feature-table filter-samples - output with no data

Hello,

I have used this very same code in the past and got results. The code is
qiime feature-table filter-samples
--i-table $FILTER/table-dada2.qza
--m-metadata-file $WORKING/sample_metadata.tsv
--p-where '"Time" IN ("5")'
--verbose
--o-filtered-table $FILTER/filtered-table-5h.qza

qiime feature-table summarize
--i-table $FILTER/filtered-table-5h.qza
--o-visualization $FILTER/filtered-table-5h.qzv

using qiime2/2019.4 currently. I do get output, but there are no samples in the qzv file output.. I do not get any errors either.

Uploaded are the qzv output and metatable.qzv (524.6 KB) table-dada2.qza (184.1 KB) data file.
I have consulted:

Filtering data — QIIME 2 2018.4.0 documentation, and all the help questions from other users.
filtered-table-5h.qzv (365.8 KB) sample_metadata.tsv (6.8 KB)

Hi @SetaPark,
Your metadata file doesn't seem to have any instances where Time=5. This is why your output table is empty because no samples were at time 5.
Using 10 instead for time as follows does work as expected:

qiime feature-table filter-samples \
--i-table table-dada2.qza \
--m-metadata-file sample_metadata.tsv \
--p-where "Time='10'" \
--o-filtered-table time10table.qza

time10table.qza (104.5 KB) | time10table.qzv (475.7 KB)

2 Likes

Thank you @Mehrbod_Estaki. But of course. you are absolutely right.

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