ERROR LSMatFormat file

[manojndsu (Manoj Kumar)]

Hi, I have txt file of different samples which is not generated from qiime. I need to convert this txt file to .qza so I can calculate Shannon diversity using qiime diversity alpha --i-table.

If I use following command it is showing error...

qiime tools import --input-path ..qiime/N.txt --output-path ..qiime/N_distance_matrix.qza --type DistanceMatrix

----ERROR-----
There was a problem importing /home/kumarm/MinION-data/qiime/otu_table.txt:

/home/kumarm/MinION-data/qiime/otu_table.txt is not a(n) LSMatFormat file

---Input file---

[Nicholas_Bokulich]

Hi @manojndsu,
This error is occurring because the file you are attempting to import is NOT a distance matrix, nor is it LSMatFormat. It is an "OTU Table". I have already recommended that you read the importing tutorial at qiime2.org to learn more about how to import various data types into QIIME 2. In your case, you will want to follow the instructions shown here to first convert your OTU table to biom-format before importing to QIIME 2:

error when running 'biom convert'

Hi again The same commands I wrote earlier worked biom convert -i otu_table.biom -o otu_table.tsv --to-tsv otu_table.tsv (75.8 KB) If you are going to convert a .tsv back to .biom: biom convert -i feature-table.tsv -o feature-table.biom --table-type="OTU table" --to-hdf5 And if you want to import a .biom to Qiime2: qiime tools import \ --input-path feature-table.biom \ --type 'FeatureTable[Frequency]' \ --input-format BIOMV210Format \ --output-path table.qza

Good luck!

[manojndsu (Manoj Kumar)]

Thank you for updates!

[manojndsu (Manoj Kumar)]

Hi, I converted the OTUs table to .biom and .biom to Qiime2. Now, I am able to use this file to calculate Shannon Index. However, I am looking to calculate UniFrac and bray_curtis_distance_matrix. Please let know if I can use this converted feature table to calculate the distances. I am using following command…

---

qiime diversity beta-group-significance --i-distance-matrix …/qiime2/table.qza --m-metadata-file …/qiime2/sequence-metadata.tsv --m-metadata-column BodySite --p-pairwise --o-visualization …/qiime2/beta-2016.qzv

[Nicholas_Bokulich]

@manojndsu

Please let know if I can use this converted feature table to calculate the distances. I am using following command…

Yes, you can use a feature table to calculate distances but you are not doing this the correct way.

I have recommended a few times already that you read through the tutorials at docs.qiime2.org, in particular the "overview" tutorial would be useful for you to learn about basic concepts and workflows in QIIME 2, and the "moving pictures" tutorial will give you some specific examples, including the answer to your question. Please read through these tutorials and use those workflows as templates for your own analysis.

Your question is in some ways a duplicate of other posts you have made recently. Please do not make duplicate posts.

[manojndsu (Manoj Kumar)]

Hi, Yes! I already gone through Moving Picture Tutorial. However, I am not sure if I am able to find how to use feature table to calculate distance matrix. For docs.qiime2.org, sure I will go though later for my next analysis however for urgent assistance I posted my query on QIIME2 Fourm, therefore, if I can get specific part to read in tutorial that will help me in my current work. Thanks !