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.
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.
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’.
@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.
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.
