The program 'qiime' is currently not installed.

Hi everyone,
I installed qiime2 in my new desktop and was trying to do analysis.
However, when I am trying to run qiime tools import command it is giving me error that “qiime is not installed”. Please see below. It appears using command that qiime is installed properly. I tried other solutions suggested in forum but I am not able to fix it. Can somebody please give a suggestion on how to fix this? thank you. Regards.

[email protected]:~$ qiime tools import \

–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path manifest_file.tsv
–output-path paired-end-demux.qza
–input-format PairedEndFastqManifestPhred33V2
The program ‘qiime’ is currently not installed. You can install it by typing:
sudo apt-get install qiime

[email protected]:~$ --t

System information

     Platform:	linux2

Python version: 2.7.3 (default, Dec 18 2014, 19:10:20) [GCC 4.6.3]
Python executable: /usr/bin/python

QIIME default reference information

For details on what files are used as QIIME’s default references, see here:

Dependency versions

      QIIME library version:	1.9.1
       QIIME script version:	1.9.1

qiime-default-reference version: 0.1.2
NumPy version: 1.9.2
SciPy version: 0.15.1
pandas version: 0.16.1
matplotlib version: 1.4.3
biom-format version: 2.1.4
h5py version: 2.4.0 (HDF5 version: 1.8.4)
qcli version: 0.1.1
pyqi version: 0.3.2
scikit-bio version: 0.2.3
PyNAST version: 1.2.2
Emperor version: 0.9.51
burrito version: 0.9.1
burrito-fillings version: 0.1.1
sortmerna version: SortMeRNA version 2.0, 29/11/2014
sumaclust version: SUMACLUST Version 1.0.00
swarm version: Swarm 1.2.19 [May 26 2015 13:50:14]
gdata: Installed.

QIIME config values

For definitions of these settings and to learn how to configure QIIME, see here:

                 blastmat_dir:	/qiime_software/blast-2.2.22-release/data
  pick_otus_reference_seqs_fp:	/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
                     sc_queue:	all.q
  topiaryexplorer_project_dir:	None
 pynast_template_alignment_fp:	/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta

pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp: /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue: friendlyq
jobs_to_start: 1
slurm_time: None
denoiser_min_per_core: 50
assign_taxonomy_id_to_taxonomy_fp: /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir: /tmp/
slurm_memory: None
slurm_queue: None
blastall_fp: /qiime_software/blast-2.2.22-release/bin/blastall
seconds_to_sleep: 1

QIIME base install test results

Ran 9 tests in 0.007s

[email protected]:~$

Hello @Sky23. This all looks like it’s referring to Qiime not Qiime2. I notice it says you’re using a virtual box. Are you using a prepackaged virtual box, or did you create your own and install Qiime on it? If you are using a prepackaged one, can you link to it?

1 Like

Hi oddant1,
Thank you for quick response.
I am using a prepacked virutal box from oracle. please see the link below.


How did you install Qiime2 on the virtualbox?

I used 3 links mentioned below for installation. Please check them.

I used these tutorials for installing qiime2 in my laptop and it works fine.
However, when i followed the same tutorials for installing qiime in my desktop it is not working.
Please give suggestion on how to do a proper installation.

Those are unofficial videos giving instructions on how to install the original QIIME. This page discusses how to install QIIME 2 using VirtualBox Please use these instructions and create a new thread if you run into issues with them. Thank you!

1 Like

thank you very much. Let me re-install it again using official intructions.

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