Hello, I am a novice in performing bioinformatic analysis and therefore in the use of tools such as qiime. I recently installed on my computer qiime 1.9.1 VirtualBox, following the recommendations that appear on qiime web and other tutorials. I installed the last version of Oracle VirtualBox for Windows, I created the virtual machine for qiime, and my problem arose when I tried to install the VB Guest Additions, when I executed autorun, the installation was not completed and the following message appeared:

Verifying archive integrity... All good. Uncompressing VirtualBox 5.2.8 Guest Additions for Linux........ VirtualBox Guest Additions installer Removing installed version 5.2.8 of VirtualBox Guest Additions... vboxadd-service.sh: Stopping VirtualBox Guest Addition service. You may need to restart your guest system to finish removing the guest drivers. Copying additional installer modules ... Installing additional modules ... VirtualBox Guest Additions: Building the VirtualBox Guest Additions kernel modules. VirtualBox Guest Additions: Look at /var/log/vboxadd-setup.log to find out what went wrong VirtualBox Guest Additions: Running kernel modules will not be replaced until the system is restarted VirtualBox Guest Additions: Starting. You may need to restart the Window System (or just restart the guest system) to enable the Guest Additions.

Press Return to close this window...

Then I executed sudo /media/VBox_GAs_5.2.8/VBoxLinuxAdditions.run

Despite this, I tried to continue with the installation of qiime, using the commands: pip install numpy pip install qiime

And when using print_qiime_config.py –t , this is the information that get:

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.

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 base install test results

.........

Ran 9 tests in 0.078s

I don’t know if everything is correct.

As a first contact with this tool, I tried to follow the steps described in the 454 Overview Tutorial: de novo OTU picking and diversity analyses using 454 data (http://qiime.org/tutorials/tutorial.html)

But when trying to run the script:

pick_de_novo_otus.py -i split_library_output/seqs.fna -o otus

....... 01:05:12 2.6Gb 67.7% Reading lib, 67415 seeds 01:05:13 2.6Gb 67.7% Reading lib, 67416 seeds 01:05:17 2.6Gb 67.7% Reading lib, 67417 seeds 01:05:22 2.6Gb 67.7% Reading lib, 67418 seeds 01:05:28 2.6Gb 67.7% Reading lib, 67419 seeds Killed

the workflow is not executed correctly, and I do not obtain the biom tables, the rep_set, etc

Then I tried to pick up otus step by step using the following commands:

pick_otus.py -i split_library_output/seqs.fna pick_rep_set.py -i uclust_picked_otus/seqs_otus.txt -f split_library_output/seqs.fna -o rept_set.fna

And I have no problems, until I try to perform the OTU assignment using the command:

assign_taxonomy.py -i rep_set.fna -o taxonomy_results

I am not able to perform the assignment, it returns these errors on the screen:

Traceback (most recent call last): File "/usr/local/bin/assign_taxonomy.py", line 417, in 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 1304, in call '--uc': uc_path}) File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 285, in call 'StdErr:\n%s\n' % open(errfile).read()) burrito.util.ApplicationError: Unacceptable application exit status: 137 Command: cd "/home/qiime/qiime_tutorial/qiime_overview_tutorial/"; uclust --input "rept_set.fna" --id 0.9 --rev --maxaccepts 3 --allhits --libonly --lib "/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta" --uc "/tmp/UclustConsensusTaxonAssigner_bqfzjZ.uc" > "/tmp/tmpWyyKUSfxKtN6pa5534Ae.txt" 2> "/tmp/tmpInClYEwXzShfiZAkJ0Of.txt" StdOut:

I don’t know what is wrong or how I can solve it. I don’t have much bioinformatic knowledge. Could someone help me?

Thanks for your attention. I am looking forward to your respons.

Regards,

Sandra

biocore / qiime

Problems with 454 Overview Tutorial: de novo OTU picking and diversity analyses using 454 data in Qiime 1.9.1 VirtualBox #2213