biom command not found

Other Bioinformatics Tools
1

Hi,
I am using qiime/2.2019.04 . When I run:
$ biom add-metadata -i exported/feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp exported/taxonomy.tsv --sc-separated taxonomy

I get following error:
-bash: biom: command not found

Regards,
Amin Ferdous

5

The biom-format package doesnā€™t come with Qiime 2, but you can still install it.

conda install biom-format

Let me know if that install works for you!

Colin

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7

Hey @amin,

The above will certainly work to install biom, however biom is a pretty core dependency of QIIME 2, so Iā€™m very surprised that it isnā€™t available (the biom library always ships the command line interface as well).

Are you certain that things are available inside that environment? What does conda list say? I kind of expect something to be very wrong with your installation (or perhaps activation just went wrong?)

10

@colinbrislawn and @ebolyen
Thanks a lot for your reply. I am using a cluster of high performance computing system. I did not install Qiime 2 by myself, it has been installed by them. Surprisingly when I tried to install biom-format package by
$ conda install biom-format
It gave me the error message
-bash: conda: command not found
Therefore, I am assuming conda is not installed here but how come it possible, I am using qiime 2 plug in commands and they are working perfectly. I e-mailed them informing my problem, hopefully they will get back to me soon.

Regards,
Amin Ferdous

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11

Yeah... it sounds like the people who deployed qiime 2 may need to install some more software.

Great solution :+1:

Let me know how it goes!
Colin

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12

Hi,
HPCC support contacted me and asked me to check Biom by running following command:
singularity exec /opt/apps/nfs/singularity/qiime/2.2019.04/qiime biom --help

I checked and it shows
Usage: biom [OPTIONS] COMMAND [ARGS]ā€¦

Options:
ā€“version Show the version and exit.
-h, --help Show this message and exit.

Commands:
add-metadata Add metadata to a BIOM table.
convert Convert to/from the BIOM table format.
from-uc Create a BIOM table from a vsearch/uclust/usearch BIOMā€¦
head Dump the first bit of a table.
normalize-table Normalize a BIOM table.
show-install-info Provide information about the biom-format installation.
subset-table Subset a BIOM table.
summarize-table Summarize sample or observation data in a BIOM table.
table-ids Dump IDs in a table.
validate-table Validate a BIOM-formatted file.

But when I give command ā€œbiom add-metadataā€ it shows " biom: command not found" also still it does not recognize ā€˜condaā€™

Do you guys have any solution what I should do.

Regards,
Amin

13

Sounds like you need to add the singularity prefix to make this work:

singularity exec /opt/apps/nfs/singularity/qiime/2.2019.04/qiime biom add-metadata ...

See?

14

It is working nowā€¦Thanks a lot.

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