Q2-PRICRUSt2 output cannot add descriptions for Ko numbers

96 views
Skip to first unread message

hanyan li

unread,
Mar 30, 2021, 3:27:36 PM3/30/21
to picrus...@googlegroups.com
Hi Gavin, 

I have a problem in adding the description to the KOs in the generated KO_metagenomic file. 

Here are what I did:

 1: I run the qiime vsearch cluster-feature-closed-reference and used the clustered sequence and tables for the picrust2 full-pipeline analysis.

 

 2. Then I did the following two steps to get the KO metageonomic prediction table, which are shown in the tutorial. 

$qiime tools export --input-path ko_metagenome.qza --output-path ko_output &

$biom convert -i feature-table.biom  -o feature-table_ko.biom.tsv --to-tsv &

 

3. Then I found the generated table only has KO numbers but no name or description. 

I tried to add them by using the following command 

 

$add_descriptions.py -i feature-table_ko.biom.tsv -o feature-table_ko_description.biom.tsv --custom_map_table /usr/local/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/default_files/description_mapfiles/KEGG_pathways_info.tsv.gz &

$add_descriptions.py -i feature-table_ko.biom.tsv -o feature-table_ko_description.biom.tsv -m ko &

 

However, none of them work and gives me errors of Error: no function ids in input table are found in the provided mapfile

 

Is there a way that I can fix the problem?

 

Thanks a lot, 

 

Hanyan Li

Gavin Douglas

unread,
Mar 31, 2021, 9:06:39 AM3/31/21
to picrus...@googlegroups.com
Hey there,

That script is meant to add the description column to the output of the standalone version of PICRUSt2. The headerline is slightly different from the biom table you’re working with.


Specifically if you change your BIOM file to start like this then it should work:

function        100CHE6KO       101CHE6WT       102CHE6WT       ...
EC:1.1.1.1      1432.0  1967.5  1408.5  ...
EC:1.1.1.100    2034.0  2748.16 2443.5  ...
EC:1.1.1.103    0.0     0.0     0.0     ...


Cheers,

Gavin

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/CABHN4s7fJ6rEM2sF2PVv-Vawv4z%3DV6GfcH6uXkHcManNDM7skw%40mail.gmail.com.

hanyan li

unread,
Mar 31, 2021, 10:49:54 AM3/31/21
to picrus...@googlegroups.com
Thanks, it works now.


Cheers,

Gavin

To unsubscribe from this group and stop receiving emails from it, send an email to picrust-users+unsubscribe@googlegroups.com.

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-users+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/C582645C-AA60-4512-8604-F3098D77645F%40gmail.com.

Mashuk Siddiquee

unread,
Apr 6, 2021, 7:17:01 PM4/6/21
to picrus...@googlegroups.com
Hi hanyan,
Could you please share your script to resolve the issue? I am also facing the same issue.
Thanks 
Mashuk



Cheers,

Gavin

To unsubscribe from this group and stop receiving emails from it, send an email to picrust-user...@googlegroups.com.

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-user...@googlegroups.com.

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/CABHN4s4ngjj8cXv0B%2BYjNQaY3_N6OeaHsS9x2_STf%2BdhpJp5og%40mail.gmail.com.


--





-------------------------------------------------------

Regards

Mashuk Siddiquee

E-mail: mashu...@gmail.com  

hanyan li

unread,
Apr 6, 2021, 8:44:26 PM4/6/21
to picrus...@googlegroups.com
Hi Mashuk,

I just manually edited the header, basically you just need to deleted the first line and type ‘’function” into the first cell in the row with all other sample names.

Thanks,
Hanyan


Cheers,

Gavin

To unsubscribe from this group and stop receiving emails from it, send an email to picrust-users+unsubscribe@googlegroups.com.

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-users+unsubscribe@googlegroups.com.

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-users+unsubscribe@googlegroups.com.


--





-------------------------------------------------------

Regards

Mashuk Siddiquee

E-mail: mashu...@gmail.com  

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-users+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/CALtY15wPw8B7p6pm%2BcxcxQ8CnQk_CaKTzscS1o1t5hSxbugOxQ%40mail.gmail.com.
Reply all
Reply to author
Forward
0 new messages