Cannot find formatdb. Is it installed? Is it in your path? (Qiime 1.9.1 in virtual box)

[Rum Wei]

Hi, qiimer. 

I am a new qiimer. And I installed the virtual box version on our server.

I met this problem when I tried to run assign_taxonomy.py with -m blast method. Here is the command line and the error messages:

qiime@qiime-190-virtual-box:~/Desktop/Shared_Folder/rum/qiime_overview_tutorial/split_lib_output/otus$ sudo assign_taxonomy.py -i rep_set/seqs_rep_set.fasta -m blast

Traceback (most recent call last):

  File "/usr/local/bin/assign_taxonomy.py", line 417, in <module>

    main()

  File "/usr/local/bin/assign_taxonomy.py", line 394, in main

    log_path=log_path)

  File "/usr/local/lib/python2.7/dist-packages/qiime/assign_taxonomy.py", line 500, in __call__

    abspath(reference_seqs_path), output_dir=blast_db_dir)

  File "/usr/local/lib/python2.7/dist-packages/bfillings/formatdb.py", line 116, in build_blast_db_from_fasta_path

    fdb = FormatDb(WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 201, in __init__

    self._error_on_missing_application(params)

  File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 468, in _error_on_missing_application

    "Is it in your path?" % command)

burrito.util.ApplicationNotFoundError: Cannot find formatdb. Is it installed? Is it in your path?

Then, I checked the qiime configuration:

qiime@qiime-190-virtual-box:~$ print_qiime_config.py -tf 

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:

 https://github.com/biocore/qiime-default-reference/releases/tag/0.1.2

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.

RDP Classifier version (if installed): rdp_classifier-2.2.jar

          Java version (if installed): 1.6.0_35

QIIME config values

===================

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

 http://qiime.org/install/qiime_config.html

 http://qiime.org/tutorials/parallel_qiime.html

                     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 full install test results

===============================

..........................F

======================================================================

FAIL: test_usearch_supported_version (__main__.QIIMEDependencyFull)

usearch is in path and version is supported

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

Traceback (most recent call last):

  File "/usr/local/bin/print_qiime_config.py", line 650, in test_usearch_supported_version

    "which components of QIIME you plan to use.")

AssertionError: usearch not found. This may or may not be a problem depending on which components of QIIME you plan to use.

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

Ran 27 tests in 0.588s

FAILED (failures=1)

I also checked the BLAST and fromatdb:

qiime@qiime-190-virtual-box:/usr/local/lib/python2.7/dist-packages/burrito$ which blastall

/qiime_software/blast-2.2.22-release/bin/blastall

qiime@qiime-190-virtual-box:/usr/local/lib/python2.7/dist-packages/burrito$ which formatdb

/qiime_software/blast-2.2.22-release/bin/formatdb

qiime@qiime-190-virtual-box:/usr/local/lib/python2.7/dist-packages/burrito$ echo $PATH | grep "blast"

/qiime_software/sourcetracker-1.0.0-release/.:/qiime_software/qiime-galaxy-0.0.1-repository-de3646d3/scripts:/qiime_software/SeqPrep-v1.1-release/.:/qiime_software/cdhit-3.1-release/.:/qiime_software/rdpclassifier-2.2-release/.:/qiime_software/muscle-3.8.31-release/.:/qiime_software/infernal-1.0.2-release/bin:/qiime_software/blast-2.2.22-release/bin:/qiime_software/bwa-0.6.2-release/.:/qiime_software/mothur-1.25.0-release/.:/qiime_software/ea-utils-1.1.2-537-release/.:/qiime_software/vienna-1.8.4-release/.:/qiime_software/drisee-1.2-release/.:/qiime_software/raxml-7.3.0-release/.:/qiime_software/chimeraslayer-4.29.2010-release/ChimeraSlayer:/qiime_software/chimeraslayer-4.29.2010-release/NAST-iEr:/qiime_software/cytoscape-2.7.0-release/.:/qiime_software/rtax-0.984-release/.:/qiime_software/cdbtools-10.11.2010-release/.:/qiime_software/ampliconnoise-1.27-release/Scripts:/qiime_software/ampliconnoise-1.27-release/bin:/qiime_software/blat-34-release/.:/qiime_software/tax2tree-1.0-release/bin:/qiime_software/pprospector-1.0.1-release/bin:/qiime_software/clearcut-1.0.9-release/.:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games

Thus, I suppose the virtual box version already contained BLAST, however, I don't know why the util.py cannot find formatdb.

Thanks

[Antonio González Peña]

Hi Rum,

I think the problem is that you are running with sudo, not sure why. Have you tried running without it? 

sudo assign_taxonomy.py -i rep_set/seqs_rep_set.fasta -m blastsudo assign_taxonomy.py -i rep_set/seqs_rep_set.fasta -m blast

->

assign_taxonomy.py -i rep_set/seqs_rep_set.fasta -m blastsudo assign_taxonomy.py -i rep_set/seqs_rep_set.fasta -m blast

Thanks! 

[Rum Wei]

It worked! Thank you very much! 

First, I did not have the permission for qiime to work in the Shared Folder. I have to run sudo every time in such folder. 

Then, I google how to get the permission for qiime in Shared Folder on VirtualBox and I found your answer in another post: https://groups.google.com/forum/#!topic/qiime-forum/RqNz-YK1UJc.

I followed the instructions and I ran the assign_taxonomy.py directly without sudo and it worked.

Many thanks for your help. This problem haunted me for a whole week. I have tried to install BLAST again manually, it didn't work.

Rum

[Antonio González Peña]

Glad it worked! 

[m. salomez]

Hello,

I have also the same problem. I have tried modifying the script following : https://groups.google.com/forum/#!topic/qiime-forum/RqNz-YK1UJc

When trying editing the script, I have noticed that this one is empty :

#!/bin/sh -e
#
# rc.local
#
# This script is executed at the end of each multiuser runlevel.
# Make sure that the script will "exit 0" on success or any other
# value on error.
#
# In order to enable or disable this script just change the execution
# bits.
#
# By default this script does nothing.

exit 0

Someone would send me how the script should look like?

Regards,

Melanie

[m. salomez]

Hello again,

I finded the solution to my problem. I needed in fact to install blast running this command : conda install -c bioconda blast-legacy=2.2.22 then to create a .ncbirc document. I have tired at the beginning to install a newer version but it did not work. We have to install the old one.

Cheers

Melanie