Combine seq fna files

Hello all
I am trying to analysis my microbiome data and my data is about fish microbiome from skin and gut, so I have 300 fish but I did the skin and gut microbiome on different chips with same barcode. Now I have two fasq files with sames barcodes, what I did I used diffeenet sample name (like s1 for skin fish 1, and g1 for gut fish1) and I did the split library with QIIME 1. Now I have two seq fna and I open the saq fna files and it seems everything is fine. My question is, can I combine the two seq fna file and then use qiime 2 for further analysis? If yes please could send me the command that I need to follow? I used Ion Torrent s5 for sequencing and my variable region was V5-V6.

Kind regards,


I would suggest reversing the order of that - you can import each of the seqs.fna files by following this tutorial:

Once you import and dereplicate, then you can merge the feature tables and representative sequences:

Then you can proceed with something like OTU clustering (in the first tutorial linked to above). Keep us posted! :t_rex:

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Hello All
I am trying to import my seq fna files from qiime 1 to qiime 2 but I am getting below error. Any help would really be appreciated. I also read this page ( but did not help me too much.

(qiime2-2020.6) [email protected]:~/Desktop/Shared_Folder/Swab_samples/Split_Library_Output$ qiime tools import --input-path sequences.fna --output-path sequences.qza --type ‘SampleData[sequences]’
Traceback (most recent call last):
File “/home/glier_ubuntu/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/builtin/”, line 158, in import_data
File “/home/glier_ubuntu/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/”, line 213, in import_data
output_dir_fmt = pm.get_directory_format(type_)
File “/home/glier_ubuntu/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/”, line 313, in get_directory_format
% semantic_type)
TypeError: Semantic type SampleData[sequences] does not have a compatible directory format.

An unexpected error has occurred:

Semantic type SampleData[sequences] does not have a compatible directory format.

See above for debug info.

Hi @Javad32 - when following the tutorial you have to do exactly as described in the document:

SampleData[sequences] is not the same as SampleData[Sequences] - you have a typo that needs to be fixed.

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Thank you so much for your help. It is so embarrassing I did not catch this error!