Question: Error when running Bismark with pair end/Full parameter list
0
gravatar for tuto345
3.8 years ago by
tuto34520
France
tuto34520 wrote:

Hi,

When trying to launch a Bismark with bowtie2 I get the following error:

Error executing tool: Required dependency 'mate_list[0]' not found in incoming values

I can't see any problem in the bismark_bowtie2_wrapper.xml and the problem only occurs when selecting "paired-end" AND selecting "Full parameter list".

Any ideas what might be wrong?

Thanks,

Cristian

software error • 986 views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by tuto34520
1
gravatar for Bjoern Gruening
3.8 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Thanks for the bug-report.

Are you able to test the latest release from: https://testtoolshed.g2.bx.psu.edu/view/bgruening/bismark

ADD COMMENTlink written 3.8 years ago by Bjoern Gruening5.1k
0
gravatar for tuto345
3.8 years ago by
tuto34520
France
tuto34520 wrote:

Hi Bjoern,

I could not install the latest release as it failed at compiling bowtie and bowtie2 (which were already compiled). It messed up the installation of version 0.10.1 rev 91f07ff056ca. So I reinstalled the stable version.

The log in web0.log is as follows:

galaxy.tools.actions DEBUG 2015-01-27 17:30:15,348 Dataset output filter failed: 'supressed_read_file'
galaxy.tools ERROR 2015-01-27 17:30:15,425 Exception caught while attempting tool execution:
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2240, in handle_single_execution
    job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2804, in execute
    return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 270, in execute
    handle_output( name, output )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 264, in handle_output
    output.actions.apply_action( data, output_action_params )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 28, in apply_action
    action.apply_action( output_dataset, other_values )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 90, in apply_action
    case.apply_action( output_dataset, other_values )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 61, in apply_action
    return super( ToolOutputActionConditionalWhen, self ).apply_action( output_dataset, other_values )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 28, in apply_action
    action.apply_action( output_dataset, other_values )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 261, in apply_action
    value = self.option.get_value( other_values )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 188, in get_value
    assert ref_name in value, "Required dependency '%s' not found in incoming values" % ref_name
AssertionError: Required dependency 'mate_list[0]' not found in incoming values

Hope this helps,

Cristian

ADD COMMENTlink written 3.8 years ago by tuto34520

HI Christian,

it's not yet on the main Tool Shed. I would like to test it before, but will release it as soon as possible to the main ToolShed.

ADD REPLYlink written 3.8 years ago by Bjoern Gruening5.1k

Thank you very much Bjoern,

I'll be waiting for the update!

Cheers,

Cristian

ADD REPLYlink written 3.8 years ago by tuto34520

Hi Bjoern,

I got a new look at the wrapper today and found the problem.

In the output filter there is a missing p in supressed_read_file. I added the missing p and it is working! I read that part of the code a dozen times and I did not see the missing p till now!

Cheers!

Cristian

ADD REPLYlink written 3.8 years ago by tuto34520

Oh intesting! Do you mind to create a pull request? https://github.com/bgruening/galaxytools/tree/master/bismark_wrapper. Otherwise I will patch it tomorrow.

Thanks!

ADD REPLYlink written 3.8 years ago by Bjoern Gruening5.1k

Hi Bjoern,

The diff below is against the toolshed version. Your github version is already corrected.

Cheers and thanks a lot for your work!

Cristian

diff -r 91f07ff056ca bismark_bowtie2_wrapper.xml
--- a/bismark_bowtie2_wrapper.xml    Mon Apr 14 16:43:14 2014 -0400
+++ b/bismark_bowtie2_wrapper.xml    Sun Feb 08 16:13:53 2015 +0100

@@ -286,7 +286,7 @@

     <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
       <filter>singlePaired['sPaired'] == "paired"</filter>
       <filter>params['settingsType'] == "custom"</filter>
-      <filter>params['supressed_read_file'] is True</filter>
+      <filter>params['suppressed_read_file'] is True</filter>
       <actions>
         <conditional name="singlePaired.sPaired">
           <when value="single">

ADD REPLYlink written 3.8 years ago by tuto34520

Hi Christian,

I updated the Main TS. Would be nice if you can test it.

Thanks,

Bjoern

ADD REPLYlink written 3.8 years ago by Bjoern Gruening5.1k
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