the number of taxonomy.tsv is less than that of feature-table.tsv

[111 (jbz)]

2269 feature-table.tsv
2269 taxonomy.tsv
There are two head lines in feature-table.tsv while there is only one head line in taxonomy.tsv, so the sequence numbers are not equal.

for feature-table.tsv:

# Constructed from biom file
#OTU ID S1 S2 S3  S4 S5
9fb03a9b98d92c703211dd01f1852d32        0.0     0.0     0.0     3922.0  5656.0
65661f6c4ecc9a6b8eb95cd423b03c5b        0.0     0.0     0.0     3176.0  6892.0

for taxonomy.tsv:

Feature ID      Taxon   Consensus
896b60ebb935551e88ca46e13f9c9269        k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s_
977336411d8cdd798bcd44ec4dcba0c2        k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s_
59d3d9dd8d69b45b3f0395805b414d5e        k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus
80e4bb11f09da9fde6eeef18816b7f49

I want to add annotation info into the out tables following this URL:

Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)

Creating a TSV BIOM table The following is based on a post by @gregcaporaso. $ qiime tools export table.qza --output-dir ./ $ biom convert -i feature-table.biom -o feature-table.tsv --to-tsv $ biom head -i feature-table.tsv # Constructed from biom file #OTU ID L1S105 L1S140 L1S208 L1S257 L1S281 4b5eeb300368260019c1fbc7a3c718fc 2222.0 0.0 0.0 0.0 0.0 fe30ff0f71a38a39cf1717ec2be3a2fc 5.0 0.0 0.0 0.0 0.0 d29fe3c70564fc0f69f2c03e0d1e5561 0.0 0.0 0.0 0.0 0.0 868528ca947bc57b69ffdf83e6b73bae 0.0 2276…

But the annotation info was not added.

Thanks

commands:
qiime feature-classifier classify-consensus-vsearch
–i-query ./rep-seqs.qza
–i-reference-reads ./silva.nr_v132.qza
–i-reference-taxonomy ./silva.nr_v132.tax.qza
–o-classification ./taxonomy.qza
–p-threads 24 --p-perc-identity 0.97
–verbose

qiime info
System versions
Python version: 3.6.7
QIIME 2 release: 2019.10
QIIME 2 version: 2019.10.0
q2cli version: 2019.10.0

Installed plugins
alignment: 2019.10.0
composition: 2019.10.0
cutadapt: 2019.10.0
dada2: 2019.10.0
deblur: 2019.10.0
demux: 2019.10.0
diversity: 2019.10.0
emperor: 2019.10.0
feature-classifier: 2019.10.0
feature-table: 2019.10.0
fragment-insertion: 2019.10.0
gneiss: 2019.10.0
longitudinal: 2019.10.0
metadata: 2019.10.0
phylogeny: 2019.10.0
quality-control: 2019.10.0
quality-filter: 2019.10.0
sample-classifier: 2019.10.0
taxa: 2019.10.0
types: 2019.10.0
vsearch: 2019.10.0

[thermokarst (Matthew Ryan Dillon)]

Hi @111!

There are two head lines in feature-table.tsv while there is only one head line in taxonomy.tsv, so the sequence numbers are not equal.

How did you count the line numbers?

This is a robust method, that uses the source Artifacts and counts the feature IDs:

# transpose feature table to get features as primary axis
qiime feature-table transpose \
  --i-table table.qza \
  --o-transposed-feature-table transposed-table.qza

qiime tools inspect-metadata transposed-table.qza | grep ID | awk '{ print $2 }'
qiime tools inspect-metadata taxonomy.qza | grep ID | awk '{ print $2 }'

When you run these you should get a number for each inspect-metadata command (2), which should match. For example, using moving pictures tutorial, I see 770 as the result for both.

Keep us posted!

[111 (jbz)]

Hi, @thermokarst, thanks for your reply!!!
I used ‘qiime tools export’ and ‘biom convert’ to get the ‘taxonomy.tsv’ and ‘feature-table.tsv’(from the table.qza) and then used the linux ‘wc -l’ to count the lines.

Yes, I used the methods you provided and the number is the same.
When I unzip the table.qza to feature-table.tsv, there are two lines:

Constructed from biom file

#OTU ID S1 S2 S3 S4 S5
Although the number of lies of feature-table.tsv is the same as taxonomy.tsv, but I check the all the seq id in feature-table.tsv can be found in taxonomy.tsv. So I guess the last line of feature-table.tsv might lack of ‘\n’ and it was not counted by ‘wc -l’.

Thanks !

[111 (jbz)]

@thermokarst, hello, Could you tell me how to add taxonomic infos to the table.qza?
I followed your methods as described before, but it did not work out.

Thanks!

[thermokarst (Matthew Ryan Dillon)]

Did you follow all of the steps? Are you sure you are looking at the right data files? That protocol has been verified many times — please double check your workflow.

[111 (jbz)]

Thanks, I will try it again !!! Probably is my fault.