Oligotyping error information

[Yiyuan Li]

Hi Meren

I'm using oligotyping on environmental DNA data. 

When I used the following command, it ran perfectly fine with correct output. 

oligotype Etheostoma.fas.uc.namelist.aligned.fas Etheostoma.fas.uc.namelist.aligned.fas-ENTROPY -C 227,233,327 -M 500 --gen-html -s 3

Then I added one more position, then I got the following error information

oligotype Etheostoma.fas.uc.namelist.aligned.fas Etheostoma.fas.uc.namelist.aligned.fas-ENTROPY -C 193,227,233,327 -M 500 --gen-html -s 3

Traceback (most recent call last):

  File "/afs/crc.nd.edu/x86_64_linux/p/python/2.7.11/gcc/4.9.2/bin/oligotype", line 51, in <module>

    oligotyping.run_all()

  File "~/.local/lib/python2.7/site-packages/oligotyping-2.0-py2.7.egg/Oligotyping/lib/oligotyping.py", line 442, in run_all

    self._generate_html_output()

  File "~/.local/lib/python2.7/site-packages/oligotyping-2.0-py2.7.egg/Oligotyping/lib/oligotyping.py", line 1451, in _generate_html_output

    index_page = generate_html_output(self.run.info_dict, html_output_directory = output_directory_for_html)

  File "~/.local/lib/python2.7/site-packages/oligotyping-2.0-py2.7.egg/Oligotyping/utils/html/for_oligotyping.py", line 336, in generate_html_output

    rendered = render_to_string('index_for_oligo.tmpl', html_dict)

  File "~/.local/lib/python2.7/site-packages/django/template/loader.py", line 97, in render_to_string

    return template.render(context, request)

  File "~/.local/lib/python2.7/site-packages/django/template/backends/django.py", line 95, in render

    return self.template.render(context)

  File "~/.local/lib/python2.7/site-packages/django/template/base.py", line 206, in render

    return self._render(context)

  File "~/.local/lib/python2.7/site-packages/django/template/base.py", line 197, in _render

    return self.nodelist.render(context)

  File "~/.local/lib/python2.7/site-packages/django/template/base.py", line 992, in render

    bit = node.render_annotated(context)

  File "~/.local/lib/python2.7/site-packages/django/template/base.py", line 959, in render_annotated

    return self.render(context)

  File "~/.local/lib/python2.7/site-packages/django/template/defaulttags.py", line 326, in render

    return nodelist.render(context)

  File "~/.local/lib/python2.7/site-packages/django/template/base.py", line 992, in render

    bit = node.render_annotated(context)

  File "~/.local/lib/python2.7/site-packages/django/template/base.py", line 959, in render_annotated

    return self.render(context)

  File "~/.local/lib/python2.7/site-packages/django/template/defaulttags.py", line 220, in render

    nodelist.append(node.render_annotated(context))

  File "~/.local/lib/python2.7/site-packages/django/template/base.py", line 959, in render_annotated

    return self.render(context)

  File "~/.local/lib/python2.7/site-packages/django/template/defaulttags.py", line 326, in render

    return nodelist.render(context)

  File "~/.local/lib/python2.7/site-packages/django/template/base.py", line 992, in render

    bit = node.render_annotated(context)

  File "~/.local/lib/python2.7/site-packages/django/template/base.py", line 959, in render_annotated

    return self.render(context)

  File "~/.local/lib/python2.7/site-packages/django/template/defaulttags.py", line 319, in render

    match = condition.eval(context)

  File "~/.local/lib/python2.7/site-packages/django/template/defaulttags.py", line 951, in eval

    return self.value.resolve(context, ignore_failures=True)

  File "~/.local/lib/python2.7/site-packages/django/template/base.py", line 736, in resolve

    new_obj = func(obj, *arg_vals)

  File "~/.local/lib/python2.7/site-packages/oligotyping-2.0-py2.7.egg/Oligotyping/utils/html/for_oligotyping.py", line 69, in has_perfect_hit

    return b6_entry_list[0].identity == 100.0 if len(b6_entry_list) else False

TypeError: object of type 'NoneType' has no len()

I tried to change the -M from 500 to 50, and the command works fine. 

oligotype Etheostoma.fas.uc.namelist.aligned.fas Etheostoma.fas.uc.namelist.aligned.fas-ENTROPY -C 193,227,233,327 -M 50 --gen-html -s 3

So I wonder in this case, if the error is because the oligotype didn't have enough abundance? If that happens, could we say the oligotype converge?  

YY

[A. Murat Eren]

Hi Yiyuan,

This is odd. Which version of the oligotyping pipeline are you using? (oligotype -v)

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

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[Yiyuan Li]

Hi Meren

I'm using version 2.0.

YY

[A. Murat Eren]

Can you please upgrade it and try again?

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

To view this discussion on the web visit https://groups.google.com/d/msgid/oligotyping/fa4b8f8d-a272-4bce-9e2b-a9cbb91e9677%40googlegroups.com.

[Yiyuan Li]

Hi Meren

Where can I find the latest version? Didn't find it here http://oligotyping.org/files/downloads/

YY

[A. Murat Eren]

Oh. I am sorry. Please try this to get the source package:

https://pypi.python.org/pypi/oligotyping

or alternatively you can type this:

sudo pip install --upgrade oligotyping

Thanks,

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

To view this discussion on the web visit https://groups.google.com/d/msgid/oligotyping/b173694b-e6f8-4b0e-9709-109f1d09f0f4%40googlegroups.com.

[Yiyuan Li]

Thank you Meren. I'll let you know if the new version solves the problem. 

YY

[Jarrod]

Greetings. 

I am experiencing a similar problem  using oligotype pipeline v 2.1, OS X 10.10.5. Except I receive the error when using the --do-blast-search (see below for the log). Howver if I use the -T flag I do not get an error. Thanks!

oligotype input.fasta-TRIMMED input.fasta-TRIMMED-ENTROPY -a 0.0 -s 5 -M 26 -C 201,112,193,211,189,95,343,155,175,123,91,100,231,153,173,196 --do-blast-search 

aceback (most recent call last):

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/oligotype", line 51, in <module>

    oligotyping.run_all()

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Oligotyping/lib/oligotyping.py", line 441, in run_all

    self._generate_html_output()

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Oligotyping/lib/oligotyping.py", line 1450, in _generate_html_output

    index_page = generate_html_output(self.run.info_dict, html_output_directory = output_directory_for_html)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Oligotyping/utils/html/for_oligotyping.py", line 358, in generate_html_output

    rendered = render_to_string('index_for_oligo.tmpl', html_dict)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/loader.py", line 97, in render_to_string

    return template.render(context, request)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/backends/django.py", line 95, in render

    return self.template.render(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/base.py", line 206, in render

    return self._render(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/base.py", line 197, in _render

    return self.nodelist.render(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/base.py", line 992, in render

    bit = node.render_annotated(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/base.py", line 959, in render_annotated

    return self.render(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/defaulttags.py", line 326, in render

    return nodelist.render(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/base.py", line 992, in render

    bit = node.render_annotated(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/base.py", line 959, in render_annotated

    return self.render(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/defaulttags.py", line 220, in render

    nodelist.append(node.render_annotated(context))

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/base.py", line 959, in render_annotated

    return self.render(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/defaulttags.py", line 326, in render

    return nodelist.render(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/base.py", line 992, in render

    bit = node.render_annotated(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/base.py", line 959, in render_annotated

    return self.render(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/defaulttags.py", line 319, in render

    match = condition.eval(context)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/defaulttags.py", line 951, in eval

    return self.value.resolve(context, ignore_failures=True)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/django/template/base.py", line 736, in resolve

    new_obj = func(obj, *arg_vals)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Oligotyping/utils/html/for_oligotyping.py", line 91, in has_perfect_hit

    return b6_entry_list[0].identity == 100.0 if len(b6_entry_list) else False

TypeError: object of type 'NoneType' has no len()

[A. Murat Eren]

Hi Jarrod!

There seems to be an issue with multithreading on Mac OS X systems. I will try to reproduce it and fix it soon. Thanks for reporting, and sorry for the inconvenience.

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

To view this discussion on the web visit https://groups.google.com/d/msgid/oligotyping/d87b8a13-4a5b-40b4-954f-5f38c385dd73%40googlegroups.com.

[Jarrod]

No inconvenience. Just an evolving project. Thanks for the help.

Jarrod

[John Gaby]

Hi Meren,

I also experience this problem when multi-threading the oligotype command on Biolinux with an ASUS laptop, so it appears not to be limited to Mac OS X systems. I can confirm that using the -T parameter does fix the error, and then the oligotype command successfully produces the html index of the output.

Cheers,

Chris