURANA

How to get the otu network map from this information?

I haven't had a chance to play with this yet, but would this plugin help?

https://library.qiime2.org/plugins/q2-scnic/11/

@HIMANI_KHURANA

I have been struggling with this since past one month for now, please help me at the earliest.

We asked you for supporting materials 25 days ago and did not hear back from you.

@HIMANI_KHURANA

Should I stop because fragment insertion step as it is taking a lot of time and no other work am I able to do because of the server being occupied.

We can't answer that question for you - you will need to make that call yourself. Based on my experience with q2-fragment-insertion this doesn't seem too crazy for runtime. Just one question though, is your server able to handle 60 concurrent threads? If not, that can cause a huge bottleneck...

In the future can you please try to limit your posts to one or two questions at a time? This will allow us to get back to you as quickly as we can, and will help future users discover our conversations more easily. Thanks!