# sidle tutorial missing aligned sequence file
**URL:** https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604
**Category:** Library Support
**Tags:** sidle
**Created:** [August 31, 2021, 9:30am UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604 "2021-08-31T09:30:15Z")
**Posts on this page:** 12
**Page:** 1
### Author:  [@elsamdea](https://forum.qiime2.org/u/elsamdea)
#### Post date: [August 31, 2021, 9:30am UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/1 "2021-08-31T09:30:15Z")
Hi @lam and @jwdebelius,
I am working with q2-sidle and right now some doubts has arisen for me. In the same step that @lam mentioned before:
qiime sidle reconstruct-fragment-rep-seqs \ [...]
--i-aligned-sequences **database/sidle-db-aligned-sequences.qza**
[...]
I could not find any place (in the "Database Preparation" or "Sequences Reconstruction" parts) inside the documentation that indicates how I can obtain the _database/sidle-db-aligned-sequences.qza_ file. Could you, please, help me?
Thank you so much.
Regards,
Elsa
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [September 1, 2021, 7:48am UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/2 "2021-09-01T07:48:52Z")
Hi @elsamdea,
The `sidle-db-aligned-sequences.qza` should be in the database folder you downloaded; please double check with `ls`. If it's not, then we can troubleshoot from there. The aligned sequence file is from the database and so it's something that gets provided during that step.
Best,
Justine
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### Author:  [@elsamdea](https://forum.qiime2.org/u/elsamdea)
#### Post date: [September 1, 2021, 11:08am UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/3 "2021-09-01T11:08:49Z")
Hi @jwdebelius!
Perhaps I didn't explain myself correctly. I mean how I can build/obtain this file with my one database?
In other words, not this file: `sidle-db-aligned-sequences.qza` particulary, but a file with contains my database aligned-sequences.
Maybe should I re-do the alignment step (from the "Sequence Reconstruction" Section) with the reconstructed-table and the database file without separating in regions?
Sorry for the missunderstanding!
Thank you!
Elsa
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [September 1, 2021, 12:00pm UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/4 "2021-09-01T12:00:17Z")
Hi @elsamdea,
As always, it depends on the database. If you're working with greengenes 13\_8, there should be a directory called `rep_set_aligned` which will have a list of files showing a percent identity; pick the one that matches your identity (probably 99). If you're using Silva 128, I think it's in the downloaded QIIME 2 folder. (Remember that tree building only works with greengenes 13\_8 and Silva 128 right now. At somepoint we'll hopefully have more SEPP references, but this is where things are right now. 🤷♀️
Best,
Justine
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### Author:  [@elsamdea](https://forum.qiime2.org/u/elsamdea)
#### Post date: [October 28, 2021, 11:54am UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/5 "2021-10-28T11:54:36Z")
Hi again!
I think my question is also useful in this post, because it is related to another database. So that is the reason why I am posting this here and do not in a new post.
I would love to reproduce the last step of sidle documentation's `Phylogenetic Tree Reconstruction`. However I could not find the `rep_set_aligned` folder in NCBI 16S database or neither the `SEPP references` file. That’s the crux of the matter.
I have found some post as:
> [@rescript get-ncbi-data](https://forum.qiime2.org/t/rescript-get-ncbi-data/20788):
>
> Dear qiime team, I am trying using the code below to download functional gene sequence by accession number, but it can only do 1000 number, if more than that, the timeout error will appear, how can i solve this problem; Thank you very much. qiime rescript get-ncbi-data \ --m-accession-ids-file "/home/rodrigues-lab/Laibin\_Project/data/urec\_accnum.txt" \ --o-sequences /home/rodrigues-lab/Laibin\_Project/data/urec-refseqs.qza \ --o-taxonomy /home/rodrigues-lab/Laibin\_Project/data/urec-ta…
> [@Reference Alignments: Best Way to Download Many Sequences from NCBI GenBank](https://forum.qiime2.org/t/reference-alignments-best-way-to-download-many-sequences-from-ncbi-genbank/19824/2):
>
> Welcome to the forum @alexkrohn ! Sounds like you are on the right track with RESCRIPt! I'd go for the latter. Would be slow to loop 400 times, also slow to merge. Also your provenenance graph would look really ugly! stuck_out_tongue_closed_eyes Probably not faster. merge-seqs is correct, but merge will merge feature tables, not FeatureData[Taxonomy] artifacts. There is a separate merge-taxa action (one in RESCRIPt with more complex functionality, one in q2-taxa that has simpler functio…
But didn't find a solution.
Maybe I need to `merge-seqs`? What approximation could I use?
Any help would be appreciated!! 🙂
Thank you so much!
Elsa
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [October 28, 2021, 1:33pm UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/6 "2021-10-28T13:33:50Z")
Hi @elsamdea,
I hope you're well! 👋
As I think is documented in the Sidle docs (and if not I will add it): tree reconstruction only works for databases that have SEPP reference trees. This means you can reconstruct using Silva 128 or Greengenes 13\_8 if you want a tree. If you'd like to build the backbone for fragment insertion with another database or database version, you're able to do that. I don't think there's a clean solution at the moment; the last thread i can find on building is from last year.
> [@q2-fragment-insertion with silva v138](https://forum.qiime2.org/t/q2-fragment-insertion-with-silva-v138/17581/6):
>
> Thank you @Nicholas_Bokulich I'm working with the Silva v128 reference right now. But will I be upgrading and making some new reference databases with the v138 release and some in-house data - this will come in handy in the near future
there's also a github issue:
>
>
> Is it possible to either get scripts to do the alignment or get the new Silva 13…8 release? Silva updates about annually and it would be really nice to be able to update things that rely on sepp and a consistent database along side that
Best,
Justine
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### Author:  [@elsamdea](https://forum.qiime2.org/u/elsamdea)
#### Post date: [October 28, 2021, 3:24pm UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/7 "2021-10-28T15:24:44Z")
Hi @jwdebelius!
I am good! How have you been? 🙂
> [@jwdebelius](#):
>
> As I think is documented in the Sidle docs (and if not I will add it): tree reconstruction only works for databases that have SEPP reference trees.
I might be wrong, but I think I did not read that in the Sidle docs. But you are right, you wrote that in this post, in the answer 4.
> [@jwdebelius](#):
>
> (Remember that tree building only works with greengenes 13\_8 and Silva 128 right now. At somepoint we'll hopefully have more SEPP references, but this is where things are right now. 🤷♀️)
I am so sorry!! I was confusing about `SEPP references`. But this explanation has resolved my doubts!!
> [@jwdebelius](#):
>
> tree reconstruction only works for databases that have SEPP reference trees. This means you can reconstruct using Silva 128 or Greengenes 13\_8 if you want a tree.
Also, I will keep an eye on the threads you have recommended me!
Thank you so much again 😊
Best,
Elsa
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### Author:  [@nandreani](https://forum.qiime2.org/u/nandreani)
#### Post date: [January 12, 2022, 4:57pm UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/8 "2022-01-12T16:57:48Z")
> [@jwdebelius](#):
>
> mepoint we'll hopefully have more SEPP referen
Dear Elsa and Justine,
I was confused by this last part of the tutorial. Would it be enough to align the sequences in the DB (Silva in my case) by myself in qiime? Where can I find the SEPP reference tree?
Thanks in advance,
Nadia
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [January 13, 2022, 8:14am UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/9 "2022-01-13T08:14:33Z")
Hi @nandreani,
It sounds like I need to make it more clear in the documentation 🙂.
You need the aligned sequences for hte database; I think for Silva 128, they can be downloaded from the [Silva website](https://www.arb-silva.de/download/archive/qiime). The insertion scaffold is available from the [resources page](https://docs.qiime2.org/2021.11/data-resources/#sepp-reference-databases).
Best,
Justine
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### Author:  [@nandreani](https://forum.qiime2.org/u/nandreani)
#### Post date: [January 15, 2022, 9:37am UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/10 "2022-01-15T09:37:16Z")
thank you very much Justine!
Nadia
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [May 22, 2023, 12:44pm UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/11 "2023-05-22T12:44:32Z")
An off-topic reply has been split into a new topic: [Getting the correct Silva 128 file for Sidle following the rescript download](https://forum.qiime2.org/t/getting-the-correct-silva-128-file-for-sidle-following-the-rescript-download/26543)
Please keep replies on-topic in the future.
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [May 22, 2023, 12:44pm UTC](https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/12 "2023-05-22T12:44:47Z")