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 print_qiime_config.py 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.
qiime@qiime-190-virtual-box:~$ 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
qiime@qiime-190-virtual-box:~$ print_qiime_config.py --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:
Release qiime-default-reference 0.1.2: template alignment bug fix (alpha release) · biocore/qiime-default-reference · GitHub
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:
Setting up your qiime config file — Homepage
Using parallel QIIME — Homepage
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
cluster_jobs_fp: start_parallel_jobs.py
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
OK
qiime@qiime-190-virtual-box:~$
