qiime install problem

[Alissa Cait]

I'm struggling to install qiime.

I followed the directions posted on https://github.com/qiime/qiime-deploy

When I run :

print_qiime_config.py -tb


it returns:



System information
==================
         Platform:    linux2
   Python version:    2.7.3 (default, Sep 16 2014, 16:32:30)  [GCC 4.6.3]
Python executable:    /home/alissa/qiime_software/python-2.7.3-release/bin/python

Dependency versions
===================
             PyCogent version:    1.5.3
                NumPy version:    1.7.1
           matplotlib version:    1.3.1
          biom-format version:    1.3.1
                 qcli version:    0.1.0
        QIIME library version:    1.8.0
         QIIME script version:    1.8.0
PyNAST version (if installed):    1.2.2
              Emperor version:    0.9.3

QIIME config values
===================
                     blastmat_dir:    /home/alissa/qiime_software/blast-2.2.22-release/data
                         sc_queue:    all.q
      topiaryexplorer_project_dir:    None
     pynast_template_alignment_fp:    /home/alissa/qiime_software/core_set_aligned.fasta.imputed
                  cluster_jobs_fp:    /home/alissa/qiime_software/qiime-1.8.0-release/bin/start_parallel_jobs.py
pynast_template_alignment_blastdb:    None
assign_taxonomy_reference_seqs_fp:    /home/alissa/qiime_software/gg_otus-13_8-release/rep_set/97_otus.fasta
                     torque_queue:    friendlyq
   template_alignment_lanemask_fp:    /home/alissa/qiime_software/lanemask_in_1s_and_0s
                    jobs_to_start:    1
                cloud_environment:    False
                qiime_scripts_dir:    /home/alissa/qiime_software/qiime-1.8.0-release/bin
            denoiser_min_per_core:    50
                      working_dir:    /tmp/
                    python_exe_fp:    /home/alissa/qiime_software/python-2.7.3-release/bin/python
                         temp_dir:    /tmp/
                      blastall_fp:    /home/alissa/qiime_software/blast-2.2.22-release/bin/blastall
                 seconds_to_sleep:    60
assign_taxonomy_id_to_taxonomy_fp:    /home/alissa/qiime_software/gg_otus-13_8-release/taxonomy/97_otu_taxonomy.txt
...............
----------------------------------------------------------------------
Ran 15 tests in 0.019s

OK





when I run:
 
tests$ python all_tests.py


it returns:
 
Ran 312 commands to test 124 scripts. 14 of these commands failed.
Failed scripts were: parallel_identify_chimeric_seqs.py pick_closed_reference_otus.py parallel_map_reads_to_reference.py start_parallel_jobs_torque.py assign_taxonomy.py pick_open_reference_otus.py pick_otus.py identify_chimeric_seqs.py map_reads_to_reference.py parallel_pick_otus_usearch61_ref.py


But when I try to run qiime:


alissa@bm-z400b-linux:~$ qiime
The program 'qiime' is currently not installed.  You can install it by typing:
sudo apt-get install qiime




Clearly qiime is installed.. but how do I get it to run?



Many thanks in advance!

[Katherine Amato]

Hi Alissa,

To use qiime, you don't need call it like you were trying (by typing 'qiime'). All you need to do is type the specific command from qiime that you want to use (e.g. split_libraries_fastq.py).

Try using one of those commands. It should work.

Best,

Katie

[zillur rahman]

Hi,

I am trying to install qiime on my mac. Here is my files and command lines. Can you tell me what I am missing?

Best Regards

Zillur

mds-macbook-pro:~ ZILLURRAHMAN$ cd desktop/qiime/macqiime

mds-macbook-pro:macqiime ZILLURRAHMAN$ ls

README.txt install.s macqiime scripts

mds-macbook-pro:macqiime ZILLURRAHMAN$ Run ./install.s 

-bash: Run: command not found

mds-macbook-pro:macqiime ZILLURRAHMAN$ 

[Justine Debelius]

Hi Zillur,

It looks like you have macqiime installed. Try typing "print_qiime_config.py" and then call "summarize_taxa.py -h". These should both give you printed outputs. If they do, qiime is installed.

I'd recommend practicing with the qiime tutorials, especially the 454 overview.

Cheers,

Justine

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[zillur Rahman]

Thank you very much for the quicker response. But still here is the problem. What would I do now?

mds-macbook-pro:~ ZILLURRAHMAN$ cd desktop/qiime/macqiime

mds-macbook-pro:macqiime ZILLURRAHMAN$ ls

README.txt install.s macqiime scripts

mds-macbook-pro:macqiime ZILLURRAHMAN$ print_qiime_config.py

-bash: print_qiime_config.py: command not found

mds-macbook-pro:macqiime ZILLURRAHMAN$ cd macqiime

mds-macbook-pro:macqiime ZILLURRAHMAN$ ls

QIIME microbiomeutil_2010-04-29

bin pprospector

blat rdp_classifier_2.2

configs rtax-0.984

greengenes share

include sw

lib version.txt

mds-macbook-pro:macqiime ZILLURRAHMAN$ print_qiime_config.py

-bash: print_qiime_config.py: command not found

mds-macbook-pro:macqiime ZILLURRAHMAN$ summarize_taxa.py -h

-bash: summarize_taxa.py: command not found

mds-macbook-pro:macqiime ZILLURRAHMAN$ cd

mds-macbook-pro:~ ZILLURRAHMAN$ print_qiime_config.py

-bash: print_qiime_config.py: command not found

mds-macbook-pro:~ ZILLURRAHMAN$ summarize_taxa.py -h

-bash: summarize_taxa.py: command not found

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[Justine Debelius]

Hi Zillur,

Please try typing the command "macqiime" in the prompt, and then try "summarize_taxa.py -h".

Please let me know what the outcome is.

Thanks,

Justine

[zillur Rahman]

Thank you very much. I have done it but still....

mds-macbook-pro:~ ZILLURRAHMAN$ cd desktop/qiime/macqiime

mds-macbook-pro:macqiime ZILLURRAHMAN$ ls

README.txt install.s macqiime scripts

mds-macbook-pro:macqiime ZILLURRAHMAN$ print_qiime_config.py

-bash: print_qiime_config.py: command not found

mds-macbook-pro:macqiime ZILLURRAHMAN$ cd macqiime

mds-macbook-pro:macqiime ZILLURRAHMAN$ ls

QIIME microbiomeutil_2010-04-29

bin pprospector

blat rdp_classifier_2.2

configs rtax-0.984

greengenes share

include sw

lib version.txt

mds-macbook-pro:macqiime ZILLURRAHMAN$ print_qiime_config.py

-bash: print_qiime_config.py: command not found

mds-macbook-pro:macqiime ZILLURRAHMAN$ summarize_taxa.py -h

-bash: summarize_taxa.py: command not found

mds-macbook-pro:macqiime ZILLURRAHMAN$ cd

mds-macbook-pro:~ ZILLURRAHMAN$ print_qiime_config.py

-bash: print_qiime_config.py: command not found

mds-macbook-pro:~ ZILLURRAHMAN$ summarize_taxa.py -h

-bash: summarize_taxa.py: command not found

mds-macbook-pro:~ ZILLURRAHMAN$ macqiime print_qiime_config.py

-bash: macqiime: command not found

mds-macbook-pro:~ ZILLURRAHMAN$ qiime print_qiime_config.py

-bash: qiime: command not found

mds-macbook-pro:~ ZILLURRAHMAN$ cd ..

mds-macbook-pro:Users ZILLURRAHMAN$ cd desktop/qiime/macqiime

-bash: cd: desktop/qiime/macqiime: No such file or directory

mds-macbook-pro:Users ZILLURRAHMAN$ cd desktop

-bash: cd: desktop: No such file or directory

mds-macbook-pro:Users ZILLURRAHMAN$ ls

Shared ZILLURRAHMAN

mds-macbook-pro:Users ZILLURRAHMAN$ cd zillurrahman/desktop/qiime/macqiime

mds-macbook-pro:macqiime ZILLURRAHMAN$ qiime print_qiime_config.py

-bash: qiime: command not found

mds-macbook-pro:macqiime ZILLURRAHMAN$ macqiime print_qiime_config.py

-bash: macqiime: command not found

mds-macbook-pro:macqiime ZILLURRAHMAN$ 

[Tony Walters]

Hello Zillur,

Close your current terminals and open a new one.

type:

macqiime

and post the output. If it says "command not found" you probably need to reinstall macqiime.

[zillur Rahman]

Thank you very much. I closed the terminal and opened a new one. But

regulus:~ ZILLURRAHMAN$ macqiime

-bash: macqiime: command not found

regulus:~ ZILLURRAHMAN$ macqiime print_qiime_config.py

-bash: macqiime: command not found

regulus:~ ZILLURRAHMAN$ 

what should I do now?

[Tony Walters]

I'd suggest reinstalling macqiime.

It should not error out when you start the instance of it by typing "macqiime"

[zillur Rahman]

Thank you very much. Now I got it.