TypeError: 'NoneType' object has no attribute '__getitem__'

[pezhmansafdari]

Hi,

I am trying to run rapclust but I am getting an error like this:
Traceback (most recent call last):
File "/usr/bin/RapClust", line 89, in
processQuant()
File "/usr/lib/python2.7/site-packages/click/core.py", line 716, in call
return self.main(*args, **kwargs)
File "/usr/lib/python2.7/site-packages/click/core.py", line 696, in main
rv = self.invoke(ctx)
File "/usr/lib/python2.7/site-packages/click/core.py", line 889, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/lib/python2.7/site-packages/click/core.py", line 534, in invoke
return callback(*args, **kwargs)
File "/usr/bin/RapClust", line 34, in processQuant
samples = cfg['samples'][c]
TypeError: 'NoneType' object has no attribute 'getitem'
Would you please help me with the posible cause of the problem?

BR,
Pezhman

[k3yavi]

Hi Pezhman,

On the first look of your trace, it looks like yaml file has not been configured correctly.
Can you please check that the input yaml file has been configured according to these requirements.

Let us know how it worked out.

[pezhmansafdari]

Hi,

I attach my yaml file. I don't see anything wrong with it.

BR,
Pezhman

On Tue, Nov 15, 2016 at 3:42 PM, Avi Srivastava notifications@github.com
wrote:

Hi Pezhman,

On the first looks of your trace, it looks like yaml file has not been
configured correctly.
Can you please check that the input yaml file has been configured
according to these
https://github.com/COMBINE-lab/RapClust#using-rapclust requirements.

Let us know how it worked out.

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[k3yavi]

I think you forgot to attach.

[pezhmansafdari]

Hi,

conditions:

• contorol
• Infected
  samples:
  control:
  • A019
  • A020
  • A021
  • A022
  • A023
  • A024
  • A025
  • A026
  • A027
  • A028
  • A029
  • A030
  • A031
  • A032
  • A033
  • A034
  • A035
  • A036
    Infected:
  • A001
  • A002
  • A003
  • A004
  • A005
  • A006
  • A007
  • A008
  • A009
  • A010
  • A011
  • A012
  • A013
  • A014
  • A015
  • A016
  • A017
  • A018
    outdir: Plantago_rapclust

BR,
Pezhman

On Tue, Nov 15, 2016 at 4:17 PM, Avi Srivastava notifications@github.com
wrote:

I think you forgot to attach.

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[k3yavi]

Hi Pezhman,

Please use the below attached yaml file for your analysis.
I hope it'll work for you now.

Let us know how it works out.

rapclust.yaml.zip

[pezhmansafdari]

Hi Avi,

It is still not working. now I get the following error message:
Traceback (most recent call last):
File "/usr/bin/RapClust", line 89, in
processQuant()
File "/usr/lib/python2.7/site-packages/click/core.py", line 716, in
call
return self.main(_args, *_kwargs)
File "/usr/lib/python2.7/site-packages/click/core.py", line 696, in main
rv = self.invoke(ctx)
File "/usr/lib/python2.7/site-packages/click/core.py", line 889, in invoke
return ctx.invoke(self.callback, *_ctx.params)
File "/usr/lib/python2.7/site-packages/click/core.py", line 534, in invoke
return callback(_args, **kwargs)
File "/usr/bin/RapClust", line 19, in processQuant
cfg = yaml.load(yamCfg)
File "/usr/lib64/python2.7/site-packages/yaml/init.py", line 71, in
load
return loader.get_single_data()
File "/usr/lib64/python2.7/site-packages/yaml/constructor.py", line 37,
in get_single_data
node = self.get_single_node()
File "/usr/lib64/python2.7/site-packages/yaml/composer.py", line 36, in
get_single_node
document = self.compose_document()
File "/usr/lib64/python2.7/site-packages/yaml/composer.py", line 55, in
compose_document
node = self.compose_node(None, None)
File "/usr/lib64/python2.7/site-packages/yaml/composer.py", line 84, in
compose_node
node = self.compose_mapping_node(anchor)
File "/usr/lib64/python2.7/site-packages/yaml/composer.py", line 133, in
compose_mapping_node
item_value = self.compose_node(node, item_key)
File "/usr/lib64/python2.7/site-packages/yaml/composer.py", line 84, in
compose_node
node = self.compose_mapping_node(anchor)
File "/usr/lib64/python2.7/site-packages/yaml/composer.py", line 133, in
compose_mapping_node
item_value = self.compose_node(node, item_key)
File "/usr/lib64/python2.7/site-packages/yaml/composer.py", line 64, in
compose_node
if self.check_event(AliasEvent):
File "/usr/lib64/python2.7/site-packages/yaml/parser.py", line 98, in
check_event
self.current_event = self.state()
File "/usr/lib64/python2.7/site-packages/yaml/parser.py", line 449, in
parse_block_mapping_value
if not self.check_token(KeyToken, ValueToken, BlockEndToken):
File "/usr/lib64/python2.7/site-packages/yaml/scanner.py", line 116, in
check_token
self.fetch_more_tokens()
File "/usr/lib64/python2.7/site-packages/yaml/scanner.py", line 257, in
fetch_more_tokens
% ch.encode('utf-8'), self.get_mark())
yaml.scanner.ScannerError: while scanning for the next token
found character '\t' that cannot start any token
in "rapclust.yaml", line 6, column 1

BR,
Pezhman

On Wed, Nov 16, 2016 at 7:06 PM, Avi Srivastava notifications@github.com
wrote:

Hi Pezhman,

Please use the below attached yaml file for your analysis.
I hope it'll work for you now.

Let us know how it works out.

rapclust.yaml.zip
https://github.com/COMBINE-lab/RapClust/files/595298/rapclust.yaml.zip

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[k3yavi]

looks like yaml doesn't like tabs and want spaces in its files.
I've replaced tabs with spaces and attached the relevant file.
rapclust.yaml.zip

[pezhmansafdari]

Hi Avi,

We figured the same out yesterday. We used for space instead of tabs and
the config file worked. The clustering results also seems very promising.
Thanks a lot.

Cheers,
Pezhman

On Thu, Nov 17, 2016 at 9:41 PM, Avi Srivastava notifications@github.com
wrote:

looks like yaml doesn't like tabs and wan't spaces in it's files.
I've replaced tabs with spaces and attached the relevant file.
rapclust.yaml.zip
https://github.com/COMBINE-lab/RapClust/files/598269/rapclust.yaml.zip

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[k3yavi]

Glad to hear that!