biom convert: command not found

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mandi...@gmail.com

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Jan 25, 2017, 11:09:29 PM1/25/17
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Hi,

I have recently installed Qiime 1.2.1 in my windows machine through Oracle VirtualBox ( 5.1.14), following all the steps in QIIME VirtualBox Install Tutorial.
I have then successfully run a Usearch script and am now trying to run the Qiime script. However, I am getting an error message related to the first command which is to convert my OTU table into Biom table.

-This is the command I am using: 
biom convert --table-type="OTU table" -i Tryp2_otu_table.txt -o Tryp2_otu_table.biom --to-hdf5

-Error message says: "biom: command not found"

According to what I have read and have been told by more experienced users, the BIOM utility should be already included in Qiime package and therefore I would not have to download anything separately. Is that correct?
I have tried re installing Qiime to see if the issue stops, but it did not. I also tried the command: convert_biom.py instead but got the same message.


Any help will be very much appreciated!

Cheers,
Amanda


P.S.Here is my "print_qiime_config.py -t" info:

qiime@linux:~$ print_qiime_config.py -t

System information
==================
         Platform: linux2
   Python version: 2.6.4 (r264:75706, Feb 23 2011, 13:48:52)  [GCC 4.4.3]
Python executable: /software/python-2.6.4-release/bin/python

Dependency versions
===================
               PyCogent version: 1.5.0
                  NumPy version: 1.3.0
             matplotlib version: 0.98.5.3
          QIIME library version: 1.2.1
           QIIME script version: 1.2.1
  PyNAST version (if installed): 1.1
Denoiser version (if installed): 0.851

QIIME config values
===================
                     blastmat_dir: /software/blast-2.2.22-release/data/
                rdp_classifier_fp: /software/rdpclassifier-2.0.1-release/rdp_classifier-2.0.jar
   template_alignment_lanemask_fp: /software/lanemask_in_1s_and_0s
                  cluster_jobs_fp: None
     pynast_template_alignment_fp: /software/core_set_aligned.fasta.imputed
                 seconds_to_sleep: 60
pynast_template_alignment_blastdb: None
                pyronoise_data_fp: /software/denoiser-0.851-release/Data/LookUp.dat
                    jobs_to_start: 1
                qiime_scripts_dir: /software/qiime-1.2.1-release/bin
                      working_dir: /tmp/
                    python_exe_fp: /software/python-2.6.4-release/bin/python
                         temp_dir: /tmp/
                      blastall_fp: blastall


running checks:

FastTree is in path and version is supported ... ok
INFERNAL is in path and version is supported ... ok
blast is in path and version is supported ... ok
blastall_fp is set to a valid path ... ok
blastmat_dir is set to a valid path. ... ok
cdbtools is in path and version is supported ... ok
cd-hit is in path and version is supported ... ok
no obvious problems with ChimeraSlayer install ... ok
clearcut is in path and version is supported ... ok
cluster_jobs_fp is set to a valid path and is executable ... ok
denoiser is in path and version is supported ... ok
dotur is in path and version is supported ... ok
local qiime_config has no extra params ... ok
mothur is in path and version is supported ... ok
muscle is in path and version is supported ... ok
pynast_template_alignment_blastdb is set to a valid path ... ok
pynast_template_alignment is set to a valid path ... ok
pyrnoise2 is in path and version is supported ... ok
python_exe_fp is set to a working python env ... ok
python is in path and version is supported ... ok
qiime_scripts_dir is set to a valid path ... ok
raxmlHPC is in path and version is supported ... ok
rdp_classifier is set to a valid path ... ok
template_alignment_lanemask is set to a valid path ... ok
uclust is in path and version is supported ... ok
working_dir is set to a valid path ... ok

----------------------------------------------------------------------
Ran 26 tests in 0.536s

OK








Justine Debelius

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Jan 26, 2017, 1:30:18 PM1/26/17
to Qiime 1 Forum
Hi Amanda,

We no longer provide support from QIIME 1.2.1. The most current version is QIIME 1.9.1. 
The biom convert command is part of the later versions of the software.

Best,
Justine
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