# Representative sequences file too large after combining studies
**URL:** https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010
**Category:** User Support
**Created:** [May 2, 2018, 12:09pm UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010 "2018-05-02T12:09:45Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@gilberto\_solano](https://forum.qiime2.org/u/gilberto_solano)
#### Post date: [May 2, 2018, 12:09pm UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/1 "2018-05-02T12:09:45Z")
Hello,
I have been working to train a classifier using the qiime alignment mafft plugin, and have continuously received errors because the process takes too much memory. Most recently it has been running for over 12 hours. I asked about this in another topic: [Mafft error for alignment of rep-seqs](https://forum.qiime2.org/t/mafft-error-for-alignment-of-rep-seqs/3915)
I believe the problem is that my rep-seqs file is too large. I created it by combining rep-seq files generated over several studies in QIITA. This was one study with 6 plates that were each given an individual prep template in qiita, so to analyze these data I downloaded each deblurred table and rep-seqs file, then combined them using qiime feature-table merge-seqs. I am concerned that it simply added the 6 tables together instead of truly combining the information, because my rep-seqs file now contains over 120,000 representative sequences. In other words, I think there may be redundant sequences listed, and that is why my file is so large. Is there a better way to merge the files, or is there a way to reduce the number of sequences so I can use this for further processing?
I tried to attach the rep-seqs.qzv file, but it was too large 😶
Thank you!
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [May 2, 2018, 12:21pm UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/2 "2018-05-02T12:21:55Z")
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### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [May 4, 2018, 11:32pm UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/3 "2018-05-04T23:32:45Z")
Hi @gilberto_solano,
> [@gilberto\_solano](#):
>
> . I am concerned that it simply added the 6 tables together instead of truly combining the information, because my rep-seqs file now contains over 120,000 representative sequences. In other words, I think there may be redundant sequences listed, and that is why my file is so large. Is there a better way to merge the files, or is there a way to reduce the number of sequences so I can use this for further processing?
That merge command won't record the same sequence twice, _however_ because you have that many representative sequences (from I assume similar plates of the same environment and amplicon), it does suggest that something is wrong. How many sequences were found in a single plate? I would expect the number of unique sequences to still be in the same ballpark after merging (it sounds like this is not the case?)
Are each of these plates for the same amplicon, and where they all filtered/trimmed/denoised to the same length? If the lengths don't match then you won't be able to compare across plates.
> [@gilberto\_solano](#):
>
> I tried to attach the rep-seqs.qzv file, but it was too large 😶
Make sense 😉
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### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [May 4, 2018, 11:32pm UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/4 "2018-05-04T23:32:46Z")
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### Author:  [@jessicalmetcalf](https://forum.qiime2.org/u/jessicalmetcalf)
#### Post date: [May 8, 2018, 3:54am UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/5 "2018-05-08T03:54:52Z")
Hi Evan, Gilberto has been trying to analyze a published QIITA data set as part of a class. The one he chose (as a dairy systems student) is [Qiita](https://qiita.ucsd.edu/study/description/10485). The challenge is that the study has 6 prep templates and it is not clear how to combine them for a final rep\_seqs. It seems something has gone wrong. Perhaps you could walk through the workflow of pulling data off QIITA when prep template within a single study need to be combined?
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### Author:  [@antgonza](https://forum.qiime2.org/u/antgonza)
#### Post date: [May 8, 2018, 11:34am UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/6 "2018-05-08T11:34:00Z")
Hi @jessicalmetcalf and @gilberto_solano,
To merge multiple preparations from a single or multiple studies in Qiita, you need to create an analysis. There are a couple of guides for this: one in the [tutorial](https://qiita.ucsd.edu/static/doc/html/analyzingsamples/index.html) and another in the [help](http://cmi-workshop.readthedocs.io/en/latest/qiita-16S-analysis.html), suggest taking a look. Once you have an analysis created you can download the merged biom and QIIME mapping file. Note that an Analysis can be also public like the [Qiita's main paper analysis](https://qiita.ucsd.edu/analysis/description/15093/), which combines 7 preparations from 7 different studies.
Hope this helps.
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### Author:  [@jessicalmetcalf](https://forum.qiime2.org/u/jessicalmetcalf)
#### Post date: [May 9, 2018, 6:11am UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/7 "2018-05-09T06:11:56Z")
Hi @antgonza Here is the public qiita meta-analysis [Qiita](https://qiita.ucsd.edu/analysis/description/16799/). One issue we ran into here is that the only phylogenetic tree option for alpha and beta tree-based metrics looked like a closed ref 97% similarity gg tree. Is that correct, or is the tree created using the deblur rep\_set sequences? I am trying to download the support\_files.zip to see if a tree is in there, but I am at a hotel with very slowwwwww internet. @gilberto_solano.
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [May 9, 2018, 3:48pm UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/8 "2018-05-09T15:48:20Z")
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### Author:  [@antgonza](https://forum.qiime2.org/u/antgonza)
#### Post date: [May 9, 2018, 4:51pm UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/9 "2018-05-09T16:51:59Z")
Currently in Qiita we only support phylogenetic analyses with close reference because we need to create a new phylogeny with the combined datasets when using other techniques, in this case deblur. Note that this is something that we are actively working on and should be available soon in the system.
Now, you can combine your deblur bioms from all studies and preparations and then download the resulting files to continue analysis in your local machine, suggest checking out these posts:
> [@Importing deblur data from QIITA](https://forum.qiime2.org/t/importing-deblur-data-from-qiita/3221):
>
> I'm working on a meta-analysis of datasets from QIITA for analysis in qiime2. I've been able to download datasets processed using deblur from QIITA as well as their respective metadata files. I've merged the BIOM and metadata files but in order to continue with my analysis, I require a rep-seqs file. It looks like this file isn't generated by QIITA from data processed with Deblur. Is there a way I could extract the rep-seqs file from the deblur BIOM file in order to run "qiime diversty core-metr…
> [@Extract tree used to create deblurred biom from deblurred biom artifact](https://forum.qiime2.org/t/extract-tree-used-to-create-deblurred-biom-from-deblurred-biom-artifact/3367):
>
> I have a deblurred reference hit biom table in Qiita but have no biom tables prior to that (I combined a few studies so I only have the combined reference hit artifact). Is there a way to extract the tree used or the representative sequences from deblurred biom table from the artifact so I can use it in my Qiime2 commands? I've tried doing this on my own by importing my biom table and then using the imported .qza to create a tree but I get an error. I import the biom using this command: qiime…
Hope this helps.
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### Author:  [@antgonza](https://forum.qiime2.org/u/antgonza)
#### Post date: [May 9, 2018, 4:52pm UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/10 "2018-05-09T16:52:09Z")
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [June 9, 2018, 10:52pm UTC](https://forum.qiime2.org/t/representative-sequences-file-too-large-after-combining-studies/4010/11 "2018-06-09T22:52:10Z")
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