biom version error

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sohini banerjee

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Oct 24, 2016, 2:31:03 PM10/24/16
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Hi,
 I have been wanting to use picrust on my data analysed on qiime. I was having error running normalize_by_copy_number.py and I read that it will work on biom 1.3.1, so I reinstalled biom. I am still unable to run the command. The error I am getting is as follows:

Traceback (most recent call last):

  File "/usr/local/bin/normalize_by_copy_number.py", line 4, in <module>

    import pkg_resources

  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 2607, in <module>

    yield Requirement(project_name, specs, extras)

  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 565, in resolve

    keys2 = self.entry_keys.setdefault(dist.location,[])

pkg_resources.DistributionNotFound: biom-format>=2.1.4,<2.2.0


print_qiime_config.py output is:

   PyCogent version:        1.5.3

                        NumPy version:        1.8.2

                   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

                      Emperor version:       Not installed.

RDP Classifier version (if installed):          rdp_classifier.jar

          Java version (if installed):   1.7.0_95

 

QIIME config values

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

                     blastmat_dir:                /usr/share/ncbi/data

                    jobs_to_start:               1

pynast_template_alignment_blastdb:   None

                qiime_scripts_dir:            /usr/lib/qiime/bin/

   template_alignment_lanemask_fp:     None

                      working_dir:                .

     pynast_template_alignment_fp:         None

                    python_exe_fp:           python

                         temp_dir:   /tmp

                      blastall_fp:    blastall

                 seconds_to_sleep:        60

                  cluster_jobs_fp:             None


If I am using an updated version of biom as mentioned in the error report, I still get an error.


Please help.

Morgan Langille

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Oct 24, 2016, 2:36:11 PM10/24/16
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The newest version of PICRUSt (1.1) now depends on biom-format >2.1.4

-------------------------------------------
Dr. Morgan Langille
Canada Research Chair in Human Microbiomics
Assistant Professor
Department of Pharmacology, Dalhousie University

Director
Integrated Microbiome Resource (IMR)

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Victoria Byrd

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Oct 24, 2016, 3:36:38 PM10/24/16
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Hi, brand new QIIME and PICRUSt user here. I also encountered an issue when I tried to run this script: 

normalize_by_copy_number.py -i closed_otu_table_json.biom -o closed_otu_table_json_normalized.biom


I got the following message:

Traceback (most recent call last):

  File "/usr/local/bin/normalize_by_copy_number.py", line 4, in <module>

    __import__('pkg_resources').run_script('PICRUSt==1.0.0.dev0', 'normalize_by_copy_number.py')

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 2797, in <module>

    parse_requirements(__requires__), Environment()

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 576, in resolve

    raise DistributionNotFound(req)

pkg_resources.DistributionNotFound: biom-format==1.3.1

MacQIIME lri-106100:FilteredMin1000Reads $ predict_metagenomes.py -i closed_otu_table_json_normalized.biom -o metagenome_predictions.biom

Traceback (most recent call last):

  File "/usr/local/bin/predict_metagenomes.py", line 4, in <module>

    __import__('pkg_resources').run_script('PICRUSt==1.0.0.dev0', 'predict_metagenomes.py')

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 2797, in <module>

    parse_requirements(__requires__), Environment()

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 576, in resolve

    raise DistributionNotFound(req)

pkg_resources.DistributionNotFound: biom-format==1.3.1

MacQIIME lri-106100:FilteredMin1000Reads $ pkg_resources.DistributionNotFound: biom-format==1.3.1

bash: pkg_resources.DistributionNotFound:: command not found


First I tried validating my biom file (I got the message "this file is a valid BIOM-formatted file") and then I tried converting to a .txt format and back to .biom format. Neither worked. So I ran biom show-install-info:

System information

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

          Platform: darwin

Python/GCC version: 2.7.10 |Anaconda 2.2.0 (x86_64)| (default, May 28 2015, 17:04:42)  [GCC 4.2.1 (Apple Inc. build 5577)]

 Python executable: /macqiime/anaconda/bin/python


Dependency versions

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

 pyqi version: 0.3.2

NumPy version: 1.9.2

SciPy version: 0.15.1

 h5py version: 2.4.0


biom-format package information

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

biom-format version: 2.1.4


MacQIIME lri-106100:FilteredMin1000Reads $ pip freeze

You are using pip version 7.0.1, however version 8.1.2 is available.

You should consider upgrading via the 'pip install --upgrade pip' command.

abstract-rendering==0.5.1

appscript==1.0.1

argcomplete==0.8.4

astropy==1.0.1

backports.ssl-match-hostname==3.4.0.2

bcolz==0.8.1

beautifulsoup4==4.3.2

binstar==0.10.1

biom-format==2.1.4

bitarray==0.8.1

blaze==0.7.3

blz==0.6.2

bokeh==0.8.1

boto==2.36.0

burrito==0.9.1

burrito-fillings==0.1.1

cdecimal==2.3

certifi==14.5.14

cffi==0.9.2

clyent==0.3.4

cogent==1.5.3

colorama==0.3.3

conda==3.12.0

conda-build==1.11.0

conda-env==2.1.4

configobj==5.0.6

cryptography==0.8

Cython==0.22

cytoolz==0.7.2

DataShape==0.4.4

decorator==3.4.0

docutils==0.12

emperor==0.9.51

enum34==1.0.4

fastcache==1.0.2

Flask==0.10.1

funcsigs==0.4

future==0.14.3

futures==2.2.0

gdata==2.0.18

gevent==1.0.1

gevent-websocket==0.9.3

greenlet==0.4.5

grin==1.2.1

h5py==2.4.0

ipython==3.1.0

itsdangerous==0.24

jdcal==1.0

jedi==0.8.1

Jinja2==2.7.3

jsonschema==2.4.0

llvmlite===0.2.2-1-gbcb15be

lxml==3.4.2

MarkupSafe==0.23

matplotlib==1.4.3

mistune==0.5.1

mock==1.0.1

multipledispatch==0.4.7

natsort==3.5.0

networkx==1.9.1

nltk==3.0.2

nose==1.3.4

numba==0.17.0

numexpr==2.3.1

numpy==1.9.2

odo==0.3.1

openpyxl==1.8.5

pandas==0.16.1

patsy==0.3.0

pep8==1.6.2

Pillow==2.7.0

ply==3.4

psutil==2.2.1

ptyprocess==0.4

py==1.4.26

pyasn1==0.1.7

PyAudio==0.2.7

pycosat==0.6.1

pycparser==2.10

pycrypto==2.6.1

pycurl==7.19.5.1

pyflakes==0.8.1

Pygments==2.0.2

pynast==1.2.2

pyOpenSSL==0.14

pyparsing==2.0.3

pyqi==0.3.2

pytest==2.6.4

python-dateutil==2.4.2

pytz==2015.4

PyYAML==3.11

pyzmq==14.5.0

qcli==0.1.1

qiime==1.9.1

qiime-default-reference==0.1.2

redis==2.10.3

requests==2.7.0

rope==0.9.4

runipy==0.1.3

scikit-bio==0.2.3

scikit-image==0.11.2

scikit-learn==0.15.2

scipy==0.15.1

six==1.9.0

sockjs-tornado==1.0.1

Sphinx==1.2.3

spyder==2.3.4

SQLAlchemy==0.9.9

statsmodels==0.6.1

sympy==0.7.6

tables==3.1.1

terminado==0.5

toolz==0.7.1

tornado==4.1

ujson==1.33

unicodecsv==0.9.4

Werkzeug==0.10.1

xlrd==0.9.3

XlsxWriter==0.6.7

xlwings==0.3.4

xlwt==0.7.5


Based on what you're saying, Biom 2.1.4 should have worked with my version of PICRUSt (1.1.0). But it didn't work, so like Sohini, I uninstalled Biom 2.1.4 and reinstalled version 1.3.1 based on what I've been reading on Github and Google forums. Of course, that didn't work either (I get the exact same "DistributionNotFound: biom-format==1.3.1" message). 

I'm not sure what to try next. Any suggestions would be greatly appreciated! Thank you.

Gavin Douglas

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Oct 24, 2016, 3:54:26 PM10/24/16
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Hey Victoria,

It looks like you're running v1.0.0-dev from what I can I tell. If you install the latest release version of PICRUSt (v1.1.0) it should work with the latest biom.


Gavin

sohini banerjee

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Oct 25, 2016, 4:36:36 AM10/25/16
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Dear Morgan,

Thank you for your reply. I have updated the picrust version and now everything works fine. I am really happy with the results.

I have a query, picrust 1.1.0 uses gg-13-5 release version. Can this be updated by simply replacing 16S_13_5_precalculated.tab.gz with 16S_13_8_precalculated.tab.gz  in the picrust-1.1.->picrust>data folder or is there any command-based method?

sohini banerjee

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Oct 25, 2016, 4:50:16 AM10/25/16
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Thank you Gavin for your reply. I did as you suggested and problem is solved.


On Tuesday, 25 October 2016 01:24:26 UTC+5:30, Gavin Douglas wrote:

Victoria Byrd

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Oct 25, 2016, 8:50:08 AM10/25/16
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Thanks Gavin! Looks like that was the issue. I thought I'd successfully installed Picrust 1.1.0 but turns out I was just running a previously installed version of Picrust. I've now installed 1.1.0. Thanks for your help.

Mi Z.

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Nov 8, 2016, 3:54:33 PM11/8/16
to picrust-users
Hi Morgan,

I've converted by biom file using the biom convert command to get the json.biom to run PICRUSt, but still got the same error when running normalization step.

Traceback (most recent call last):
  File "/galaxy-central/tools/picrust/scripts/normalize_by_copy_number.py", line 146, in <module>
    main()
  File "/galaxy-central/tools/picrust/scripts/normalize_by_copy_number.py", line 98, in main
    count_table =

Attached is the converted file.
Would you please give some suggestions on this?

Thanks a lot!
Mi




Morgan Langille於 2016年10月24日星期一 UTC-6下午12時36分11秒寫道：
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otujson.biom

Gavin Douglas

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Nov 8, 2016, 4:08:20 PM11/8/16
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Hi Mi,

I think you’re responding to the wrong thread, just so you know for next time.

I tried running that file with galaxy and got this full error:

Traceback (most recent call last):
  File "/galaxy-central/tools/picrust/scripts/normalize_by_copy_number.py", line 146, in <module>
    main()
  File "/galaxy-central/tools/picrust/scripts/normalize_by_copy_number.py", line 98, in main
    count_table = convert_precalc_to_biom(count_table_fh,ids_to_load)
  File "/galaxy_venv/local/lib/python2.7/site-packages/picrust/util.py", line 87, in convert_precalc_to_biom
    raise ValueError,"One or more OTU ids were not found in the precalculated file!\nAre you using the correct --gg_version?\nExample of (the {0}) unknown OTU ids: {1}".format(len(ids_to_load),', '.join(list(ids_to_load)[:5]))
ValueError: One or more OTU ids were not found in the precalculated file!
Are you using the correct --gg_version?
Example of (the 1177) unknown OTU ids: 680225, 181586, 339889, 120439, 527102

These ids don’t seem to be in either supported database used by PICRUSt, what database did you use for OTU assignment?


Gavin


<otujson.biom>

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